Assessing wild barley germplasm in multiparent and advanced backcross populations for mapping, gene discovery, and improvement of malting barley

University of Minnesota Ph.D. dissertation. May 2015. Major: Applied Plant Sciences. Advisor: Gary Muehlbauer. 1 computer file (PDF); xii, 139 pages.Wild barley (Hordeum vulgare ssp. spontaneum), the progenitor of cultivated barley (Hordeum vulgare ssp. vulgare), is a rich source of genetic diversity. This diversity is not easily exploited due to challenges inherent in identifying and extracting beneficial alleles from widely unadapted germplasm. Wild barley germplasm has been shown to contain valuable alleles for several disease resistance and abiotic stress tolerance traits, and due to its extensive diversity, it is a key target for expanding the limited diversity of cultivated breeding germplasm. Therefore, our aim was to create and characterize populations that incorporate diverse sources of wild barley germplasm into cultivated barley backgrounds using advanced backcross (AB) and nested association mapping (NAM) techniques. To do this, we created a wild barley AB-NAM population by backcrossing 25 wild barley accessions to the 6-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected to capture approximately ~90% of the allelic content of the wild barley diversity collection (WBDC), which contains 318 accessions sourced from across wild barley’s native range. The resulting set of 796 BC2F4:6 lines were genetically characterized and analyzed in augmented field trials for agronomic, yield, grain protein, and wax production traits. Additionally, we analyzed the Harrington (2-rowed malting barley cultivar) x OUH-602 (wild barley accession), biparental AB population for yield and malting quality characteristics. The AB-NAM population was genotyped with 384 SNP markers and 263,531 markers were imputed onto the population from exome capture sequence of the parents. Linkage disequlibrium in the AB-NAM was significantly lower than the HOUH biparental mapping population, indicating a higher potential mapping resolution. Qualitative traits were mapped to candidate gene resolution and beneficial alleles were identified for several quantitative traits. Ultimately, the AB-NAM population will serve as a community resource for barley breeders and geneticists to explore a large proportion of wild barley germplasm in a single, relatively adapted mapping population.Nice, Liana. (2015). Assessing wild barley germplasm in multiparent and advanced backcross populations for mapping, gene discovery, and improvement of malting barley. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/181787

Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation.

Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, Glyma.15G107200, and Glyma.19G121200.1 (Table 4). Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, and Glyma.19G121200.1 are best candidates. To the best of our knowledge, this is the first report highlighting SNP markers associated with tolerance index based on biomass reduction under SCN infestation in soybean. This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance