Tesi: "Barley Disease and pest resistance Genetic aspects"

1

Collins, Nicholas C. "The genetics of barley yellow dwarf virus resistance in barley and rice." Title page, table of contents and summary only, 1996. http://hdl.handle.net/2440/46063.

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Barley yellow dwarf virus (BYDV), an aphid transmitted luteovirus, is the most widespread and economically damaging virus of cereal crops. The work in this thesis aims to characterise the basis of the naturally occurring resistance to BYDV in cereals in three ways: Firstly, by facilitating the isolation of the Yd2 gene for BYDV resistance from barley by a map-based approach. Secondly, by determining if a BYDV resistance gene in rice is orthologous to Yd2. Thirdly, by establishing if other BYDV resistance genes in non- Ethiopian barleys are allelic to Yd2. It is hoped that the information generated in this study will ultimately assist in the production of BYDV resistant cereal cultivars. A detailed genetic map of the Yd2 region of barley chromosome 3 was constructed, containing 19 RFLP loci, the centromere and the Yd2 gene. Yd2 mapped on the long arm, 0.5 cM from the centromere, and in the mapping population of 106 F2 individuals, perfectly cosegregated with the RFLP loci XYlp, and Xwg889. This map represents the first stage in a project to isolate the Yd2 gene by a map-based approach. The isolation of Yd2 could help to elucidate the molecular mechanism of the Yd2-mediated BYDV resistance, and may allow the production of BYDV resistant cereals by genetic transformation. The RFLP markers mapped closest to Yd2 could also be useful in barley breeding, by enabling selection for both the presence of Yd2 and the absence of agronomically undesirable traits known to be closely linked to Yd2. Genetically Directed Representational Difference Analysis (GDRDA) is a technique based on subtractive hybridisation, which can be used to identify RFLP markers closely linked to a gene of interest. Two GDRDA experiments were performed with the intention of generating additional RFLP markers close to Yd2. However, the first experiment yielded RFLP probes that were not derived from the barley genome, while the second experiment yielded probes that detected repetitive sequences. It was concluded that GDRDA is of limited use in generating further markers close to Yd2. To isolate the Yd2 gene by a map-based approach, a much larger mapping population will need to be analysed to genetically resolve markers tightly linked to Yd2. If the two morphological markers uzu dwarf and white stripe,,j flank Yd2, then they could assist in this task by enabling the visual identification of F2 seedlings resulting from recombination close to Yd2. However, in this study, both morphological markers were found to be located distal to Yd2. Therefore, these two morphological markers can not be used together to facilitate high resolution genetic mapping of the Yd2 locus. It may be possible to use large-insert genomic DNA clones from the relatively small genome of rice to generate further RFLP markers close to the Yd2 gene in barley, provided that the order of orthologous sequences in barley and rice is conserved close to the Yd2 locus. To assess the feasibility of this approach, RFLP probes used to identify loci close to Yd2 were mapped in rice using a segregating rice F2 population. Five of the RFLP loci mapped together and in the same order as RFLP loci mapped close to Yd2 in barley using the same probes. By comparing the location of RFLPs mapped by other researchers in rice using probes mapped close to Yd2, the region of conserved linkage between rice and the Yd2 region was tentatively identified as the central portion of rice chromosome 1. The collinearity shown by orthologous sequences in barley and rice indicated that it may indeed be possible to use rice to assist in generating RFLP markers close to Yd2. Of all the cereals, rice is the most amenable to map-based gene isolation, due to its small genome, well developed physical and genetic maps, and its ability to be genetically transformed with high efficiency. If a BYDV resistance gene that is orthologous to Yd2 could be identified in rice, this gene could be isolated with relative ease, and then used to identify barley cDNA clones corresponding to Yd2 gene by virtue of the sequence homology expected between these genes. To test if a BYDV resistance gene from an Italian rice line is orthologous to Yd2, recombinant-inbred rice lines previously characterised for this gene were analysed using probes mapped close to Yd2 in barley. No genetic linkage was detected between the RFLP loci and the BYDV resistance gene, indicating that the gene is unlikely to be orthologous to Yd2. BYDV resistance alleles at the Yd2 locus which are of a non-Ethiopian origin may show interesting differences to Ethiopian Yd2 resistance alleles. To identify barleys which may contain resistance alleles of Yd2, ten BYDV resistant barleys not known to contain Yd2 were assessed for their resistance to the PAVadel isolate of BYDV in the glasshouse. CI 1179, Rojo, Perry, Hannchen, Post and CI 4228 were found to be the most resistant under these conditions, and were analysed further. If the resistance from these barleys is controlled by alleles of Yd2, RFLP markers close to Yd2 will be expected to cosegregate with the resistance in F2 families derived from crosses between these resistant barleys and the BYDV susceptible barleys Atlas and Proctor. RFLPs suitable for use in these allelism tests were identified using probes mapped close to Yd2. However, time did not permit the analysis of these F2 populations. Thesis (Ph.D.) -- University of Adelaide, Dept. of Plant Science, 1996

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2

King, Brendon James. "Towards cloning Yd2 : a barley resistance gene to barley yellow dwarf virus." Title page, contents and summary only, 2001. http://web4.library.adelaide.edu.au/theses/09PH/09phk523.pdf.

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3

Rathjen, John Paul. "Aspects of luteovirus molecular biology in relation to the interaction between BYDV-PAV and the Yd2 resistance gene of barley /." Title page, contents and summary only, 1995. http://web4.library.adelaide.edu.au/theses/09PH/09phr2342.pdf.

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4

Hossain, Mohammad Abul. "Powdery mildew on barley : pathogen variability in South Australia : resistance genes in cv. Galleon /." Title page, contents and abstract only, 1986. http://web4.library.adelaide.edu.au/theses/09PH/09phh8287.pdf.

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5

Jenkin, Mandy Jane. "Genetics of boron tolerance in barley / by Mandy Jane Jenkin." Thesis, Adelaide Thesis (Ph.D.) -- University of Adelaide, Department of Plant Science, 1993. http://hdl.handle.net/2440/21652.

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6

Jenkin, Mandy Jane. "Genetics of boron tolerance in barley /." Adelaide : Thesis (Ph.D.) -- University of Adelaide, Department of Plant Science, 1993. http://web4.library.adelaide.edu.au/theses/09PH/09phj514.pdf.

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7

Shams-Bakhsh, Masoud. "Studies on the structure and gene expression of barley yellow dwarf virus." Title page, contents and abstract only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09phs5275.pdf.

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Bibliography: leaves 118-132. This thesis examines the structure and gene expression of barley yellow dwarf viruses (BYDVs)-PAV in order to gain a better understanding of the interaction between the virus and the Yd2 resistance gene. The protein products of open reading frame (ORF)3, ORF4 and ORF5 are expressed in bacterial cells, in order to characterise the BYDV-PAV virion-associated proteins. The effect of the Yd2 resistance gene on the expression of the BYDV-PAV viral proteins in infected cells is also studied.

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8

Golegaonkar, Prashant G. "Genetic and molecular analysis of resistance to rust diseases in barley." University of Sydney, 2007. http://hdl.handle.net/2123/3549.

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Doctor of Philosophy The responses of 92 barley genotypes to selected P. hordei pathotypes was assessed in greenhouse tests at seedling growth stages and in the field at adult plant growth stages to determine known or unknown resistances. On the basis of multipathotype tests, 35 genotypes were postulated to carry Rph2, Rph4, Rph5, Rph12, RphCantala alone or combinations of Rph2 + Rph4 and Rph1 + Rph2, whereas 52 genotypes lacked detectable seedling resistance to P. hordei. Five genotypes carried seedling resistance that was effective to all pathotypes tested, of which four were believed to carry uncharacterised resistance based on pedigree information. Field tests at adult plant growth stages indicated that while 28 genotypes were susceptible, 57 carried uncharacterised APR to P. hordei. Pedigree analysis indicated that APR in the test genotypes could have been derived from three different sources. The resistant responses of seven cultivars at adult plant growth stages were believed to be due to the presence of seedling resistance effective against the field pathotypes. Genetic studies conducted on 10 barley genotypes suggested that ‘Vada’, ‘Nagrad’, ‘Gilbert’, ‘Ulandra (NT)’ and ‘WI3407’ each carry one gene providing adult plant resistance to P. hordei. Genotypes ‘Patty’, ‘Pompadour’ ‘Athos’, ‘Dash’ and ‘RAH1995’ showed digenic inheritance of APR at one field site and monogenic inheritance at a second. One of the genes identified in each of these cultivars provided high levels of APR and was effective at both field sites. The second APR gene was effective only at one field site, and it conferred low levels of APR. Tests of allelism between resistant genotypes confirmed a common APR gene in all genotypes with the exception of ‘WI3407’, which based on pedigree information was genetically distinct from the gene common in ‘Vada’, ‘Nagrad’, ‘Patty’, ‘RAH1995’ and ‘Pompadour’. An incompletely dominant gene, Rph14, identified previously in an accession of Hordeum vulgare confers resistance to all known pathotypes of P. hordei in Australia. The inheritance of Rph14 was confirmed using 146 and 106 F3 lines derived from the crosses ‘Baudin’/ ‘PI 584760’ (Rph14) and ‘Ricardo’/‘PI 584760’ (Rph14), respectively. Bulk segregant analysis on DNA from the parental genotypes and resistant and susceptible DNA bulks from F3 lines using diversity array technology (DArT) markers located Rph14 to the short arm of chromosome 2H. Polymerase chain reaction (PCR) based marker analysis identified a single simple sequence repeat (SSR) marker, Bmag692, linked closely to Rph14 at a map distance of 2.1 and 3.8 cM in the populations ‘Baudin’/ ‘PI 584760’and ‘Ricardo’/‘PI 584760’, respectively. Seedlings of 62 Australian and two exotic barley cultivars were assessed for resistance to a variant of Puccinia striiformis, referred to as BGYR, which causes stripe rust on several wild Hordeum species and some genotypes of cultivated barley. With the exception of six Australian barley cultivars and an exotic cultivar, all displayed resistance to the pathogen. Genetic analyses of six Australian barley cultivars and the Algerian barley ‘Sahara 3771’, suggested that they carried either one or two major seedling resistance genes to the pathogen. A single recessive seedling resistance gene, Bgyr1, identified in ‘Sahara 3771’ was located on the long arm of chromosome 7H and flanked by restriction fragment length polymorphism (RFLP) markers wg420 and cdo347 at genetic distances of 12.8 and 21.9 cM, respectively. Mapping resistance to BGYR at adult plant growth stages using a doubled haploid population derived from the cross ‘Clipper’/‘Sahara 3771’ identified two major QTLs on the long arms of chromosomes 3H and 7H that explained 26 and 18% of total phenotypic variation, respectively. The QTL located on chromosome 7HL corresponded to the seedling resistance gene Bgyr1. The second QTL was concluded to correspond to a single adult plant resistance gene designated Bgyr2, originating from cultivar ‘Clipper’.

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9

Singh, Rampal. "Characterization of virus disease resistance in Lactuca sativa." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=55529.

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Little is known about the mechanism of virus disease resistance in plants. The aim of the work presented here was to answer whether disease resistance is offered within the cell or at the level of intercellular movement of the virus. The protoplast system was used for this purpose. Conditions were optimized to isolate viable protoplasts from the leaves of Lactuca sativa cultivars. Protoplasts and leaves from resistant and susceptible Lactuca sativa cultivars were inoculated separately with turnip mosaic virus (TuMV) and lettuce mosaic virus (LMV), Virus multiplication was examined over time using enzyme-linked immunosorbent assay. Resistant cv. Kordaat did not support TuMV multiplication in protoplasts as well as in leaves. The results indicated that resistance to TuMV is available within the cell. The results ruled out the possibility of involvement of cell to cell movement and resistance to TuMV seems to be constitutive. On the other hand, protoplasts and leaves from both resistant and susceptible lettuce cultivars supported LMV multiplication. This suggested that resistance to LMV may not be offered within the cell. The results also indicated that the resistance to LMV was partly due to a hypersensitive response though virus was still able to spread systemically. To contribute towards mapping of the Tu resistance gene, the genotype of F$ sb2$ individuals was determined by screening an F$ sb3$ population from 71 F$ sb2$ individuals of a cross between cv. Calmar and cv. Kordaat for TuMV-infection. These data were useful for the production of bulks around the Tu locus to facilitate the search for new molecular markers linked to the Tu gene.

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10

Marchione, Wesley A. "Pathogen resistance genes and proteins in orchids." Virtual Press, 2003. http://liblink.bsu.edu/uhtbin/catkey/1260625.

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To study resistance (R) genes that are expressed when Sophrolaeliacattleya Ginny Champion 'Riverbend' orchid tissue was infected with the tobacco mosaic virus (TMV0), a subtraction library of cDNA clones was previously constructed using mRNA isolated before and after infection (Shuck, unpublished). From 200 clones collected, 5 clones were randomly selected, DNA was isolated, and the cDNA insert was sequenced. These sequences were imported into BLAST to search for homology to other R genes. This search revealed clone 4A to have an 84% homology to a 54 nucleotide region from the Arabidopsis thaliana oligouridylate binding protein which is highly expressed and known to bind RNA Polymerase III transcripts and adenovirus associated RNAs. Further bioinformatics analysis was performed utilizing databases and analysis packages available on the Internet, software such as Vector NTI (Informax, Bethesda, MD), and manual searches. However, no additional domains or motifs indicative of pathogen resistance genes were located in any of the 5 clones. Subsequently, total proteins expressed at various time points following infection were examined on denaturing 5-20% gradient polyacrylamide gels stained with the ProteoSilver Plus TM silver stain kit (Sigma, St. Louis, MO) in order to examine the timing and duration of expression of proteins involved in TMV-O resistance. One protein of-18 kDa was highly expressed at 4 hr after infection that was not seen in the negative control. By 8 hr the band was no longer expressed, it was expressed again from 30 - 48 hr, but was not seen again in later time points. Finally, total mRNA isolated from pooled time points and subjected to in vitro translation indicated a reduction in translation products after infection, providing evidence of posttranscriptional gene silencing (PTGS) following TMV-O infection. Department of Biology

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11

Wang, Hongxia. "Identification of Molecular Markers Linked to X-Disease Resistance in Chokecherry." Diss., North Dakota State University, 2012. https://hdl.handle.net/10365/26565.

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X-disease, caused by phytoplasmas, is one of the destructive diseases in stone fruit trees, causing yield loss and poor fruit quality. So far no effective methods are available to control X-disease. X-disease resistance has been first discovered in chokecherry (Prunus virginiana, 2n=4x=32), which is a native woody species of North America. To identify molecular markers linked to X-disease resistance, simple sequence repeat (SSR) markers were used to construct genetic linkage maps for chokecherry and to identify markers associated with X-disease resistance in chokecherry. In this research, three segregating populations of chokecherry were developed by crossing one X-disease resistant (CL) with three susceptible chokecherry lines (a, c, and d), of which the progenies were 101, 177, and 82, respectively. In order to construct a genetic map for chokecherry, 108 pairs of SSR primers were employed from other Prunus species. Additionally, a set of 246 SSRs were developed from chokecherry sequencing by Roche 454 sequencing technology. A total of 354 pairs of SSR primers were used to screen individuals of all three populations. Two software programs, TetraploidMap and JoinMap, were used to construct linkage map based on single-dose restriction fragments (SDRFs) and two parental linkage maps were generated for each population from both software programs. Bulked segregant analysis (BSA) was applied for identification of X-disease resistance markers. As a result, one SSR marker was found to be linked to the X-disease resistance. The set of 246 chokecherry SSRs was later used to test transferability among another 11 rosaceous species (sour cherry, sweet cherry, wild cherry, peach, apricot, plum, apple, crabapple, pear, june berry, and raspberry). As a result, chokecherry SSR primers can be transferable in Prunus species or other rosaceous species. An average of 63.2% and 58.7% of amplifiable chokecherry primers amplified DNA from cherry and other Prunus species, respectively, while 47.2% of amplifiable chokecherry primers can be transferable to other rosaceous species. The genetic information, including genetic map, disease linked marker, chokecherry sequence, and confirmed transferability of the identified chokecherry SSRs to other species, will benefit the genetic research in Prunus and other rosaceous species.

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12

au, lars kamphuis@csiro, and Lars Gian Kamphuis. "Genetic dissection of disease resistance to Phoma medicaginis in Medicago truncatula." Murdoch University, 2007. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20090424.121918.

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Phoma medicaginis is a necrotrophic fungal pathogen, commonly found infecting Medicago truncatula and M. sativa in temperate regions of Australia. To identify, characterize and differentiate eight P. medicaginis isolates from Western Australia, morphological phenotypes and five gene regions (actin, â- tubulin, calmodulin, internal transcribed spacer, translation elongation factor 1-á) were examined. Sequence comparisons showed that specimens isolated from M. truncatula in Western Australia formed a group that was consistently different from, but closely allied to, a P. medicaginis var. medicaginis type specimen. Characterization of three P. medicaginis genotypes showed that all exhibited a narrow host range, causing disease only in M. sativa and M. truncatula among eight commonly cultivated legume species sampled. Infection of 85 M. truncatula accessions showed a continuous distribution in disease phenotypes, with the majority of accessions susceptible. Differences in disease phenotypes suggest that M. truncatula harbours specific and diverse sources of resistance to individual P. medicaginis genotypes. To characterize the genetic basis of resistance to P. medicaginis two F2 populations derived from crosses between the resistant accession SA27063 and the susceptible accessions SA3054 and A17 were phenotyped for disease symptoms. Highly significant recessive QTLs for resistance to P. medicaginis OMT5 were identified in each mapping population. In SA27063 x A17 a QTL named resistance to the necrotroph Phoma medicaginis one (rnpm1) was identified on the short arm of LG4. In SA27063 x SA3054 a QTL (rnpm2) was identified on the long arm of LG8. Further fine mapping of the areas surrounding the QTLs is underway to identify the genes underlying rnpm1 and rnpm2. Examination of the recombination frequencies between genetic markers on the long arms of chromosomes 4 and 8 in the SA27063 x A17 cross revealed an apparent genetic linkage between these chromosomes. Subsequent analysis of other crosses showed this unexpected linkage relationship is characteristic for genetic maps derived from A17. Furthermore F1 individuals derived from crosses involving A17 showed 50% pollen viability or less. This semisterility and the unexpected linkage relationships provide good evidence for a reciprocal translocation in A17 between chromosomes four and eight. The implications of the distinctive chromosomal rearrangement in A17 on genetic mapping, genome sequencing and comparative mapping are discussed. The Mt16kOLI1plus microarray was used to identify transcriptional changes in M. truncatula expressed in defence against P. medicaginis. Three-hundred-and-thirty-four differentially expressed transcripts showed a change of two-fold or more in either the resistant or susceptible interaction, and most of the Phoma-regulated genes could be assigned to functional categories which have been reported to be involved in plant defence responses. RT-qPCR and HPLCUV confirmed involvement of the octadecanoid and phenylpropanoid pathways in response to P. medicaginis infection. Faster induction of lipoxygenase genes and constitutively higher levels of certain phenolic metabolites were observed in resistant plants.

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13

Ubalijoro, Eliane. "Characterization of resistance to lettuce mosaic virus in Lactuca sativa." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=22821.

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Lettuce mosaic virus (LMV) is an economically important pathogen with worldwide distribution. LMV infection in L. sativa can cause significant yield losses. Resistance to LMV in L. sativa is conferred by the recessive gene mo. We attempted to position the mo gene on the L. sativa map. The ultimate goal is a better understanding of plant-virus interactions. To do so, Random Amplified Polymorphic DNA (RAPD) markers were screened in the near isogenic lines (NILs) Vanguard and Vanguard 75. These NILs differ in the presence of the mo gene in Vanguard 75. Polymorphic markers were screened for linkage to mo in two F$ sb2$ populations segregating for resistance to LMV. The F$ sb2$ populations used were derived from 2 crosses, the first one between the L. sativa cultivars Dwarf 2 (resistant to LMV via the presence of mo) and Saffier and the second one between two breeding lines 87-25M-1 (momo) and 87-1090M-1 (MoMo). In order to develop a highly stringent antibody detection system to phenotype plants infected with LMV, a plasmid construct was developed which overproduces LMV coat protein. This construct will be used in the future to produce enough recombinant LMV coat protein for antibody production. To further characterize mo, a selection of cultivars resistant and susceptible to LMV according to the literature were subjected to various temperature changes to determine the environmental influences on virus movement.

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14

Reid, Lana M. (Lana Marie). "Resistance of maize silk to Fusarium graminearum." Thesis, McGill University, 1991. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=70316.

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The characteristics and inheritance of maize silk resistance to Fusarium graminearum ear rot were investigated. In an in vitro test, genotypic differences in the degradation of detached silk tissue by F. graminearum were correlated to field evaluations of resistance. Susceptibility to infection decreased with silk age. Total phenolics of silk channel silk tissue increased in response to infection in resistant inbreds but decreased in susceptible inbreds. The flavones iso-orientin, iso-vitexin, maysin, luteolin, and apigenin were identified in the silk. No significant genotype by isolate interaction effects were found when 13 inbred lines were inoculated with three F. graminearum isolates. Simple models of quantitative and qualitative inheritance were not adequate to explain the inheritance of resistance. Disease severity ratings were bimodally distributed in the F$ sb1$, F$ sb2$, and backcross generations. In a complete diallel cross among 12 inbred lines, general and specific combining ability effects were significant for both disease incidence and disease severity. A screening of 12 accessions of exotic maize germplasm with resistance to either Aspergillus flavus or Heliothis zeae, identified several possible new sources of resistance to F. graminearum. Visual evaluations of resistance were correlated to deoxynivalenol levels of the ear.

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15

Dufresne, Philippe J. "Development and validation of molecular markers for the detection of disease resistance alleles in Lactuca sativa." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=78352.

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In this study, RAPD (Randomly Amplified Polymorphic DNA) and SCAR (Sequence Amplified Characterized Region) markers found within 5 centiMorgans of known disease resistance loci in L. sativa were tested for their potential use in MAS. Out of thirty RAPD and SCAR markers evaluated, ten were found to be reliable predictors of disease resistance or susceptibility across a wide range of commercial and reference cultivars. Direct sequencing of seven selected markers did not reveal any significant similarity with known sequences. Three SNPs (Single Nucleotide Polymorphism) associated with two markers found in close proximity to corky root (cor) and Lettuce mosaic virus resistance (mo12) genes were identified. This information was used in the development of a non-electrophoresis PCR-based assay called FRET (Fluorescence Resonance Energy Transfer) hybridization probes assay.

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16

Yu, Yong Gang. "Molecular genetic analysis of host resistance to soybean mosaic virus." Diss., Virginia Tech, 1994. http://hdl.handle.net/10919/37253.

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17

Galagedara, Nelomie Nayanathara. "Identification of Quantitative Trait Loci for Resistance to Tan Spot in Durum Wheat." Thesis, North Dakota State University, 2018. https://hdl.handle.net/10365/28765.

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Tan spot, caused by Pyrenophora tritici-repentis (Ptr), is a major foliar disease on wheat. The pathosystem involves three pairs of necrotrophic effector (NE) and host sensitivity (S) gene interactions, namely Ptr ToxA-Tsn1, Ptr ToxB-Tsc2 and Ptr ToxC-Tsc1. Additionally, genetic factors conferring race-nonspecific resistance have been identified. The objectives of this study were to map tan spot resistance QTL and investigate the role of NE-S interactions in disease in durum using association and bi-parental mapping. Evaluation of a worldwide collection of durum accessions allowed identifying highly resistant nineteen lines to multiple Ptr races. Association mapping revealed genomic regions on chromosomes 1A, 2B and 3B significantly associated with resistance to tan spot, which likely correspond to Tsc1, Tsc2 and racenonspecific resistance. Using a bi-parental population derived from Ben and PI 41025, we found that ToxA-Tsn1 interaction plays no significant role in disease, instead a major race-nonspecific QTL on chromosome 5A was identified.

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18

Horn, Marizanne. "Transfer of genetic resistance to the Russian wheat aphid from rye to wheat." Thesis, Stellenbosch : Stellenbosch University, 1997. http://hdl.handle.net/10019.1/55770.

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Thesis (MSc.) -- Stellenbosch University, 1997. ENGLISH ABSTRACT: An octoploid triticale was derived from the F1 of a Russian wheat aphid resistant rye, 'Turkey 77', and 'Chinese Spring' wheat. The alloploid was crossed (a) to common wheat, and (b) to the 'Imperial' rye to 'Chinese Spring' disomic addition lines. F2 progeny from these crosses were tested for Russian wheat aphid resistance and C-banded. Resistance was found to be associated with chromosome arm 1RS of the 'Turkey 77' rye genome. This initial work was done by MARAIS (1991) who made a RWA resistant, monotelosomic 1RS ('Turkey 77') addition plant available for the study. The F3 progeny of this monotelosomic addition plant was used to confirm the RWA resistance on chromosome 1RS. The monotelosomic addition plant was then crossed with the wheat cultivar 'Gamtoos', which has the 1BL.1 RS 'Veery' translocation. Unlike the 1RS segment in 'Gamtoos', the 'Turkey 77'- derived 1RS telosome did not express the rust resistance genes 5r31 and Lr26 which could then be used as markers. From the F1 a monotelosomic 1RS addition plant that was also heterozygous for the 1BL.1 RS translocation, was selected and testcrossed with an aphid susceptible common wheat, 'Inia 66'. Meiotic pairing between the .rye arms resulted in the recovery of five euploid, Russian wheat aphid resistant plants out of a progeny of 99 euploids. One recombinant also retained 5r31 and Lr26 and was allowed to self pollinate. With the aid of SOS-PAGE profiles, Russian wheat aphid resistant 1BL.1 RS translocation homozygotes were identified and it was possible to confirm that the Russian wheat aphid resistance gene was in fact transferred to the 1BL.1RS ('Veery') translocation. Two attempts were made to map the Russiar, wheat aphid locus or loci. (1) Telosomic mapping was attempted. For this purpose a plant with 2n = 40 + 1BL.1 RS + 1RS was obtained, and testcrossed with a Russian wheat aphid susceptible wheat. (2) A disomic, recombined 1BL.1 RS translocation line with Russian wheat aphid resistance but lacking the Lr26 and Sr31 alleles was crossed with 'Gamtoos' and the F1 testcrossed. The testcross in both strategies were done with 'Chinese Spring'. In the first experiment the Sr31 locus was located 10.42 map units from the Lr26 locus. The rust resistance data implied that the genetic distance estimates may be unreliable and therefore the laborious Russian wheat aphid resistance tests were not done. In the second experiment a Russian wheat aphid resistance gene was located 14.5 map units from the Lr26 locus. In the latter cross nonmendel ian segregation of the Russian wheat aphid resistance evidently occurred which implied that the estimated map distance may be inaccurate. It was also not possible to determine the number of genes involved from the data. Digitized at 300 dpi Colour & b/W PDF format (OCR), using ,KODAK i 1220 PLUS scanner. Digitised, Ricardo Davids on request from ILL 25 April 2013 AFRIKAANSE OPSOMMING: 'n Oktaplo"lede triticale is gemaak vanaf die F1 van 'n kruising tussen 'n Russiese koringluis-weerstandbiedende rog, 'Turkey 77', en die koringkultivar 'Chinese Spring'. Die alloplo"led is gekruis met gewone broodkoring en met 'Imperial' rog/'Chinese Spring' disomiese addissielyne. Die F2 nageslag vanaf hierdie kruisings is getoets vir Russiese koringluisweerstandbiedendheid en C-bande is ook gedoen. Weerstand is gevind wat geassosieer is met die 1RS chromosoomarm van 'Turkey 77'. Hierdie oorspronklike werk is deur MARAIS (1991) gedoen en uit sy materiaal is 'n monotelosomiese 1RS ('Turkey 77') addissieplant beskikbaar gestel vir die huidige studie. Die F3 nageslag van hierdie monotelosomiese addissieplant is gebruik om die weerstand teen die Russiese koringluis op chromosoom 1RS te bevestig. Die monotelosomiese addissieplant is ook gekruis met die koringkultivar 'Gamtoos' wat die 1BL.1 RS-translokasie dra. Hoewel die 1RS segment van 'Gamtoos' die roesweerstandsgene, Sr31 en Lr26 uitdruk, is dit nie die geval met die 'Turkey 77' 1RS telosoom nie. Hierdie gene kon dus as merkergene gebruik word. Vanuit die F1 is 'n monotelosomiese 1RS addissieplant geselekteer wat ook heterosigoties was vir die 1BL.1 RStranslokasie. Hierdie plant is getoetskruis met 'n luisvatbare gewone broodkoring, 'Inia 66'. Meiotiese paring tussen die rogarms het daartoe gelei dat vyf euplo"lede Russiese koringluis-weerstandbiedende nageslag uit 99 euplo"lede nageslag geselekteer kon word. Een rekombinant het ook Sr31 en Lr26 behou en is toegelaat om self te bestuif. Met behulp van SDSPAGE profiele is Russiese koringluis-weerstandbiedende 1BL.1 RStranslokasie homosigote ge"ldentifiseer en kon bevestig word dat die weerstandsgeen vir die Russiese koringluis oorgedra is na die 1BL.1 RS ('Veery') -translokasie. Twee strategies is gevolg om die Russiese koringluislokus of -loci te karteer: (1) 'n Telosomiese analise is gedoen. 'n Plant met 2n = 40 + 1BL.1 RS + 1RS is verkry en met 'n luisvatbare koring bestuif. (2) 'n Gerekombineerde, disomiese plant met Russiese koringluis-weerstandbiedendheid maar sonder die Lr26 en Sr31 allele is gekruis met 'Gamtoos' en die F1 getoetskruis. Die toetskruisouer in beide die strategiee was 'Chinese Spring'. In die eerste eksperiment is die Sr31-lokus 10.42 kaarteenhede vanaf die Lr26-lokus gelokaliseer. Die raesdata het ge"impliseer dat onbetraubare genetiese kaarteenhede geskat sou word en daarom is die omslagtige Russiese koringluis weerstandsbepalings nie gedoen nie. In die tweede eksperiment is die Russiese koringluis-weerstandsgeen op 14.5 kaarteenhede vanaf die Lr26-lokus gelokaliseer. Nie-Mendeliese segregasie van die Russiese koringluis-weerstand in hierdie karteringseksperiment het ge'impliseer dat die berekende kaartafstand onakkuraat mag wees. Dit was ook nie moontlik om op grand van die data die aantal gene betrakke af te lei nie.

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19

Brière, Stéphan C. "Selection of partial resistance for crown rust (Puccinia ćoronata Cda.) race 264 in oat." Thesis, McGill University, 1992. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=60678.

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Nineteen cultivars and fourteen breeding lines were evaluated for partial resistance to crown rust Puccinia coronata race 264. Multivariate statistical methods such as principal component and cluster analyses were employed to identify significant resistance parameters and to group oat genotypes with similar rust resistance characteristics. This involved two separate investigations consisting of two experiments each, the first experiment conducted under field conditions and the second conducted under growth bench conditions. From both of the investigations a group of oat genotypes with high partial resistance to P. coronata race 264 was obtained. These are OA 712-17, OA 712-33, Glen, Woodstock, QO 220.13, and QO 574.21. These oat genotypes are currently being used as parents in crosses in the Macdonald Campus of McGill University oat breeding program.

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20

Abu-Nada, Yousef. "Metabolic profiling of potato cultivars varying in horizontal resistance to late blight, Phytophthora infestans." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=102947.

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Potato is one of the most important crops grown in Canada and all over the world. Late blight caused by P. infestans is one of the major diseases of potato and is mainly managed by fungicides application. The extensive use of fungicides not only causes adverse effects on the environment but also accelerates the development of resistance in this pathogen. Horizontal resistance is considered as the best choice to control P. infestans as it is durable over years. Breeding for durable resistance requires evaluation of hundreds of breeding lines in greenhouses and in the field. This is usually done by testing several epidemiological parameters such as infection efficiency, lesion size, latent period, and area under disease progress curve (AUDPC). These methods are time-consuming and expensive. The present study reports standardization of metabolic profiling protocols and exploration of metabolic profiling based on GC/MS as an additional tool to discriminate resistance in potato against late blight. Potato cultivars varying in horizontal resistance against late blight have been inoculated with water or the pathogen and more than 100 metabolites have been tentatively identified by GC/MS. Univariate analysis has been used to identify several pathogenesis related (PR) and defense related (DR) metabolites that have potential for application as resistance biomarker metabolites. Multivariate analysis of the abundances of metabolites (the mass spectral (MS) ion trap detector outputs were obtained using Saturn Lab Software Version 5.52 and these abundances are positively proportional to the concentration of mass ions of metabolites) in cultivars were mainly used to identify pathogenesis and resistance functions. Following pathogen inoculation, several metabolites such as amino acids, organic acids, fatty acids and sugars, were significantly increased in abundances, especially in the resistant cultivar. Other metabolites such as phenylalanine, tyrosine, shikimic acid and malonic acid detected here are well known for their direct participation in the shikimic acid, the phenylpropanoid, and the malonic acid metabolic pathways. These pathways lead to the production of several defense metabolites including antimicrobial compounds including phenolics, flavonoids and phytoalexins. The metabolic profiling technology developed here has the potential application for screening of potato breeding lines for horizontal resistance against late blight.

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21

Van, Staden Derick. "AFLP and PCR markers for the Ht1, Ht2, Ht3 and Htn1 resistance genes in maize." Thesis, Stellenbosch : Stellenbosch University, 2001. http://hdl.handle.net/10019.1/52078.

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Thesis (PhDAgric)--University of Stellenbosch, 2001. ENGLISH ABSTRACT: Maize is undoubtedly South Africa's most important field crop. The identification of markers and genes for traits of interest is important to sustain the improvement of maize cultivation. Northern corn leaf blight (NClB) is a disease that occurs worldwide and can dramatically reduce yield. A number of single dominant resistance genes have been identified for NClB and some have been mapped. Currently there are no simple PCR markers for any of these resistance genes, making markerassisted selection (MAS) difficult. The aim of this study was to develop PCR markers for the NClB resistance genes Ht1, Ht2, Ht3 and Htn1 in maize. To accomplish this, the AFlP (amplified fragment length polymorphism) technique was first optimised. The results indicated that the Mlul/Msel restriction enzyme combination produces a higher percentage of polymorph isms when compared to the PstllMsel enzyme combination. It was also shown that the enzyme combination plays an important role in the percentage of polymorphic fragments observed, whereas the number of restriction enzymes used in AFlP analysis only significantly affects the total number of fragments scored. Populations segregating for the different resistance genes were not available for this study. Nearly-isogenic lines (Nils) were used in combination with AFlP technology to identify markers that map close to the genes. AFlP markers common in at least two resistant or susceptible lines were cloned and converted to PCR markers. Two commercially available recombinant inbred line (Ril) populations were then used to map the identified markers. For Htn1 fifteen polymorphic fragments were present in both resistant lines. They were selected for sequence specific marker conversion. Seven of the fifteen sequence characterized amplified region (SCAR) markers were polymorphic on the Nil pairs and five mapped to one region of maize chromosome 8.05/06. Twenty-one AFlP markers were identified for Ht1 and four SCAR markers were polymorphic In the Ht1 Nils. Three of these were mapped to chromosome 2.07. Three AFlP markers were identified for Ht2 of which two were converted to SCAR markers. Both SCAR markers were polymorphic on the Ht2 Nils and mapped to chromosome 8.05/06. On the Ht3 NILs, four AFLP markers were identified and two converted SCAR markers and one microsatellite marker (bnlg1666) were polymorphic. One of the SCAR markers and the microsatellite marker were mapped to chromosome 7.04 using a RIL population. This reports the first tentative mapping position for the Ht3 locus. The next step was to determine if a set of marker alleles could be used in a number of Htn 1 resistance lines to identify a common donor region selected by the breeders. Nine markers consisting of five SCAR markers, three converted RFLP markers and one microsatellite marker were used on 16 Htn1 resistant lines. The marker allele of us3 was in 12 of the 16 lines in coupling with Htn1 resistance. Second was the marker us5 in 11 of the 16 lines. Using this data 14 of the 16 lines shared a common introgressed region between the markers us3 and us5. A further common introgressed region between 11 of the inbred lines was found between the markers us14 and asg17. The last aim of this study was to propose a new marker technique that might be more successful than the AFLP technique in the identification of markers closely linked to genes. A new marker approach was identified where a MITE (Hbr) primer was used as an anchor primer in combination with resistance gene analog primers. This was found to be a highly polymorphic marker technique that could be used to identify markers and possibly candidate genes. It is a robust technique, which is affordable since amplifications occur from undigested genomic DNA and the primers mainly amplify fragments from genic regions. AFRIKAANSE OPSOMMING: Mielies (Zea mays) is ongetwyfeld Suid Afrika se belangrikste lanbou gewas. Vir volgehoue opbrengs verbetering is die identifisering van merkers en gene vir belangrike eienskappe noodsaaklik. Noordelike blaarskroei (NBS) kan opbrengs wesenlik kan beïnvloed. Tans is daar reeds "n aantal enkel weerstandsgene geïdentifiseer, maar geen PKR-merkers is beskikbaar vir merker gebaseerde seleksie nie. Die doelwit van hierdie studie was om PKR-merkers te ontwikkel vir vier enkel weerstands gene (Ht1, Ht2, Ht3 en Htn1) teen NBS in mielies. Om die doelstelling te bereik is die AFLP-tegniek eers geoptimiseer. Op grond van waargenome aantal polimorfismes, was Mlul/Mse/"n beter restriksie ensiem kombinasie as Pstl/Msel. In die studie is ook bewys dat die aantal (meer as twee) restriksie ensieme wat gebruik word slegs die aantal fragmente, en nie die persentasie polimorfismes, wesenlik beïnvloed nie. Geen segregerende populasie was vir die verskillende gene beskikbaar nie. Naby isogeniese lyne (NILe) is daarom in kombinasie met die AFLP-tegniek gebruik om merkers te identifiseer wat naby die gene karteer. Alleenlik polimorfiese merkers wat in ten minste twee weerstand biedende of vatbare lyne voorgekom het, is gekloneer en omgeskakel na PKR-merkers. Daarna is twee kommersiële rekombinante ingeteelde lyn populasies gebruik om die gene te karteer. Vyftien fragmente is gevind wat gekoppel was met die Htn1 weerstand. Sewe van hierdie merkers is omgeskakel in polimorfiese SCAR-merkers waarvan vyf gekarteer is in een gebied op chromosoom 8.05/06. Een-en-twintig AFLP-merkers is geïndentifiseer vir Ht1 en vier is omgeskakel na polimorfiese SCAR-merkers. Drie hiervan is gekarteer op chromosoom 2.07. Drie AFLP-merkers is geïndetifiseer vir Ht2 waarvan 2 omgeskakel is na polimorfiese SCAR-merkers. Altwee hierdie merkers is gekarteer op chromosoom 8.05/06. Op die Ht3 lyne is vier AFLP-merkers geïdentifiseer waarvan twee omgeskakel is na polimorfiese SCAR-merkers. Een mikrosatelliet merker (bnlg1666) is ook gevind wat die selfde polimorfiese patroon wys op die Ht3 lyne. Die mikrosateliet en een van die SCAR-merkers het gekarteer op chromosomale posisie 7.04. Hierdie is die eerste tentatiewe posisie vir die Ht3 lokus. Die volgende stap was om te bepaal of "n stel polimorfiese merker-allele gebruik kan word om die donor DNA-segment te identifiseer wat die plantteiers geselekteer het. Nege PKR-merkers wat bestaan het uit vyf SCAR-merkers, 3 omgeskakelde RFLP merkers en een mikrosateliet is gebruik op 16 Hnt1 weerstandslyne. Us3 was die merker alleel wat in die meeste gevalle gekoppel was met die Htn1 weerstandslyne (12/16). Tweede was die merker us5 (in 11 van die 16 lyne). Uit die data blyk dit dat 14 van die 16 lyne "n donor segment het wat beide merkers us3 en us5 bevat. Merkers us14 en asg17 het in 11 van die 16 bestande lyne saam voorgekom. Die laaste doelstelling van hierdie studie was om "n nuwe tegniek te ontwikkel wat dalk meer suksesvol as AFLPs kan wees om merkers te identifiseer nabyaan gene. "n Nuwe tegniek word voorgestel waar "n MITE (Hbr) inleier gebruik kan word in kombinasie met weerstandgeen-analoog inleiers. Dit is gevind dat hierdie kombinasie van inleiers "n hoogs polimorfiese band patroon gee en dat die merkers ook dalk kandidaat-gene kan wees. Die tegniek is maklik uitvoerbaar, relatief goedkoop en maak gebruik van onverteerde genomiese DNA. Die fragmente wat geamplifiseer word is hoofsaaklik vanaf geenryke areas.

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22

Lehmensiek, Anke. "Genetic mapping of gray leaf spot resistance genes in maize." Thesis, Stellenbosch : Stellenbosch University, 2000. http://hdl.handle.net/10019.1/51776.

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Thesis (PhD)--Stellenbosch University, 2000. ENGLISH ABSTRACT: Gray leaf spot (GLS) of maize, caused by the fungus Cercospora zeae-maydis, can reduce grain yields by up to 60% and it is now recognized as one of the most significant yield-limiting diseases of maize in many parts of the world. The most sustainable and long-term management strategy for GLS will rely heavily on the development of high-yielding, locally adapted GLS resistant hybrids. Molecular markers could be useful to plant breeders to indirectly select for genes affecting GLS resistance and to identify resistance genes without inoculation and at an early stage of plant development. Only two studies in the USA have examined quantitative trait loci (QTL) association with GLS resistance. The aim of this study was to map GLS resistance genes in a resistant Seed Co LTD, Zimbabwean inbred line. Molecular markers linked to the GLS resistance QTL were identified by using the amplified fragment length polymorphism (AFLP) technique together with bulked segregant analysis. Eleven polymorphic AFLP fragments were identified and converted to sequence-specific PCR (polymerase chain reaction) markers. Eight of the 11 converted AFLP markers were added to the maize marker database of the University of Stellenbosch. Five of the 8 converted AFLP markers were polymorphic between the resistant and the susceptible parent. They were amplified on the DNA of 230 plants of a segregating F2 population and linkage analysis was performed with MAPMAKER/EXP. Two linkage groups consisting of two markers each, with a linkage distance of 10.4 cM (LOD 22.83) and 8.2 cM (LOD 55.41) between the two markers, were identified. QTL mapping with MAPMAKER/QTL confirmed the presence of QTL in both linkage groups. Two publicly available recombinant inbred families (Burr et a/., 1988) were used to localize the converted AFLP markers on the genetic map of maize. The QTL, which were identified with the AFLP markers, were mapped to chromosomes 1 and 5. Another AFLP marker was mapped to chromosome 2 and a further to chromosome 3. To obtain more precise localizations of the QTL on chromosomes 1 and 5, sequence-tagged site markers and microsatellite markers were used. The markers were amplified on the DNA of the 230 plants of the F2 population and linkage analysis was performed with MAPMAKER/EXP. The order of the markers was in agreement with the UMC map of the Maize Genome Database. Interval mapping using MAPMAKERlQTL and composite interval mapping using QTL Cartographer were performed. The QTL on chromosome 1 had a LOD score of 21 and was localized in bin 1.05/06. A variance of 37% was explained by the QTL. Two peaks were visible for the QTL on chromosome 5, one was localized in bin 5.03/04 and the other in bin 5.05/06. Both peaks had a LOD score of 5 and 11% of the variance was explained by the QTL. To test the consistency of the detected QTL, the markers flanking each QTL were amplified on selected plants of two F2 populations planted in consecutive years and regression analysis was performed. Both the QTL on chromosome 1 and the QTL on chromosome 5 were detected in these populations. Furthermore, the presence of a QTL on chromosome 3 was confirmed with these populations. A variance of 8 -10% was explained by the QTL on chromosome 3. In this study, a major GLS resistance QTL was thus mapped on chromosomes 1 and two minor GLS resistance QTL were mapped on chromosomes 3 and 5 using a resistant Seed Co LTD, Zimbabwean inbred line. Markers were identified which could be used in a marker-assisted selection program to select for the GLS resistance QTL. AFRIKAANSE OPSOMMING: Grys blaarvlek (GBV) van mielies, veroorsaak deur die swam Cercospora zeaemaydis, kan graanopbrengs met tot 60% verlaag en word beskou as een van die vernaamste opbrengs-beperkende siektes wêreldwyd. Die toepaslikste langtermyn stragtegie vir GBV beheer sal wees om plaaslike mieliebasters met hoë opbrengs en GBV weerstand te ontwikkel. Molekulêre merkers kan nuttig deur plantetelers gebruik word om weerstandsgene te selekteer. Seleksie is moontlik in die afwesigheid van inokolum en op 'n vroeë stadium van plant ontwikkeling. Slegs twee vorige studies (in die VSA) het kwantitatiewe-kenmerk-Iokusse (KKL), vir GBVweerstand ondersoek. Die doel van hierdie studie was om die GBV weerstandsgene in 'n weerstandbiedende ingeteelde lyn (Seed Co BPK, Zimbabwe) te karteer. Molekulêre merkers gekoppel aan die GBV weerstands KKL is geïdentifiseer deur gebruik te maak van die geamplifiseerde-fragmentlengte-polimorfisme- (AFLP-) tegniek en gebulkte-segregaat-analise. Elf polimorfiese merkers is geïdentifiseer en omgeskakel na volgorde-spesifieke PKR (polimerase kettingreaksie) merkers. Agt van die elf omgeskakelde AFLP-merkers is by die mieliemerker databasis van die Universiteit van Stellenbosch gevoeg. Vyf van die 8 omgeskakelde AFLP-merkers was polimorfies tussen die bestande en vatbare ouers. Hulle is geamplifiseer op die DNA van 230 plante van 'n segregerende F2-populasie en is gebruik in 'n koppelingstudie met MAPMAKER/EXP. Twee koppelingsgroepe, elk bestaande uit twee merkers, met onderskeidelik koppelingsafstande van 10.4 eM (LOD 22.83) en 8.2 eM (LOD 55.41) tussen die merkers, is geïdentifiseer. KKL-kartering het getoon dat KKL in albei koppelingsgroepe aanwesig is. Twee kommersieël beskikbare, rekombinant-ingeteelde families (Burr et aI., 1988) is gebruik om die omgeskakelde AFLP-merkers op die mielie genetiese kaart te plaas. Die KKL wat met die AFLP-merkers geïdentifiseer is, is gekarteer op chromosome 1 en 5. 'n Verdere AFLP-merker is op chromosoom 2 gekarteer en 'n ander op chromosoom 3. Ten einde die KKL op chromosome 1 en 5 meer akkuraat te karteer, is volgordege- etikeerde en mikrosatelliet merkers gebruik. Die merkers is geamplifiseer op die DNA van die 230 plante van die F2-populasie en koppelings-analises is uitgevoer. Die volgorde van die merkers was dieselfde as die van die UMC-kaart in die Mielie Genoom Databasis. Interval kartering met MAPMAKER/QTL en komposiet interval kartering met QTL Cartographer is uitgevoer. Die KKL op chromosoom 1 het 'n LOD-telling van 21 gehad en is in bin 1.05/06 geplaas. Die KKL was verantwoordelik vir 37% van die variansie. Twee pieke was onderskeibaar vir die KKL op chromosoom 5, een in bin 5.03/04 geleë en die ander in bin 5.05/06. Elke piek het 'n LOD-telling van 5 gehad en die twee KKL was verantwoordelik vir 11% van die variansie. Om die herhaalbaarheid van die effek van die KKL te toets is die merkers naaste aan elke KKL geamplifiseer op geselekteerde plante van twee F2-populasies wat in opeenvolgende jare geplant is. Regressie analise is op die data gedoen. Beide die KKL op chromosoom 1 en die KKL op chromosoom 5 kon in hierdie populasies geïdentifiseer word. Verder kon die aanwesigheid van 'n verdere KKL op chromosoom 3 in hierdie populasies bevestig word. Laasgenoemde KKL was verantwoordelik vir 8-10% van die totale variansie. In hierdie studie is daar dus 'n hoof GBV-weerstands KKL gekarteer op chromosoom 1 en twee kleiner GBV-weerstands KKL gekarteer op chromosome 3 en 5. Merkers is geïdentifiseer wat moontlik in merker-gebaseerdetelingsprogramme gebruik kan word om plante te selekteer wat die GBVweerstands KKL het.

