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Fisk, Dianna G. "CRP1 : founding member of a novel protein family that functions in organellar gene expression /." view abstract of download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9987422.
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Islam, Mohammad Sayedul. "Genetic mapping of rooting in rice : exploiting a high throughput phenotyping in plants." Thesis, University of Aberdeen, 2016. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=229720.
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Meeting future demands of food security will require enhanced rice production that is more environmentally sustainable. To achieve this it is important to know the genetic and molecular mechanism controlling the root traits. High throughput phenotyping which can keep pace with genotyping is needed, but for many researchers this needs to be cheap as well as meaningful. Here a very simple, low cost and reliable method of assessing root depth of seedling using a layer of diuron-soaked filter paper buried 25 cm deep in a soil-filled box has been developed which is suitable for screening of hundreds of accessions. The assumption is that deep-rooting plants die quicker. This method was then used to screen five established rice panels. Deep rooted cultivars were screened from a panel of an aus panel from IRRI and a panel of Brazilian and Japanese cultivars by using this method. Root QTLs were detected by using bi-parental mapping population and GWA study was performed in two panels, the rice diversity panel (RDP-1) and Bengal Assam Association Population. Assessing 139 RILs from Bala x Azucena bi-parental population revealed heritability of 55% for herbicide symptoms where eleven QTLs were detected, many of which were co-localised with previously reported root QTLs in this population. A GWA study was performed using RDP1) of 356 accessions with 44k SNP markers. Analysis revealed 17% of phenotypic variation of herbicide score was attributable to rice sub-population where the aus showed the deepest rooting systems. A number of QTLs have been identified and a number of positional candidate gene lists were produced. A further 298 cultivars from Bengal and Assam were screened and GWA was performed using 2 M SNP database available from sequencing. ANOVA revealed 37% variation for herbicide score explained by genotype. Soil-filled rhizotron were used to assess 12 of these cultivars, revealing strong xx correlations between deep root traits and herbicide score, confirming the reliability of this method. GWA revealed a number of significant SNPs associated with the traits in this population. Finally a set of mutant gene (LOC_Os09g31478, LOC_Os05g40330, LOC_Os11g34140) which are functional candidate gene for root growth QTLs were studied. Here hydroponic phenotypic screening approach were used to identify the T-DNA mutant lines. However, no convincing mutants were revealed. The herbicide screening method has been shown to be a quick and robust system for the assessment of deep rooting rice plants in soil. This method can now be used for screening large number of cultivars and the identification of QTLs and candidate genes.
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Smith, Gavin James. "A molecular systematic study of the xylariales (ascomycota)." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B30110841.
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Song, Weining. "Genome studies of cereals /." Title page, contents and summary only, 1992. http://web4.library.adelaide.edu.au/theses/09PH/09phs6984.pdf.
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Lonergan, Paul Francis. "Genetic characterisation and QTL mapping of zinc nutrition in barley (Hordeum vulgare)." Title page, contents and abstract only, 2001. http://web4.library.adelaide.edu.au/theses/09PH/09phl847.pdf.
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Dimkpa, Stanley Obumneke Nyebuhi. "Genome wide association mapping and assessment of allelic variation in strigolactone synthesis genes involved in rice plant parasite interactions." Thesis, University of Aberdeen, 2014. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=220456.
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Donald, Tamzin. "Organisation and expression of plant B chromosomes /." Title page, table of contents and abstract only, 1999. http://web4.library.adelaide.edu.au/theses/09PH/09phd6758.pdf.
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Hanson, Christopher Jon. "Exploration of the Gossypium raimondii Genome Using Bionano Genomics Physical Mapping Technology." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/6854.
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Cotton is a crop with a large global economic impact as well as a large, complex genome. Most industrial cotton production is from two tetraploid species (Gossypium hirsutum L. and Gossypium barbadense L.) which contain two subgenomes, specifically the AT and DT subgenomes. The DT subgenome is nearly half the size of the AT subgenome in tetraploid cotton and is closely related to an extant D-genome Gossypium species, G. raimondii Ulbr. Characterization of the structural variants present in diploid D-genome should provide greater insight into the evolution of the DT subgenome in the tetraploid cotton. Bionano (BNG) optical mapping uses patterns of fluorescent labels inserted at specific endonuclease sites to create physical maps of the genomes which can then be examined for structural variation. To develop optical maps in G. raimondii, we first developed a de novo PacBio long read sequence assembly of G. raimondii. This sequence assembly consisted of 2,379 contigs, an average contig length of 413 Kb and a contig N50 of 4.9 Mb. Using BNG technology, we developed two optical maps of the diploid D genome of G. raimondii. One was created using the Nt.BssSI endonuclease and one with the Nt.BspQI endonuclease. Using the BNG optical maps, the PacBio assembly was hybrid scaffolded into 100 scaffolds (+ 5 unscaffolded contigs) with an average scaffold length of 7.5 Mb and a scaffold N50 of 13.1 Mb. A comparison between the Nt. BssSI BNG optical map and the two sequence assemblies identified 3,195 structural variants. These were used to validate the accuracy of the reference sequence of G. raimondii and structural variants were used to create a new phylogeny of nine major cotton species.
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Jean, Martine. "Genetic mapping of restorer genes for cytoplasmic male sterility in Brassica napus using DNA markers." Thesis, McGill University, 1995. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=40147.
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DNA markers tightly-linked to nuclear fertility restorer genes for cytoplasmic male sterility (CMS) are valuable tools for breeders and researchers working with these genes. Two different targeting approaches were used to identify markers linked to the Rfp1 restorer gene for the pol CMS of canola (Brassica napus L.): nearly isogenic line (NIL) comparison and bulked segregant analysis. These methods were equally efficient in identifying markers linked to Rfp1; combining them allowed a targeting efficiency of 100% to be achieved. The efficiency of bulked segregant analysis was found to be limited by the inadvertent occurrence of shared homozygosity at specific chromosomal regions in the bulks, in contrast with the efficiency of NIL comparison which was limited by the occurrence of residual DNA from the donor cultivar at scattered sites around the genome of the NILs. Eleven DNA markers linked to the Rfp1 gene were identified, one of which perfectly co-segregates with Rfp1. The linkage group on which Rfp1 is localized contains 17 DNA markers. Two restorer genes of the pol CMS, Rfp1 and Rfp2, and a Rfn restorer gene of the nap CMS were found to be at least tightly linked to one another and may all reside at the same locus. A fourth restorer gene, the Rfo restorer for the ogu CMS, was, however, found to be unlinked to the other restorer genes. Different restorer genes for the nap CMS were found in the lines 'Westar-Rf and 'Karat'. A linkage map of the B. napus genome containing 146 markers organized into 23 linkage groups covering a total length of 850.2 cM was constructed from a BC$ sb1$ population. This map contains 63 loci previously localized on the B. napus genome through analysis of an F$ sb2$ population. Comparative analysis indicates that the total length of the BC$ sb1$-derived map is smaller than that of the F$ sb2$-derived map, which suggests that a reduction in recombination frequency is occurring in male gametes. The preferential use of two or three probe-
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Surber, Lisa Marie McKinley. "Is there a genetic basis for forage quality of barley for beef cattle?" Diss., Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/surber/SurberL0806.pdf.
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Xing, Liqun 1962. "Marker density, marker distribution and QTL-by-environment interaction in QTL mapping." Thesis, McGill University, 1999. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=36734.
