Tesis: "Resistance QTL"

1

Sabry, Ahmed Mohamed-Bashir. "QTL mapping of resistance to sorghum downy mildew in maize". Diss., Texas A&M University, 2003. http://hdl.handle.net/1969.1/460.

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Sorghum downy mildew (SDM) of maize is caused by the oomycete Peronosclerospora sorghi (Weston and Uppal) C. G. Shaw. The disease can cause devastating yield losses in maize (Zea mays L.). Quantitative trait loci (QTLs) mediating resistance to SDM were mapped using both restriction fragment length polymorphisms (RFLPs), and simple sequence repeats (SSRs) in 220 F2 individual maize progeny derived from a cross between two extremes; highly susceptible inbred parent SC-TEP5-19-1-3-1-4-1-1 (white) and highly resistant inbred P345C4S2B46-2-2-1-2-B-B-B (yellow). The phenotypic expression was assessed on F2:3 families in a wide range of environments under natural field infection and in a controlled greenhouse screening method. Heritability estimates of disease reaction ranged from 93.3% in Thailand sit 1 to 48% in Thailand sit 2. One hundred and thirty three polymorphic markers were assigned to the ten chromosomes of maize with LOD scores exceeding 4.9 covering about 1265 cM with an average interval length between markers of 9.5 cM. About 90% of the genome was located within a 10 cM distance to the nearest marker. Three putative QTLs were detected in association with resistance to SDM in different environments using composite interval mapping. Despite environmental and symptom differences, one QTL on chromosome 2 bin 9 had a major effect in all trials and explained up to 70% of the phenotypic variation in Thailand where the highest disease pressure was experienced. Two other QTLs on chromosome 3 bin 5 and chromosome 9 bin 2 had a minor effect, each explaining no more than 4% of the phenotypic variation. These results revealed one major gene and two minor genes that control sorghum downy mildew resistance. These markers should be very useful in breeding programs in facilitating the introgression of the resistance genes into commercial varieties. Marker-assisted selection for these loci should be useful in incorporating SDM resistance genes in maize across environments, even in the absence of the pathogen.

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2

Gambone, Katherine. "Mapping stem rust resistance genes in ‘Kingbird’". Thesis, Kansas State University, 2016. http://hdl.handle.net/2097/32496.

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Master of Science
Department of Plant Pathology
William Bockus
Robert Bowden
Stem rust, caused by the fungus Puccinia graminis f. sp. tritici, has historically been one of the most important diseases of wheat. Although losses have been much reduced in the last fifty years, new highly virulent races of the pathogen have recently emerged in East Africa. These new races are virulent on nearly all of the currently deployed resistance genes and therefore pose a serious threat to global wheat production. The spring wheat variety ‘Kingbird’ is thought to contain multiple quantitative trait loci (QTLs) that provide durable, adult-plant resistance against wheat stem rust. Stem rust-susceptible Kansas winter wheat line ‘KS05HW14’ was backcrossed to Kingbird and 379 recombinant lines were advanced to BC₁F₅ and then increased for testing. The lines were screened for stem rust resistance in the greenhouse and field in Kansas and in the field in Kenya over multiple years. We identified 16,237 single nucleotide polymorphisms (SNPs) with the Wheat 90K iSelect SNP Chip assay. After filtering for marker quality, linkage maps were constructed for each wheat chromosome. Composite interval mapping and multiple-QTL mapping identified seven QTLs on chromosome arms 2BL, 2DS, 3BS, 3BSc, 5DL, 7BL, and 7DS. Six QTLs were inherited from Kingbird and one QTL on 7BL was inherited from KS05HW14. The location of the QTL on 2BL is approximately at locus Sr9, 3BS is at Sr2, 3BSc is at Sr12, and 7DS is at Lr34/Yr18/Sr57. Although no QTL was found on 1BL, the presence of resistance gene Lr46/Yr29/Sr58 on 1BL in both parents was indicated by the gene-specific marker csLV46. QTLs on 2DS and 5DL may be related to photoperiod or vernalization genes. Pairwise interactions were only observed with race QFCSC, most notably occurring with QTLs 2BL and 3BSc. These results confirm that there are multiple QTLs present in Kingbird. Ultimately, the identification of the QTLs that make Kingbird resistant will aid in the understanding of durable, non-race-specific resistance to stem rust of wheat.

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3

Cai, Jin. "Mapping QTL for fusarium head blight resistance in Chinese wheat landraces". Thesis, Kansas State University, 2012. http://hdl.handle.net/2097/13703.

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Master of Science
Department of Agronomy
Allan Fritz
Fusarium head blight (FHB) is one of the most devastative diseases in wheat. Growing resistant cultivars is one of the most effective strategies to minimize the disease damage. Huangcandou (HCD) is a Chinese wheat landrace showing a high level of resistance to FHB spread within a spike (type II). To identify quantitative traits loci (QTL) for resistance in HCD, a population of 190 recombinant inbred lines (RILs) were developed from a cross between HCD and Jagger, a susceptible hard winter wheat (HWW) released in Kansas. The population was evaluated for type II resistance at the greenhouses of Kansas State University. After initial marker screening, 261 polymorphic simple-sequence repeats (SSR) between parents were used for analysis of the RIL population. Among three QTL identified, two from HCD were mapped on the short arms of chromosomes 3B (3BS) and 3A (3AS). The QTL on the distal end of 3BS showed a major effect on type II resistance in all three experiments. This QTL coincides with a previously reported Fhb1, and explained 28.3% of phenotypic variation. The QTL on 3AS explained 9.7% of phenotypic variation for mean PSS over three experiments. The third QTL from chromosome 2D of Jagger explained 6.5% of phenotypic variation. Allelic substitution using the closest marker to each QTL revealed that substitution of Jagger alleles of two QTL on 3AS and 3BS with those from HCD significantly reduced the PSS. HCD containing both QTL on 3AS and 3BS with a large effect on type II resistance can be an alternative source of FHB resistance for improving FHB type II resistance in wheat. Besides, meta-analyses were used to estimate 95% confidence intervals (CIs) of 24 mapped QTL in five previously mapped populations derived from Chinese landraces: Wangshuibai (WSB), Haiyanzhong (HYZ), Huangfangzhu (HFZ), Baishanyuehuang (BSYH) and Huangcandou (HCD). Nineteen QTL for FHB type II resistance were projected to 10 QTL clusters. Five QTL on chromosomes 1A, 5A, 7A, and 3BS (2) were identified as confirmed QTL that have stable and consistent effects on FHB resistance and markers in these meta-QTL regions should be useful for marker-assisted breeding.

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4

Fytrou, Anastasia. "Drosophila immunity : QTL mapping, genetic variation and molecular evolution". Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4742.

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Drosophila is involved in a wide range of interactions with parasites and pathogens (parasitoid wasps, bacteria, fungi, viruses). Drosophila hosts vary greatly at the species, population and individual level, in their response against such organisms, and much of this variation has a genetic basis. In this thesis I explored three aspects of this variation. First, using recombination mapping based on SNPs and a variation of bulk segregant analysis, I identified a QTL region on the right arm of the third chromosome of D. melanogaster associated with resistance to at least some of the parasitoid species / strains used in the experiments. The location of the QTL was further explored with deficiency complementation mapping and was narrowed down to the 96D1-97B1 region. The success of the deficiency mapping suggests that the resistant allele is not completely dominant. Second, I investigated patterns of molecular evolution in a set of immunity-related genes, using sequences from a D. melanogaster and a D. simulans population and a set of genes without known involvement in immunity for comparison. I found evidence that several of these genes have evolved under different selection pressure in each species, possibly indicating interactions with different parasites. The immunity genes tested appear to be evolving faster compared to non-immunity genes, supporting the idea that the immune system is evolving under strong selective pressure from parasites. Finally, in a D. melanogaster – sigma virus system, I measured genetic variation in the transmission of different virus genotypes, in different environments. There was poor correlation between temperatures, suggesting that environmental heterogeneity could constraint evolution of resistance (to virus transmission). The correlation between viral genotypes was also low, although relatively stronger for more closely phylogenetically related viral strains. Such interactions between host genotypes, virus genotypes and environmental conditions can maintain genetic variation in virus transmission.

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5

Wright, Emily Elizabeth. "Identification of Native FHB Resistance QTL in the SRW Wheat Cultivar Jamestown". Thesis, Virginia Tech, 2014. http://hdl.handle.net/10919/64327.

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Fusarium Head Blight (FHB) is a devastating fungal disease of wheat (Triticum aestivum L.) and results in significant economic losses due to reductions in grain yield and the accumulation of mycotoxins, such as deoxynivalenol (DON) and nivalenol (NIV). As a result, breeding programs have been working to identify resistance genes in wheat varieties known to be resistant to FHB. Some of the major quantitative trait loci (QTL) for FHB resistance identified to date have been from exotic sources such as 'Sumai3' and the Chinese landrace Wangshuibai, and native resistance has been identified in North American cultivars such as Ernie and Truman which are being used in breeding programs. This study was conducted to characterize and map QTL for resistance to FHB in the soft red winter wheat cultivar Jamestown and to identify tightly linked DNA markers associated with those QTL so that marker-assisted selection (MAS) can be used in pyramiding these and other known QTL into elite backgrounds. Types of resistance assessed in this study include: Type I (resistance to initial infection; incidence), Type II (resistance to spread in wheat spike; severity), and decreases in mycotoxin accumulation (DON) and percentage of Fusarium damaged kernels (FDK). A population composed of 186 F5:7 recombinant-inbred lines (RILs) from the cross Pioneer Brand '25R47'/Jamestown were used to evaluate these traits in six environments (MD, NC, and VA in 2011 and 2012). This study identified a QTL for resistance to DON accumulation and FHB severity on the wheat chromosome 1B. The QTL accounted for 12.7% to 13.3% of the phenotypic variation in DON accumulation and 26.1% of the phenotypic variation in FHB severity. The most diagnostic marker for the QTL on chromosome 1B associated with resistance to FHB severity and DON accumulation is Xwmc500.6 located 7.2 cM from the QTL peak and flanked by markers Xwmc500.7 and Xgwm273.2 (28.2 cM interval).
Master of Science

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6

Asea, Godfrey Rox. "Genetic characterization of partial resistance and comparative strategies for improvement of host-resistance to multiple foliar pathogens of maize". Columbus, Ohio : Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1133833939.

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7

Lee, Jonghoon, Nur K. Izzah, Murukarthick Jayakodi, Sampath Perumal, Ho J. Joh, Hyeon J. Lee, Sang-Choon Lee et al. "Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage". BioMed Central Ltd, 2015. http://hdl.handle.net/10150/610296.

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BACKGROUND: Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. RESULTS: Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F₂:₃ progenies and identified one major QTL and three minor QTLs. CONCLUSION: We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.

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8

Singh, Gurminder. "Resistance Screening and QTL Mapping in Wheat and Triticale Against Root-Lesion Nematode". Thesis, North Dakota State University, 2020. https://hdl.handle.net/10365/31886.

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Root-lesion nematode (RLN, Pratylenchus neglectus) invades the roots of wheat and causes yield losses throughout the world. Genetic resistance is the most economical and effective means to manage RLNs. The objective of this study were to identify source of resistance to RLN in a small collection of wheat germplasm and to map quantitative trait loci (QTL) associated with RLN resistance in two; one wheat and one triticale recombinant inbred line (RIL) populations. Out of wheat lines, three were resistant, including hard red spring wheat cultivars Brennan, SY Ingmar, and SY Soren. A number of genomic regions in wheat and rye were identified as QTL for RLN resistance. My research provides a better understanding of the genetic basis of P. neglectus resistance and important tools for RLN resistance breeding.