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23

Krsikapa, Nenad. "Variation for resistance to Fusarium graminearum ear rot in selfed families from the corn population Zapalote Chico." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0021/MQ37137.pdf.

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24

Marino, Dante. "Screening of Germplasm Accessions from the Brassica Species for Resistance against PG3 and PG4 Isolates of Blackleg." Thesis, North Dakota State University, 2011. https://hdl.handle.net/10365/29053.

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Blackleg is a disease of canola and rapeseed cultivars that is caused by the fungus Leptosphaeria maculans (Desm.) Ces. & de Not., and it is by far the most destructive pathogen of canola in North America. In recent years, blackleg strains belonging to pathogenicity groups (PG) 3 and 4 have been discovered in North Dakota. Recent outbreaks of the disease have added a sense of urgency to characterize the risk these new strains represent for the canola industry and to identify sources of resistance against them. Thus, the objectives of this study were to screen germplasm collections of Brassica rapa, B. napus. and B. juncea for their reaction to PG3 and PG4 and to evaluate the reaction of a sample of currently used canola commercial cultivars grown in North Dakota to PG3 and PG4 as means to estimate the risk these new strains represent. All canola germplasm and commercial cultivars were evaluated in replicated trials in greenhouse conditions using cotyledon bioassays. In 2009 and 2010, the effect of these strains, using five inoculation sequences, on the reaction of canola seedlings was also evaluated. Field trials were not conducted because of the limited geographical distribution of the new strains. No adequate sources of resistance were identified among the 277 B. rapa and 130 B. napus accessions evaluated; however, 22 of the 406 accessions of Brassicajuncea evaluated were considered to have moderate levels of resistance. B. juncea seedlings that survived these inoculations were self-pollinated and their progeny (F1) were also screened. As before, surviving seedlings were self-pollinated. These F2 seeds are the elite materials that could be used in future breeding programs. The complementary study evaluating the role of sequence inoculations in reaction of canola seedlings to blackleg indicated that an increased susceptibility to PG3 occurred when seedlings were first inoculated with PG4; however, reaction to PG4 was not enhanced by a prior inoculation with PG3. All 75 commercial cultivars evaluated were susceptible to PG3 and PG4, indicating that the risk these new strains represent to the canola industry of the region is serious. Further, when a subsample of 16 cultivars were challenged with PG2, they were either resistant or moderately resistant, suggesting the ratings the industry are using relate to reaction of those cultivars to PG2 but not to the new strains; thus, growers should use caution when using these ratings while deciding on which cultivars to plant. North Dakota State University. Department of Plant Pathology USDA North Central Canola Research Program Northern Canola Growers Association

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25

Hinga, Clark D. "Genetic analysis of resistance to Myzus persicae (Sulzer) in Nicotiana tabacum L." Thesis, Virginia Tech, 1985. http://hdl.handle.net/10919/41552.

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Field experiments with the green peach aphid on tobacco were conducted at Blackstone, Virginia in 1983 and 1984. The objectives were to: 1) confirm and identify source materials resistant to the green peach aphid; 2) study the inheritance of aphid resistance; 3) verify heritability of resistant genotypes through F2 and advanced generation testing and 4) investigate the nature of the resistance. Results showed green peach aphid resistance in Tobacco Introductions 1462, 1118, 1112, 1024, breeding line 1-35 and cultivar NC 745. Inheritance studies showed that the resistance is a recessive trait controlled by three separate, non-linked loci; such that a homozygous recessive at any one locus will condition for the resistance reaction. Among the source materials, one locus conditioned the resistance shown by TI 1118, TI 1112 and breeding line I-35. A second independent locus conditioned the found in TI 1024 and a third independent locus conditioned the resistance observed in NC 745. Tobacco Introduction 1462 possessed alleles for resistance at both the second and third loci. Small aphid cages were of questionable value for studying the resistance reaction. Higher leaf temperatures were noted for the caged leaf surfaces and may be responsible for the unreliable results. Evaluation of F2, F3, F5, F5 populations developed from resistant x susceptible crosses indicated that aphid resistance is a heritable trait and is not closely linked to adverse agronomic quality characteristics. Master of Science

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26

Bierman, Anandi. "Mapping and survey sequencing of Dn resistance genes in Triticum aestivum L." Thesis, Stellenbosch : Stellenbosch University, 2015. http://hdl.handle.net/10019.1/96912.

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Thesis (PhD)--Stellenbosch University, 2015 ENGLISH ABSTRACT : Diuraphis noxia Kurdjumov (Russian Wheat Aphid; RWA) is a pest of wheat and barley that has spread from its home range in the fertile crescent to most wheat producing countries except Australia. Since its first introduction to South Africa and the USA in the late 20th century, breeding programs for wheat phenotypes resistant to the aphid were put in place. Conventional breeding practices rely on phenotypic screening to verify traits carried by offspring and genetic tools such as marker assisted selection (MAS) have greatly aided this process in speed and accuracy. The size and complexity of the wheat genome, its allopolyploid nature and repetitive elements have, however, posed a challenge to studies on the genetics of this cereal crop. Many studies have focused on chromosome 3B which is the largest of the wheat chromosomes and easily separated from the redundant genomic background by techniques such as flow cytometry. The similarity in size of the remaining chromosomes however, limits the application of flow cytometry to their isolation. Databases such as Grain-Genes (http://wheat.pw.usda.gov/GG2/index.shtml) house marker data from various mapping studies for all wheat chromosomes and in 2014 the International Wheat Genome Sequencing Consortium (IWGSC) completed the draft genome sequence of wheat categorized by chromosome. Sources of resistance (Dn resistance genes) against RWA are located on chromosome 7D. but despite the marker and sequence data available currently, mapping studies specific for the Dn resistance genes are few. Additionally, sequence data available is derived from cultivars susceptible to RWA and is not comprehensively annotated and assembled in many cases. In this study, we demonstrate a novel, combined approach to isolate and characterize the Dn resistance genes through the use of a genetic map constructed from Amplified Fragment Length Polymorphism (AFLP), Expressed Sequence Tag (EST) and microsatellite markers and a physical map constructed from Next Generation Sequencing (NGS) data of ditelosomic chromosomes (7DS and 7DL) isolated by microdissection on the PALM microbeam system. A 122.8 cM genetic map was produced from 38 polymorphic AFLP markers and two ESTs with the microsatellite Xgwm111 as anchor to related genetic maps. Through comparison to maps available on GrainGenes the location of the Dn1 resistance gene was narrowed down to a deletion bin (7DS5-0.36-0.62) on the short arm of chromosome 7D with an AFLP marker (E-ACT/M-CTG_0270.84) mapping closely at 3.5 cM and two ESTs mapping at 15.3 cM and 15.9 cM from Dn1. Isolation of individual chromosome arms 7DS and 7DL using the PALM Microbeam system allowed sequencing of the chromosome without the redundancy of the remainder of the hexaploid genome. Through isolating the chromosome arms in this way, a >80-fold reduction in genome size was achieved as well as a major reduction in repetitive elements. Analysis of the sequencing data confirmed that 7DL is the physically shorter arm of the chromosome though it contains the majority of protein coding sequences. AFRIKAANSE OPSOMMING : Diuraphis noxia Kurdjumov (Russiese koring-luis; RWA) is « pes wat op koring en gars voorkom. Die pes het vanaf sy tuiste in die midde Ooste na meeste koringproduserende lande behalwe Australië versprei. Sedert die eerste bekendstelling van RWA in Suid Afrika en die VSA in die vroeë 20ste eeu is teelprogramme ten gunste van koring lyne met weerstand teen RWA begin. Tradisionele teelprogramme maak op fisieise observasie van die fenotipe staat om te verifieer of plante in die nageslag die gewenste eienskap dra. Genetiese metodes soos merkerondersteunde seleksie (MAS) versnel hierdie selekteringsproses grootliks. Die grootte en kompleksiteit van die koring genoom asook die polyploïde en herhalende natuur daarvan is « groot hindernis vir genetiese studies van hierdie graangewas. Baie studies het op chromosoom 3B gefokus wat die grootste van die koring chromosome is en dus maklik vanaf die res van die oorbodige genomiese agtergond deur tegnieke soos vloeisitometrie geskei word. Die ooreenkoms in grootte tussen die res van die chromosome bemoeilik die toepassing van vloeisitometrie om hulle te isoleer. Databasisse soos GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml) bevat merker data vanaf verskeie karterings-studies vir al die chromosome en in 2014 het die "International Wheat Genome Sequencing Consortium"(IWGSC) die voorlopige basispaarvolgorde van die koring genoom bekendgestel, gekategoriseer volgens chromosoom. Weerstandsbronne (Dn weerstandsgene) teen RWA kom meestal op chromosoom 7D voor. Ten spyte van merker en basispaarvolgorde data tans beskikbaar is karterings-studies spesifiek tot die Dn gene skaars en basispaarvolgorde data is vanaf kultivars afkomstig wat nie weerstandbiedend teen RWA is nie en waarvan die annotasie en samestelling baie keer nie goed is nie. In hierdie studie demonstreer ons « nuwe, gekombineerde aanslag om die Dn weerstandsgene te isoleer en karakteriseer deur van « genetiese kaart opgestel met "Amplified Fragment Length Polymorphism"(AFLP), "Expressed Sequence Tag"(EST) en mikrosatelliet merkers asook « fisiese kaart saamgestel deur die volgende-generasiebasispaarvolgordebepaling van ditelosomiese chromosome (7DS en 7DL) geïsoleer deur mikrodisseksie met die "PALM Microbeam"sisteem gebruik te maak. « Genetiese kaart van 122.8 cM was met 38 polimorfiese AFLP merkers en twee EST merkers geskep. Die mikrosatelliet, Xgwm111, is ook ingesluit en het as anker vir verwante genetiese-kaarte gedien. Deur vergelyking met genetiese-kaarte op GrainGenes is die posisie van die Dn1 weerstandsgeen vernou na « delesie bin (7DS5-0.36-0.62) op die kort arm van chromosoom 7D met « AFLP merker (EACT/ M-CTG_0270.84) wat ongeveer 3.5 cM vanaf die geen karteer. Die twee EST merkers is 15.3 cM en 15.9 cM vanaf die geen gekarteer. Isolering van die individuele chromosoom arms, 7DS en 7DL, deur van die "PALM Microbeam"sisteem gebruik te maak het basispaarvolgordebepaling van die chromosoom toegelaat sonder die oortolligheid van die res van die hexaploïde genoom. Deur die chromosoom so te isoleer is « >80-maal verkleining in genoom grootte bereik insluitend « groot reduksie in herhalende elemente. Analise van die data vanaf basispaarvolgordebepaling het bevestig dat chromosoom 7D die fisiese kleiner chromosoom is maar dat dit die meerderheid van proteïn koderende basispaarvolgordes bevat.

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27

Montesclaros, Luz B. "Mapping of molecular markers surrounding the Tu gene conferring resistance to turnip mosaic virus in Lactuca sativa L." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=23923.

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In lettuce (Lactuca sativa), the dominant gene Tu confers resistance to turnip mosaic virus (TuMV) infection. In order to eventually clone and characterize the Tu gene using a map-based cloning strategy, the chromosome region in which Tu is located needs to be saturated with molecular markers. Random polymorphic DNA (RAPD) markers were screened using bulked segregant analysis. Nine new RAPD markers, UBC431$ rm sb{420}, UBC431 sb{940}, UBC434 sb{360}, UBC434 sb{1000}, UBC439 sb{520}, UBC448 sb{685:750}, UBC135 sb{240}, OP108 sb{410} and OP108 sb{1305},$ were identified as linked to Tu. Each marker was mapped relative to Tu using F$ sb2$ individuals previously known to be recombinant in the area surrounding the Tu locus. Three new markers, UBC431$ rm sb{420}, UBC439 sb{520} and UBC135 sb{240}$ are within a 5 cM area of Tu. As the number of DNA markers on the map increased map expansion and difficulties in determining a unique order were encountered. To increase the confidence in the estimate of genetic distances, a population of 500 F$ sb2$ plants was screened in order to identify more recombinant individuals around the Tu locus. The population was screened using markers UBC431$ sb{420}$ and UBC135$ sb{240}.$ Thirty-three recombinants were identified in an interval of 6.6 cM. Two markers, UBC346$ sb{1067}$ and OP108$ sb{634},$ tightly flanking Tu were converted to sequence characterized amplified regions (SCAR 346 and SCAR L08). No polymorphism was detected among the SCARs generated. The area surrounding Tu now includes 24 RAPD markers in an interval of 44 cM.

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28

Williams, Kevin John. "Biological and genetic studies of wheat resistance to Heterodera avenae." Title page, summary and contents only, 1994. http://web4.library.adelaide.edu.au/theses/09PH/09phw7238.pdf.

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29

Deng, Yinghai 1966. "Development and disease resistance of leafy reduced stature maize (Zea mays L.)." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=38177.

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Previous studies on Leafy reduced-stature (LRS) maize found that it had extremely early maturity and a higher harvest index (HI), leading to high yields for its maturity rating. Whether this apparent high HI is relaxed to its earliness, or can also exist among the medium or late maturity LRS maize has not been previously investigated. It was also of interest to know if the traits that produced the LRS canopy structure have pleiotropic effects on root architecture. Finally, field observations indicated that LRS maize had a lower incidence of common smut. It is not known whether this apparent resistance is specific to smut or includes other diseases. Using a wide range of the most recently developed LRS hybrids and some conventional hybrids, a two-year field experiment was conducted to examine the HI and disease resistance of LRS maize. HI, yield, and yield components were compared between the two genotype groups (LRS and conventional) under different population densities. The resistance to the natural incidence of common smut and artificially inoculated Gibberella ear rot was also tested. Morphology and fractal dimension analyses of roots at an early development stage were conducted in indoor experiments. These analyses were performed with WinRHIZO (version 3.9), an interactive scanner-based image analysis system. This work showed that: (1) There was no relationship between the HI and maturity; higher HIs can also exist among the medium and late maturity LRS hybrids. (2) While LRS maize hybrids have the potential for high yield this was not realized in the LRS hybrids used in this work. Further breeding and development of optimum management practices are needed to fully exploit this potential. (3) During early development LRS hybrids generally had more branching and more complex root systems than conventional hybrids. (4) Fractal dimension, as a comprehensive estimation of root complexity, was highly related to major root morphological variables, such as root total length, surface area, branching frequency and dry mass. (5) Of the hybrids tested the greatest resistance to both common smut and Gibberella ear rot, two major ear diseases, occurred in some of the LRS types.

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30

Robbins, Marjorie. "The location of Tu on the genetic map of Lactuca sativa and the identification of random amplified polymorphic DNA markers flanking and tightly linked to Tu /." Thesis, McGill University, 1993. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=69684.

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In Lactuca sativa, the dominant gene Tu confers resistance to infection by turnip mosaic virus (TuMV). Tu and Dm5/8, a gene for resistance to Bremia lactucae, are linked in L. sativa. The area surrounding Dm5/8 on the genetic map of L. sativa contains restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers. The orientation of Tu relative to Dm5/8 was not known. Locating Tu would indicate which markers are on the map of lettuce close to Tu. To locate Tu on the L. sativa genetic map, F$ sb3$ families from recombinant F$ sb2$ in the Dm5/8 area of a cross between TuMV-resistant (Cobbham Green) and susceptible (Calmar) cultivars were inoculated with TuMV and phenotyped for Tu by indirect enzyme-linked immunosorbent assay. Polyclonal antibodies for immunodetection were produced using turnip mosaic virus coat protein expressed in E. coli. Phenotypic ratios within F$ sb3$ families were used to determine individual F$ sb2$ genotypes for Tu. With these genotypes, Tu was located on the genetic map of L. sativa relative to data present for Dm5/8 and surrounding markers, between OPM18 and OPY13. Using bulked segregant analysis, bulks created for the Dm5/8 locus were screened for genetic polymorphisms by the RAPD technique. Five new RAPD markers, UBC346, UBC517, UBC563, UBC599, and UBC675 were found linked to Tu after mapping relative to F$ sb2$ genotypes for Tu and other RAPD markers. The resulting three-point mapping information indicates that Tu is flanked by two markers, OPM18/OPL08 and UBC346, at respective genetic distances of 0.4 and 0.7 cM.

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31

Van, Eeden C. (Christiaan). "The construction of gene silencing transformation vectors for the introduction of multiple-virus resistance in grapevines." Thesis, Stellenbosch : Stellenbosch University, 2004. http://hdl.handle.net/10019.1/53764.

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Thesis (MSc)--University of Stellenbosch, 2004. ENGLISH ABSTRACT: Viruses are some of the most important pathogens of grapevines. There are no effective chemical treatments, and no grapevine- or other natural resistance genes have been discovered against grapevine infecting viruses. The primary method of grapevine virus control is prevention by biological indexing and molecular- and serological screening of rootstocks and scions before propagation. Due to the spread of grapevine viruses through insect vectors, and in the case of GRSPaV the absence of serological screening, these methods of virus control are not always effective. In the past several methods, from cross-protection to pathogen derived resistance (PDR), have been applied to induce plant virus resistance, but with inconsistent results. In recent years the application of post-transcriptional gene silencing (PTGS), a naturally occurring plant defense mechanism, to induce targeted virus resistance has achieved great success. The Waterhouse research group has designed plant transformation vectors that facilitate specific virus resistance through PTGS. The primary focus of this study was the production of virus specific transformation vectors for the introduction of grapevine virus resistance. The Waterhouse system has been successfully utilised for the construction of three transformation vectors with the pHannibal vector as backbone. Each vector contains homologous virus coat protein (CP) gene segments, cloned in a complementary conformation upstream and downstream of an intron sequence. The primary vector (pHann-SAScon) contains complementary CP gene segments of both GRSPaV and GLRaV-3 and was designed for the introduction of multiple-virus resistance. For the construction of the primary vector the GRSPaV CP gene was isolated from RSP infected grapevines. A clone of the GLRaV-3 CP gene was acquired. The second vector (pHann- LR3CPsas) contains complementary CP gene segments of GLRaV-3. The third vector (pHann-LR2CPsas) contains complementary CP gene segments of GLRaV-2. The cassette containing the complementary CP gene segments of both GRSPaV and GLRaV-3 was cloned into pART27 (pART27-HSAScon), and used to transform N tabacum cv. Petit Havana (SRI), through A. tumefaciens mediated transformation. Unfortunately potential transformants failed to regenerate on rooting media; hence no molecular tests were performed to confirm transformation. Once successful transformants are generated, infection with a recombinant virus vector (consisting of PYX, the GFP gene as screenable marker and the complementary CP gene segments of both GRSPaV and GLRaV-3) will be used to test for the efficacy of the vectors to induce resistance. A secondary aim was added to this project when a need was identified within the South African viticulture industry for GRSPaV specific antibodies to be used in serological screening. To facilitate future serological detection of GRSPaV, the CP gene was isolated and expressed with a bacterial expression system (pETI4b) within the E. coli BL2I(DE3)pLysS cell line. The expressed protein will be used to generate GRSPaV CP specific antibodies. AFRIKAANSE OPSOMMING: Virusse is van die belangrikste patogene by wingerd. Daar bestaan geen effektiewe chemiese beheer nie, en geen wingerd- of ander natuurlike weerstandsgene teen wingerdvirusse is al ontdek nie. Die primêre metode van beheer t.o.v. wingerdvirusse is voorkoming deur biologiese indeksering, en molekulêre- en serologiese toetsing van onderstokke en entlote voor verspreiding. As gevolg van die verspreiding van wingerdvirusse deur insekvektore, en in die geval van GRSPa V die tekort aan serologiese toetsing, is dié metodes van virusbeheer nie altyd effektief nie. In die verlede is metodes soos kruis-beskerming en patogeen-afgeleide weerstand (PDR) gebruik om virusweerstand te induseer, maar met inkonsekwente resultate. In onlangse jare is post-transkripsionele geenonderdrukking (PTGS), 'n natuurlike plantbeskermingsmeganisme, met groot sukses toegepas om geteikende virusweerstand te induseer. Die Waterhouse-navorsingsgroep het planttransformasievektore ontwerp wat spesifieke virusweerstand induseer d.m.v. PTGS. Die vervaardiging van virus spesifieke tranformasievektore vir die indusering van wingerdvirusweerstand was die primêre doelwit van hierdie studie. Die Waterhouse-sisteem was gebruik vir die konstruksie van drie transformasievektore, met die pHannibal vektor as basis. Elke vektor bevat homoloë virus kapsiedproteïen (CP) geensegmente, gekloneer in 'n komplementêre vorm stroom-op en stroom-af van 'n intronvolgorde. Die primêre vektor (pHann-SAScon) bevat komplementêre CP geensegmente van beide GRSPaV en GLRaV-3, en was ontwerp vir die indusering van veelvoudige-virusweerstand. Die CP-geen van GRSPa V was vanuit RSP-geïnfekteerde wingerd geïsoleer, vir die konstruksie van die primêre vektor. 'n Kloon van die GLRa V-3 CP-geen was verkry. Die tweede vektor (pHann-LR3CPsas) bevat komplementêre CP geensegmente van GLRaV-3. Die derde vektor (pHann-LR2CPsas) bevat komplementêre CP geensegmente van GLRa V-2. Die kasset bestaande uit die komplementêre CP geensegmente van beide GRSPaV en GLRaV-3, was gekloneer in pART27 (pART27-HSAScon), en gebruik om N tabacum cv. Petit Havana (SRI) te transformeer d.m.v. A. tumefaciens bemiddelde transformasie. Ongelukkig het potensiële transformante nie geregenereer op bewortelingsmedia nie; gevolglik was geen molekulêre toetse gedoen om transformasie te bevestig nie. Na suksesvolle transformante gegenereer is, sal infeksie met 'n rekombinante-virusvektor (bestaande uit PYX, die GFP geen as waarneembare merker en die komplementêre CP geensegmente van beide GRSPa V en GLRa V-3) gebruik word om die effektiwiteit van die vektore as weerstandsinduseerders te toets. 'n Sekondêre doelwit is by die projek gevoeg toe 'n behoefte aan GRSPaV spesifieke teenliggame binne die Suid-Afrikaanse wynbedryf geïdentifiseer is, vir gebruik in serologiese toetsing. Om toekomstige serologiese toetsing van GRSPa V te bemiddel, was die CP-geen geïsoleer en in 'n bakteriële uitdrukkingsisteem (PETI4b) uitgedruk, in die E. coli BL21(DE3)pLysS sellyn. Die uitgedrukte proteïne sal gebruik word vir die vervaardiging van GRSPa V CP spesifieke antiliggame.

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32

Joubert, Dirk Albert 1973. "Regulation of the Vitis vinifera PGIP1 gene encoding a polygalacturonase-inhibiting protein." Thesis, Stellenbosch : Stellenbosch University, 2004. http://hdl.handle.net/10019.1/53759.

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Thesis (PhD)--University of Stellenbosch, 2004. ENGLISH ABSTRACT: Plant-pathogen interactions have been intensively investigated in the last decade. This major drive towards understanding the fundamental aspects involved in plant disease resistance is propelled by the obvious agricultural and economical benefits that are intrinsically linked to disease and stress resistant plants. It is, therefore, not surprising that fundamental research in this area is not just restricted to model organisms, such as Arabidopsis and tobacco, but also extends to more traditional crop plants, such as maize, bean, soybean, apples, grapevine etc. In grapevine for instance, several genes involved in disease resistance have been isolated. One of these genes, encoding for a polygalacturonase inhibiting protein (PGIP), has been studied extensively. PGIPs are cell wall bound, contain leucine rich repeats (LRR) and are found in all dicotyledonous plants so far examined. In most cases, pgip genes occur in small multigene families and expression is often tissue specific and developmentally regulated. Up-regulation of PGIP-encoding genes typically occurs upon pathogen infection, treatment with elicitors, salicylic acid (SA), jasmonic acid (JA), cold treatment and wounding. Differential regulation and specificity have been shown to occur between members of the same multigene family. Differential regulation even extends to the utilization of separate pathways to induce pgip genes from the same family in response to a single stress stimulus. PGIPs interact with cell wall macerating polygalacturonases (PGs) that are secreted by pathogenic fungi during the infection process. The antifungal action of PGIPs is thought to depend on a dual action. The physical interaction of PGIP with PGs has an inhibitionary effect, resulting in (i) a slower fungal infection rate and (ii) the prolonged existence of long chain oligogalacturonides (OGs). These oligosaccharides are able to elicit a general plant defense response, enabling the plant to further retard or curb the spread of infection. The main objective of this study was to investigate the regulatory aspects underlying PGIP expression in grapevine. Unlike most characterized PGIP encoding genes from other dicotyledonous plant species, no evidence to support the existence of a V. vinifera PGIP multigene family could be found from either genetic or biochemical analyses. Recently, a genomic DNA fragment from Vitis vinifera cv Pinotage was pathogen interactions with regards to the fundamental processes underlying defense gene regulation. AFRIKAANSE OPSOMMING: Die ooglopende voordele wat, vanuit 'n landboukundige én ekonomiese oogpunt, uit siekte- en stresbestande plante spruit, het gedurende die laaste dekade aanleiding gegee tot die ontwikkeling van plantpatogeen-interaksies as "n baie belangrike studieveld. Dit was dus ook te verwagte dat fundamentele navorsing in hierdie area nie net beperk gebly het tot modelorganismes soos Arabidopsis en tabak (ook natuurlik van landboukundige belang) nie, maar ook na meer tradisionele landbougewasse soos mielies, boontjies, sojaboontjies, appels, druiwe, ens. oorgevloei het. Verskeie siekteweerstands-verwante gene is byvoorbeeld al vanuit wingerd geïsoleer. Een só "n geen wat vir "n poligalakturonase-inhiberende proteïen (PGIP) kodeer, vorm deel van hierdie groep gene. Die funksie en regulering van PGIP's is baie goed bestudeer. Hierdie proteïene word normaalweg in die selwande van die meeste dikotiele plante aangetref. Leusienryke herhalings is algemeen in PGIP's en hierdie tipe van herhalings is kenmerkend van proteïene betrokke by proteïen-proteïen-interaksies. Verder word pgip-gene gewoonlik in klein multigeenfamilies aangetref, waar in die meeste gevalle die uitdrukking weefselspesifiek en die regulering spesifiek ten opsigte van die ontwikkelingsfase is. Verskeie faktore kan tot die induksie van pgip-gene lei, soos onder andere patogeen-infeksie, elisitoor-, salisiensuur-, jasmoonsuur- en kouebehandeling, asook verwonding. Differensiële regulering word in baie gevalle tussen lede van dieselfde multigeenfamilie aangetref. Hierdie differensiële regulering kan selfs bemiddel word deur onafhanklike reguleringsweë in reaksie op dieselfde induksiestimulus. PGIP's is in staat om te reageer met poligalakturonases (PGs), wat selwande afbreek en wat gedurende die infeksieproses deur swamme of fungi afgeskei word. Die effek van hierdie interaksie is tweeledig: (i) Die fisiese interaksie tussen PGIP en PG moduleer die aktiwiteit van die PG deur die ensiemaksie te inhibeer, en (ii) PGinhibisie lei tot die verhoogde stabiliteit van langketting-oligogalakturonades, molekules wat daartoe in staat is om die weerstandsrespons van plante te ontlok. Die inhibisie van die patogeen-PG's, tesame met die geïnduseerde weerstandrespons, stel die plant dan in staat om verdere infeksie te vertraag of te verhoed. Die doel van hierdie studie was om die onderliggende aspekte van PGIPregulering in wingerd te bestudeer. In teenstelling met die meeste plantspesies waar pgip-gene in klein multigeenfamilies aangetref word, is daar nie 'n pgip-multigeenfamilie in wingerd nie. Veelvuldige kopieë van In enkele pgip-geen word egter in die wingerdgenoom aangetref. Daar is onlangs in ons laboratorium In genoom-DNAfragment vanaf Vitis vinifera cv Pinotage geïsoleer wat die oopleesraam en 5'-stroomopsekwense van In PGIP-enkoderende geen (Vvpgip1) bevat. In hierdie studie is die uitdrukkingspatroon van Vvpgip1 ten opsigte van weefselspesifisiteit, korrelontwikkelingsfase, asook die effek van verskeie omgewings en patogeenverwante stres-stimuli ontleed. Die regulatoriese meganismes van Vvpgip1 bevat spesifieke in planta-ontwikkelingsfaseseine wat verder deur spesifieke faktore, insluitende omgewings- en patogeenstres, gereguleer word. In lyn hiermee is mRNS-transkripte van Vvpgip1 tot wortel- en korrelweefsels beperk, terwyl die mRNS-vlakke ook tussen verskillende korrelontwikkelingsfases wissel. Kumulatiewe uitdrukking kon waargeneem word in veráison-korrels in reaksie op verwonding en osmotiese stres. Die weefselspesifieke uitdrukkingspatroon tipies van wingerd-PGIP is in blare opgehef in reaksie op Botrytis cinerea-infeksie, verwonding, osmotiese stres, ouksien (indoolasynsuur) en salisiensuur. PGIP-uitdrukking word ook onderdruk deur In staurosporien-sensitiewe proteïenkinase, wat In goeie aanduiding is van die betrokkenheid van proteïenfosforilasie in die seintransduksiekaskade wat tot PGIPuitdrukking aanleiding gee. Die geïnduseerde PGIP-uitdrukkingsprofiel in wingerdblare kan ook nageboots word in tabak wat met die Vvpgip1-geen en -promotor getransformeer is. PG-inhibisie-eksperimente met membraan-geassosieerde proteïenekstrakte van geïnduseerde wingerdblare het ook dieselfde profiel getoon as dié van PGIP wat deur die Vvpgip1-geen geënkodeer is. Die uitdrukkingsprofiel van PGIP in die transgeniese tabakplante het ook bewys dat die promotor van die Vvpgip1-geen vir die geïnduseerde PGIP-uitdrukkingsprofiel in wingerdblare verantwoordelik is. In silica-analise van die promotorarea dui op die teenwoordigheid van verskeie cis-werkende elemente. Die kern promotor en transkripsie-aanvangsgedeelte is gevolglik eksperimenteel bepaal. Verder het uitdrukkingseksperimente met promotorfragmente verskeie dele van die promotor geïdentifiseer wat by stimulis-geassosieerde uitdrukking betrokke is. Posisioneel is hierdie fragmente in goeie konteks met die voorspelde cis-werkende elemente en kan dus die basis vorm vir verdere studies oor Vvpgip-regulering. Met hierdie studie word die eerste data verskaf waar die regulering van PGIP deur omgewingsverwante faktore verbind kan word met onwikkelingspesifieke toestande in die plant. Verder verskaf die resultate verdere bewyse vir die rol van PGIP in plant-patogeen-interaksies en lewer spesifieke bydraes tot die onderliggende prosesse wat by die regulering van siekteweerstandverwante gene betrokke is.

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33

Spaner, Dean Michael. "Agronomic evaluation of short season quality protein maize." Thesis, McGill University, 1992. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=61042.

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The introduction of Quality Protein Maize (QPM), hard endosperm opaque-2 maize, into northern temperate maize growing areas is a desirable breeding objective. In topcrosses with opaque-2 testers, in diallel combination, as inbreds per se, and in inbred disease screening nurseries, some QPM lines performed better than or equal to the best local checks. In general, while agronomic potential is high for some lines and gains from selection are statistically possible, longer days to flowering intervals and higher levels of moisture at harvest than check hybrids indicated a need to improve adaptation for the locations studied. Methodology experiments indicated that detasselling of check hybrids is a suitable experimental method to facilitate the inclusion of normal endosperm local checks into QPM performance tests. The screening for Fusarium graminearum resistance in the seedling stage has not been proven to be a viable alternative to field scale ear inoculation screening procedures. (Abstract shortened by UMI.)

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34

Schuck, Heather A. "Differentially expressed genes of Sophrolaeliacattleya Ginny Champion "Riverbend" in response to the odontoglossum ringspot virus." Virtual Press, 2000. http://liblink.bsu.edu/uhtbin/catkey/1164841.

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Due to the rapid destruction of native orchid habitats it has become necessary to house many endangered orchid species in greenhouse environments where enhanced spread of viral disease occurs due to the close contact between plants. This research was concerned with the construction of a library of genes whose expression is induced in response to viral challenge. In uncovering the genes that are activated during plant-pathogen interactions, it may be possible to manipulate these pathways to develop virus resistant orchids. Furthermore, this research will contribute additional information for the existing framework of plant-pathogen interactions of all plant species.In order to construct a library of genes expressed in response to viral infection, suppression subtractive hybridization was performed using the PCR-Select cDNA Subtraction Kit (CLONTECH, Palo Alto, CA) on Sophrolaeliacattleya Ginny Champion 'Riverbend' clones. RNA was isolated from plants that had been inoculated with the Odontoglossum ringspot virus (ORSV) and from control plants that had not been inoculated with ORSV. Following reverse transcription-PCR (RT-PCR) to obtain cDNA, cDNAs of the tester population (those cDNAs containing differentially expressed messages in response to ORSV) and the driver population (reference cDNAs from uninfected plants) were obtained. The two different cDNA populations are mixed together and hybridized. The sequences common to both populations were subtracted, leaving only the differentially expressed sequences available for PCR amplification.A library containing these genes was constructed, and one clone, chosen at random, was sequenced. Based on homology comparisons to known genes, we have cloned a gene that may contain a nucleotide binding site similar to that of the tobacco N gene, important for plant resistance to pathogens. In the near future, this clone will be used to construct probes for use in northern analysis to determine the timing and localization of the products of this gene. This information will aid in characterizing the function of the orchid N-gene and identifying other members of this signal cascade. In addition, many other clones await sequencing and similar characterization. Department of Biology

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35

Heyns, I. C. "Mapping and restructuring of an Ae. kotschyi derived translocation segment in common wheat." Thesis, Stellenbosch : University of Stellenbosch, 2010. http://hdl.handle.net/10019.1/5172.

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Thesis (PhD (Genetics))--University of Stellenbosch, 2010. Includes bibliography. ENGLISH ABSTRACT: The wild relatives are an important source of new genes for the genetic improvement of wheat. At Stellenbosch University the leaf and stripe rust resistance genes Lr54 and Yr37 were transferred from Aegilops kotschyi to chromosome 2DL of wheat. In an attempt to reduce the size of the whole-arm translocation on which the resistance genes occur, homoeologous pairing was induced between the wheat and corresponding Ae. kotschyi chromatin. The purpose of this study was to: (i) Evaluate the testcross progeny thus obtained; identify translocation recombinants that retained Lr54/Yr37 and to characterize these using molecular markers (ii) Test for the presence of genes for photoperiod insensitivity (Ppd) and reduced height (Rht) believed to be associated with the translocation (iii) Develop a SCAR marker for the most useful recombinant that could be recovered. Ten putative translocation recombinants were identified following the screening of 159 hemizygous testcross F1 plants with three microsatellite markers specific for chromosome arm 2DL. The recombinants were then characterized with another five microsatellite markers. Using the eight microsatellite markers the recombinants were ordered in two size categories with recombinant #74 being the shortest and having retained only proximal alien chromatin on 2DL. In addition to microsatellite markers, RAPDs, RGAs, AFLPs and SCAR markers were genetically mapped to the translocation and further resolved the recombinants into three size categories. In an attempt to find suitable markers linked to the shortest recombinant (#74) a polymorphic 410 bp AFLP fragment produced with the enzyme/selective nucleotide combination EcoRI – AAC/MseI – CAT, was converted into a dominant SCAR marker. In addition three microsatellite markers that mapped to recombinant #74 provided a useful recessive molecular marker system to detect Lr54/Yr37. Evaluation of the 10 recombinants with four 2DS-specific microsatellite markers revealed a large deletion of this chromosome arm in recombinant #74. This deletion may affect plant phenotypic characteristics and a strategy to replace the deleted region in recombinant #74 is proposed. To test for the presence of a gene for photoperiod insensitivity on the translocation, translocation-carriers plus controls were subjected to long and short day treatments, and the effect on time to flowering was studied. However, no evidence was found for the presence of such a gene. A height experiment to test for the presence of an Rht gene on the translocation confirmed its presence. This gene (designated H) appeared to be different from Rht8 on chromosome 2DS and was mapped on 2DL. While H does not occur in a chromosome region that corresponds with the location of Rht8, it does not rule out the possibility that they could be orthologous loci. Plant height data obtained for recombinant #74 suggested that H was lost through recombination in this particular recombinant. A greenhouse experiment suggested that the full-length translocation increased 100 kernel mass but had a detrimental effect on overall plant yield. Since a much shorter recombinant (#74) has been obtained, this will also have to be evaluated for associated effects. Such an evaluation needs to be done under commercial growing conditions and should involve the comparison of near-isogenic bulks with and without recombinant chromosome #74. The stripe rust resistance gene (Yr37) was mapped by screening hemizygous TF2 progeny of the 10 recombinants with Puccinia striiformis pathotype 6E22A+. Recombinant #74 retained both Lr54 and Yr37 and the two genes therefore occur towards the centromere. AFRIKAANSE OPSOMMING: Wilde verwante spesies is ‘n belangrike bron van nuwe gene vir die genetiese verbetering van koring. By die Universiteit van Stellenbosch is die blaar-roes en streep-roes weerstandsgene Lr54 en Yr37 vanaf Aegilops kotschyi na chromosoom 2DL van koring oorgedra. ‘n Poging is vervolgens aangewend om die vol-armtranslokasie waarop die weerstandsgene voorkom te verklein deur homoeoloë paring tussen die koring en ooreenstemmende Ae. kotschyi chromatien te induseer. Die doelstelling van hierdie studie was daarom as volg: (a) Evaluering van die verkreë toetskruis-nageslag asook die identifisering en karakterisering van translokasie rekombinante wat Lr54/Yr37 behou het. (b) Toetsing vir fotoperiode onsensitiwiteits- (Ppd) en verkorte plant-hoogte (Rht) gene wat moontlik op die translokasie kon voorkom. (c) Die ontwikkeling van ‘n volgorde-spesifieke polimerase kettingreaksie (PKR) vir die mees bruikbare rekombinant. Tien translokasie rekombinante is geïdentifiseer nadat 159 hemisigotiese toetskruis F1-plante met drie mikrosatelliet-merkers, spesifiek vir chromosoom-arm 2DL, ge-evalueer is. Die rekombinante is hierna met vyf verdere mikrosatellietmerkers getoets. Die data van die agt mikrosatelliet-loci het die rekombinante in twee grootte-kategorieë geplaas waarvan rekombinant #74 die kortste was met slegs die proksimale gedeelte van 2DL wat uit vreemde chromatien bestaan. Behalwe mikrosatellite-merkers is toevallig-geamplifiseerde polimorfiese DNS (RAPD), weerstandsgeen-analoog (RGA), geamplifiseerde volgordelengte polimorfisme (AFLP) en volgorde-gekarakteriseerde geamplifiseerde-streke (SCAR) merkers ook geneties op die translokasie gekarteer. Data van die addisionele merkers het dit moontlik gemaak om die rekombinante in drie grootte-kategorieë te skei. Pogings om ‘n merker vir die kortse rekombinant (#74) te vind, het gelei tot die omskakeling van ‘n 410 bp polimorfiese AFLP-fragment (geproduseer met die ensiem/selektiewenukleotied kombinasie EcoRI - AAC/MseI - CAT), na ‘n dominante, volgordespesifieke PKR-merker. Hierbenewens kan drie mikrosatelliet-merkers wat op rekombinant #74 karteer as resessiewe merkers vir die identifisering van Lr54/Yr37 gebruik word. Die evaluering van die 10 rekombinante met vier chromosoom 2DSspesifieke mikrosatelliet-merkers het ‘n groot delesie van chromosoom-arm 2DS in rekombinant #74 uitgewys. Die delesie mag plant fenotipiese kenmerke beïnvloed en daarom is ‘n strategie vir die vervanging daarvan in rekombinant #74 voorgestel. Ten einde te toets of ‘n geen vir fotoperiode-onsensitiwiteit op die translokaie voorkom is translokasie-draers en kontroles aan lang- en kortdag-behandelings onderwerp en is die effek hiervan op dae-tot-blom gemeet. Geen bewyse vir so ‘n geen kon gevind word nie. ‘n Hoogte-eksperiment om te toets vir die teenwoordigheid van ‘n Rht-geen op die translokasie, het bevestig dat so ‘n geen wel voorkom. Die geen (voorgestelde simbool H) is gekarteer op 2DL en verskil oënskynlik van Rht8 op chromosoom 2DS. Die verskillende chromosoom-ligging van H en Rht8 skakel egter nie die moontlikheid dat hulle ortoloë loci mag wees uit nie. Plant-hoogte data vir rekombinant #74 het daarop gedui dat H nie meer in hierdie rekombinant voorkom nie. Data van ‘n glashuis-eksperiment het daarop gedui dat die vollengte-translokasie 100-korrel-massa verhoog maar dat dit plant-opbrengs verlaag. Aangesien ‘n aansienlike korter rekombinant (#74) verkry is, sal dit ook vir gekoppelde effekte getoets moet word. So ‘n evaluering moet egter onder kommersiële toestande gedoen word met gebruik van naby isogeniese-lyne met en sonder rekombinante chromosoom #74. Die streep-roes weerstandgeen (Yr37) is gekarteer deur hemisigotiese TF2- nageslag van die 10 rekombinante te toets vir weerstand teen Puccinia striiformis patotipe 6E22A+. Rekombinant #74 het beide Lr54 en Yr37 behou en die twee gene karteer dus naby die sentromeer.

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36

Filkowski, Jody, and University of Lethbridge Faculty of Arts and Science. "The effect of pathogens on plant genome stability." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Biological Sciences, 2004, 2004. http://hdl.handle.net/10133/254.

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Resistance (R) genes, a key factor in determining the resistance of plants, have been shown often to be highly allelic entities existing in duplicated regions of the genome. This characteristic suggests that R-gene acquisition may have arisen through frequent genetic rearrangements as a result of transient, reduced genome stability. Tabacco plants transgenic for a recombination construct exhibited reduced genome stability upon infection with a virulent pathogen (tobacco mosaic virus). The reduced genome stability manifested as an increase in recombination events in the transgene. Such increases were observed following a virulent pathogen attack. This increase in recombination was shown to be systemic and was observed prior to systemic viral movement suggesting the presence of a systemic recombination signal. Further molecular analyses revealed that specific R-gene loci experience a large frequency of rearrangements following a virulent pathogen encounter. The possible targeting of instability to R-gene regions may be controlled through epigenetic processes, in particular, DNA methylation. xiii, 119 leaves ; 29 cm.

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37

Beeck, Cameron. "Simultaneous improvement in black spot resistance and stem strength in field pea (Pisum sativum L.)." University of Western Australia. School of Plant Biology, 2006. http://theses.library.uwa.edu.au/adt-WU2006.0057.

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[Truncated abstract] Field pea (Pisum sativum) has many benefits when included in the crop rotation system in broadacre grain farming. These benefits include a disease break and improved weed control for cereals and less dependence on nitrogenous fertilisers due to the leguminous nature of pea. Currently, field pea adoption in Australia is low because the crop is susceptible to the fungal disease `black spot’ (Mycosphaerella pinodes) and has low stem strength and a lodged canopy. Black spot causes yield losses averaging 10-15% per year. Lodging results in difficult and costly harvesting, increased disease pressure and increased wind erosion from exposed soil surface when stems break at the basal nodes. This project aimed to address these problems through breeding, and through the application of quantitative genetics theory to a recurrent selection program. A quantitative measurement of relative stem strength was developed which could be used effectively in the field on single plants. Accurate laboratory measurements of stem strength were closely correlated with the field measure of compressed stem thickness in the basal node region. A diallel analysis of stem strength of the progeny of crosses among a range of pea lines with different values of compressed stem thickness concluded that the genetic control of stem strength was additive, with no maternal inheritance or dominance or epistasis effects.

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38

Saxon, Herbert. "The molecular biology of orchids : transformation by Agrobacterium Tumefaciens and DNA fingerprinting." Virtual Press, 1995. http://liblink.bsu.edu/uhtbin/catkey/941575.

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The work reported here was done at the Wheeler Orchid Collection and Species Bank and the Department of Biology at Ball State University. We have developed a research teaching program with two applied research goals: genetically transforming and DNA fingerprinting orchid tissue. As part of their molecular biology education, students have investigated the genetic transformation of orchids for mitigating viral symptoms and the identification of unknown orchids by DNA fingerprinting. In a second application of the technology, DNA fingerprinting has been used to determine evolutionary relationships and to quantify genetic diversity among orchids.This dissertation details the background and need for this project and the research that was done to start it. As the early work has, developed and students have added their contributions, the data have developed into two papers formatted for submission to scientific journals. They are included as results.The first is a project designed to insert exognenous DNA into orchid tissue. The soil microbe Agrobacterium tumefaciens causes crown-gall tumors to develop in its plant hosts by inserting DNA into their cells which then controls the biosynthesis of development-controlling hormones. A. tumefaciens which has been disarmed has been routinely used to bioengineer dicotyledonous plants but its use has been rare on monocotyledons. In this paper, we report that A. tumefaciens transformed embryonic orchid tissue and caused alteration in its normal developmental course.The second paper details the DNA fingerprinting of tissue from Aplectrum hymale, a terrestrial orchid native to this climate. Three populations of A. hymale have been sampled and DNA extracted from the tissue samples. RAPD primers were used to prime PCR amplifications of random sequences of the DNA and the amplified DNA was visualized by gel electrophoresis. Loci of the resulting bands were treated as potentially multiallelic gene loci and heterozygosity between and within subpopulations was calculated. We report that the three populations could be partially differentiated by this procedure and that the two populations located nearest to each other yielded the least between -ubpopulation heterozygosity. We report very high levels of genetic diversity between individuals within small subpopulations in spite of the fact that these subpopulations are considered to be primarily clonal in reproductive nature. Department of Biology

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39

Khan, Imtiaz Ahmed. "Utilisation of molecular markers in the selection and characterisation of wheat-alien recombiant chromosomes." Title page, contents and summary only, 1996. http://web4.library.adelaide.edu.au/theses/09PH/09phk451.pdf.

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Bibliography: leaves 137-163. his is a comprehensive study of induced homoeologous recombination along most of the complete genetic length of two homoeologous chromosomes in the Triticeae (7A of common wheat and 7Ai of Agropyron intermedium), using co-dominant DNA markers. Chromosome 7Ai was chosen as a model alien chromosome because is has been reported to carry agronomically important genes conferring resistance to stem rust and barley yellow dwarf virus on its short and long arms, respectively.

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40

Ramburan, Viresh Premraj. "Genetic mapping of adult plant stripe rust resistance in the wheat cultivar Kariega." Thesis, Stellenbosch : Stellenbosch University, 2003. http://hdl.handle.net/10019.1/53438.

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Thesis (PhD (Agric)) -- Stellenbosch University, 2003. ENGLISH ABSTRACT: Stripe (yellow) rust of wheat, caused by Puccinia striiformis f.sp. tritici, was first detected as a single introduction into South Africa in 1996. Two additional pathotypes have since been identified. Control of the disease may be achieved by use of genetic adult plant resistance (APR) as is present in the local cultivar 'Kariega'. The aim of this project was to understand the genetic basis of the APR in 'Kariega' to facilitate breeding of new varieties with genetic resistance to stripe rust. A partial linkage map of a 'Kariega X Avocet S' doubled haploid population covering all 21 wheat chromosomes was generated using 208 DNA markers, viz, 62 SSR, 133 AFLP, 3 RGA and 10 SRAP markers, and 4 alternative loci. The different marker techniques detected varying polymorphism, viz, overall SSR: 46%, AFLP: 7%, SRAP: 6% and RGA: 9%, and the markers produced low levels of missing data (4%) and segregation distortion (5%). A significant feature of the linkage map was the low polymorphism found in the D genome, viz, 19% of all mapped DNA markers, 11% of all AFLP markers and 30% of the total genome map distance. A region exhibiting significant segregation distortion was mapped to chromosome 4A and a seedling resistance gene for stem rust (Puccinia graminis f.sp . tritici), Sr26, mapped to chromosome 6A close to three SSR markers. The leaf tip necrosis gene, Ltn, which was also segregating in the population, mapped to chromosome 7D. Protocols for SRAP and RGA were optimised, and SRAP marker use in wheat genetic linkage studies is reported for the first time. The linkage map was used together with growth chamber and replicated field disease scores for QTL mapping. Chromosomes showing statistically significant QTL effects were then targeted with supplementary SSR markers for higher resolution mapping. The quality of disease resistance phenotypic data was confirmed by correlation analysis between the different scorers for reaction type (0.799±0.023) and for transformed percentage leaf area infected (0.942±0.007). Major QTL were consistently identified on chromosome 7D (explaining some 25-48% of the variation) and on chromosome 2B (21-46%) using transformed percentage leaf area infected and transformed reaction type scores (early and final) with interval mapping and modified interval mapping techniques. Both chromosomal regions have previously been identified in other studies and the 7D QTL is thought likely to be the previously mapped APR gene Yr 18. Minor QTL were identified on chromosomes lA and 4A with the QTL on 4A being more prominent at the early field scoring for both score types. A QTL evidently originating from 'Avocet S' was detected under growth chamber conditions but was not detected in the field, suggesting genotype-environment interaction and highlighting the need for modifications of growth chamber conditions to better simulate conditions in the field. The genetic basis of the APR to stripe rust exhibited by 'Kariega' was established by mapping of QTL controlling this trait. The linkage map constructed will be a valuable resource for future genetic studies and provides a facility for mapping other polymorphic traits in the parents of this population with a considerable saving in costs. AFRIKAANSE OPSOMMING: Streep of geelroes van koring word veroorsaak deur Puccinia striiformis f. sp tritici, en is die eerste keer in 1996 in Suid-Afrika na introduksie van 'n enkele patotipe waargeneem. Twee verdere patotipes is sedertdien in Suid-Afrika gei"dentifiseer. Beheer van die siekte word veral moontlik gemaak deur die gebruik van genetiese volwasseplantweerstand soos gei"dentifiseer in die plaaslike kultivar 'Kariega'. Die doel van hierdie studie was om die genetiese grondslag van die streeproesweerstand te ontrafel ten einde die teling van nuwe bestande kultivars moontlik te maak. 'n Verdubbelde haplo1ede populasie uit die kruising 'Kariega X Avocet S' is aangewend om 'n gedeeltelike koppelingskaart vir die volle stel van 21 koring chromosome saam te stel. Die kaart het uit 208 DNA merkers, nl., 62 SSR, 133 AFLP, 3 RGA, 10 SRAP merkers en 4 ander lokusse bestaan. Totale polimorfisme wat deur die verskillende merkersisteme opgespoor is, was as volg: SSR: 46%, RGA: 9%, AFLP: 7% en SRAP: 6%. Die mate van ontbrekende data was gering (4%) asook die mate van segregasie distorsie (5%) van 'n enkele geval wat op chromosoom 4A gekarteer is. 'n Prominente kenmerk van die koppelingskaart is die relatiewe gebrek aan polimorfiese merkers op die D-genoom, nl., slegs 19% van alle DNA merkers en 11% van alle AFLP merkers wat slegs 30% van die totale genoom kaartafstand bestaan het. Die stamroes (Puccinia graminis f. sp. tritici) saailingweerstandsgeen, Sr26, karteer op chromosoom 6A naby drie SSR merkers. Die geen vir blaartipnekrose, Ltn, karteer op chromosoom 7D. Protokolle vir SRAP en RGA merkers is ge-optimiseer en gebruik van SRAP merkers in koppelings-analise word vir die eerste keer in koring gerapporteer. Die koppelingskaart is in kombinasie met groeikamerdata en gerepliseerde veldproefdata gebruik om die gene (QTL) vir volwasseplant streeproesweerstand te karteer. Chromosome met statisties betekenisvolle QTL is met aanvullende SSR merkers geteiken om die resolusie van kartering verder te verhoog. Die kwaliteit van fenotipiese data, soos in die proewe aangeteken, is bevestig deur korrelasies te bereken tussen lesings geneem deur onafhanklike plantpataloe (0.799 ± 0.023 vir reaksietipe en 0.942 ± 0.007 vir getransformeerde persentasie blaaroppervlakte besmet). Hoofeffek QTL vir die twee maatstawwe van weerstand is deur middel van die metodes van interval QTL kartering en gemodifiseerde interval QTL kartering konsekwent op chromosome 7D (25-48% van variasie verklaar) en 2B (21-46% van variasie verklaar) ge"identifiseer. In vorige studies is aangetoon dat beide chromosome 7D en 2B QTL vir volwasseplant streeproesweerstand dra. Die 7D QTL is waarskynlik die weerstandsgeen, Yr 18. QTL met klein effekte op weerstand is op chromosome lA en 4A ge"identifiseer. Die effek van laasgenoemde geen was meer prominent in die velddata in die vroee datum van weerstandsbeoordeling. Een QTL, afkomstig van 'Avocet S', is slegs onder groeikamertoestande identifiseerbaar. Dit dui op moontlike genotipe-omgewing wisselwerking en beklemtoon die noodsaaklikheid om aanpassings te maak in groeikamertoestande vir beter simulasie van veldproeftoestande. Die genetiese grondslag van volwasseplantweerstand teen streeproes in die kultivar 'Kariega' is deur QTL kartering bepaal. Die 'Kariega X Avocet S' koppelingskaart kan as 'n waardevolle basis dien vir toekomstige genetiese ontledings van ander polimorfiese kenmerke in die populasie.

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41

Carroll, Audra L. "Sense and antisense oligonucleotide inhibition of the Odontoglossum ringspot virus (ORSV) coat protein gene via microprojectile bombardment of orchid callus tissue." Virtual Press, 1999. http://liblink.bsu.edu/uhtbin/catkey/1210536.

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A major goal of our laboratory is to confer resistence specifically to the Odontoglossum ringspot virus [ORSV; sometimes referred to as tobacco mosaic virus strain O (TMV-O)] in orchids. The chosen strategy may also provide cross-protection to other pathogens. The experimental design for the entire project is presented here along with the results obtained in several preliminary experiments performed in this research. Our approach involved RT-PCR amplification of the viral coat protein gene with gene-specific primers and digestion of the cDNAs into oligonucleotides. These fragments were cloned into the selectable vector pG35barB (which confers herbicide resistence) in both sense and antisense orientations. The cloned DNA was coated with tungsten beads and shot into orchid callus tissue using a makeshift biolistic gun. Tranformant callus cells were selected for by herbicide resistance. Unfortunately the potential transformants became contaminated with fungus and could nto be analyzed to determine which oligonucleotide was received and the effect each oligonucleotide had on pathogen resistance. Due to the uncertainty of the relatedness between ORSV and TMV-O, we also sequenced the coat protein gene of TMV-O and compared the amino acid sequence with those of several strains of ORSV: the Japanese strain had the highest percent amino acid similarity (99.4%), the Type strain the second highest (98.7%), and the Korean strain the lowest (96.9%). It was concluded that TMV-O is most likely one strain of ORSV, the Japanese strain. Department of Biology

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42

Collins, Nicholas Charles. "The genetics of barley yellow dwarf virus resistance in barley and rice." Thesis, 1996. http://hdl.handle.net/2440/46063.