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Two studies were conducted on gene mapping analysis. For the first study, genetic simulation experiments were conducted to address the effects of marker density, method of mapping analysis, and gaps in a marker map on the efficiency of QTL detection and the accuracy of QTL parameter estimation. The simulated genome consisted of seven chromosomes with seven or eight segregating QTL affecting the simulated quantitative trait. A set of six randomly segregating QTL outside the test region was consistently used to represent 40% of phenotypic variation. An individual QTL or a linkage block of two QTL on a target chromosome contributed 10% of phenotypic variation. The marker map was either dense (with markers every 4 cM) or sparse (with markers every 20 cM). The gap in the marker map was either 32 cM or 56 cM. Interval mapping and composite interval mapping were used to map QTL on the target chromosome. A dense map provided more power of QTL detection, better accuracy of QTL parameter estimation, and higher false-positive error rates for the target chromosome than a sparse map. Composite interval mapping provided more power of QTL detection, better accuracy of QTL parameter estimation, and lower false-positive error rates than interval mapping. Presence of a large gap in a marker map affected QTL detection and QTL parameter estimation for a QTL inside or near the gap. The use of a dense map with composite interval mapping was the most efficient combination tested in this study. For the second study, a mixed factorial regression model for interval mapping was developed for conducting QTL-by-environment interaction analysis and for providing inferences about QTL that are applicable beyond the environments used in the experiments. Genetic simulation was used to test the model for the power of detecting QTL-by-environment interaction and identifying the types of such interaction as crossover or non-crossover, and for the accuracy of estimating QTL parameters. The model prov
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Schneerman, Martha June Cook Weber David F. "Identification of quantitative trait loci (QTLs) of corn oil in Zea mays L." Normal, Ill. Illinois State University, 1996. http://wwwlib.umi.com/cr/ilstu/fullcit?p9720812.
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Thesis (Ph. D.)--Illinois State University, 1996.Title from title page screen, viewed May 31, 2006. Dissertation Committee: David F. Weber (chair), Alan J. Katz, Marjorie A. Jones, Radheshyam K. Jayaswal, Jefferey A. Dole. Includes bibliographical references (leaves 96-108) and abstract. Also available in print.
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Campeol, Nadia. "Detection of markers in a low-density region of the barley (Hordeum vulgare L.) genome and their effects on the mapping of quantitative traits." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0002/MQ44137.pdf.
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Pollock, Stephanie. "A study of genetic diversity and genome organization of Brassica napus using EST (expressed sequence tags) of Arabidopsis and SSR (simple sequence repeat) markers of B. napus /." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=33023.
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Arabidopsis expressed sequence tags (ESTs) and microsatellites of Brassica napus have been developed and used as PCR-based markers for both mapping and genetic diversity studies in B. napus . Out of 300 random Arabidopsis ESTs screened, 43 markers were mapped onto a genetic map of B. napus and then used in a diversity study involving 48 B. napus cultivars. A second set of EST markers were developed from chromosome 1 of Arabidopsis and used in genetic mapping studies of B. napus. From 192 primer pairs developed, 50 markers were added onto the B. napus reference map. Microsatellite markers were developed using a "GA" enriched genomic library from B. napus. From 152 designed primer pairs, 23 markers were added onto the B. napus reference map. Microsatellite markers were also used in genetic diversity studies of B. napus, where, from the 152 primer pairs, 40 revealed polymorphism between the 48 B. napus cultivars.
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Hraber, Peter T. "Discovering molecular mechanisms of mututalism with computational approaches to endosymbiosis /." Color figures, full content, and supplementary materials are available online, 2001.
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Thesis (Ph. D.)--University of New Mexico, 2001."July, 2001." Includes bibliographical references (leaves 112-121). Color figures, full content, and supplementary materials are available online via www.santafe.edu/p̃th/dss.
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Wargachuk, Richard Burns. "Fine mapping and functional analysis of the radish Rfo nuclear restorer locus." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=81454.
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Cytoplasmic male sterility (CMS) is a widespread, maternally inherited trait that results in an inability of plants to produce functional pollen. The Ogura CMS system originated in radish, but has since been transferred to, and confers male sterility on, plants in the related genus Brassica . A gene which restores male fertility is needed for the Ogura CMS system to be exploited commercially for hybrid seed production in oilseed species such as Brassica napus. The restorer gene Rfo is a dominant radish nuclear gene that restores the male fertility to plants with Ogura cytoplasm. This gene has been transferred into Brassica napus through intergeneric crosses; however the introgressed segment of radish DNA contains an unknown number of genes, some of which confer undesirable traits, such as an elevated content of seed glucosinolates, antinutritive compounds that render the seed meal unusable as animal feed. A fine scale linkage map of the region in radish containing Rfo was constructed, and a map-based cloning approach relying on synteny between radish and Arabidopsis was used to clone Rfo. A radish gene encoding a 687 amino acid protein with a predicted mitochondrial targeting presequence was found to confer male fertility upon transformation into Ogura CMS B. napus . This gene, codes for a pentatricopeptide repeat (PPR)-containing protein with multiple, in this case 16, PPR domains. Two similar genes that do not appear to function as Rfo flank this gene. A transcript representing a non-functional allele (rfo) was detected in sterile radish plants. Comparison of the Rfo region with the syntenic Arabidopsis region indicates that a PPR gene is not present at the Rfo-equivalent site in Arabidopsis , although a smaller and related PPR gene is found about 40 kb from this site.
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Sadeghzadeh, Behzad. "Mapping of chromosome regions associated with seed zinc accumulation in barley." University of Western Australia. School of Earth and Geographical Sciences, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0204.
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[Truncated abstract] Zinc deficiency in crops is the most widespread micronutrient deficiency, with about 50% of the cereal-growing areas worldwide containing low levels of plant-available Zn. Zinc plays multiple key roles in different metabolic and physiological processes; its deficiency in crops reduces not only grain yield, but also the nutritional quality of grains. Insufficient micronutrient intake, particularly Zn and Fe, afflicts over 3 billion people in the world, mainly in developing countries. Increasing the amount of Zn in food crops can contribute to improving the Zn status of people. Furthermore, Zn-dense seeds have agronomic benefits, resulting in greater seedling vigour, bigger root system and higher crop yield when sowed to soils with low plant-available Zn. Enhancing nutrient content and nutritional quality of crops for human nutrition is a global challenge currently, but it was mostly ignored during the breeding process in the past. There is a significant genotypic variation for seed Zn accumulation in several crops (including barley) which could be exploited in the breeding programs to produce genotypes with higher seed Zn concentration and content. However, the progress in Zn efficiency until now has mainly relied on conventional plant breeding approaches that have had limited success. Therefore, reliable alternative methods are required. Enhancing mineral nutrition through plant biotechnology may be a sustainable and beneficial approach in developing Zn-dense seeds in the staple crops. ... This DNA band was sequenced and converted into a simple sequence-specific PCR-based marker, which was designated as SZnR1 (seed Zn-regulator1). The developed marker is very easy to score, is inexpensive to run and amenable for a large number of plant samples. The successful development of SZnR1 molecular marker linked to chromosome region associated with seed Zn concentration and content using MFLP in this study illustrates the advantage of this technique over some other DNA fingerprinting methods used for identification of molecular markers for marker-assisted selection (MAS). In conclusion, the greater Zn efficiency of Sahara over Clipper under sufficient Zn supply may be attributed to its higher uptake of Zn. It appears that soil-based pot experiments under controlled condition may offer potential improvements over field experiments in screening for seed Zn accumulation. Shoot and seed Zn concentration and content can be used to diagnose the Zn statues of barley genotypes, and may be a useful selection criterion for Zn efficiency in large populations like doubled-haploid populations aimed at developing molecular markers for Zn efficiency. Identified QTLs influencing seed Zn concentration were repeatable in the field and glasshouse conditions, suggesting their robustness across environments as well as their value in marker-assisted selection. The developed PCR-based marker SZnR1 and other molecular markers associated with the QTLs on the short and long arms of chromosome 2H have the potential to be used for marker-assisted selection in breeding for Zn-dense seed in barley.