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9

Pirseyedi, Seyed Mostafa. "QTL Analysis for Fusarium Head Blight Resistance in Tunisian-Derived Durum Wheat Populations". Diss., North Dakota State University, 2014. https://hdl.handle.net/10365/27014.

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Durum (2n=4x=28; AABB) wheat is the grain of choice for the production of high-quality pasta products. Fusarium spp. are causal pathogens for Fusarium Head Blight (FHB). Limited host resistance to this disease exists among adapated durum cultivars. The use of Tunisian-derived durum lines for integration of FHB resistance in cultivars was evaluated. The genetic characterization of FHB resistance was evaluated, and markers assosciated with FHB resistance are presented in two populations. Two backcross inbred line (BIL) populations derived from cross between a resistant durum genotype `Tunisian 108' and susceptible durum wheat cultivars `Ben' and `Lebsock' were screened to identify QTL for FHB resistance. Analysis of variance showed significant effect of genotypes on FHB severity and incidence despite high level of interaction between environment and genotypes. A total of 329 and 331 DArT and microsatellite markers covered a distance of 1887.6 and 1748 cM in two populations respectively. Composite interval mapping using two linkage maps and the phenotypic data revealed 11 different FHB resistance QTL on seven different chromosomes (1A, 1B, 2B, 3B, 5A, 5B, and 7B) in Tunisian/Ben derived population and 15 different FHB resistant QTL on seven different chromosomes (1A, 1B, 3A, 3B, 4A, 5A, and 6B) in population derived from cross between Tunisian/Lebsock. At least two novel QTL were identified on chromosome 2B (Qfhb.ndsu-2B) 4A (Qfhs.ndsu-4A) in Tunisian/Ben//Ben and Tunisian/Lebsock//Lebsock population respectively. Location of the two FHB resistance QTL on chromosome 1B and two QTL on 5A were identical in both populations. Owing to cumulative effects of resistance QTL, high level of transgressive segregation was observed in both populations. Our finding revealed an alternative tetraploid FHB resistance source from Tunisian genomic background that can be utilized with associated markers for wheat geremplasm enhancement.

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10

Wang, Hehe. "Identification and Dissection of Soybean QTL Conferring Resistance to Phytophthora sojae". The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1321389470.

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11

Thumma, Bala Reddy. "QTL analysis of physiological and biochemical traits contributing to drought resistance in stylosanthes /". [St. Lucia, Qld.], 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16386.pdf.

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12

Prat, Noémie. "Genetic characterization of Fusarium head blight resistance in durum wheat". Thesis, Clermont-Ferrand 2, 2016. http://www.theses.fr/2016CLF22744/document.

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La fusariose de l’épi est une maladie fongique qui touche toutes les cultures de céréales à paille à travers le monde entrainant des baisses de rendements et de la qualité des grains. La fusariose pose également un problème pour la sécurité alimentaire lié à la contamination des grains infectés par des mycotoxines. Le développement de variétés résistantes est considéré comme la méthode la plus efficace et la plus durable pour réduire les dommages causés par la maladie et pour limiter la contamination par les mycotoxines. L’amélioration de la résistance à la fusariose chez le blé dur (Triticum durum Desf.) demeure un défi du fait de son extrême sensibilité à la maladie et de la faible variabilité génétique disponible pour ce caractère. L’objectif principal de cette thèse a été d’évaluer l’effet de Fhb1, le QTL majeur de résistance à la fusariose chez le blé tendre (Triticum aestivumL.), au sein de fonds génétiques de blé dur élite. Pour cela, trois populations de cartographie, comprenant chacune environ 100 F7-RIL (lignées pures recombinantes ou « recombinant inbred lines »), ont été développées à partir de croisements entre la lignée expérimentale de blé dur DBC-480, portant une introgression de Fhb1, et les cultivars de blé dur Karur, Durobonus et SZD1029K. Les lignées ont été évaluées au champ, sur trois saisons, pour leur résistance globale à la fusariose après inoculation en spray de Fusarium culmorum. Des notations morphologiques (date de floraison, hauteur des plantes) ont également été réalisées afin d'évaluer leur influence sur l'infestation. Les lignées ont été génotypées à l’aide de marqueurs SSR et de marqueurs GBS (génotypage par séquençage ou « genotyping-by-sequencing ») développés par DArTseq. L’analyse de liaison a permis d’identifier des QTL de résistance sur les bras des chromosomes 2BL, 3BS, 4AL, 4BS, 5AL et 6AS. DBC-480 contribuait à l’allèle de résistance à tous ces loci. Le QTL sur 3BS a été détecté au sein des trois populations centré sur l’intervalle de Fhb1, confirmant, pour la première fois, son introgression dans le blé dur. L’évaluation de la résistance à la propagation après inoculation ponctuelle, réalisé au sein d’une des trois populations, a également permis de valider l’effet de Fhb1 sur la résistance de type 2 chez le blé dur. La hauteur des plantes influe fortement sur la résistance globale à la fusariose et, en particulier, l’allèle de nanisme Rht-B1b est associé à une plus grande sensibilité à la maladie dans les trois populations. Cependant, l’effet négatif de Rht-B1b sur la résistance est largement compensé dans les lignées possédant Fhb1. Des lignées semi-naines avec un meilleur niveau de résistance ont été sélectionnées et favoriseront le développement de cultivars de blé dur résistants à la fusariose
Fusarium head blight (FHB) is a devastating disease affecting small-grain cereals worldwide causing yield and quality losses. FHB affects food safety due to the contamination of infected grains by mycotoxins. Host plant resistance is considered the most efficient and sustainable approach to contain FHB and mycotoxin contaminations. In durum wheat (Triticum durum Desf.) breeding for FHB resistance remains a challenge due to its extreme susceptibility and to lack of genetic variation available in the primary durum wheat gene pool. The primary goal of this thesis was to evaluate the effect of Fhb1, the major common wheat (Triticum aestivum L.) FHB resistance QTL, in elite durum wheat background. Three F7-RIL (recombinant inbred lines) mapping populations of about 100 lines were developed from crosses between the durum wheat experimental line DBC-480, harboring Fhb1, and the durum wheat cultivars Karur, Durobonus and SZD1029K. The RILs were tested under field conditions by artificial spray inoculation with Fusarium culmorum in three seasons. Morphological traits (flowering date, height) were also recorded to assess their influence on FHB infestation. Genotyping of the lines was performed with SSR and genotyping-by-sequencing (GBS) DArTseq markers. QTL analysis identified genomic regions associated with FHB resistance on chromosome arms 2BL, 3BS, 4AL, 4BS, 5AL and 6AS. DBC-480 contributed the resistant allele at all loci. Fhb1 was detected in all three populations, demonstrating for the first time its successful deployment in durum wheat. The effect of Fhb1 on FHB resistance in durum wheat was further verified by evaluating type 2 resistance in one of the three populations. Plant height had a strong influence in modulating FHB severity. Although the semi-dwarf allele Rht-B1b was associated with increased FHB susceptibility, its negative effect was efficiently counterbalanced in lines carrying Fhb1. Semi-dwarf lines with enhanced levels of resistance were selected and will assist the development of FHB resistant cultivars

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13

Baranwal, Deepak Kumar. "Molecular mapping of rust resistance and genome-wide association study for grain mineral concentration in wheat". Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/25444.

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This investigation included characterisation of diverse sources for rust resistance and identification of genomic regions underpinning rust resistance in wheat. Markers linked to the adult plant leaf rust resistance gene Lr49 were identified using the 90K SNP (single nucleotide polymorphisms) array genotyping of the VL404/WL711 RIL population and alignment of flow-sorted chromosome sequences of chromosome 4B of parents VL404 and WL711. The Lr49-linked markers were tested on a large VL404/Avocet ‘S’ F2 population for fine mapping of the region. A RIL population of VL404/Avocet ‘S’ was evaluated against stripe rust pathotypes in the greenhouse and the underlying locus was named YrVL. Molecular mapping using the 40K Illumina XT SNP array placed YrVL (769.08-779.3 Mb) on the chromosome arm 2BL and found likely to be a new locus. A stripe rust resistant Tunisian landrace Aus26670 was crossed with the susceptible parent Avocet ‘S’ to develop the Aus26670/AvS RIL population. Seedling tests on this population indicated the presence of a single seedling stripe rust resistance gene and this locus was named YrAW12. Targeted genotyping-by-sequencing assay mapped YrAW12 in the 754.9-763.9 Mb region of chromosome 2BL. QTL (Quantitative trait loci) mapping of adult plant stripe rust response variation suggested the involvement of four QTL for stripe rust resistance in chromosomes 1BL, 5AL, 5BL and 6DS. Two QTL, QYr.sun-5AL (654.5Mb) and QYr.sun-6DS (1.4Mb), appear to be new. Genome-wide association study (GWAS) in a HarvestPlus panel was also undertaken to identify genomic regions conferring rust resistance and 10 minerals. This panel was genotyped using the 90K Infinium SNP array and 13 markers linked with rust resistance genes. GWAS identified six new QTL for rust resistance and 27 known genes/QTL. Forty-one known and 76 new QTL were identified for mineral content. Accessions carrying alien translocations (1B:1R and 2NS) displayed higher accumulation of some minerals.

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14

Haghdoust, Rouja. "Genetic and molecular analysis of resistance to adapted and non-adapted (heterologous) rust pathogens in barley". Thesis, University of Sydney, 2020. https://hdl.handle.net/2123/24387.

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Rust diseases caused by Puccinia spp. are specialised to different economically important crops such as wheat and barley and can cause significant crop failure when severe. For many decades, genetic resistance has proven effective in protecting crops against rust pathogens. However, the ability of rust pathogens to evolve rapidly can lead to the emergence of new virulent races that can overcome genetic resistance. Therefore, the identification of new durable sources of resistance is essential for crop production and food security. Barley is a diploid crop with a reference genome sequence that is a near non-host to some non-adapted rust pathogens. Thus, the barley-Puccinia pathosystem is amenable for studies of the genetic architecture of resistance to rust pathogens. This thesis aims to determine the genetic basis of specificity of resistance in different barley-Puccinia pathosystems and to identify valuable sources of resistance in barley that can be used for genetic improvement of cereal crops. Chapter one contains a detailed review of the literature, addressing aspects of biology of barley and rust pathogens as well as mechanisms of host and non-host resistance. Chapter two investigates the genetic architecture of non-host resistance in barley using diverse Puccinia isolates and identifies non-host resistance (NHR) QTL that are suitable for either map-based or rapid cloning approaches. Chapter three examines the isolate specificity and polygenic inheritance of resistance in barley to different P. striiformis isolates. Chapter four generates a high-density linkage map using DArT-Seq markers with the aim of mapping loci for seedling and adult plant resistance to adapted stripe, leaf and stem rust pathogens. Chapter five delivers an overall conclusion based on the findings of the thesis and includes future paths and perspectives.

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15

Galal, Ahmed Abdelrahman [Verfasser]. "Mapping Root-Lesion Nematode Resistance QTL in Barley (Hordeum vulgare L.) / Ahmed Abdelrahman Galal". Kiel : Universitätsbibliothek Kiel, 2014. http://d-nb.info/1053326254/34.