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Barley yellow dwarf virus (BYDV), an aphid transmitted luteovirus, is the most widespread and economically damaging virus of cereal crops. The work in this thesis aims to characterise the basis of the naturally occurring resistance to BYDV in cereals in three ways: Firstly, by facilitating the isolation of the Yd2 gene for BYDV resistance from barley by a map-based approach. Secondly, by determining if a BYDV resistance gene in rice is orthologous to Yd2. Thirdly, by establishing if other BYDV resistance genes in non- Ethiopian barleys are allelic to Yd2. It is hoped that the information generated in this study will ultimately assist in the production of BYDV resistant cereal cultivars. A detailed genetic map of the Yd2 region of barley chromosome 3 was constructed, containing 19 RFLP loci, the centromere and the Yd2 gene. Yd2 mapped on the long arm, 0.5 cM from the centromere, and in the mapping population of 106 F2 individuals, perfectly cosegregated with the RFLP loci XYlp, and Xwg889. This map represents the first stage in a project to isolate the Yd2 gene by a map-based approach. The isolation of Yd2 could help to elucidate the molecular mechanism of the Yd2-mediated BYDV resistance, and may allow the production of BYDV resistant cereals by genetic transformation. The RFLP markers mapped closest to Yd2 could also be useful in barley breeding, by enabling selection for both the presence of Yd2 and the absence of agronomically undesirable traits known to be closely linked to Yd2. Genetically Directed Representational Difference Analysis (GDRDA) is a technique based on subtractive hybridisation, which can be used to identify RFLP markers closely linked to a gene of interest. Two GDRDA experiments were performed with the intention of generating additional RFLP markers close to Yd2. However, the first experiment yielded RFLP probes that were not derived from the barley genome, while the second experiment yielded probes that detected repetitive sequences. It was concluded that GDRDA is of limited use in generating further markers close to Yd2. To isolate the Yd2 gene by a map-based approach, a much larger mapping population will need to be analysed to genetically resolve markers tightly linked to Yd2. If the two morphological markers uzu dwarf and white stripe,,j flank Yd2, then they could assist in this task by enabling the visual identification of F2 seedlings resulting from recombination close to Yd2. However, in this study, both morphological markers were found to be located distal to Yd2. Therefore, these two morphological markers can not be used together to facilitate high resolution genetic mapping of the Yd2 locus. It may be possible to use large-insert genomic DNA clones from the relatively small genome of rice to generate further RFLP markers close to the Yd2 gene in barley, provided that the order of orthologous sequences in barley and rice is conserved close to the Yd2 locus. To assess the feasibility of this approach, RFLP probes used to identify loci close to Yd2 were mapped in rice using a segregating rice F2 population. Five of the RFLP loci mapped together and in the same order as RFLP loci mapped close to Yd2 in barley using the same probes. By comparing the location of RFLPs mapped by other researchers in rice using probes mapped close to Yd2, the region of conserved linkage between rice and the Yd2 region was tentatively identified as the central portion of rice chromosome 1. The collinearity shown by orthologous sequences in barley and rice indicated that it may indeed be possible to use rice to assist in generating RFLP markers close to Yd2. Of all the cereals, rice is the most amenable to map-based gene isolation, due to its small genome, well developed physical and genetic maps, and its ability to be genetically transformed with high efficiency. If a BYDV resistance gene that is orthologous to Yd2 could be identified in rice, this gene could be isolated with relative ease, and then used to identify barley cDNA clones corresponding to Yd2 gene by virtue of the sequence homology expected between these genes. To test if a BYDV resistance gene from an Italian rice line is orthologous to Yd2, recombinant-inbred rice lines previously characterised for this gene were analysed using probes mapped close to Yd2 in barley. No genetic linkage was detected between the RFLP loci and the BYDV resistance gene, indicating that the gene is unlikely to be orthologous to Yd2. BYDV resistance alleles at the Yd2 locus which are of a non-Ethiopian origin may show interesting differences to Ethiopian Yd2 resistance alleles. To identify barleys which may contain resistance alleles of Yd2, ten BYDV resistant barleys not known to contain Yd2 were assessed for their resistance to the PAVadel isolate of BYDV in the glasshouse. CI 1179, Rojo, Perry, Hannchen, Post and CI 4228 were found to be the most resistant under these conditions, and were analysed further. If the resistance from these barleys is controlled by alleles of Yd2, RFLP markers close to Yd2 will be expected to cosegregate with the resistance in F2 families derived from crosses between these resistant barleys and the BYDV susceptible barleys Atlas and Proctor. RFLPs suitable for use in these allelism tests were identified using probes mapped close to Yd2. However, time did not permit the analysis of these F2 populations. Thesis (Ph.D.) -- University of Adelaide, Dept. of Plant Science, 1996

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43

March, Timothy. "The genetic basis of barley black point formation." 2008. http://hdl.handle.net/2440/50740.

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Abstract (sommario):

Black point of barley grain refers to a discolouration of the embryo end of the grain. Historically black point has been proposed to be due to fungal colonisation of the grain. However, Koch’s postulates have yet to be satisfied. The discolouration occurs during grain fill in response to high humidity or rainfall during the grain filling period. In wheat, which is also affected by black point, the discolouration has been proposed to be due to the oxidation of phenolic acids within the grain to form discoloured end products. Within this study, two approaches were investigated in order to understand the proteins and genes associated with this disorder. Firstly, a proteomics approach enabled the identification of individual proteins associated with black point. Two-dimensional gel electrophoresis was used to compare the proteome of the husk and whole grain tissue of mature black pointed and healthy grain. Very little watersoluble protein was extracted from the husk tissue. However, a significantly larger amount of protein was extracted using a salt extraction buffer, indicating the husk proteins were mostly cell wall bound. Due to the effect of residual salt and low protein concentrations these proteins were not conducive to analysis using two-dimensional gel electrophoresis. Further experiments using acid hydrolysis of the husk tissue and subsequent amino acid analysis revealed that the proteins were bound to the husk cell walls via covalent bonds. In contrast, large quantities of protein were obtained from the whole grain samples. This allowed statistically significant comparisons to be made between gels from healthy and black pointed grains. Two proteins were identified as being more abundant in black pointed grains. Mass spectrometry identified these as isoforms of barley grain peroxidase 1 (BP1). In addition, three proteins were identified as being more abundant in healthy grain. Mass spectrometry revealed these to be isoforms of the same protein with sequence similarity to a partial EST sequence from barley. Using 3' RACE the entire coding sequence of the gene was isolated which revealed that it encoded a novel putative late embryogenesis abundant (LEA) protein. Northern blot analysis was performed for BP1 and LEA and showed that gene expression differences could not account for the differences seen in protein quantities. Western blot analysis revealed that the LEA protein was biotinylated in vivo which is consistent with similar LEA proteins from other plant species. To further understand the role of these proteins in black point, antibodies were raised against the two proteins. Subsequent immunolocalisation studies indicated BP1 was present throughout all tissues of the grain whilst LEA was most abundant in the embryo and aleurone tissue. The second major area of investigation within this thesis was to further delineate the previously identified quantitative trait loci (QTL) associated with black point in barley. Previous studies have reported QTL for black point and kernel discolouration in both barley and wheat. Comparison of the published QTL revealed a locus on the short arm of chromosome 2H to be of particular interest. To identify genes underlying this QTL the genomes of barley, wheat and rice were compared. An in silico approach showed that the QTL shared macro-synteny with rice chromosomes 4 and 7. From the rice genome sequence, barley ESTs with sequence similarity were selected. In total, 20 ESTs were selected based on two main criteria: their putative role in black point and also being evenly spread across the region of the QTL length. These QTL were mapped within the Alexis x Sloop double haploid population. This approach revealed that there was some conservation of synteny but also identified clear boundaries where synteny between barley and rice had been lost since divergence. Significantly, the additional markers mapped to this region have enabled the initial black point QTL to be reduced from approximately 30cM to 20cM. In conclusion, this study has added significant knowledge our understanding of the genetics of black point in barley through the use of two approaches. The proteomics approach has aided in understanding the biochemical processes occurring within the grain in response to black point. The comparative genetics approach has aided in understanding the genetic control of an important region of the genome influencing black point susceptibility. Combined, these findings will direct future research endeavours aimed at producing black point resistant barley cultivars. http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1323053 Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

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44

March, Timothy. "The genetic basis of barley black point formation." Thesis, 2008. http://hdl.handle.net/2440/50740.

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Abstract (sommario):

Black point of barley grain refers to a discolouration of the embryo end of the grain. Historically black point has been proposed to be due to fungal colonisation of the grain. However, Koch’s postulates have yet to be satisfied. The discolouration occurs during grain fill in response to high humidity or rainfall during the grain filling period. In wheat, which is also affected by black point, the discolouration has been proposed to be due to the oxidation of phenolic acids within the grain to form discoloured end products. Within this study, two approaches were investigated in order to understand the proteins and genes associated with this disorder. Firstly, a proteomics approach enabled the identification of individual proteins associated with black point. Two-dimensional gel electrophoresis was used to compare the proteome of the husk and whole grain tissue of mature black pointed and healthy grain. Very little watersoluble protein was extracted from the husk tissue. However, a significantly larger amount of protein was extracted using a salt extraction buffer, indicating the husk proteins were mostly cell wall bound. Due to the effect of residual salt and low protein concentrations these proteins were not conducive to analysis using two-dimensional gel electrophoresis. Further experiments using acid hydrolysis of the husk tissue and subsequent amino acid analysis revealed that the proteins were bound to the husk cell walls via covalent bonds. In contrast, large quantities of protein were obtained from the whole grain samples. This allowed statistically significant comparisons to be made between gels from healthy and black pointed grains. Two proteins were identified as being more abundant in black pointed grains. Mass spectrometry identified these as isoforms of barley grain peroxidase 1 (BP1). In addition, three proteins were identified as being more abundant in healthy grain. Mass spectrometry revealed these to be isoforms of the same protein with sequence similarity to a partial EST sequence from barley. Using 3' RACE the entire coding sequence of the gene was isolated which revealed that it encoded a novel putative late embryogenesis abundant (LEA) protein. Northern blot analysis was performed for BP1 and LEA and showed that gene expression differences could not account for the differences seen in protein quantities. Western blot analysis revealed that the LEA protein was biotinylated in vivo which is consistent with similar LEA proteins from other plant species. To further understand the role of these proteins in black point, antibodies were raised against the two proteins. Subsequent immunolocalisation studies indicated BP1 was present throughout all tissues of the grain whilst LEA was most abundant in the embryo and aleurone tissue. The second major area of investigation within this thesis was to further delineate the previously identified quantitative trait loci (QTL) associated with black point in barley. Previous studies have reported QTL for black point and kernel discolouration in both barley and wheat. Comparison of the published QTL revealed a locus on the short arm of chromosome 2H to be of particular interest. To identify genes underlying this QTL the genomes of barley, wheat and rice were compared. An in silico approach showed that the QTL shared macro-synteny with rice chromosomes 4 and 7. From the rice genome sequence, barley ESTs with sequence similarity were selected. In total, 20 ESTs were selected based on two main criteria: their putative role in black point and also being evenly spread across the region of the QTL length. These QTL were mapped within the Alexis x Sloop double haploid population. This approach revealed that there was some conservation of synteny but also identified clear boundaries where synteny between barley and rice had been lost since divergence. Significantly, the additional markers mapped to this region have enabled the initial black point QTL to be reduced from approximately 30cM to 20cM. In conclusion, this study has added significant knowledge our understanding of the genetics of black point in barley through the use of two approaches. The proteomics approach has aided in understanding the biochemical processes occurring within the grain in response to black point. The comparative genetics approach has aided in understanding the genetic control of an important region of the genome influencing black point susceptibility. Combined, these findings will direct future research endeavours aimed at producing black point resistant barley cultivars. Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

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45

Abbott, David Colin. "Pyramiding scald resistance genes in barley." Phd thesis, 1997. http://hdl.handle.net/1885/145297.

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46

Castro, Tabo Ariel Julio. "Stripe rust resistance pyramids in barley." Thesis, 2002. http://hdl.handle.net/1957/29789.

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47

Toojinda, Theeryut. "Mapping and introgression of disease resistance genes in barley (Hordeum vulgare L.)." Thesis, 1998. http://hdl.handle.net/1957/33275.

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Abstract (sommario):

Molecular tools, coupled with unique germplasm stocks and rigorous phenotyping, are useful for developing a better understanding of qualitative and quantitative disease resistance genes in plants. The identification of molecular markers linked to all types of resistance genes provides opportunities for implementing a range of resistance breeding strategies, ranging from gene pyramiding to gene deployment. This thesis consists of two chapters. The first describes a disease resistance gene mapping effort and the second describes a disease resistance gene introgression effort. The number, location, and effects of genes determining resistance to stripe rust, leaf rust and Barley Yellow Dwarf Virus were determined using a population of doubled haploid (DH) lines from the cross of Shyri x Galena. Resistance to leaf rust was qualitatively inherited, and the locus was mapped to the long arm of chromosome 1. Resistance to stripe rust and BYDV was quantitatively inherited. Multiple QTLs were detected for each type of resistance. The principal stripe rust resistance QTL was on the short arm of chromosome 5 and the principal BYDV resistance QTL was on the long arm of chromosome 1, linked in repulsion phase with the leaf rust resistance gene. Additional QTLs and QTL x QTL interactions were detected. The majority of the qualitative and quantitative resistance loci detected in the Shyri x Galena population coincided with Resistance Gene Analog Polymorphisms (RGAPs) mapped in the same population. These RGAPs were based on degenerate primers derived from cloned resistance gene sequence motifs. These associations should be useful for efficient resistance gene mapping and provide an approach for ultimately isolating and describing quantitative and qualitative resistance genes. The second chapter describes a molecular marker assisted selection (MMAS) effort to introgress stripe rust resistance QTLs on chromosomes 4 and 7 into susceptible germplasm. DH lines were derived form a MMAS backcross-one (BC-1) population, extensively phenotyped for stripe rust resistance, and genotyped for the introgressed QTLs and background genome. The resistance QTLs that were introgressed were significant determinants of resistance in the new genetic background. Additional resistance QTLs were also detected. Together, these chapters describe an integrated approach to disease resistance gene characterization and utilization. Graduation date: 1999

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48

Prehn, Doris A. "Analysis of genetic resistance to barley stripe rust (Puccinia striiformis f. sp. hordei)." Thesis, 1993. http://hdl.handle.net/1957/36114.

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Abstract (sommario):

Stripe rust (Puccinia striiformis f. sp. hordei) is a serious disease of barley that can cause up to 70% yield loss in susceptible varieties. The fungus is moving northward, threatening major barley production areas in the US, where most cultivars are susceptible. Fungicides are available for control of stripe rust, but economic and environmental considerations favor genetic resistance. Two stripe rust resistance quantitative trait loci (QTLs) located in chromosomes 4 and 7 have previously been reported. One hundred and ten doubled haploid progeny from a stripe rust susceptible x resistant cross were derived using the Hordeum bulbosum technique and phenotyped for agronomic and malting quality traits in order to assess the importance of linkage drag associated with the mapped stripe rust resistance QTLs. Data on 33 markers were combined with phenotypic data for QTL analysis. A molecular marker-assisted backcross program was implemented to initiate the transfer of the stripe rust resistance loci into susceptible US germplasm. No negative QTLs for agronomic or malting quality traits were detected within or adjacent to the intervals that were targeted for marker-assisted selection. A minor leaf rust resistance QTL, however, was found adjacent to the stripe rust locus on chromosome 7. Linkage drag in this region could operate in favor of the breeder. Epistatic interaction between the two stripe rust resistance QTLs confirms the necessity of introgressing both chromosome intervals. Graduation date: 1994

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49

Paltridge, Nicholas G. (Nicholas Geoffrey). "The development of molecular markers for barley Yd2, the barley yellow dwarf virus resistance gene." 1998. http://web4.library.adelaide.edu.au/theses/09APSP/09apspp183.pdf.

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Abstract (sommario):

Includes bibliographical references (l5 leaves) The aim of the work presented in this thesis was to develop molecular genetic markers for YD2 (the gene in barley which provides protection against barley yellow dwarf luteovirus) which could be used for the marker assisted selection of the gene in breeding programs and enable the gene to be cloned via a map-based approach.

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50

Choe, Y. W. (Young Won). "DNA markers for cereal cyst nematode (Heterodera avenae Woll.) resistance gene in barley." 1995. http://web4.library.adelaide.edu.au/theses/09PH/09phc545.pdf.

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Tesi sul tema "Barley Disease and pest resistance Genetic aspects"

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