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Veereshlingam, Harita. "Characterization of Infection Arrest Mutants of Medicago Truncatula and Genetic Mapping of Their Respective Genes." Thesis, University of North Texas, 2005. https://digital.library.unt.edu/ark:/67531/metadc5567/.
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In response to compatible rhizobia, leguminous plants develop unique plant organs, root nodules, in which rhizobia fix nitrogen into ammonia. During nodule invasion, the rhizobia gain access to newly divided cells, the nodule primordia, in the root inner cortex through plant-derived cellulose tubes called infection threads. Infection threads begin in curled root hairs and bring rhizobia into the root crossing several cell layers in the process. Ultimately the rhizobia are deposited within nodule primordium cells through a process resembling endocytosis. Plant host mechanisms underlying the formation and regulation of the invasion process are not understood. To identify and clone plant genes required for nodule invasion, recent efforts have focused on Medicago truncatula. In a collaborative effort the nodulation defect in the lin (lumpy infections) mutant was characterized. From an EMS-mutagenized population of M. truncatula, two non-allelic mutants nip (numerous infections with polyphenolics) and sli (sluggish infections) were identified with defects in nodule invasion. Infection threads were found to proliferate abnormally in the nip mutant nodules with only very rare deposition of rhizobia within plant host cells. nip nodules were found to accumulate polyphenolic compounds, indicative of a host defense response. Interestingly, nip was also found to have defective lateral root elongation suggesting that NIP has a role in both nodule and lateral root development. NIP was found to map at the upper arm of chromosome 1. In sli, infection threads were observed to bring rhizobia from infection threads to newly divided nodule primordium cells in the roots inner cortex. Polyphenolic accumulation in sli nodule/bumps was found. Lateral roots in sli were found to be clustered at the top of the root, indicating that sli like nip may be defective in lateral root development.
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Wilson, Dale 1972. "Early-flowering mutants of a late-flowering ecotype of Arabidopsis thaliana." Monash University, Dept. of Biological Sciences, 2001. http://arrow.monash.edu.au/hdl/1959.1/8976.
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Geddy, Rachel Gwyneth. "Location and expression of genes related to the cytoplasmic male sterility system of Brassica napus." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=100608.
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Cytoplasrnic male sterility (CMS) is a maternally inherited defect in the production of pollen, the male gamete of the flower. This sterility can be suppressed by nuclear Restorer of Fertility (Rf) genes that normally downregulate the expression of the CMS-associated novel mitochondrial gene. In Brassica napus, nap CMS and pol CMS are associated with related chimeric mitochondrial genes orf222 and orf224, respectively. CMS in both nap and pol is associated with a polar loss of locule development, loss of synchronous locule development and clumping of sporogenous tissue away from the tapetal cell layer, as well as secondary effects on petal and bud formation. In nap CMS, early accumulation of orf222 transcripts in the locule regions of developing anthers is associated with sterility, while the absence of orf222 transcripts from the locules is associated with fertility restoration. Accumulation of novel antisense transcripts of atp6 in a cell specific manner which matches that of sense transcripts of orf222 and atp6 in nap CMS anthers may be indicative of a post-transcriptional regulatory mechanism associated with CMS in flower buds.Restoration of fertility in Brassica napus nap and pol CMS is associated with nuclearly encoded genes Rfn and Rfp, respectively. These restorers are very closely linked to one another, and may be allelic. Further efforts to isolate Rfp have narrowed the genomic region to approximately 105 kb of a syntenic region in Arabidopsis thaliana. Cosmid clones isolated from a library of Brassica rapa genomic DNA introgressed with Rfp have been successfully sorted into contigs through the application of the amplified fragment length polymorphism technique. The region to which Rfp is mapped is syntenic to a region of Arabidopsis DNA that is a duplication of a second location at the 23 megabase region of chromosome 1 of that genome. This region contains pentatricopeptide (PPR) motif-encoding genes that are highly related to other restorers of fertility of other species. By inference, Rfp from Brassica napus may encode PPR motifs. The PPR genes related to these previously characterized restorers of fertility are often found alongside the restorer genes existing as mini-clusters of several PPR-encoding genes. This is likely caused by selective pressure acting on PPR-encoding genes that resulted in diversification and multiplication of these genes. In addition, the PPR genes of this duplicated region are not syntenically located, whereas the non-PPR-encoding genes maintain their syntenic locations. The same is true for orthologous comparisons between Arabidopsis and other plant species. PPR genes are therefore malleable and capable of alteration in response to changing environmental pressures, such as the evolution of sterility inducing genes.
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Boyko, Oleksandr, and University of Lethbridge Faculty of Arts and Science. "The versatile role of homologous recombination in plant cell : repair of DNA damage, stress-directed genome evolution and foreign DNA integration." Thesis, Lethbridge, Alta. : University of Lethbridge, Faculty of Arts and Science, 2008, 2008. http://hdl.handle.net/10133/724.
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Homologous recombination represents a DNA repair pathway. Its role in a plant cell is not limited to double strand break repair. It also extends to genome evolution via rearranging of DNA sequences, and has an important application in foreign DNA integration in the plant genome. Our study demonstrated that effects exerted by stress on homologous recombination and genome stability are not restricted to the exposed generation. The progeny of plants exposed to stress exhibited elevated spontaneous homologous recombination, changes in DNA methylation and higher tolerance to stress. These heritable changes are mediated by an unknown stress-inducible epigenetic signal. Furthermore, we demonstrated that using factors that enhance homologous recombination can improve the efficiency of genetic transformation by Agrobacterium. We have developed and patented a plant growth medium enhancing homologous recombination and significantly increasing the transformation frequency. The role of several other chemicals for the improvement of transformation was also evaluated.xxi, 246 leaves : ill. ; 29 cm. --
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Nualsri, Charassri. "Inheritance of rhizome expression in birdsfoot trefoil (Lotus corniculatus l.) /." free to MU campus, to others for purchase, 1996. http://wwwlib.umi.com/cr/mo/fullcit?p9717176.
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Hayes, Alec J. "Characterization of the soybean genome in regions surrounding two loci for resistance to soybean mosaic virus." Diss., Virginia Tech, 1998. http://hdl.handle.net/10919/11275.
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Soybean mosaic virus (SMV), has been the cause of numerous and often devastating disease epidemics, causing reduction in both the quality and quantity of soybeans worldwide. Two important genes for resistance to SMV are Rsv1 and Rsv4. Alleles at the Rsv1 locus have been shown to control resistance to all but the most virulent strain of SMV. This locus has been mapped previously to the soybean F linkage group. Rsv4 is an SMV resistance locus independent of Rsv1 and confers resistance to all strains of SMV. This locus has not been mapped previously. The purpose of this study is to investigate the two genomic regions that contain these vitally important resistance genes.