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16

Lopez-Gerena, Jershon. "Mapping QTL controlling durable resistance to rice blast in the cultivar Oryzica Llanos 5". Diss., Manhattan, Kan. : Kansas State University, 2006. http://hdl.handle.net/2097/163.

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17

Stasko, Anna K. "Functional Gene Analysis of Resistance QTL towards Phytophthora sojae on SoybeanChromosome 19". The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1524139406566913.

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18

Fatima, Nosheen. "Identification and deployment of QTL for Fusarium head blight resistance in U.S. hard winter wheat". Thesis, Kansas State University, 2016. http://hdl.handle.net/2097/32679.

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Master of Science
Agronomy
Guihua Bai
Guorong Zhang
Fusarium head blight (FHB) is one of the most damaging diseases in wheat, which impacts both grain yield and quality drastically. Recently, the disease has become more prevalent in the hard winter wheat (HWW) grown areas of the United States including Oklahoma where FHB has not been reported before. Growing resistant cultivars is the most economical and effective strategy for disease management. To dissect quantitative trait loci (QTL) for FHB resistance in a moderately resistant hard winter wheat (HWW) cultivar, Overland, a population of 186 recombinant inbred lines (RILs) was developed from the cross between Overland and Overley, a susceptible HWW cultivar from Kansas. The RILs were evaluated for FHB type II resistance in one field and three greenhouse experiments and genotyped using genotyping-by-sequencing (GBS) markers. Three FHB resistance QTLs were mapped on Chromosomes 4DL, 4AL, and 5BL. The QTL on 4DL was the most consistent one and explained up to 13% of the phenotypic variation for type II resistance and 14 % for low Fusarium damaged kernels (FDK). Two GBS markers closely linked to the 4DL QTL were successfully converted to Kbioscience competitive allelic specific PCR (KASP) assays and can be used in marker-assisted breeding. In breeding, a single QTL may provide only partial resistance and pyramiding of several resistance QTLs in a cultivar can provide more protection in FHB epidemics. Fhb1 is a major QTL for FHB resistance from a Chinese source and Fhb3 is an alien gene from wild rye grass (Leymus racemosus). To study the effects of these QTLs individually and cumulatively in hard winter wheat backgrounds, they were transferred into two HWW cultivars Overland and Jagger. The results show that Fhb1 significantly increased FHB resistance, but Fhb3 did not. Thus, Fhb3 is not an effective gene for improvement of FHB resistance in HWW.

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19

Lee, Yi-Chen. "MENDELIZING QUANTITATIVE TRAIT LOCI THAT UNDERLIE RESISTANCE TO SOYBEAN SUDDEN DEATH SYNDROME". OpenSIUC, 2016. https://opensiuc.lib.siu.edu/theses/1999.

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Soybean (Glycine max [L.] Merr.) cultivars differ in their resistance to sudden death syndrome (SDS). The syndrome is caused by root colonization by Fusarium virguliforme (ex. F. solani f. sp. glycines). Breeding for improve SDS response has proven challenging, possible due to interactions among the 18 known loci for resistance. Four loci for resistance to SDS (cqRfs to cqRfs3) were found clustered within 20 cM of the rhg1 locus underlying resistance to soybean cyst nematode (SCN) on chromosome 18. Another locus on chromosome 20 (cqRfs5) was reported to interact with this cluster. The aims of this study were to compare the inheritance of resistance to SDS in a near isogenic line (NIL) population that was fixed for resistance to SCN but still segregated at 2 of the 4 loci (cqRfs1 and cqRfs) for resistance to SDS on chromosome 18; to examine the interaction with the locus on chromosome 20; and to identify candidate regions underlying quantitative trait loci (QTL). Used were a near isogenic line population derived from residual heterozygosity in an F5:7 recombinant inbred line EF60 1-40; SDS response data from 2 locations and years; four microsatellite markers and six thousand SNP markers. Polymorphic regions were found from 2,788 to 8,938 Kbp on chromosome 18 and 33,100 to 34,943 Kbp on chromosome 20. Both regions were significantly (0.005 < P > 0.0001) associated with resistance to SDS. A fine map was constructed that Mendelized the three loci. Substitution maps suggested the two loci on chromosome 18 were actually 3 loci (cqRfs, cqRfs1 and cqRfs19). Candidate genes for cqRfs19 were identified in a small region of the genome sequence of soybean. An epistatic interaction was inferred where the allele of loci on chromosome 18 determined the value of the locus on chromosome 20. It was concluded that SDS loci are both complex and interacting which may explain the slow progress in breeding for resistance to SDS.

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Farquhar, Alex Graham Lennox. "Locating genes for carrot fly resistance and agronomic performance in carrots using molecular markers". Thesis, University of Birmingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369718.

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Santos, Karla Gasparini dos. "Mapeamento fino de QTL associados à resistência ao carrapato em bovinos de leite". Universidade Federal de Juiz de Fora (UFJF), 2011. https://repositorio.ufjf.br/jspui/handle/ufjf/2499.

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Em países de clima tropical, os prejuízos causados pelo carrapato Riphichephalus (Boophilus) microplus causam grande impacto nos sistemas de produção bovino. A identificação de regiões genômicas e marcadores de DNA associados à resistência ao parasita poderão ser utilizados como estratégia para seleção de animais mais resistentes. Já foram descritos sete QTL relacionados à resistência ao carrapato bovino, porém, os estudos iniciais geralmente detectam QTL com uma resolução baixa ou moderada, sendo necessário o posterior refinamento da região onde o mesmo foi detectado. Dessa forma, esse trabalho teve como objetivo refinar a posição dos QTL previamente identificados com a adição de marcadores microssatélites em uma população bovina F2 formada a partir do cruzamento entre animais Gir e Holandês. Amostras de sêmen e sangue foram submetidas à extração de DNA e posterior PCR com os marcadores microssatélites. Os produtos de PCR foram detectados utilizando o seqüenciador automático de DNA MegaBACE 1000 e as análises estatísticas foram feitas utilizando o software GridQTL. As análises realizadas nos cromossomos 2, 5, 10, 11, 21, 23 e 27 confirmaram a presença dos QTL encontrados anteriormente e reduziram significativamente os intervalos de confiança da maioria dos QTL. Os QTL encontrados no BTA 2 e 27 foram significativos a Pc<0.05, aqueles localizados no BTA 5, 10, 11, 21 e 23 foram significativos a Pc<0.01. O BTA 2 sofreu redução no intervalo de confiança de 12 cM passando de 22 para 10 cM, assim como o BTA 5 que passou de 20 para 8 cM. No BTA 10 foi confirmada a presença de dois picos de QTL com intervalo de confiança de 27cM anteriormente detectado em 47 cM. O BTA 11 passou a apresentar um intervalo de confiança de 19 cM e BTA 21 de 36 cM sofreu redução para 26 cM. O BTA 23 apresentou a menor redução no intervalo de confiança na estação de chuva passando de 17 para 14 cM e na seca manteve inalterado com I.C. de 12 cM, assim como o BTA 27 que sofreu redução de apenas 1 cM passando para 7 cM. A adição de marcadores e a redução no intervalo de confiança de QTL previamente encontrados é um importante passo para a identificação de genes relacionados à resistência ao carrapato.
In tropical countries, losses caused by tick Rhipichephalus (Boophilus) microplus causes a great impact on cattle production systems. The identification of genomic regions and DNA markers associated to the parasite resistance may be used to select resistant animals. Seven QTL associated with tick resistance were described, however, the initial studies detect QTL with low or moderate resolution, being necessary the refinement of the regions where the QTL were detected. Thus, the aim of this work was refine the position of QTL previous identified with addiction of microsatellite markers in Gir X Holstein F2 population. Semen and blood samples were submitted to DNA extraction and then, the PCR were done using microsatellite markers. The PCR products were detected using DNA automatic sequencer MegaBACE1000 and the statistical analysis was performed using GridQTL software. The analysis performed on chromosome 2, 5, 10, 11, 21, 23 and 27 confirmed the presence of QTL previously found and the confidence intervals were significantly reduced in most of QTL. The QTL found on the BTA 2 and 27 were significant at Pc<0.05 and those located on BTA 5, 10, 11, 21 and 23 were significant at Pc<0.01. The BTA 2 was reduced 12 cM in the C.I., from 22 to 10 cM, and BTA 5 from 20 to 8. In BTA 10 was confirmed the presence of two QTL peaks with C.I. 27 cM, previously detected in 47 cM. BTA 11 reduced C.I. to 19 cM and BTA 21 reduced from 36 cM to 26 cM. BTA 23 showed the smallest reduction in C.I. in the rainy season, from 17 to 14 cM and in dry season the C.I remained unchanged with 12 cM, as the BTA 27 that reduced only 1 cM reaching 7 cM. The addiction of markers and the reduction in the confidence interval of QTL previously found is an important step to identify genes related to ticks resistance.

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22

Yu, Jianbin. "Identification of new sources and mapping of QTL for FHB resistance in Asian wheat Germplasm". Diss., Manhattan, Kan. : Kansas State University, 2007. http://hdl.handle.net/2097/258.

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23

Ashtari, Mahini Rahil. "Analysis and Identification of QTL for Resistance to Sclerotinia Sclerotiorum in Pea (Pisum sativum L.)". Diss., North Dakota State University, 2018. https://hdl.handle.net/10365/28867.

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Document incorrectly classified as a thesis on title page (decision to classify as a dissertation from NDSU Graduate School)
White mold caused by Sclerotinia sclerotiorumi s one of the most devastating diseases infecting field pea (Pisum sativum L.) which causes severe yield loss worldwide. Population 17 (Lifter/ PI240515), and Population 19 (PI169603/ Medora) were developed by single seed descent and screened by greenhouse evaluation and detached stem assay to identify potential sources of white mold resistance. Twenty-two partial resistant inbred lines were identified with short internode which met at least two resistance criteria based on lesion expansion inhibition (LEI) and nodal transmission inhibition (NTI). To find SNPs (single nucleotide polymorphism) responsible for white mold resistance, Populations 17 and 19 were genotyped using GBS (genotyping by sequencing) methodology and analyzed with the GBS-SNP-CROP pipeline. Linkage maps were constructed for each population and a composite map based on shared SNPs between the two populations was also generated. Nineteen QTL were identified as contributing to resistance to white mold. Seventeen were associated with LEI and two were associated with NTI. The QTL responsible for lesion expansion on LG VII were duplicated in the short internode subset of both populations. Partially resistant inbred lines and QTL responsible for white mold resistance identified in this study can be useful as resources for resistance to S. sclerotiorum in further experiments aimed at developing resistant cultivars.
National Sclerotinia Initiative in USDA ARS

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24

Gessese, Mesfin Kebede. "Characterization of wheat landraces for resistance to biotic and abiotic stresses". Thesis, The University of Sydney, 2017. http://hdl.handle.net/2123/17198.

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This study covered genetic and molecular analyses of stripe rust and leaf rust resistance in common wheat landraces and investigation of response of drought and short term leaf temperature changes among a set of 20 durum wheat genotypes. Three all stage resistance genes (YrAW5 in Aus27430 and YrAW6 and YrAW7 in Aus27492) were identified. YrAW5 and YrAW7 were located on chromosomes 6AS and 5AL, respectively. The location of YrAW6 was inconclusive. While Aus27430 was concluded to carry Yr18, Aus27492 appears to carry an uncharacterized adult plant resistance gene. Four QTL for stripe rust resistance (QYr.sun-1BL, QYr.sun-2AL, QYr.sun-5AL and QYr.sun-3BS) were detected in Aus28166/AvS RIL population. QYr.sun-1BL and QYr.sun-5AL also conferred resistance to leaf rust in Aus28166. QYr.sun-1BL and QLr.sun-1BL corresponded to the pleiotropic locus Lr46/Yr29/Sr58/Pm39/Ltn. The co-located loci QYr.sun-5AL and QLr.sun-5AL appear to represent a new pleiotropic resistance locus. Durum wheat genotypes showed significant variation for mesophyll conductance in response to water stress and short-term variation of leaf temperature highlighting the potential for improving durum wheat for drought and heat stress.

