|BANDILLO, NONOY - University Of Nebraska|
|JARQUIN, DIEGO - University Of Nebraska|
|CREGAN, PERRY - Retired ARS Employee|
|SPECHT, JAMES - University Of Nebraska|
|LORENZ, AARON - University Of Nebraska|
Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/15/2015
Publication Date: 9/25/2015
Publication URL: http://doi:10.3835/plantgenome2015.04.0024
Citation: Bandillo, N., Jarquin, D., Song, Q., Cregan, P., Nelson, R.L., Specht, J., Lorenz, A. 2015. A population structure and genome-wide association analysis on the USDA soybean germplasm collection. The Plant Genome. 8(3):1-13.
Interpretive Summary: We have analyzed the USDA Soybean Germplasm Collection with >42,000 Single Nucleotide Polymorphism (SNP) DNA markers. The USDA Soybean Germplasm Collection consists of more than 18,000 cultivated soybean accessions and among these nearly 13,000 accessions were measured for seed protein content and oil content. The resulting dataset is publically available in the USDA, ARS Germplasm Resources Information Networkdatabase. Using the seed protein and oil and the molecular marker datasets, we studied the association of the seed protein content and oil content with molecular markers and were able to narrow down regions of the soybean chromosomes containing genes affecting the seed protein content and oil content and to identify molecular marker patterns that were associated with protein and oil content. In addition, this research provides a fuller understanding of the distribution of genetic variation contained within the soybean germplasm collection. This knowledge will ultimately facilitate a more efficient and effective use of this diversity in the development of genetically improved elite soybean varieties.
Technical Abstract: Genotype-phenotype associations within the soybean (Glycine max) germplasm collection could provide valuable information on the frequency and distribution of alleles affecting economically important traits. Here we performed a genome-wide association study (GWAS) for seed protein and oil content in the USA soybean collection comprised of nearly 13,000 unique accessions with available genotype and phenotype information. A region previously reported to be important for protein and oil content was further narrowed to a 450 kb region containing only two candidate genes. The haplotype effects show a strong negative relationship between oil and protein at this locus, indicating negative pleiotropic effects. The vast majority of accessions carry the haplotype allele conferring lower protein and higher oil. Results from a population structure analysis provide a fuller understanding of the distribution of genetic variation contained within the collection.