A population of 281 F2 individuals that had previously been genotyped for reaction to SMV was evaluated in a mapping study which combined bulk segregant analysis with Amplified Fragment Length Polymorphism (AFLP). A Rsv4-linked marker, R4-1, was identified that mapped to soybean linkage group D1b using a reference mapping population. More than 40 markers were mapped in the Rsv4 segregating population including eleven markers surrounding Rsv4. This will provide the necessary framework for the fine mapping of this important genetic locus.
Previous work has located Rsv1 to a genomic region containing several important resistance genes including Rps3, Rpg1, and Rpv. An RFLP probe, NBS5, whose sequence closely resembles that of several cloned plant disease resistance genes has been mapped to this chromosomal region. The efficacy of using this sequence to identify potential disease resistance genes was assessed by screening a cDNA library to uncover a candidate disease resistance gene which corresponds to this NBS5 sequence. Two related sequence classes were identified that correspond to NBS5. Interestingly, one class corresponds to a full length gene closely resembling other previously cloned disease resistance genes offering evidence that this NBS5-derived clone is a candidate disease resistance gene.
A new marker technique was developed by combining the speed and efficiency of AFLP with DNA sequence information from cloned disease resistance genes. Using this strategy, three new markers tightly linked to Rsv1 were identified. One of these markers, which maps 0.6 cM away from Rsv1, has motifs consistent with other cloned disease resistance genes, providing evidence that this approach is an efficient method for targeting genomic regions where disease resistance genes are located.Ph. D.
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Karps, Jennifer Michelle. "Regeneration Patterns and Facilitation Following Blowdown in a Self- Replacing Lodgepole Pine (Pinus contorta) Stand in Central Oregon." PDXScholar, 2006. https://pdxscholar.library.pdx.edu/open_access_etds/1482.
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Nurse plant and object facilitation is an important factor mitigating abiotic stress, improving seedling recruitment, and shaping the fine-scale spatial patterns of many plant communities. I investigate the role of facilitation on lodgepole pine regeneration following blowdown in central Oregon. My objective is to examine the importance of nurse objects on seedling recruitment under varying stand conditions. I base my analysis on 1) the mapped locations and attributes of seedlings, saplings, trees, shrubs, snags, stumps, and sound and decomposed logs in each of five, 500 m2 circular plots, 2) water holding capacity estimates of woody and leafy litter and pumice soil, and 3) growing-season air temperatures. My analysis identifies seedling patterns at multiple spatial scales (~0-8 m) using nearest neighbor and Ripley’s K statistics and identifies differences in canopy structure, seedling development, and temperature using non-parametric rank-sum tests.
My results show blowdown severity varies with pre-disturbance stand structure, resulting in a multi-modal stand structure with a wide range of canopy and seedling microhabitat conditions. Stand-wide, post-blowdown regeneration patterns reveal >80% of seedlings grow near nurse shrubs, logs, and woody litter, suggesting preferential germination and survival in these microhabitats. High seedling densities correspond with median shrub diameters, and up to 38% of seedlings grow near recently downed logs, indicating both shrubs and logs serve as important nurse objects. The role of nurse objects in mitigating moisture stress is implicated by the potentially high evaporative stress under extreme growing season temperatures in areas of severe blowdown and by the high moisture-holding capacity of woody litter relative to the pumice soil. Stand-wide, 91% of all seedlings and 87% of all shrubs grow on woody litter, and seedlings growing on woody litter show the greatest development.
The positive spatial correlation of seedlings and shrubs with nurse plants and woody litter supports the assertion that both are important facilitators for seedling regeneration and emerging spatial patterns of stand recovery. These results have important management implications, suggesting that the removal of nurse plants and objects through salvage logging or prescribed burning may have negative long-term impacts on local and regional forest regeneration.
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Morris, Viktoriya. "Map-based cloning of the NIP gene in model legume Medicago truncatula." Thesis, University of North Texas, 2007. https://digital.library.unt.edu/ark:/67531/metadc3638/.
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Large amounts of industrial fertilizers are used to maximize crop yields. Unfortunately, they are not completely consumed by plants; consequently, this leads to soil pollution and negative effects on aquatic systems. An alternative to industrial fertilizers can be found in legume plants that provide a nitrogen source that is not harmful for the environment. Legume plants, through their symbiosis with soil bacteria called rhizobia, are able to reduce atmospheric nitrogen into ammonia, a biological nitrogen source. Establishment of the symbiosis requires communication on the molecular level between the two symbionts, which leads to changes on the cellular level and ultimately results in nitrogen-fixing nodule development. Inside the nodules hypoxic environment, the bacterial enzyme nitrogenase reduces atmospheric nitrogen to ammonia. Medicago truncatula is the model legume plant that is used to study symbiosis with mycorrhiza and with the bacteria Sinorhizobium meliloti. The focus of this work is the M. truncatula nodulation mutant nip (numerous infections and polyphenolics). The NIP gene plays a role in the formation and differentiation of nodules, and development of lateral roots. Studying this mutant will contribute knowledge to understanding the plant response to infection and how the invasion by rhizobia is regulated. Previous genetic mapping placed NIP at the top of linkage group 1 of the M. truncatula genome. A NIP mapping population was established with the purpose of performing fine mapping in the region containing NIP. DNA from two M. truncatula ecotypes A17 and A20 can be distinguished through polymorphisms. Positional mapping of the NIP gene is based on the A17/A20 genetic map of M. truncatula. The NIP mapping population of 2277 plants was scored for their nodulation phenotype and genotyped with flanking molecular genetic markers 146o17 and 23c16d, which are located ~1.5 cM apart and on either side of NIP. This resulted in the identification of 170 recombinant plants, These plants' DNAs were tested further with different available genetic markers located in the region of interest, to narrow the genetic interval that contains the NIP gene. Segregation data from genotyping analysis of recombinant plants placed NIP in the region between 4L4 and 807 genetic markers.
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Sharp, Aaron Robert. "Improving Cotton Agronomics with Diverse Genomic Technologies." BYU ScholarsArchive, 2016. https://scholarsarchive.byu.edu/etd/5845.
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Agronomic outcomes are the product of a plant's genotype and its environment. Genomic technologies allow farmers and researchers new avenues to explore the genetic component of agriculture. These technologies can also enhance understanding of environmental effects. With a growing world population, a wide variety of tools will be necessary to increase the agronomic productivity. Here I use massively parallel, deep sequencing of RNA (RNA-Seq) to measure changes in cotton gene expression levels in response to a change in the plant's surroundings caused by conservation tillage. Conservation tillage is an environmentally friendly, agricultural practice characterized by little or no inversion of the soil prior to planting. In addition to changes in cotton gene expression and biological pathway activity, I assay the transcriptional activity of microbial symbiotes living in and around the cotton roots. I found a large degree of similarity between cotton individuals in different treatments. However, under conventional disk tillage I did find significantly greater activity of cotton phosphatase and sulfate transport genes, as well as greater abundance of the microbes Candidatus Burkholderia brachynathoides and Arthrobacter species L77. This study also includes the use of high-throughput physical mapping of DNA to examine the genomic structure of a wild cotton species, Gossypium raimondii, which is closely related to the economically significant crop species Gossypium hirsutum. This technology characterizes genomic regions by assembling large input DNA molecules labeled at restriction enzyme recognition sites. I created an efficient algorithm and generated 812 whole genome assemblies from two datasets. The best of these assemblies allowed us to detect 3,806 potential misassemblies in the current release of the G. raimondii genome sequence assembly.