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25

Burrage, Lindsay. "Genetic Resistance to Diet-Induced Obesity in Mice". Case Western Reserve University School of Graduate Studies / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=case1151680415.

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26

Kandiah, Pakeerathan. "Characterisation and molecular mapping of leaf rust and stripe rust resistance in wheat". Thesis, The University of Sydney, 2017. http://hdl.handle.net/2123/16915.

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This investigation was carried out for the characterisation and chromosomal locations of resistance to rust diseases in common wheat and durum wheat recombinant inbred line (RIL) populations. A new seedling stripe rust resistance gene (tentatively named YrAW10) was identified in common wheat landrace Aus27696. This gene is effective against both pre-2002 and post-2002 Australian Puccinia striiformis f. sp. tritici (Pst) pathotypes. YrAW10 was located in 3BL-A02-FL-0.22 deletion bin of chromosome 3B and was flanked by SNP markers KASP_13376 and KASP_8775. Yr29/Lr46-linked marker SNPLr46G22 indicated the presence of this gene in Aus27696. The presence of Lr16 was confirmed on the basis of infection type produced by Aus91433 and controls (Thatcher + Lr16 and Exchange) against Puccinia triticina (Pt) pathotype 104-1,3,4,6,7,8,9,10,12+Lr37 and linked marker location in the short arm of chromosome 2B. Lr16 was not effective against the Pt pathotypes used in field study. Genotype C16.14 was proved to carry at least two adult plant resistance (APR) genes located on chromosomes 1D and 3B through iSelect 90K SNP based selective genotyping of C16.14/Aus91433 RILs. The chromosome 3B located resistance was proved to be Lr74 through genotyping of markers closely linked with this gene. In addition to Yr29/Lr46, two other consistent QTL for stripe resistance were detected in Arrivato/Bansi RIL population through DArTseq mapping. QYr.sun-1BS.1 corresponded to Yr24 and QYr.sun-1BS.2 was temporarily named YrAr. Both of these genes produced intermediate responses when present alone. Two QTL located on different linkage groups of chromosome 2B were identified in addition to Lr46/Yr29. QLr.sun-2B.1 appeared to be either a new gene or an allele of Lr16. Aus27506 was shown to carry QLr.sun-2D in addition to Lr46 and QLr.sun-2B was contributed by Aus27229 in Aus27506/Aus27229 population. QLr.sun-2D and QLr.sun-2B appears to be new loci. Comparison of chitin accumulation in the flag leaves with the performance of QTL indicated that combination of two QTL prevent the fungal growth resulting in low disease severity.

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27

Clinesmith, Marshall. "Genetic mapping of QTL for Fusarium head blight resistance in winter wheat cultivars Art and Everest". Thesis, Kansas State University, 2016. http://hdl.handle.net/2097/32563.

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Master of Science
Agronomy
Allan Fritz
Fusarium head blight (FHB) is a fungal disease, mostly commonly associated with F. graminearum, which affects cereal crops such as wheat resulting in substantial yield losses and reductions in grain quality. The onset of the disease can occur rapidly when warm, wet or humid weather coincides with flowering in the spring. The pathogen also produces mycotoxins such as deoxynivalenol (DON) that accumulate in the grain and can be toxic to humans and animals. This results in additional economic losses as contaminated grain must be discarded or blended to reduce the amount of toxin in order to meet federal regulatory limits. Development and deployment of resistant cultivars has proved to be an effective method to combat the disease, and many resistant sources have been reported in the literature with the majority of major resistance coming from Chinese landraces. Transferring resistance from these sources into cultivars adapted to the U.S. has been a slow process due to linkage of FHB resistance genes with poor agronomic traits. Therefore, it is important for breeders to search for sources of resistance in native material adapted to their local conditions. In this study, we aimed to identify quantitative trait loci (QTL) for resistance to spread of FHB within the head (Type II resistance), accumulation of DON toxin in grain (Type III resistance), and resistance to kernel infection (Type IV resistance). Plant material consisted of 148 doubled haploid (DH) lines from a cross between the two moderately resistant hard red winter wheat (HRWW) cultivars Art and Everest. The study was conducted for two years using a point inoculation technique in a greenhouse in Manhattan, KS. Three QTL conferring resistance to FHB traits were detected on chromosomes 2D, 4B, and 4D. The QTL on chromosomes 4B and 4D overlapped with the major height genes Rht1 and Rht2, respectively. Plant height has shown previous associations with FHB, though the underlying cause of these associations is not well understood. The majority of results have reported increased susceptibility associated with shorter plant types; however, in this study, the haplotype analysis for the Rht-B1 and Rht-D1 loci showed an association between the dwarfing alleles and increased resistance to FHB. This suggests either pleiotropic effects of these loci or perhaps linkage with nearby genes for FHB resistance. Markers close to the peaks of the FHB resistance QTL have the potential for Kompetitive Allele Specific PCR (KASP) marker development and subsequent use in marker assisted selection (MAS) to help improve overall FHB resistance within breeding programs.

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Shao, Mingqin. "QTL mapping of pre-harvest sprouting and stripe rust resistance in wheat cultivars Danby and Tiger". Diss., Kansas State University, 2017. http://hdl.handle.net/2097/38205.

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Doctor of Philosophy
Department of Agronomy
Guihua Bai
Guorong Zhang
Wheat yield and quality is influenced by many abiotic and biotic environmental factors. Pre-harvest sprouting (PHS) occurs when physiologically matured spikes are exposed to wet field conditions before harvest, which results in seed germination and causes significant losses in yield and end-use quality. Wheat stripe rust is one of the most important biotic factors reducing grain yield and quality. To investigate the genetic basis of the resistance to PHS and stripe rust in hard white winter wheat cultivars Danby and Tiger and develop molecular markers for marker- assisted breeding, a double haploid (DH) population, derived from those two cultivars, was genotyped with simple sequence repeats (SSR) markers and simple nucleotide polymorphism (SNP) markers. This DH population was assessed for resistance to PHS and stripe rust in both greenhouse and field experiments. For PHS, one major resistant quantitative trait locus (QTL) was consistently detected on the short arm of chromosome 3A in all three experiments conducted and explained 21.6% to 41.0% of the phenotypic variation (PVE). This QTL is corresponding to a previously cloned gene, TaPHS1. A SNP in the promoter of TaPHS1 co- segregated with PHS resistance in this mapping population. Meanwhile, two other QTLs, Qphs.hwwg-3B.1 and Qphs.hwwg-5A.1, were consistently detected on the chromosome arms 3BS and 5AL in two experiments. These two QTLs showed significant additive effects with TaPHS1 in improving PHS resistance. For stripe rust, three major QTLs were consistently detected in four out of six environments for infection type (IT) or disease severity (DS). Two of them, QYr.hwwg-2AS1 and QYr.hwwg-4BL1, contributed by the Danby allele explained up to 28.4% of PVE for IT and 60.5% of PVE for DS. The third QTL, QYr.hwwg-3BS1, contributed by the Tiger allele, had PVE values up to 14.7% for IT and 22.9% for DS. QYr.hwwg-2AS1 and QYr.hwwg- 4BL1 are likely the same resistance genes reported previously on chromosome arms 2AS and 4BL. However, QYr.hwwg-3BS1 might be different from the reported gene cluster near the distal end of 3BS where Yr57, Yr4, Yr30 and Sr2 were located. Significant additive effects on reducing IT and DS were observed among these three major QTLs. In order to pyramid multiple QTLs in breeding, user-friendly Kompetitive allele specific PCR (KASP) markers were successfully developed for several QTLs identified in this study. The QTLs and their interactions found in this study together with those novel flanking KASP markers developed will be useful not only for understanding genetic mechanisms of PHS and stripe rust resistance but also for marker- assisted breeding to improve wheat resistance to PHS and stripe rust by gene pyramiding.

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Singh, Gurpreet. "Identification of Quantitative Trait Loci (QTL) associated with resistance to Vascular Streak Dieback disease of cacao". Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/29254.

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Vascular-Streak Dieback (VSD) disease of cacao, caused by the fungus Ceratobasidium theobromae, has devastating impacts on cacao production in southeast Asia and Oceania. This study aimed to identify genomic regions associated with resistance to VSD using a population derived from a cross between the cocoa genotypes S1 (VSD resistant) and CCN51 (VSD susceptible). QTL analysis was performed using a genetic linkage map constructed with 8,698 DArT markers and 1,470 SNP markers. Two QTL were detected, one on linkage group 8 and the other on linkage group 9. The QTL on linkage group 8 explained 15-16% of the phenotypic variation while the QTL on linkage group 9 explained 16-18% of the phenotypic variation. Five polymorphic microsatellite (SSR) markers were identified within the QTL regions. SSR markers showed clear polymorphism among the VSD resistant and susceptible lines in the two populations, S1 x CCN51 and CCN51 x M07. These results suggest that these markers could be closely associated with VSD resistance and therefore used in marker-assisted selection for cacao breeding programs in response to VSD disease. Further, genomes of the S1 and CCN51 genotypes were sequenced using paired end short reads. Both S1 and CCN51 whole genome sequencing generated 383 and 367 million clean reads, respectively, and 93% of reads from both S1 and CCN51 mapped to the reference genome Matina 1-6. Alignment to the reference genome enabled the detection of 1.87 million polymorphic SNVs/Indels and 8,363 polymorphic structural variants (SVs) among the two genomes. The resequencing of the genomes of cacao genotypes S1 and CCN51 provides a valuable resource to narrow the search for candidate genes that underlie VSD resistance.

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Sun, Xiaochun. "Genetic characterization of wheat genes resistance to tan spot and leaf rust". Thesis, Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1606.

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Cai, Jin. "Meta-analysis of QTL for Fusarium head blight resistance in Chinese wheat landraces using genotyping by sequencing". Diss., Kansas State University, 2016. http://hdl.handle.net/2097/32166.

