Browsing by Subject "QTL mapping"

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    Genetic Relationship Of Adult Plant Resistance To Wheat Rusts And Validation Of Stem Rust Qtl
    (2019-05) Rauf, Yahya
    Cereal rusts are among the most important fungal diseases worldwide and pose a major threat to global food security. Wheat is attacked by three rusts known as stripe rust, leaf rust, and stem rust caused by fungal pathogens, Puccinia striiformis f. sp. tritici (Pst), Puccinia triticina (Pt), and Puccinia graminis f. sp. tritici (Pgt), respectively. These pathogens are widely distributed across the world, produce spores with the ability to travel long distances, rapidly multiply under favorable environmental conditions, and evolve new races that overcome the resistant genes in cultivated varieties. The rapid appearance of new races of rust pathogens with virulence for the major seedling resistance genes in wheat has intensified the focus to breeding for durable resistance. Durable rust resistance is more likely to be of adult plant resistance (APR) rather than seedling resistance, and not associated with the genes conferring hypersensitive reaction. Two projects were developed to identify and map the genetic sources and dissect the mechanism of APR to rusts. The first project utilized a bi-parental mapping population derived from a cross of COPIO x Apav#1. It consisted of 178, F4:F5 recombinant inbred lines (RIL) developed at the International Maize and Wheat Improvement Centre (CIMMYT) in Mexico. The objectives of this study were to map the APR genes in ‘COPIO’ and to understand the genetic relationship of APR genes conferring resistance to all three rusts. The parents of the RIL mapping population were tested against selected Pgt, Pst, and Pt races at the seedling stage and were also assayed for the known APR genes and 2NS/2AS translocation using molecular markers. The RIL population was also evaluated under field conditions in six environments for leaf and stem rust and nine environments for stripe rust. Genotyping of the population and parents was carried out through genotyping-by-sequencing (GBS) and 762 resulting polymorphic markers each representing a unique locus, were used for the downstream QTL mapping analysis. Molecular characterization and quantitative/qualitative analysis revealed that COPIO harbors some important pleiotropic and APR genes along with qualitative genes for Pgt, Pst, and Pt. Pleiotropic gene Lr46/Yr29/Sr58 on chromosome 1BL reduced disease severities of all three rusts with R2 values ranging from 10 to 42%. The APR genes Sr2/Yr30 for stem and stripe rust along with either a new gene for leaf rust resistance or due to pleiotropic effects of Sr2/Yr30 resulted in reduced severities of all three rusts. The 2NS/2AS translocation segment on chromosome 2AS containing the race-specific resistance genes Sr38, Lr37, and Yr17 is present in COPIO. A new putative stripe rust APR QTL (QYr.umn.2A) in the same region, along with partial effects of Yr17, significantly reduced stripe rust severities in all nine environments. We also postulated the presence of Lr13 on chromosome 2B and Yr31, Yr45, and Yr60 on chromosomes 2B, 3D, and 4B respectively in COPIO. This study also detected minor effect QTL, both previously reported (for stem rust; QSr.umn.3B.2; QSr.umn.4B, for stripe rust; QYr.umn.1A; QYr.umn.3B.3) and potentially new sources of resistance (for stem rust; QSr.umn.2A.3; QSr.umn.7A, for leaf rust; QLr.umn.2A.1, QLr.umn.3B, for stripe rust; QYr.umn.1B.1; QYr.umn.3A.2) in COPIO. These QTLs are also contributing quantitative resistance to all three rusts in COPIO. Our findings show that wheat line COPIO contains pleiotropic, APR and seedling genes along with small to medium effect QTL that are working in combination to enhance genetic resistance against rust pathogens. Broad spectrum resistance against wheat rust diseases in COPIO makes it a valuable source of resistance and its utilization in recombination breeding can potentially enhance durable resistance. Development of diagnostic markers, particularly for the 2A