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Herzig, Paul [Verfasser], Klaus [Gutachter] Pillen, and Jens [Gutachter] Léon. "Genome-wide association studies in a wild barley nested association mapping (NAM) population to reveal the genetic architecture of plant development and quality traits / Paul Herzig ; Gutachter: Klaus Pillen, Jens Léon." Halle (Saale) : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2021. http://d-nb.info/1238074561/34.
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Howie, John Allan. "Adult plant resistance to fungal pathogens of wheat." Thesis, Open University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.388302.
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Bassi, Filippo Maria. "Radiation Hybrid Fine Mapping of Two Fertility-Related Genes: Marking the Path to Wheat Hybrids." Diss., North Dakota State University, 2012. https://hdl.handle.net/10365/26535.
Full textAbstract:
Over one billion people, more than 1/9th of the global population, are undernourished. Feeding the ever increasing population has to be the most important goal of plant sciences. Since cultivated areas are not likely to increase, I will need to produce more with what is available. This can be summarized in one word: yield. Unfortunately, wheat?s yield is expected to increase only 1.13% by 2019, a prediction that if converted into reality will likely indicate that I failed to cope with the world demographic increase. A new strategy to revolutionize wheat production is required, and some believe that this change might be represented by wheat hybrids. Achieving adequate commercial production of wheat hybrids has the potential to nearly double the yield of one of the world?s most important staple food. The first fundamental step toward this goal is to develop feasible methodologies to sterilize the male part of the complete wheat flowers. Two fertility-related genes are the primary target of this study, namely the species cytoplasm specific on chromosome 1D, and the desynaptic locus on chromosome 3B. This dissertation summarizes the important achievements obtained toward the cloning of the two loci by means of radiation hybrid functional analysis. Radiation hybrid is a technique that employs radiation to create genetic diversity along the targeted chromosome. Chapter 1 explains in details how this methodology can be applied to plants. The use of radiation hybrid mapping permitted creating a comprehensive map of wheat chromosome 3B, as discussed in Chapter 2, and then expanded the mapping information to identify the 2 Mb location of the desynaptic locus desw2, as discussed in Chapter 3. A similar approach on chromosome 1D allowed first to pinpoint the location of the species cytoplasm specific gene to a region of 2 Mb, as discussed in Chapter 4, and then ultimately to find a strong candidate for this locus, as discussed in Chapter 5. Now that the molecular locations of these genes have been unraveled by this study, their sequence can be streamlined into transformation to ultimately produce female wheat plants, and consequently hybrids.
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Kuraparthy, Vasu. "Genomic targeting and mapping of agronomically important genes in wheat." Diss., Manhattan, Kan. : Kansas State University, 2007. http://hdl.handle.net/2097/311.
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Bickel, Cory Lyn. "Identification of Genomic Regions Involved in Stress Responsiveness in Flax by Genetic Mapping." Case Western Reserve University School of Graduate Studies / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=case1301676557.
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Balimponya, Elias George. "Application of Genomic Selection and Association Mapping to Breeding for Resistance to Rice Blast and Bacterial Blight of Rice (Oryza sativa L.)." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1449138999.
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Gagliardi, Paulo Roberto. "Análise estrutural e comparativa do genoma de Leifsonia xyli subsp. xyli." Universidade de São Paulo, 2003. http://www.teses.usp.br/teses/disponiveis/11/11135/tde-20102003-165028/.
Full textAbstract:
Leifsonia xyli subsp. xyli (Davis et al.; 1984; Evtushenko et al.; 2000) é agente causal de uma das mais importantes doenças da cana-de-açúcar: o raquitismo-da-soqueira (Gillaspie Jr. & Davis, 1992; Davis et al.; 1994). O presente trabalho teve como objetivo principal usar métodos de análise cromossômica para corroborar o mapa genômico da estirpe CTC B07 de L. xyli subsp. xyli obtido através do seqüenciamento por shotgun, realizado pelo grupo de seqüenciamento de Genomas Agronômicos e do Meio-ambiente (AEG) da rede ONSA-FAPESP. A identidade do isolado foi confirmada com a amplificação e seqüenciamento da região 23S do rRNA bem como por meio de testes sorológicos de microaglutinação com antissoro específico. Além destes, foram realizados testes de microscopia eletrônica de varredura da bactéria cultivada em meio líquido para confirmar a pureza do isolado. O tamanho do genoma de L. xyli subsp. xyli foi estimado com base na análise de fragmentos de restrição gerados por digestões com as enzimas de restrição XbaI e SpeI e eletroforese de campo pulsado (PFGE). As estimativas de 2.540 kb e 2.530 kb com XbaI e SpeI respectivamente ficaram próximas ao valor obtido pelo seqüenciamento genômico (2.596.959 pb). Em adição, o número de seqüências repetidas e de genes ribossomais identificados pelo projeto genoma foram confirmados por meio de hibridizações com sondas apropriadas. Comparações genômicas de L. xyli subsp. xyli, L. xyli subsp. cynodontis e duas espécies de Clavibacter também foram objetivos deste trabalho. As comparações foram baseadas em análise de RFLPs após a hibridização do DNA genômico utilizando como sondas elementos genéticos móveis presentes no genoma de L. xyli subsp. xyli. As estimativas dos números estimado de cópias destes elementos no genoma de L. xyli subsp. xyli obtidas por hibridizações concordam com aquelas obtidas pelo seqüenciamento, considerando fragmentos RFLPs menores que 9 kb. Informações referentes à fragmentos maiores não foram obtidas uma vez que estes não foram adequadamente resolvidos na corrida eletroforética. Finalmente, comparações através de análise de RFLP e rep-PCR mostraram diferenças entre L. xyli subsp. xyli e L. xyli subsp. cynodontis bem como entre estas e espécies de Clavibacter. Não foram verificadas diferenças entre a estirpe CTC B07 de L. xyli subsp. xyli e a estirpe australiana.Leifsonia xyli subsp. xyli (Davis et al.; 1984; Evtushenko et al.; 2000) is the causal agent of one of the most economically important disease of sugarcane worldwide, i.e, ratoon stunting disease (Gillaspie Jr. & Davis, 1992; Davis et al.; 1994). The main objective of this study was to confirm the assembly of the genome of L. xyli subsp. xyli obtained after shotgun sequencing by the Agronomic and Enviromental Genomes group of the ONSA/FAPESP network. The identity of the strain was confirmed by amplification and sequencing of the 23S rRNA region as well as by microaglutination serological tests with specific antiserum. Besides this, scanning electron microscopic analysis was used to assess the purity of the strain culture. The size of the genome of L. xyli subsp. xyli was estimated based on restriction analysis after digestion of genomic DNA with SpeI and XbaI followed by pulsed-field gel electrophoresis. The estimates of 2,530 kb and 2,540 kb, respectively for SpeI and XbaI, are in agreement with the one obtained by whole genome sequencing (2,596 kb). In addition, the number of repeated sequences and ribossomal genes predicted by thesequencing project was confirmed by hybridization experiments with the appropriate probes. Genomic comparisons of L. xyli subsp. xyli, L. xyli subsp. cynodontis and two Clavibacter species comprised a second objective of this study. Comparisons were based on RFLP analysis after hybridization of digested genomic DNA using mobile genetic elements present in the genome of L. xyli subsp. xyli as probes. The estimates of number of copies of these elements in the genome of L. xyli subsp. xyli obtained by this approach agreed with the ones obtained by sequencing if RFLP fragments smaller than 9 kb are considered. Data from larger fragments were not obtained since they were not adequately resolved by electrophoresis. Finally, RFLP and rep-PCR comparisons unveiled differences between L. xyli subsp. xyli and L. xyli subsp. cynodontis as well as between these and Clavibacter. No differences were found between strain CTC B07 of L. xyli subsp. xyli and an Australian strain.
