Browsing by Subject "genomic selection"

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    Evaluating genomewide marker-based breeding methods in traditional and wild relative-derived barley populations
    (2016-04) Tiede, Tyler
    The genetic improvement of plants for human use is the primary goal of plant breeding. Through repeated processes of population development and selection, breeders have produced highly productive plants that are adapted to a vast array of environments and cultivation practices. The challenges that drove plant breeders in the past, such as increasing production, novel or increasingly prevalent abiotic and biotic stresses, and evolving end-user demands persist today and are compounded with unprecedented population growth. Genomic selection (GS), a genomewide marker-based selection method, has been shown to be an efficient and effective breeding tool. Its general applicability to plant breeding and principles guiding its use have been established by simulation and empirical cross-validation studies. More recently, studies have demonstrated genetic gains over multiple cycles of selection in a variety of crop species. In the first chapter we provide additional evidence for the effectiveness of GS in an actual breeding program by demonstrating significant gains of 164.74 kg ha-1 and -1.41 ppm for grain yield and DON, respectively, two unfavorably correlated quantitative traits, across three cycles of selection in a spring six-row barley breeding population. With its general effectiveness established, the next step is to increase the accuracy of GS and thereby increase genetic gains. For this, we first showed that updating the training population (TP) with phenotyped lines from recent breeding cycles, specifically selected lines, had an overall positive effect on prediction accuracy. Additionally, we investigated four recently-proposed algorithms that seek to optimize the composition of a TP. Overall the optimization algorithms improved prediction accuracy when compared to a randomly selected TP subset of the same size, but which algorithm performed best was dependent on the trait being predicted and other factors discussed within. This retrospective investigation highlighted the importance of maintaining and optimizing the TP when using GS in real breeding situations to maximize prediction accuracy, thereby maximizing gain from selection and resource utilization. Furthermore, genetic gains depend on genetic variation. Exotic germplasm can be exploited to introduce genetic variability into elite breeding populations to drive genetic gains and address new or changing breeding targets. Wide crosses between elite and exotic germplasm have been widely used to identify large-effect QTL and breed for improved disease or insect resistance. The utility of exotic germplasm to improve quantitative traits, which includes many important agronomic traits, has not been tested as widely. In the second chapter we select parents from an advanced backcross population constructed from 25 wild barley (Hordeum vulgare L. spp spontaneum) accessions crossed to the common high-yielding malting barley cultivar, Rasmusson. We extended the genomic selection framework to identify parent combinations that, with ideal recombination, should produce progeny with large numbers of exotic introgressions with favorable effects. We compared the marker-based crossing strategy to the traditional methods of crossing the topmost performing parents or the most genetically diverse parents. After one round of marker-based progeny selection from these crosses we identified breeding lines, harboring exotic introgressions, which consistently yielded higher than Rasmusson across five trial locations. While none of these lines were statistically better than Rasmusson, there is compelling evidence that the introgression of wild alleles contributed to increased yield. The three parent selection strategies were not significantly different for their ability to identify superior progeny.
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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.