QTL (QYr.umn.2A), will be useful for marker assisted selection in breeding programs. The second project involved a bi-parental mapping population developed by crossing a wheat line ‘MN06113-8’ and cultivated wheat variety ‘Sabin’. The wheat breeding program at the University of Minnesota previously mapped a large effect stem rust APR QTL (QSr.umn-2B.2) on chromosome 2B in wheat line ‘MN06113-8’. This QTL is effective against the North American, Kenyan and Ethiopian stem rust pathogen races. The objectives of this study were to:1) understand the genetics of APR to wheat stem rust in the breeding line ‘MN06113-8’ and cultivated wheat variety ‘Sabin’; and 2) validate 2B QTL in MN06113-8. A total of 184 recombinant inbred lines (RILs) from the cross Sabin/MN06113-8 were tested in stem rust nurseries in Kenya, Ethiopia and Saint Paul. Both parental lines were highly susceptible to Ug99 races TTKSK, TTKST, and TTKTT at the seedling stage but MN06113-8 exhibited adult plant resistance (APR) in Kenya and Ethiopia under field testing conditions. Genotyping by sequencing (GBS) was used to genotype the population and both parents. A total of 4,100 polymorphic GBS markers were assigned to 21 wheat chromosomes to develop the linkage maps. The GBS single nucleotide polymorphism (SNP) markers covered 2,931 cM of the genome with an average of 0.71 markers cM-1. Composite interval mapping detected six quantitative trait loci (QTL) on chromosomes 2A, 3B, 4A, 4B, and 6B associated with stem rust resistance. Among these seven QTL, three were detected in African environments and four were detected in Saint Paul against the North American stem rust pathogen races. We could not validate QSr.umn-2B.2, discovered in a previous study involving MN06113-8 because the QTL region was monomorphic in our population. A large effect QTL (QSr.umn.3B) was mapped on chromosome 3B conferring resistance to Ug99 and North American Pgt races. The QTL (QSr.umn.4A.1) detected in Kenya on chromosome 4A has not been previously reported. Development of diagnostic markers and pyramiding of these genes through marker assisted selection will accelerate the development of durable rust resistance.
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    Genetics of Resistance to Fusarium Head Blight and Spot Blotch in Hordeum
    (2016-05) Haas, Matthew
    Fusarium head blight (FHB) and spot blotch are two important diseases of barley (Hordeum vulgare) in the Upper Midwest. FHB is caused by Fusarium graminearum which produces deoxynivalenol (DON), a toxin harmful to humans and animals. To characterize the genetic architecture of resistance to FHB and DON accumulation, two wild barley (PI 466423 and W-365) accessions with partial resistance were used as donor parents in advanced backcross populations with six-rowed Minnesota malting barley cultivars. The largest effect quantitative trait locus (QTL) identified in the populations was mapped at or near the photoperiod response gene Ppd-H1, which affects heading date and plant height. This result suggests that the QTL for reduced FHB and DON are a pleiotropic effect of that locus. For over 50 years, spot blotch, caused by Cochliobolus sativus, has been controlled in the Upper Midwest through the deployment of durable resistance derived from the breeding line NDB112. Recently, C. sativus isolates (e.g. ND4008) with virulence for the NDB112 resistance have been reported in the region. PI 466423 is resistant to isolate ND4008; therefore, the Rasmusson/PI 466423 population was used to map QTL for resistance to virulent isolate. Four resistance QTL were identified in chromosomes 1H, 2H, 4H, and 5H. The QTL on chromosomes 1H, 4H, and 5H were contributed by PI 466423, while the one on chromosome 2H was contributed by Rasmusson. A gamma radiation-induced susceptibility mutant from cultivar Morex was used in an RNAseq experiment to study the early infection response of barley to C. sativus. Differential expression analysis between the two genotypes revealed a role for lipid signaling in the resistance response, which may activate the jasmonic acid pathway.