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Laurent, Benoit. "Base génétique et potentiel d’évolution de la pathogénicité de Fusarium graminearum, bio-agresseur fongique des céréales." Thesis, Bordeaux, 2016. http://www.theses.fr/2016BORD0317/document.
Full textAbstract:
Le champignon Fusarium graminearum est l'un des principaux agents responsables de la fusariose des épis, une maladie nécrosante des céréales associée à une contamination des grains et des aliments par des mycotoxines. De récentes observations suggèrent une évolution de l’agressivité des populations de ce pathogène, questionnant l’efficacité et la durabilité des moyens de luttes actuels. Mieux anticiper cette évolution nécessite une meilleure caractérisation de la diversité phénotypique et génotypique existante entre souches. Six nouveaux génomes de F. graminearum ont été séquencés et ont permis l’identification et la caractérisation de 243 000 variations génétiques. La majorité de ces variants (77%) est concentrée dans des îlots de polymorphisme, représentant 32% du génome et enrichis en probables effecteurs liés à la pathogénicité de F. graminearum. La construction d’une population recombinante, et son génotypage avec 1 300 marqueurs moléculaires, ont permis le développement de la première carte génétique à haute-densité de l’espèce. La corrélation entre le taux de recombinaison et le polymorphisme a mis en évidence une organisation « à deux-vitesses » du génome de cette espèce. Finalement, l’intégration de ces données dans une approche de génétique quantitative a permis l’identification d’un locus polymorphe, affectant le gène FgVeA, et responsable de 90% de la variation d’agressivité et de la production de mycotoxine observée. Les différents résultats obtenus durant ces travaux font l’objet d’une discussion générale sur le potentiel adaptatif et d’évolution de ce pathogèneF. graminearum is one of the main causal agents of the fusarium head-blight (FHB), a cereal disease leading to head necrosis, in addition to grain and food/feed contamination by stable and toxic metabolites. Recent observations refer to an increase of pathogenicity, questioning efficiency and durability of current management practices. In order to anticipate this evolution, we must bring a deeper characterization of the currently existing diversity. Six new genomes of F. graminearum were sequenced, and 243,000 genetic variations have been identified and characterized. Seventy seven percent of the total number of the variants was located within 32% of the genome, delineating highly polymorphic islands. These islands are enriched with probable effectors linked to Fusarium’s pathogenicity. The construction and the genotyping on 1,300 molecular markers of a recombinant population have enabled the development of the first high-density genetic map of the species. The remarkable correlation between polymorphism and recombination rate highlighted the 'two-speed' genome organization of this pathogen. Finally, the integration of these data through a quantitative genetic approach allowed the discovery of one quantitative trait locus, likely to affect the gene FgVeA, and responsible for 90% of the observed variation of aggressiveness and mycotoxin production. These results are discussed in the light of F. graminearum’s adaptive potential and evolution
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Gilmore, Scott R. "Genetic mapping of plant transpiration efficiency." Phd thesis, 2005. http://hdl.handle.net/1885/149993.
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Jaccoud, Damian Francois. "Diversity arrays technology (DArT) in a model plant and animal." Phd thesis, 2006. http://hdl.handle.net/1885/150431.
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Donald, Tamzin. "Organisation and expression of plant B chromosomes / by Tamzin Donald." Thesis, 1999. http://hdl.handle.net/2440/19416.
Full textAbstract:
Copy of previously published article by author, inserted.Bibliography: leaves 217-233.
xix, 233 leaves : ill. (some col.) ; 30 cm.
The rDNA work presented aimed to determine if B chromosome sequences of Brachycome dichromosomatica were transcriptionally active.
Thesis (Ph.D.)--University of Adelaide, Dept. of Genetics, 1999
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Oziel, Adeline M. "Mapping of quantitative trait loci for malting quality in a winter X spring barley (Hordeum vulgare, L.) cross." Thesis, 1993. http://hdl.handle.net/1957/35753.
Full textAbstract:
Making quality and winterhardiness in barley are "ultimate" phenotypes composed of
component, quantitatively inherited traits. A 69-point genome map of the seven chromosomes of
barley was used, in conjunction with multi-environment phenotypes for grain yield and malting
quality, to determine the chromosome locations of quantitative trait loci (QTLs). A combined
analysis of the two environments identified QTLs that were both common and unique to each
environment. Dispersed QTLs with positive relationships provide ready targets for marker-assisted
selection. Overlapping QTLs for agronomic and making quality QTLs with favorable
alleles contributed by alternate parents will require further, higher resolution mapping to
determine if negative relationships are due to linkage or pleiotropy. There is preliminary evidence
for orthologous agronomic trait and malting QTLs in barley. This QTL analysis will hopefully
assist in the rapid development of winter making varieties that will maximize the profitability of
Oregon barley production.Graduation date: 1994
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"Genome sequence of shiitake mushroom Lentinula edodes and comparative mushroom genomics with platform construction." Thesis, 2011. http://library.cuhk.edu.hk/record=b6075378.
Full textAbstract:
Au, Chun Hang.Thesis (Ph.D.)--Chinese University of Hong Kong, 2011.
Includes bibliographical references (leaves 124-146).
Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Abstract also in Chinese.
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"Generation and sequencing of cDNA matching SAGE tags for gene identification in Lentinula edodes." 2005. http://library.cuhk.edu.hk/record=b5896450.
Full textAbstract:
Hui Cheung.Thesis (M.Phil.)--Chinese University of Hong Kong, 2005.
Includes bibliographical references (leaves 166-172).
Abstracts in English and Chinese.
