Browsing by Subject "association mapping"

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    Implementing Association Mapping and Genomic Selection to Advance Breeding for Complex Traits in Barley
    (2016-07) Falcon, Celeste
    To efficiently respond to challenges presented by global climate change, plant breeders can implement methods that utilize genome-wide marker data to discover and deploy useful genes. We investigated the use of genome-wide association mapping and genomic selection to improve two traits related to protecting natural resources: nitrogen use efficiency (NUE) and winter hardiness. In our first study, we identified quantitative trait loci (QTL) for improved NUE using phenotypic data and calculated stress indices in conjunction with genome-wide marker data for 250 six-row and 250 two-row barley breeding lines. We identified a QTL for grain protein concentration (GPC) on chromosome 6H that has been mapped previously in barley and is collinear with the well-characterized Gpc-B1 locus in wheat. Groups of lines defined by marker haplotypes at this locus exhibited significant differences in GPC but not in grain yield. Overall, our results indicated that potentially effective breeding strategies for NUE include selection based on stress indices, marker assisted selection for desirable alleles, and genomic selection to capture small effect loci. In a second study, we assessed the utility of genomic selection to initiate a breeding program for winter barley based on observed gains from selection, changes in phenotypic variation, and changes in marker allele frequencies. After conducting two cycles of genomic selection for a selection index that combined predictions for low temperature tolerance, malt extract, grain yield, heading date, and plant height, we assessed the selected sets of lines in field trials. Between cycles 0 and 2, genomic selection improved low temperature tolerance and malt extract while maintaining the other selection index traits. Phenotypic variance fluctuated but did not change significantly. Three markers previously shown to be linked to winter hardiness traits shifted in genotypic frequency over the cycles of selection. Based on all marker data, the population shifted toward similarity with the winter growth-type parent lines after two cycles of genomic selection. Overall, this study demonstrated that genomic selection is an effective method for improving trait values in a population at the initiation of a breeding program. Together, these studies support the use of marker-based breeding strategies to improve genetically complex traits that contribute to sustainable agricultural systems that will address climate change.
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    Utilizing Biparental And Association Mapping To Identify Leaf Rust Resistance In Diverse Wheat Accessions
    (2015-07) Turner, M. Kathryn
    Leaf rust is a common disease of wheat, consistently reducing yields by 5-15% with higher losses in some years. In hard red spring wheat growing regions of the U.S., farmers apply fungicides annually to mitigate crop losses, but genetic resistance can provide less expensive, effective control. Our objectives were to map leaf rust resistance genes and evaluate the utility of association and biparental mapping approaches. Biparental mapping populations were created by crossing resistant T. aestivum accessions from the National Small Grains Collection with the susceptible cultivar Thatcher. Race specific resistance was evaluated at the seedling plants in five F2:3 populations and resistance gene locations identified using bulk segregant analysis. Two F6 populations with potential race non-specific resistance were evaluated at the adult plant stage and mapped using composite interval mapping. The race specific seedling resistance populations identified three potentially novel loci on chromosomes 2DS, 3BL and 6AL. The resistance, in the two populations targeted for race non-specific resistance at the adult stage, was explained by Lr34 and Lr46. No potentially novel adult plant resistance loci were identified. A core panel of 1,032 T. aestivum accessions was selected for association mapping from the larger worldwide set of 3,040 Triticum accessions from the National Small Grains Collection and was evaluated for leaf rust resistance in Minnesota. Of the 1,032 accessions, 712 were susceptible at the seedling stage and were selected to create a smaller subset panel to target adult plant resistance. There were 113 accessions with resistance at the seedling stage to race BBBDB, which were targeted for seedling resistance and tested with additional races. Association mapping detected five potentially novel resistance loci on chromosomes 2BL, 2DL, 4AS, 5DL, and 7AS. Three of the four characterized race non-specific resistance genes (Lr34, Lr46, and Lr68) were detected. Eight putative adult plant resistance loci were identified by selecting loci with field resistance that lacked seedling resistance; the KaspLr34 marker was detected in this group. Three of the five seedling loci detected in biparental mapping (on chromosomes 2BL, 3BL, and 6AL) were also detected through association mapping (AM). No loci for adult plant resistance were detected with both approaches, but slightly different positions were identified for Lr46 and with additional markers Lr34 was also detected with both approaches. Selection of a subset of the core panel was useful in targeting adult plant resistance and seedling resistance genes. Both biparental and association mapping proved useful approaches that identified novel and race non-specific resistance genes. Association mapping provided better resolution to identify closely linked markers for resistance loci, but the majority of these markers are at a high frequency in the worldwide germplasm panel and may not be very useful in marker assisted selection. All loci identified in biparental mapping were also significant in at least one environment in AM, indicating that a lower threshold of significance would detect more true resistance loci but would also detect more false positives as well. Loci detected in both association mapping and biparental mapping were validated through the independent identification using different methods. Potentially novel seedling resistance loci will be confirmed through allelism tests. Potentially novel adult plant resistance will be verified by developing biparental mapping populations or a small nested association mapping panel from accessions with favorable alleles and resistance consistent with the locus identified. Supplementary information regarding the accessions selected for the association mapping core, adult plant resistance, and seedling resistance panels can be found in Supplemental Table 1.