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    Mapping Quantitative Trait Loci and Assessing the Prospects of Genomic Prediction for Resistance to Goss’s Wilt of Maize
    (2017-07) Singh, Amritpal
    Goss’s wilt is a bacterial disease of maize caused by the Gram-positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn). Goss’s wilt was discovered for the first time in South Central Nebraska in 1969. Following its discovery, the disease spread to the neighboring states over the next decade. Maize germplasm was screened for resistance to Goss’s wilt, and possibly due to the deployment of partially resistant hybrids, Goss’s wilt did not cause any significant damage during the 1980s and 1990s. However, Goss’s wilt re-emerged around 2006 and has been spreading to major maize growing areas in the United States and Canada. It is important to understand the genetic basis of resistance to Goss’s wilt to devise strategies for breeding resistance into maize hybrids. The main objectives of this dissertation were to (i) map quantitative trait loci (QTL) for resistance to Goss’s wilt using linkage mapping, joint linkage mapping, and genome-wide association mapping; (ii) identify differentially expressed genes in resistant and susceptible inbred lines in response to Cmn using RNA-seq; and (iii) to explore the prospects of genomic prediction of resistance to Goss’s wilt. Three bi-parental linkage mapping families including B73 x Oh43, B73 x HP301, and B73 x P39 that were evaluated for Goss’s wilt were used for joint linkage and linkage mapping. Eleven QTL were detected for resistance to Goss’s wilt on chromosomes 1, 2, 3, 4, 5, and 10 through joint linkage mapping. Linkage mapping in each of the three families identified nine, six, and four QTL in the families B73 × Oh43, B73 × HP301, and B73 × P39, respectively. Genome-wide association analysis conducted using a diversity panel of 555 maize inbred lines and 450 recombinant inbred lines (RILs) from three bi-parental mapping populations found three SNPs in the diversity panel and 10 SNPs in the combined dataset of diversity panel and RILs that were associated with Goss’s wilt resistance. Two modules of correlated genes were discovered that showed differential regulation in response to Cmn between resistant (N551) and susceptible (B14A) inbred lines using a weighted gene co-expression network analysis. Gene ontology analysis revealed that the genes inside one of the modules were enriched in defense related functions. Genomic prediction of Goss’s wilt resistance was conducted on the data obtained from bi-parental families and the diversity panel. Highest predictive ability of 0.56 and 0.64 was achieved in the diversity panel and B73 x Oh43 population respectively. Effect of training population size, composition, and adding diverse lines to training population on predictive ability was also assessed. Results indicated that predictive ability is not highly benefited when training population is designed by adding equal number of lines from each of the three families. Adding diverse lines to the training population lead to minor changes in predictive ability. Overall, the results improved our understanding of the genetic architecture of Goss’s wilt resistance and showed that the resistance to Goss’s wilt is a complex trait, controlled by small effect QTL.
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    Validation of rice blast resistance genes in barley using a QTL mapping population and near-isolines
    (Breeding Science, 2009) Steffenson, Brian; Kongprakhon, Phinyarat; Cuesta-Marcos, Alfonso; Hayes, Patrick M.; Richardson, Kelley L.; Sirithunya, Pattama; Sato, Kazuhiro; Toojinda, Theerayuth
    There are prior reports of Pyricularia grisea—the causal agent of blast of rice—causing disease in barley. In order to determine the specificity of this resistance in barley, we extended our previous mapping efforts to include blast isolates from barley and rice grown in Thailand and we assessed two resistance phenotypes: leaf blast (LB) and neck blast (NB). The largest-effect resistance QTL, on chromosome 1H, was associated with NB and LB and is located in a region rich in resistance genes, including QTL conferring resistance to stripe rust (incited by Puccinia striiformis f. sp. hordei) and the mildew (Blumeria graminis f. sp. hordei) resistance gene Mla. The LB, NB and mildew resistance alleles trace to one parent (Baronesse) whereas the stripe rust resistance allele traces to the other parent (BCD47) of the mapping population. Baronesse is the susceptible recurrent parent of a set of near-isogenic lines (NILs) for three stripe rust resistance QTL, including one on 1H. Unigene (EST) derived single nucleotide polymorphism haplotypes of these NILs were aligned with the blast mapping population QTL using Mla as an anchor. Baronesse and all NILs without the 1H introgression were resistant to LB and NB. However, two NILs with the 1H introgression were resistant to LB and NB. Both are resistant to stripe rust. Therefore, the QTL conferring resistance to stripe rust is separable by recombination from the blast resistance QTL.