Abstract --- p.iii
Acknowledgments --- p.vi
Abbreviations --- p.vii
Table of Contents --- p.viii
Table of Figures --- p.xiii
Table of Tables --- p.xviii
Chapter Chapter 1. --- Literature Reviews
Chapter 1.1 --- Functional Genomics and Its Developments --- p.1
Chapter 1.1.1 --- Introduction --- p.1
Chapter 1.1.2 --- "Transcriptomics, Proteomics and Metabolomics" --- p.1
Chapter 1.1.3 --- Gene-perturbing Strategies --- p.3
Chapter 1.1.4 --- Applications of Functional Genomics --- p.4
Chapter 1.2 --- Serial Analysis of Gene Expression (SAGE) and Generation of Longer cDNA Fragments from SAGE tags for Gene Identification (GLGI) --- p.6
Chapter 1.2.1 --- Introduction --- p.6
Chapter 1.2.2 --- Principles and Methods of SAGE --- p.6
Chapter 1.2.3 --- Data Analysis --- Bioinformatics --- p.9
Chapter 1.2.4 --- Applications of SAGE --- p.9
Chapter 1.2.5 --- Modifications of SAGE --- p.10
Chapter 1.2.6 --- Principles and Methods of GLGI --- p.11
Chapter 1.2.7 --- Applications and Improvements of GLGI --- p.14
Chapter 1.3 --- Transformation --- p.15
Chapter 1.3.1 --- Introduction --- p.15
Chapter 1.3.2 --- Different Methods of Transformation --- p.15
Chapter 1.3.2.1 --- General Transformation Strategy --- p.15
Chapter 1.3.2.2 --- Polyethylene Glycol (PEG)-mediated Transformation --- p.16
Chapter 1.3.2.3 --- Restriction Enzyme Mediated Integration (REMI) --- p.16
Chapter 1.3.2.4 --- Electroporation --- p.17
Chapter 1.3.2.5 --- Particle Bombardment --- p.17
Chapter 1.3.3 --- The Future Needs of Transformation --- p.18
Chapter 1.4 --- RNA Silencing --- p.20
Chapter 1.4.1 --- Introduction --- p.20
Chapter 1.4.2 --- Major Components and Principles of RNAi --- p.21
Chapter 1.4.3 --- Applications of RNA Silencing --- p.23
Chapter 1.5 --- The Target Organism Lentinula edodes --- p.25
Chapter 1.5.1 --- Introduction --- p.25
Chapter 1.5.2 --- The Life Cycle of L. edodes --- p.26
Chapter 1.5.3 --- Biochemical and Molecular Studies on L. edodes --- p.27
Chapter 1.5.4 --- Prospectus --- p.29
Chapter Chapter 2. --- Development of Methods for Studying Gene Function in Lentinula edodes
Chapter 2.1 --- Introduction --- p.30
Chapter 2.2 --- Materials and Methods --- p.32
Chapter 2.2.1 --- Cultivation of Lentinula edodes --- p.32
Chapter 2.2.2 --- Proplast Release and Regeneration --- p.32
Chapter 2.2.3 --- Preparation of Plasmid DNA --- p.33
Chapter 2.2.4 --- Selectable Marker …Bialaphos --- p.35
Chapter 2.2.5 --- Transformation --- p.35
Chapter 2.2.5.1 --- Electroporation --- p.35
Chapter 2.2.5.2 --- PEG-mediated Transformation --- p.36
Chapter 2.3 --- Results --- p.37
Chapter 2.3.1 --- Cultivation of Lentinula edodes --- p.37
Chapter 2.3.2 --- Proplast Release and Regeneration --- p.37
Chapter 2.3.3 --- Preparation of Plasmid DNA --- p.43
Chapter 2.3.4 --- Selectable Marker--- Bialaphos --- p.43
Chapter 2.3.5 --- Transformation --- p.46
Chapter 2.3.5.1 --- Electroporation --- p.46
Chapter 2.3.5.2 --- PEG-mediated Transformation --- p.46
Chapter 2.4 --- Discussions and Conclusions --- p.57
Chapter Chapter 3. --- Identification of Interested Genes in Expression Profile of SAGE using GLGI Method.
Chapter 3.1 --- Introduction --- p.61
Chapter 3.1.1 --- Results of SAGE Analysis --- p.61
Chapter 3.1.2 --- Use of GLGI Method for Extension of SAGE Tags --- p.63
Chapter 3.1.3 --- 5´ة Extension of GLGI (5'GLGI) --- p.65
Chapter 3.1.3.1 --- Introduction --- p.65
Chapter 3.1.3.2 --- "Overall strategy of 5, GLGI Method" --- p.67
Chapter 3.1.3.3 --- Two-Steps PCR Method --- p.69
Chapter 3.2 --- Generation of Longer cDNA Fragments from SAGE tags for Gene Identification (GLGI) --- p.71
Chapter 3.2.1 --- Materials and Methods (GLGI Analysis) --- p.71
Chapter 3.2.1.1 --- Total RNA Extraction --- p.71
Chapter 3.2.1.2 --- Messenger RNA (mRNA) Extraction --- p.72
Chapter 3.2.1.3 --- Preparation of 3´ة cDNA for GLGI --- p.73
Chapter 3.2.1.4 --- NIaIII digestion of double strand cDNA --- p.74
Chapter 3.2.1.5 --- PCR amplification of the 3'-cDNAs (Optional) --- p.77
Chapter 3.2.1.6 --- GLGI Amplification of The Target Template --- p.80
Chapter 3.2.1.7 --- DNA Cloning (Optional) --- p.82
Chapter 3.2.1.8 --- Sequencing of GLGI PCR products --- p.85
Chapter 3.2.2 --- 5' Materials and Methods (5' GLGI Analysis) --- p.86
Chapter 3.2.2.1 --- Preparation of unique antisense primers --- p.86
Chapter 3.2.2.2 --- 5' extension of GLGI products --- p.87
Chapter 3.2.2.3 --- DNA Cloning (Optional) --- p.89
Chapter 3.2.2.4 --- Sequencing of 5' GLGI PCR products --- p.89
Chapter 3.2.3 --- Results (GLGI Analysis) --- p.90
Chapter 3.2.3.1 --- Total RNA Extraction --- p.90
Chapter 3.2.3.2 --- Messenger RNA Extraction --- p.90
Chapter 3.2.3.3 --- Preparation of 3' cDNA for GLGI --- p.90
Chapter 3.2.3.4 --- NIaIII digestion of double strand cDNA --- p.94
Chapter 3.2.3.5 --- GLGI Amplification of The Target Template --- p.94
Chapter 3.2.3.6 --- Sequencing of GLGI PCR products --- p.103
Chapter 3.2.4 --- Results (5' GLGI Analysis) --- p.111
Chapter 3.2.4.1 --- 5' extension of GLGI products --- p.111
Chapter 3.2.4.2 --- Sequencing of 5´ة GLGI PCR products --- p.116
Chapter 3.3 --- Discussions and Conclusions --- p.126
Chapter 3.3.1 --- GLGI amplification of the target template --- p.126
Chapter 3.3.2 --- 5' extension of GLGI products --- p.129
Chapter 3.3.3 --- Two-Steps PCR Method --- p.130
Chapter 3.3.4 --- Sequencing results of GLGI method and 5' GLGI method --- p.131
Chapter Chapter 4. --- Identification of Unknown EST Using PCR Method With cDNA Library
Chapter 4.1 --- Introduction --- p.134
Chapter 4.2 --- Materials and Methods --- p.134
Chapter 4.2.1 --- Extension of 5' end of EST sequence by PCR method --- p.134
Chapter 4.2.2 --- Purification of PCR products --- p.136
Chapter 4.2.3 --- Sequencing of Extended EST products --- p.136
Chapter 4.3 --- Results --- p.137
Chapter 4.3.1 --- Extension of 5' end of EST sequence by PCR method --- p.137
Chapter 4.3.2 --- Sequencing of Extended EST products --- p.137
Chapter 4.4 --- Discussions and Conclusions --- p.147
Chapter Chapter 5. --- General Discussions --- p.151
Appendix I --- p.156
Reference --- p.166
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Zurek, Paul Roman. "Quantitative Trait Locus Mapping Reveals Regions of the Maize Genome Controlling Root System Architecture." Diss., 2014. http://hdl.handle.net/10161/9399.