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Doctor of Philosophy
Department of Agronomy
Guihua Bai
Guorong Zhang
Fusarium head blight (FHB) is a devastating fungal disease in wheat, reducing not only grain yield but also quality. The pathogen produces the mycotoxin deoxynivalenol (DON) that induces severe toxicological problems in human and animals. Using host resistance has been the most efficient way to control the disease. To identify quantitative trait loci (QTLs) for FHB resistance in Chinese landrace Haiyanzhong (HYZ), a recombinant inbred lines (RILs) population derived from a cross between HYZ and Wheaton was developed. The RILs were evaluated for percentage of symptomatic spikelets (PSS) in three greenhouse experiments, and genotyped using simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) developed from genotyping-by-sequencing (GBS). Eight QTLs were identified for type II (PSS) resistance on chromosomes 5A, 6B, 7D, 2B (2), 3B, 4B, and 4D, with 5A as the major QTL. Ten SNPs closely linked to 5A, 6B, and 2B QTLs were successfully converted to Kompetitave allelic specific PCR (KASP) assays. To identify common QTLs across different populations, we constructed high-density GBS-SNP maps in an additional four RIL populations derived from the Chinese landraces, Wangshuibai (WSB), Baishanyuehuang (BSYH), Huangfangzhu (HFZ), and Huangchandou (HCD) and conducted meta-analysis of the QTLs for FHB resistance using a consensus map developed from the five populations. We identified six MQTLs on chromosomes 3BS (2), 3A, 3D, 2D, and 4D and 23 tightly linked GBS-SNPs to the MQTLs. These GBS-SNPs were successfully converted to KASPs. The KASPs linked to MQTLs can be used for pyramiding these QTL in breeding programs. To quickly reduce FHB damage in U.S. hard winter wheat (HWW), we transferred Fhb1, a major QTL with stable effects on FHB resistance, from Ning7840 into three adapted HWW cultivars Overland, Jagger, and Overley, by marker-assisted backcross (MAB), and assessed the effect of Fhb1 on FHB resistance in these different backgrounds. The results showed that Fhb1 can significantly lower FHB severity, Fusarium-damaged kernel (FDK), and DON accumulation in the all the three HWW backgrounds. Some of the selected lines showed high levels of FHB resistance, but agronomically similar traits as recurrent parents, can be used as resistant parents to improve HWW FHB resistance.

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SCHIFF, CELINE. "Bases genetiques de la resistance a l'oidium chez arabidopsis thaliana : analyse de qtl et caracterisation de mutants". Paris, Institut national d'agronomie de Paris Grignon, 2001. http://www.theses.fr/2001INAP0002.

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L'oidium est un pathogene qui affecte la plupart des plantes cultivees. Deux approches complementaires ont ete menees pour mieux comprendre les bases genetiques de la resistance a erysiphe cichoracearum chez arabidopsis thaliana. Des analyses de qtl (quantitative trait loci) menees chez kas-1 et wa-1, des ecotypes resistants d'arabidopsis, montrent que la resistance a l'oidium est specifiee par des multiples locus, nommes les rpw (recognition of powdery mildew) locus. Ces etudes ont permis d'identifier cinq qtl (trois chez kas-1 et deux chez wa-1) qui expliquent environ 65% de la variation phenotypique totale dans chacun des cas. La cartographie fine du qtl majeur suggere que le meme gene soit responsable de la resistance a l'oidium chez kas-1 et wa-1. Cependant, la presence de plusieurs qtl mineurs ayant des effets additifs pour le phenotype de resistance indique que les ecotypes d'arabidopsis possedent une importante variation genetique pour la resistance a l'oidium. La seconde approche consiste en la creation de resistance par mutations d'une plante au depart sensible. Le mutant mil1 (mildew induced lesions) est plus resistant a l'oidium que la plante sauvage. Cette resistance est accompagnee par la necrose des tissus infectes et par l'hyper-activation de la voie de signalisation de l'acide salicylique associee a la defense contre les pathogenes. Le gene mil1 code une nouvelle proteine possedant deux domaines hypothetiques qui sont impliques dans differentes branches de signalisation. Mil1 pourrait integrer les niveaux de stress engendres par les attaques de pathogenes et ensuite generer un message regulant la mort cellulaire et les reactions de defense. Ces deux types d'approches permettent d'isoler des genes fonctionnellement differents. En plus de permettre de mieux comprendre les interactions entre plantes et pathogenes, ces genes peuvent etre utilises pour ameliorer la resistance a l'oidium chez les plantes cultivees.

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Gunnaiah, Raghavendra. "Functional characterization of wheat, fusarium head blight resistance (QTL) «Fhb1» based on non-target metabolomics and proteomics". Thesis, McGill University, 2013. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=119639.

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Fusarium head blight (FHB) caused by Fusarium graminearum is a dreadful disease of wheat (Triticum aestivum L.). Host resistance to FHB in wheat is quantitatively inherited. Though more than 100 QTLs have been identified, only a few have been validated. However, the resistance mechanisms governed by these QTLs are poorly understood. A type II FHB resistance QTL Fhb1 is the most consistent and largest effect QTL in wheat against FHB spread in wheat. Non-targeted metabolic and proteomic profiling of wheat near isogenic lines (NILs) with resistant and susceptible Fhb1 alleles was used to functionally characterize Fhb1 using a high resolution LC-MS. The Fhb1 from a moderately resistant cultivar Nyubai was associated with cell wall thickening, mainly at the rachis, due to deposition of hydroxycinnamic acid amides (HCAAs), phenolic glucosides and flavonoids. A hypothetical protein coding gene (GenBank: CBH32656.1) near Fhb1 locus was putatively identified as hydroxycinnamoyl transferase, which catalyzes the biosynthesis of HCAAs. Deoxynivalenol (DON) accumulation was high in both the NILs, eliminating DON detoxification as a mechanism associated with Fhb1 (Chapter III). For additional confirmation, the Fhb1 resistant allele, from a highly FHB resistant cultivar Sumai-3 was profiled. Even though the DON accumulation was low in resistant NIL, the detoxification of DON by host UDP-glycosyltransferase was moderately high in both the NILs, with no significant difference. Interestingly, unlike in the resistant NIL, constitutively present glycerophospholipids were absent in the susceptible NIL following pathogen inoculation due to degradation of membrane. Membrane degradation was caused due to programmed cell death as evidenced by DNA laddering in the susceptible NIL. A locus TAA_ctg0954b.00390.1 was identified as an Fhb1 candidate gene that contains a calmodulin binding motif and two nucleolar localization signal motifs and hence re-annotated as calmodulin binding protein (TaCaMBP_Fhb1). The TaCaMBP_Fhb1 is induced following pathogen infection, binds to Ca2+ bound calmodulin, and triggers Ca2+ signalling cascade including transcriptional activation of endonucleases that cleaves the genomics DNA and cause programmed cell death. The resistant allele of TaCaMBP_Fhb1 lacks part of the promoter region and is non-functional in triggering Ca2+ signalling. While the susceptible allele of TaCaMBP_Fhb1, with functional promoter region is capable of triggering Ca2+ signalling and programmed cell death. The necrotrophic pathogen F. graminearum feeds on the dead tissue, multiply in the host and produce more DON, following a repeated cycle in the susceptible genotype (Chapter IV). The wheat resistance mechanisms against FHB were further confirmed, based on metabolic profiling of rachis, from a resistant cultivar Sumai-3 and a susceptible cultivar Roblin, for resistance against spread of a trichothecene producing (Wild: FgTri5+) and a trichothecene non- producing (mutant: FgTri5-) isolates of F. graminearum. The wild isolate repressed several host resistance mechanisms in both the cultivars due to production of DON. The FHB resistance to spread in Sumai-3 was mainly because of increased cell wall thickening, especially at rachis, due to deposition of lignin, HCAAs and flavonoids, and partially, due to induced RR metabolites which in turn reduced the fungal biomass and toxin biosynthesis. The resistance was not attributed to DON detoxification by UDP-glycosyltransferase, as it was not significant in both the cultivars confirming our previous studies (Chapter V). The resistant alleles of two Fhb1 candidate genes, identified in this study, can be suitably stacked into genome of elite cultivars to enhance FHB resistance in wheat.
La fusariose de l'épi est une maladie fongique attaquant le blé (Triticum aestivum) induite par Fusarium graminearum. La fusariose cause de sévères pertes économiques dues à la réduction de la qualité et des rendements suite à la contamination par les mycotoxines trichothecene. La résistance du blé face à la fusariose est un trait quantitatif. Plus de 100 LCQ on été identifiés et un petit nombre a été validé. Cependant, les mécanismes de résistance gouvernés par ces LCQ sont peu connus. Fhb1 est le LCQ le plus consistent qui produit le plus grand effet face à la fusariose du blé. Une caractérisation fonctionnelle à l'aide d'un LC-MS à haute résolution de lignées isogéniques avec ou sans l'allèle susceptible Fhb1 a générée des profils de métabolites non ciblés ainsi que protéomique. Le Fhb1 d'un cultivar modérément résistant, Nyubai, a été associé avec le développement de la paroi cellulaire plus épaisse, surtout au niveau du rachis due à la déposition d'acides amides hydroxycinnamic (HCAAs), de glucosides phénolique ainsi que de flavonoïdes. Le gène codant pour une protéine hypothétique (GenBank: CBH32656.1) située près du locus Fhb1 a été identifiée comme étant possiblement une hydroxycinnamoyle transférase. Cette protéine déclencherait la biosynthèse de HCAAs. L'accumulation de DON a été plus élevée dans les deux lignes isogéniques. La détoxification de DON est un mécanisme associé avec Fhb1 (Chapitre III). Pour confirmer, l'allèle Fhb1 la résistance du cultivar Sumai-3 a été profilé. Contrairement aux lignes iso géniques, aucune présence constitutive de glycérophospholipides, n'a été détectée chez les lignées susceptibles en raison de la dégradation des membranes. La dégradation de membrane s'est avérée être causée par la mort cellulaire programmée comme le démontre le patron de dégradation de l'ADN de la variété susceptible NIL. Le locus TAA_ctg0954b.00390.1 fut identifié comme candidat pour le gène Fhb1 qui contient un domaine de liaison à la calmoduline et deux signaux de localisation nucléaire. Ce dernier fut donc annoté en tant que protéine de liaison à la calmoduline (TaCaMBP_Fhb1). TaCaMBP_Fhb1 est induit suite à l'infection du pathogène pour ensuite se lier à la calmoduline liée au Ca2+ pour ensuite initier une cascade de signaux qui inclut l'activation transcriptionnelle d'endonucléases qui clivent l'ADN génomique causant ainsi la mort cellulaire programmée. L'allèle résistante de TaCaMBP_Fhb1 présente une délétion au niveau du promoteur ce qui la rend non fonctionnel pour l'activation du signalement Ca2+ impliqué dans la mort cellulaire programmée. Le pathogène nécrotrophe F. graminearum se nourrit des tissus morts, se multiplie et produit plus de DON pour faciliter l'infection; perpétuant ainsi un cercle vicieux chez le génotype susceptible (Chapitre IV). C'est résultats on été confirmés à l'aide d'un profilage métabolique des rachis de la lignée résistante Sumai-3 et la lignée susceptible Roblin lors de l'infection avec (Wild : FgTri5+) trichothécène producteur et (Mutant :FgTri5- ) trichothécène non producteur qui sont deux isolats de F. graminearum. L'isolat producteur est parveu à inhiber plusieurs mécanismes de résistance de l'hôte dans les deux cultivars grâce à la production de DON. La résistance FHB à l'infection dans Sumai-3 était principalement lié à l'augmentation des parois cellulaires particulièrement au niveau des rachis à cause de la déposition de lignine, HCAAs et de flavonoïdes et partiellement due à l'augmentation des métabolite RR qui réduisent la biomasses des champignons ainsi que la synthèse des toxines. La résistance n'a pas été attribuée à détoxification de DON par l'UDP-glycosyltransferase, puisque les résultats étaient similaires dans les deux cultivars (Chapitre V). Les allèles résistants, des deux gènes candidats Fhb1 identifiés dans cette étude, pourraient-être ajoutés au génome de cultivars élites de blé pour augmenter leur résistance au FHB.

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34

Lemes, Da Silva Cristiano. "Genomic approaches for mapping and predicting disease resistance in wheat (Triticum aestivum L.)". Diss., Kansas State University, 2017. http://hdl.handle.net/2097/38555.

