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Distribution of genomic variation in the USDA Soybean Germplasm Collection and relationship with phenotypic variation

Nonoy B Bandillo, University of Nebraska - Lincoln


The USDA Soybean Germplasm Collection harbors a large stock of genetic diversity with potential to accelerate soybean cultivar development. The extent and nature of favorable alleles contained in the collection are not well known nor is the distribution of genetic variation and how it relates to phenotypic variation. The genotyping of the entire USDA Soybean Germplasm Collection marked the beginning of a systematic exploration of genetic diversity for genetic research and breeding. In this research, we conducted the first comprehensive analysis of population structure on the collection of ~14,400 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold & Zucc.] that were genotyped using a 50KSNP chip. Accessions originating from Japan and Korea diverged from the Chinese accessions. The ancestry of founders of the American accessions derived mostly from two Chinese subpopulations, which reflects the composition of the American accessions as a whole. A genome-wide association study on ~12,000 accession conducted on seed protein and oil is the largest reported to date in plants and identified strong single nucleotide polymorphisms (SNPs) signals on chromosomes 20 and 15. The haplotype effects of the chromosome 20 region show a strong negative relationship between oil and protein at this locus, indicating negative pleiotropic effects or multiple closely linked loci in repulsion phase linkage. Genome-wide association mapping for ten descriptive traits identified a total of 23 known genes and unknown genes controlling the phenotypic variants. Because some of those genes had been cloned, we were able to show that the narrow SNP signal regions had chromosomal base pair spans that, with few exceptions, bracketed the base pair region of the cloned gene coding sequences, despite variation in SNP distribution of chip SNP set. We also elucidate the genetic basis of local adaptation in soybean by exploring the natural variation available in 3,012 locally adapted landrace accessions from across the geographical range of soybean. Our approach using selection mapping and landscape genomic association methods identified important candidate genes related to abiotic stresses, and revealed important signatures of directional selection that are likely involved on geographic divergence of soybean.

Subject Area

Agronomy|Genetics|Plant sciences

Recommended Citation

Bandillo, Nonoy B, "Distribution of genomic variation in the USDA Soybean Germplasm Collection and relationship with phenotypic variation" (2016). ETD collection for University of Nebraska-Lincoln. AAI10241022.