Full textAbstract:
Root system architecture (RSA) is the spatial distribution of roots of individual plants. As part of a collaborative effort I adapted a gellan gum based system for imaging and phenotyping of root systems in maize. This system was first used to perform a survey of 26 distinct maize varieties of the Nested Association Mapping (NAM) population. The analysis of these data showed a large amount of variation between different RSA, in particular demonstrating tradeoffs between architectures favoring sparse, but far reaching, root networks versus those favoring small but dense root networks. To study this further I imaged and phenotyped the B73 (compact) x Ki3 (exploratory) mapping population. These data were used to map 102 quantitative trait loci (QTL). A large portion of these QTL had large, ranging from 5.48% to 23.8%. Majority of these QTLs were grouped into 9 clusters across the genome, with each cluster favoring either the compact of exploratory RSA. In summary, our study demonstrates the power of the gellan based system to locate loci controlling root system architecture of maize, by combining rapid and highly detailed imaging techniques with semi-automated computation phenotyping.
Dissertation
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Mumm, Anina. "Promoter analysis of members of a plant defense-related LRR-RLK gene cluster in Arabidopsis thaliana." Thesis, 2014. http://hdl.handle.net/10210/11414.
Full textAbstract:
M.Sc. (Biochemistry)A 14-member, closely-spaced cluster of genes coding for leucine-rich repeat receptor-like kinases (LRR-RLKs) is located on chromosome 1 of Arabidopsis thaliana. Following on from previous microarray studies that found some of the members of this cluster to be upregulated in response to biotic stressors, including the bacterial elicitor flg22, the present study sought to confirm, using a luciferase-based protoplast assay, that flg22 does in fact induce the expression of the genes, and then to investigate the promoters of the genes. The promoters of At1g51790, At1g51850 and At1g51890 responded positively in this particular assay, and bioinformatic analyses determined that W-boxes are over-represented in the cloned regions. Mutational inactivation of individual W-boxes in the promoter of At1g51790 drastically reduced the flg22 response, except for the W-box closest to the start site, which seemed to increase both basal and flg22-inducible expression. In the promoter of At1g51850, mutational inactivation of either or both of its W-box dyads resulted in virtually no flg22 inducibility. The deletion of 6 W-boxes in the promoter of At1g51890, done via truncation, drastically reduced both its basal expression and its inducible response to flg22. These results provide evidence that W-box cis-elements are responsible for the upregulation of these LRR-RLKs in response to flg22. WRKYs -7, -11, -22,and -26 were found bioinformatically to have similar expression patterns to some of the genes in the cluster, and are thus good candidates to investigate as transcriptional regulators of the cluster in future studies.
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Song, Weining 1958. "Genome studies of cereals." 1992. http://web4.library.adelaide.edu.au/theses/09PH/09phs6984.pdf.
Full textAbstract:
Bibliography: leaves 93-114. This thesis investigates genome analysis of wheat, rye and barley. The objective is to evaluate the feasibility of using polymerase chain reaction (PCR) as a tool for studying cereal genomes. Results are compared for PCR and RFLP (restriction fragment length polymorphism)
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Lonergan, Paul F. "Genetic characterisation and QTL mapping of zinc nutrition in barley (Hordeum vulgare) / Paul Francis Lonergan." 2001. http://hdl.handle.net/2440/21718.
Full textAbstract:
Includes bibliographical references (leaves 192-211).x, 211 leaves : ill. ; 30 cm.
Title page, contents and abstract only. The complete thesis in print form is available from the University Library.
Maps major genes or quantitative trait loci associated with zinc nutrition in the vegetative and reproductive tissues of barley (Hordeum vulgare)
Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 2001
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Lee, Young-Kwang. "Molecular and functional studies of low molecular weight glutenin subunits from A-genome diploid wheats." Phd thesis, 1997. http://hdl.handle.net/1885/145939.
Full text
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Song, Weining 1958. "Genome studies of cereals / by Song Weining." Thesis, 1992. http://hdl.handle.net/2440/21422.
Full textAbstract:
Bibliography: leaves 93-114.114, [43] leaves, [30] leaves of plates : ill. ; 30 cm.
This thesis investigates genome analysis of wheat, rye and barley. The objective is to evaluate the feasibility of using polymerase chain reaction (PCR) as a tool for studying cereal genomes. Results are compared for PCR and RFLP (restriction fragment length polymorphism)
Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 1994
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Araneda, Loreto P. "Comparative Genome Analysis between Agrostis stolonifera and Members of the Pooideae Subfamily Including Brachypodium distachyon." 2011. https://scholarworks.umass.edu/theses/661.
Full textAbstract:
Understanding of grass genome structure and evolution has been significantly advanced through comparative genomics. The genomes of most cool-season forage and turf grasses, belonging to the Pooideae subfamily of the grasses, remain understudied. Creeping bentgrass (Agrostis stolonifera) is one of the most important cool-season turfgrasses due to its low mowing tolerance and aggressive growth habit. An RFLP genetic map of creeping bentgrass using 229 RFLP markers derived from cereal and creeping bentgrass EST-RFLP probes was constructed for a comparative genome analysis. This genetic map was compared with those of perennial ryegrass, oat, wheat, and rice. Large-scale chromosomal rearrangements between the map of creeping bentgrass and the respective maps of the Triticeae, oat, and rice were observed. However, no evidence of chromosomal rearrangements between the maps of creeping bentgrass and perennial ryegrass was detected, suggesting that these recently domesticated species might be closely related than expected. Further comparative genome analysis of creeping bentgrass was performed with the genome sequences of Brachypodium distachyon using sequences of the above-mentioned RFLP mapped markers and 8,470 publicly available A. stolonifera EST (AgEST) sequences. A total of 24 syntenic blocks were identified between the Agrostis linkage groups and the B. distachyon chromosomes. Orthologous loci of AgESTs (678) were identified in the B. distachyon genome, and these loci can be utilized in further comparative mapping of Pooideae species. Insights from comparative genomics with B. distachyon will be useful for genetic improvement of Agrostis spp. and provide a better understanding of the evolution of the Pooideae species.
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Ming, Reiguang. "Restriction fragment length polymorphism analysis of host-plant resistance to four maize pathogens." Thesis, 1995. http://hdl.handle.net/10125/9273.
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Long, Nigel R. "Characterisation and mapping of chromosome regions associated with improved growth and grain yield of barley on sandy soils of low fertility / by Nigel Richard Long." Thesis, 2003. http://hdl.handle.net/2440/21993.
Full textAbstract:
"August, 2003"Includes bibliographical references (leaves 260-292)
v, 294 leaves : ill. (some col.), plates (col.), maps (col.) ; 30 cm.
Thesis (Ph.D.)--University of Adelaide, School of Agriculture and Wine, 2003
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Long, Nigel R. "Characterisation and mapping of chromosome regions associated with improved growth and grain yield of barley on sandy soils of low fertility / by Nigel Richard Long." 2003. http://hdl.handle.net/2440/21993.
Full textAbstract:
"August, 2003"Includes bibliographical references (leaves 260-292)
v, 294 leaves : ill. (some col.), plates (col.), maps (col.) ; 30 cm.
Title page, contents and abstract only. The complete thesis in print form is available from the University Library.
Thesis (Ph.D.)--University of Adelaide, School of Agriculture and Wine, 2003