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Doctor of Philosophy
Genetics Interdepartmental Program
Allan K. Fritz
Wheat diseases cause significant economic losses every year. To ensure global food security, newly released cultivars must possess increased levels of broadly-effective resistance against wheat pathogens, acceptable end-use quality, and high yield potential. Genetic host resistance stands out from other management strategies as the most viable option for controlling diseases. New genotyping platforms allow whole genome marker discovery at a relatively low cost, favoring the identification of novel loci underlying traits of interest. The work presented here describes genomic approaches for mapping and predicting the resistance to Fusarium head blight (FHB) and wheat rusts. The first study used biparental mapping to identify quantitative trait loci (QTL) associated with Fusarium head blight (FHB) resistance. A doubled haploid population (DH) was originated from a cross of Everest and WB-Cedar, which are widely grown wheat cultivars in Kansas with moderately resistant and moderately susceptible reactions to FHB, respectively. We confirmed that neither of the parents carry known large-effect QTLs, suggesting that FHB resistance is native. Eight small-effect QTLs were identified as associated with multiple mechanisms of FHB resistance. All QTLs had additive effects, providing significant improvements in levels of resistance when they were found in combinations within DH lines. In the second study, a genome-wide association mapping (GWAS) and genomic selection (GS) models were applied for FHB resistance in a panel of 962 elite lines from the K-State Wheat Breeding Program. Significant single nucleotide polymorphisms (SNPs) associated with the percentage of symptomatic spikelets were identified but not reproducible across breeding panels tested in each year. Accuracy of predictions ranged from 0.25 to 0.51 depending on GS model, indicating that it can be a useful tool to increase levels of FHB resistance. GWAS and GS approaches were also applied to a historical dataset to identify loci underlying resistance to leaf and stem rust at seedling stage in a panel of elite winter wheat lines. Infection types of multiple races of wheat rusts from the last sixteen years of the Southern Regional Performance Nursery (SRPN) were used in this study. A total of 533 elite lines originating from several breeding programs were tested in the SRPN during this period of time. GWAS identified significant SNP-trait associations for wheat rusts, confirming the effectiveness of already known genes and revealing potentially novel loci associated with resistance.

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35

Mensah, Clarice. "Inheritance of aphid resistance in PI 567541B and PI 567598B, identification of aphid resistance QTL in PI 567598B, and a new aphid biotype in Michigan". Diss., Connect to online resource - MSU authorized users, 2008.

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36

Frey, Travis J. "Finemapping, cloning, verification, and fitness evaluation of a QTL, Rcg1, which confers resistance to Colletotrichum graminicola in maize". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 1.30 Mb., 164 p, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3220625.

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37

Agostinelli, Andres Mateo. "PHENOTYPIC AND GENOTYPIC SELECTION FOR HEAD SCAB RESISTANCE IN WHEAT". UKnowledge, 2009. http://uknowledge.uky.edu/gradschool_theses/582.

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Fusarium Head Blight (FHB) is a destructive disease caused by Fusarium graminearum that affects wheat (Triticum aestivum L.) worldwide. Breeding for resistance to FHB is arguably the best way to combat this disease. However, FHB resistance is highly complex and phenotypic screening is difficult. Molecular markers are a promising tool but breeding programs face the challenge of allocating resources in such a way that the optimum balance between phenotypic and genotypic selection is reached. An F2:3 population derived from a resistant x susceptible cross was subjected to phenotypic and genotypic selection. For phenotyping, a novel air separation method was used to measure percentage of damaged kernels (FDK). Heritability estimates were remarkably high, which was attributed to the type of cross and the quality of phenotyping. Genotypic selection was done by selecting resistance alleles at quantitative trait loci (QTL) on the 3BS (Fhb1) and the 2DL chromosomes. Fhb1 conferred a moderate but stable FHB resistance while the 2DL QTL conferred a surprisingly high level of resistance but with significant interaction with the environment. Phenotypic selection conferred higher or lower genetic gains than genotypic selection, depending on the selection intensity. Based on these results, different selection strategies are discussed.

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38

Shrestha, Subidhya. "Identification of Quantitative Trait Loci (QTL) Associated with Resistance to Initial Infection of Fusarium Head Blight in Spring Wheat". Diss., North Dakota State University, 2017. http://hdl.handle.net/10365/25980.

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Video summarizing a Ph.D. dissertation for a non-specialist audience.
Triticeae CAP
US Wheat and Barley Scab Initiative (USWBSI)
State Board of Agricultural Research and Education
NDSU Agriculture
North Dakota Wheat Commission

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39

Wright, Drew Welsey. "EVALUATION AND GENETIC ANALYSIS OF TWO SOYBEAN [Glycine max (L.) Merr.] RECOMBINANT INBRED LINE POPULATIONS SEGREGATING FOR RESISTANCE TO ROOT KNOT NEMATODE (Meloidogyne incognita)". OpenSIUC, 2012. https://opensiuc.lib.siu.edu/theses/1046.

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One of the most economically important pathogens of US soybeans is the Southern Root Knot Nematode [(Meloidogyne incognita) (Kofoid and White) Chitwood] (Mi). Evaluation and identification of resistance is highly important to the plant breeding program at SIUC. The main objective of this study was to screen within the greenhouse two F5:7 recombinant inbred line (RIL) (n=96) from crosses between LS90-1920 or LS97-1610 (resistant parents) with `Spencer' (susceptible parent) to identify sources of resistance for Mi. Additionally, the RILs were evaluated in two locations in southern Illinois (Harrisburg and Dowell) in 2011 for several agronomic characteristics including yield performance. The phenotypic data collected from field and greenhouse experiments was used to select for superior lines within the two populations. The screening data was also used to identify single nucleotide polymorphism (SNP) markers associated with Mi resistance. Initial screening of the 5,361 SNP markers indicated four SNP markers (ss247062763, ss247064854, ss247077423 and ss247067293) highly associated with resistance to Mi. The results will help accelerating selection practices, and have provided high yielding resistant lines for the creation of resistant commercial varieties.

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40

MASCHIETTO, VALENTINA. "Identificazione di geni, QTL e metaboliti per la resistenza alla fusariosi della spiga in mais". Doctoral thesis, Università Cattolica del Sacro Cuore, 2013. http://hdl.handle.net/10280/1731.

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Fusarium verticillioides è responsabile della fusariosi della spiga in mais e della contaminazione della granella con micotossine. Sono state individuate le regioni geniche e i geni candidati per la resistenza a Fusarium dal confronto tra una linea di mais resistente (CO441) e una suscettibile (CO354), impiegando tre diversi approcci: analisi QTL, analisi trascrittomica (RNASeq) e analisi metabolomica. 184 famiglie F2:3 (CO441xCO354) sono state valutate in due diversi ambienti nell’anno 2011 e inoculate artificialmente con due diverse tecniche (forchetta e stuzzicadente). E’ stata rilevata una significativa variazione genotipica in risposta all’infezione. Sulla base di una mappa preliminare di linkage molecolare contenente 74 marcatori microsatelliti polimorfici, sono stati determinati 8 QTLs comuni alla resistenza alla fusariosi della spiga e alla riduzione della contaminazione da fumonisine. Sono stati considerati geni candidati per la resistenza i geni differenzialmente espressi, risultanti dall’ RNASeq, in semi di mais CO441 prima e 72 ore dopo l’infezione. I metaboliti putativi correlati alla resistenza sono stati rilevati tramite high resolution LC-MS in entrambe le linee di mais. I geni candidati e i metaboliti mappano in pathway coinvolti nei meccanismi di difesa: fenilalanina, tirosina e triptofano biosintesi, fenilpropanoidi e flavonoidi biosintesi, metabolismo dell’acido linoleico e α-linolenico. Abbondanti trascritti derivano dalla biosintesi dei terpenoidi e dei diterpenoidi. Nei geni candidati verranno ricercati polimorfismi fra le due linee di mais e che andranno ad arricchire la mappa di linkage molecolare.
Fusarium verticillioides is responsible for Fusarium ear rot in maize and mycotoxin contamination of grain. Genomic regions and candidate genes for resistance to Fusarium were detected through the comparison of resistant (CO441) and susceptible (CO354) maize lines, by following three different approaches: Quantitative Trait Locus (QTL), transcriptomic (RNASeq) and metabolomic analyses. 184 F2:3 families (CO441xCO354) were evaluated in two different environments in 2011 and artificially infected with two side-needle inoculation methods (pin-bar and toothpick). Significant genotypic variation in response to infection was detected. On the basis of a genetic draft map containing 74 polymorphic SSRs markers, 8 common QTLs for Fusarium ear rot resistance and fumonisin contamination reduction were revealed. Candidate genes for resistance resulted from differentially expressed genes before and 72 hours post infection of CO441 kernels through RNASeq technology. Putative metabolites related to resistance were detected through high resolution LC-MS in both maize lines. Candidate genes and metabolites mapped in pathways involved in defense mechanism: phenylalanine, tyrosine and tryptophan biosynthesis, phenylpropanoid and flavonoid biosynthesis, linoleic and α-linolenic acid metabolism. Abundant genic transcripts derived from terpenoid and diterpenoid biosynthesis. Candidate genes will be screened for polymorphisms between the two maize lines in order to enrich the linkage map.

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41

MASCHIETTO, VALENTINA. "Identificazione di geni, QTL e metaboliti per la resistenza alla fusariosi della spiga in mais". Doctoral thesis, Università Cattolica del Sacro Cuore, 2013. http://hdl.handle.net/10280/1731.

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Fusarium verticillioides è responsabile della fusariosi della spiga in mais e della contaminazione della granella con micotossine. Sono state individuate le regioni geniche e i geni candidati per la resistenza a Fusarium dal confronto tra una linea di mais resistente (CO441) e una suscettibile (CO354), impiegando tre diversi approcci: analisi QTL, analisi trascrittomica (RNASeq) e analisi metabolomica. 184 famiglie F2:3 (CO441xCO354) sono state valutate in due diversi ambienti nell’anno 2011 e inoculate artificialmente con due diverse tecniche (forchetta e stuzzicadente). E’ stata rilevata una significativa variazione genotipica in risposta all’infezione. Sulla base di una mappa preliminare di linkage molecolare contenente 74 marcatori microsatelliti polimorfici, sono stati determinati 8 QTLs comuni alla resistenza alla fusariosi della spiga e alla riduzione della contaminazione da fumonisine. Sono stati considerati geni candidati per la resistenza i geni differenzialmente espressi, risultanti dall’ RNASeq, in semi di mais CO441 prima e 72 ore dopo l’infezione. I metaboliti putativi correlati alla resistenza sono stati rilevati tramite high resolution LC-MS in entrambe le linee di mais. I geni candidati e i metaboliti mappano in pathway coinvolti nei meccanismi di difesa: fenilalanina, tirosina e triptofano biosintesi, fenilpropanoidi e flavonoidi biosintesi, metabolismo dell’acido linoleico e α-linolenico. Abbondanti trascritti derivano dalla biosintesi dei terpenoidi e dei diterpenoidi. Nei geni candidati verranno ricercati polimorfismi fra le due linee di mais e che andranno ad arricchire la mappa di linkage molecolare.
Fusarium verticillioides is responsible for Fusarium ear rot in maize and mycotoxin contamination of grain. Genomic regions and candidate genes for resistance to Fusarium were detected through the comparison of resistant (CO441) and susceptible (CO354) maize lines, by following three different approaches: Quantitative Trait Locus (QTL), transcriptomic (RNASeq) and metabolomic analyses. 184 F2:3 families (CO441xCO354) were evaluated in two different environments in 2011 and artificially infected with two side-needle inoculation methods (pin-bar and toothpick). Significant genotypic variation in response to infection was detected. On the basis of a genetic draft map containing 74 polymorphic SSRs markers, 8 common QTLs for Fusarium ear rot resistance and fumonisin contamination reduction were revealed. Candidate genes for resistance resulted from differentially expressed genes before and 72 hours post infection of CO441 kernels through RNASeq technology. Putative metabolites related to resistance were detected through high resolution LC-MS in both maize lines. Candidate genes and metabolites mapped in pathways involved in defense mechanism: phenylalanine, tyrosine and tryptophan biosynthesis, phenylpropanoid and flavonoid biosynthesis, linoleic and α-linolenic acid metabolism. Abundant genic transcripts derived from terpenoid and diterpenoid biosynthesis. Candidate genes will be screened for polymorphisms between the two maize lines in order to enrich the linkage map.

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42

Souza, Adenilson Mroginski. "MAPEAMENTO DE QTLs PARA TOLERÂNCIA À MURCHA BACTERIANA (Ralstonia solanacearum Smith) EM TABACO". Universidade Estadual de Ponta Grossa, 2018. http://tede2.uepg.br/jspui/handle/prefix/2706.

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Os objetivos deste trabalho foram a obtenção de um mapa genético de alta densidade utilizando marcadores SNP (Single Nucleotide Polymorphism) obtidos através de genotipagem por sequenciamento (GBS) e identificar as regiões genômicas ligadas à tolerância à murcha bacteriana (Ralstonia solanacearum Smith) em uma população de duplo-haploides (DH) de tabaco. As linhagens endogâmicas NC95 (tolerante) e NC2326 (suscetível) foram cruzadas entre si gerando a população F1, anteras foram coletadas destas plantas para produção de haploides e posterior duplicação cromossômica através da cultura de anteras, gerando 180 famílias duplo-haploides que foram avaliadas em ambiente controlado quanto à tolerância à murcha bacteriana, após inoculação com R. solanacearum, através de uma escala de notas com amplitude de 0 a 4. As famílias DH foram genotipadas utilizando a metodologia de GBS e os dados resultantes desta genotipagem foram alinhados com o genoma de referência do tabaco para posterior obtenção dos marcadores SNP utilizados na construção do mapa de ligação. O mapa de ligação juntamente com os dados de fenotipagem foram utilizados para realizar o mapeamento de QTLs através do mapeamento por intervalo composto. Foram identificados 6.842 SNPs, utilizados para construção de um mapa de ligação com 70.583 cM, sendo este o maior mapa de ligação utilizando marcadores SNP disponível para tabaco e com o maior número de marcadores. Utilizando este mapa de ligação foram mapeados 13 QTLs para tolerância à murcha bacteriana em oito grupos de ligação, dos quais oito QTLs ainda não tinham sido identificados na literatura especializada. Os locos presentes nos grupos de ligação 3, 17 e 22 apresentaram os maiores efeitos na variação fenotípica. O elevado número de QTLs mapeados nesta população confirma o padrão de herança quantitativa da tolerância de tabaco à murcha bacteriana causada por R. solanacearum.
The objectives of this work were to obtain a high-density genetic map using SNP (Single Nucleotide Polymorphism) markers obtained through Genotyping-by-Sequencing (GBS) and to identify the genomic regions linked to bacterial wilt tolerance (Ralstonia solanacearum Smith) in a tobacco double-haploid (DH) population. The inbred lines NC95 (tolerant) and NC2326 (susceptible) were crossed generating the F1 population, anthers were collected from these plants for haploid production and subsequent chromosomic duplication using anthers culture, generating 180 double-haploid families that were evaluated in a controlled environment for tolerance to bacterial wilt after inoculation with R. solanacearum, using an assessment scale from 0 to 4. The DH families were genotyped using the GBS methodology and the resulting data from this genotyping were aligned with the reference genome and then to obtain the SNP markers used to construct the genetic linkage map. The linkage map jointly with the phenotyping data were used to QTL mapping through the composite interval mapping method. A total of 6,842 SNPs was identified and used to construct a linkage map with 70,583 cM, being the largest SNP-based genetic linkage map available for tobacco and presenting the highest number of markers. Using this linkage map, 13 QTLs were mapped for bacterial wilt tolerance in eight linkage groups, from those eight QTLs had not yet been identified in the specialized literature. The loci present in linkage groups 3, 17 and 22 had the highest effects on phenotypic variation. The high number of QTLs mapped in this population confirms the quantitative genetic control of tobacco tolerance to bacterial wilt caused by R. solanacearum.

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43

Poudel, Bikash. "Understanding Host Resistance and Pathogen Biology in the Wheat-Fusarium graminearum Pathosystem". Diss., North Dakota State University, 2020. https://hdl.handle.net/10365/31811.

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Fusarium head blight (FHB) is a major challenge in global wheat production. In the United States, the disease is predominantly caused by the fungus Fusarium graminearum. Utilization of FHB-resistant wheat cultivars integrated with other measures such as fungicide application is the most effective approach for the management of this disease. This study aimed to 1) identify novel quantitative trait loci (QTL) for resistance to FHB in a Brazilian spring wheat cultivar ‘Surpresa’ through bi-parental mapping, 2) detect QTL for FHB resistance in a global panel of 233 spring wheat accessions by genome-wide association analysis (GWAS), and 3) localize genomic regions governing traits associated with virulence in Fusarium graminearum. Using phenotypic and genotypic data from 187 recombinant inbred lines derived from the cross between Surpresa and a susceptible spring wheat cultivar ‘Wheaton’, four QTL (Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, Qfhb.ndwp-3B, and Qfhb.ndwp-4D) were mapped on chromosomes 2A, 3B, and 4D of Surpresa, respectively. Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, and Qfhb.ndwp-3B were found to be novel based on physical locations of the markers tightly linked to these QTL. Two significant marker-trait associations (Qfhb.ndwp-3A and Qfhb.ndwp-2BL) were detected by GWAS of 233 spring wheat accessions, which conferred type II and type III FHB resistance and mapped on chromosomes 3A and 2B, respectively. Both QTL were novel based on the physical locations of tightly linked markers. GWAS of virulence and fungicide sensitivity using 183 F. graminearum isolates collected from North Dakota identified two significant marker-trait associations in chromosomes 1 and 3 for virulence, and two for fungicide sensitivity. The genes associated with virulence that were detected in this study were not previously reported. Identification of these novel genes in metabolic pathways of F. graminearum could help to develop new strategies for the management FHB.

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Lenz, Ryan Rae. "A Novel Genetic Linkage Map of Chokecherry (Prunus Virginiana L.) and QTL Mapping for X-Disease (Candidatus Phytoplasma Pruni) Resistance". Thesis, North Dakota State University, 2016. https://hdl.handle.net/10365/28063.

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A novel chokecherry genetic linkage map was constructed using 565 molecular markers and a previously published mapping population (n=101). Chokecherry (Prunus virginiana L.) is a potential model for genetic research of phytoplasmic diseases because of its natural resistance to X-disease (Candidatus Phytoplasma pruni). The novel chokecherry map was developed using JoinMap 4.0 and contains a complete set of 16 linkage groups. In total, the map spans a genetic distance of 2,172 cM with an average marker density of 3.97 cM. Three significant quantitative trait loci (QTL) associated with X-disease resistance were identified on linkage groups 15, 5, and 4 contributing to a total of 45.9% of the phenotypic variation. This novel genetic linkage map and the identified QTL linked to X-disease resistance will provide the framework needed to facilitate molecular genetics, genomics, and breeding research concerning X-disease in chokecherry and other Prunus species.

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45

Bruschi, Martina <1986&gt. "Fine mapping of QSbm.ubo-2BS, a major QTL for resistance to Soil-Borne Cereal Mosaic Virus (SBCMV) in durum wheat". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2018. http://amsdottorato.unibo.it/8564/1/Bruschi_Martina_tesi.pdf.

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QSbm.ubo-2BS, a major QTL controlling the response to Soil-Borne Cereal Mosaic Virus in durum wheat, maps within a 2 cM-wide interval in the distal region of chromosome arm 2BS. The consensus map developed by Maccaferri et al. (2015) allowed to enrich QSbm.ubo-2BS interval with SNPs from the 90K Illumina array common to several linkage maps. Eleven SNPs were successfully converted to KASP markers, which provided fluorescent high-throughput assays spanning the QTL region. Marker-assisted selection was performed on ~3,000 RILs from the Svevo (resistant) x Ciccio (medium-susceptible) population with two KASP markers flanking the QTL interval, KUBO 9 and KUBO 13. MAS identified a total of 521 lines recombinant between the two markers. In particular, 320 and 189 of these lines were characterized for SBCMV response in a field nursery under severe and uniform SBCMV infection in 2016 and 2017, respectively. The lines were scored for symptom severity on a 0 to 5 scale, where 0 = very resistant and 5 = very susceptible. The same lines were genotyped with six KASP markers distributed along the QTL interval (KUBO 1, KUBO 3, KUBO 27, KUBO 29, KUBO 40 and KUBO 41) and with the DArT marker wPt-2106. The fine mapping conducted on Svevo x Ciccio allowed to locate the most probable QSbm.ubo-2BS support interval to 0.2 cM between the markers KUBO 27 and KUBO 41. Single-marker analysis showed that all markers in the interval are strongly associated with the QTL. Markers order was confirmed through genotyping of Meridiano x Claudio RILs with recombinant events in the interested interval. QSbm.ubo-2BS support interval corresponds to 3.2 Mb on the physical map of Svevo genome, a region that harbors 93 genes, including defensins, proteins belonging to NBS-LRR family and NBS-LRR-like resistance proteins. This work provides the foundation for the positional cloning of QSbm.ubo-2BS.

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46

Kurz, Jacqueline P. "Bovine Mastitis Resistance: Novel Quantitative Trait Loci and the Role of Bovine Mammary Epithelial Cells". DigitalCommons@USU, 2018. https://digitalcommons.usu.edu/etd/6910.

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Bovine mastitis, or inflammation of the mammary gland, has substantial economic and animal welfare implications. A genetic basis for mastitis resistance traits is recognized and can be used to guide selective breeding programs. The discovery of regions of the genome associated with mastitis resistance, and knowledge of the underlying molecular mechanisms responsible, can facilitate development of efficient mastitis control and therapeutic strategies. The objectives of this dissertation research were to identify sites of genetic variation associated with mastitis resistance, and to define the contributions of the milk-secreting epithelial cells to mammary gland immune responses and mastitis resistance. Twenty seven regions of the bovine genome potentially involved in mastitis resistance were identified in Holstein dairy cattle. Additionally, this research demonstrates a role of bovine mammary epithelial cells in mastitis resistance, and provides guidance for the use of an in vitro model for mastitis studies. Primary bovine mammary epithelial cells from mastitis-resistant cows have differential expression of 42 inflammatory genes compared with cells from mastitis-susceptible cows, highlighting the importance of epithelial cells in mastitis resistance. Bovine mammary epithelial cells display both similarities and differences in pro-inflammatory gene expression compared to fibroblasts, and their expression of inflammatory genes is influenced by administration of the enzyme phospholipase A2. The growth potential of milk-derived bovine mammary epithelial cells in vitro can be extended, facilitating their use in mastitis studies, by transfection with a viral protein. Collectively, this research contributes to current knowledge on bovine mastitis resistance and in vitro models.

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47

Braga, Marcelo Fideles. "Mapeamento de QTL (Quantitative Trait Loci) associados à resistência do maracujá-doce à bacteriose". Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-02082011-103816/.

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O maracujá-doce (Passiflora alata Curtis) é uma espécie nativa no Brasil. Seu cultivo tem crescido nos últimos anos devido a sua valorização no mercado in natura e seus usos na fitoterapia. Entretanto, os cultivos comerciais enfrentam problemas devido a ocorrência da bacteriose (Xanthomonas axonopodis pv. passiflorae). O patógeno é endêmico no país, apresentando considerável variabilidade genética em suas populações naturais. Este trabalho teve como objetivo identificar QTL relacionados à resistência de P. alata à bacteriose em uma população F1 segregante oriunda do cruzamento entre acessos não endogâmicos. Foram avaliados os caracteres: área total da folha (TA), idade de queda da folha inoculada (IK), área total da lesão foliar (LA), área de clorose foliar (CA) e área da necrose foliar (NEA). Apenas um dos isolados apresentou diferenças de severidade em relação aos demais, sendo o menos agressivo (PA8-2). A inoculação do isolado M-129 mostrou que há variação significativa na resposta da população ao patógeno, sendo possível a identificação de genótipos transgressivos. A herdabilidade dos caracteres variou de 45% a 71%%. Foi construído um mapa de ligação integrado com 1.786 cM e uma densidade média de 4,5 cM. A análise de marcas individuais indicou a associação de 51 marcas aos fenótipos avaliados. O mapeamento de QTL, realizado por intervalo composto e utilizando uma estratégia diferenciada para populações F1 segregantes, identificou regiões associadas a 26 QTL para os cinco caracteres avaliados, sendo 16 deles referentes à LA, CA e NEA. A variação fenotípica explicada individualmente pelos marcadores variou de 0,8% a 16,7%. Sugere-se que a resistência à bacteriose é quantitativa, com predominância de efeitos genéticos aditivos.
The sweet passion fruit (Passiflora alata Curtis) is a specie native to Brazil. Its cultivation has increased in recent years due to its market valuation in natura and their uses in herbal medicine. However, crops are facing problems due to the occurrence of bacterial blight (Xanthomonas axonopodis pv. passiflorae). The pathogen is endemic in the country, with considerable genetic variability in their natural populations. This study aimed to identify QTL related to resistance of P. alata to bacterial blight in an F1 segregant population from the cross between outbred accessions. Five traits were evaluated: total area of the leaf (TA), age of inoculated leaf fall (IK), area of the leaf´s lesion (LA), area of the leaf´s chlorosis (CA) and area of the leaf´s necrosis (NEA). Only one of the isolates showed differences in severity in relation to others, being the least aggressive (PA8-2). The inoculation of the isolate M-129 showed significant variation in population response to the pathogen, making it possible to identify transgressive genotypes. The heritability of characters ranged from 45% to 71%. An integrated linkage map was constructed, with a length of 1,786 cM and an average density of 4.5 cM. The analysis of individual marks indicated the association of 51 markers to phenotypes. The QTL mapping was performed using composite interval and a special strategy for segregating F1 populations, identified 26 regions associated with QTL for the five traits, 16 of them related to LA, CA and NEA. The phenotypic variation explained by individual markers ranged from 0,8% to 16,7%. It is suggested that the resistance to bacterial blight is quantitative, with a predominance of additive genetic effects.

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48

CRUZ, I. A. PACHECO. "PEACH FRUIT RESISTANCE TO BROWN ROT (MONILINIA SPP.): A GENOMICS APPROACH". Doctoral thesis, Università degli Studi di Milano, 2010. http://hdl.handle.net/2434/150118.

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Brown Rot disease (BR) caused by the necrotrophic fungus Monilinia spp. is a major problem for the peach fruit market, causing significant losses at post-harvest level. Previous work demonstrated the possibility of discriminating between susceptible and tolerant peach genotypes, suggesting a quantitative nature of the BR resistance. In order to uncover genomic regions associated with this trait and identify molecular markers for marker assisted selection (MAS), an F1 segregating population from the intra-specific Contender (tolerant cultivar) x Elegant Lady (susceptible cultivar) peach cross has been chosen for QTL analysis. Phenotypic analysis was performed over two harvest seasons, using an artificial infection procedure that measured skin and flesh resistance to a M. fructigena field isolate. Significant correlations were found between the data obtained in the two years and between the two traits. Maturity date (MD) was also highly correlated with resistance traits. Genotyping 110 CxEL individuals allowed the construction of a linkage map (CxEL map), containing 78 SSR, covering a total genetic distance of 317.7 cM, and having an average marker density of 4.7 cM/marker. Both parametric (interval mapping) and non-parametric (Kruskal-Wallis analysis) QTL analysis using genotypic and phenotypic data from CxEL revealed two QTL clusters: a QTL underlying skin resistance located on LG CxEL-2 (explaining a 15% - 22% of the total phenotypic variability), and a QTL associated with flesh resistance (explaining a 30% - 35.2% of the total phenotypic variability), collocating with a major MD QTL on LG CxEL-4. These results suggest that resistance to BR has at least two main components: the first related to avoidance of fungal penetration, and a second earliness-associated factor associated with fungal spread after penetration. Furthermore, markers M1a (CxEL-2) and UDAp-439 (CxEL-4) may provide useful tools for MAS for BR-resistance breeding programmes.

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49

Pumphrey, Michael Odell. "Towards map-based cloning of Fusarium head blight resistance QTL Fhb1 and non-additive expression of homoeologous genes in allohexaploid wheat". Diss., Kansas State University, 2007. http://hdl.handle.net/2097/32793.

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Doctor of Philosophy
Department of Plant Pathology
Bikram S. Gill
Wheat is the most widely grown and consumed grain crop in the world. In order to meet future agricultural production requirements of a growing population, it is essential that we achieve an increased understanding of the basic components and mechanisms shaping growth and productivity of the polyploid wheat plant. Fusarium head blight (FHB) (syn. "scab") poses a serious threat to the quantity and safety of the world's food supply. The resistance locus Fhb1 has provided partial resistance to FHB of wheat for nearly four decades. Map-based cloning of Fhb1 is justified by its significant and consistent effects on reducing disease levels, the importance of FHB in global wheat production and food safety, and because this gene confers partial resistance to this disease and does not appear to behave in a gene-for-gene manner. A bacterial artificial chromosome (BAC) contig spanning the Fhb1 region was developed from the cultivar 'Chinese Spring', sequenced and seven candidate genes were identified in an ~250 kb region. Cosmid clones for each of the seven candidate genes were isolated from a line containing Fhb1 and used for genetic transformation by biolistic bombardment. Transgenic lines were recovered for five candidate genes and evaluated for FHB resistance. All failed to complement the Fhb1 phenotype. Fhb1 is possibly one of the two remaining candidate genes, an unknown regulatory element in this region, or is not present in Chinese Spring. Traditional views on the effects of polyploidy in allohexaploid wheat have primarily emphasized aspects of coding sequence variation and the enhanced potential to acquire new gene functions through mutation of redundant loci. At the same time, the extent and significance of regulatory variation has been relatively unexplored. Recent investigations have suggested that differential expression of homoeologous transcripts, or subfunctionalization, is common in natural bread wheat. In order to establish a timeline for such regulatory changes and estimate the frequency of non-additive expression of homoeologous transcripts in newly formed T. aestivum, gene expression was characterized in a synthetic T. aestivum line and its T. turgidum and Aegilops tauschii parents by cDNA-SSCP and microarray expression experiments. The cDNA-SSCP analysis of 30 arbitrarily selected homoeologous transcripts revealed that four (~13%) showed differential expression of homoeoalleles in seedling leaf tissue of synthetic T. aestivum. In microarray expression experiments, synthetic T. aestivum gene expression was compared to mid-parent expression level estimates calculated from parental expression levels. Approximately 16% of genes were inferred to display non-additive expression in synthetic T. aestivum. Six homoeologous transcripts classified as non-additively expressed in microarray experiments were characterized by cDNA-SSCP. Expression patterns of these six transcripts suggest that cis-acting regulatory variation is often responsible for non-additive gene expression levels. These results demonstrate that allopolyploidization, per se, results in rapid initiation of differential expression of homoeologous loci and non-additive gene expression in synthetic T. aestivum.

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50

Liu, Sixin. "Molecular marker analysis of adult plant resistance to powdery mildew in common wheat". Diss., Virginia Tech, 1999. http://hdl.handle.net/10919/11236.

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Powdery mildew, caused by Blumeria graminis (DC.) E.O. Speer f. sp. tritici E'm. Marchal (syn. Erysiphe graminis f. sp. tritici), is one of the major diseases of wheat (Triticum aestivum L.) worldwide. The use of cultivars with resistance to powdery mildew is an efficient, economical and environmentally safe way to control powdery mildew. Race-specific resistance has been extensively used in breeding programs; however, it is ephemeral. Adult plant resistance (APR) to powdery mildew is more durable as demonstrated by the cultivar Massey, which has maintained its APR to powdery mildew since its release in 1981. To develop an efficient breeding strategy, it is essential to understand the genetic basis of APR. The objectives of this study were to identify molecular markers associated with APR to powdery mildew in common wheat Massey and to verify their association using recombinant inbred (RI) lines. A cross was made between the powdery mildew susceptible cultivar Becker and Massey. One hundred and eighty F2:3 lines were rated for disease severity under natural pressure of powdery mildew in field. Using both restriction fragment length polymorphism (RFLP) and microsatellite markers, three quantitative trait loci (QTL), designated as QPm.vt-1B, QPm.vt-2A and QPm.vt-2B, were identified in the Becker x Massey F2:3 generation. These loci are located on chromosomes 1B, 2A and 2B, respectively, and explained 17%, 29% and 11% of the total variation among F2:3 lines for powdery mildew resistance, respectively. Cumulatively, the three QTLs explained 50% of the phenotypic variation among F2:3 lines in a multi-QTL model. The three QTLs associated with APR to powdery mildew were derived from Massey and displayed additive gene action. QPm.vt-2B also fits a recessive model for APR to powdery mildew. In the second part of this study, 97 RI lines were developed from the Becker x Massey cross. The RI lines were evaluated for APR to powdery mildew under natural disease pressure for three years. Both single marker analysis and interval mapping confirmed the presence of the three QTLs identified in the F2:3 generation. The three QTLs, QPm.vt-1B, QPm.vt-2A and QPm.vt-2B, accounted for 15%, 26% and 15% of the variation of mean powdery mildew severity of the RI lines over three years. In a multi-QTL model, the three QTLs explained 44% of the phenotypic variation of the RI lines. The RI lines were grouped according to the genotype of the three QTLs, represented by markers GWM304a, KSUD22 and PSP3100, respectively. The RI lines with Massey alleles at all three loci had a mean disease severity of 3.4%, whereas the RI lines with Becker alleles at all three loci had a mean disease severity of 22.3%. These severity values are similar to those of the corresponding parents. The molecular markers identified and verified as to their association with APR to powdery mildew in Massey have the potential for use in marker-assisted selection for resistance to powdery mildew and in pyramiding powdery mildew resistance genes, as well as facilitating a better understanding of the molecular basis of APR to powdery mildew.
Ph. D.

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