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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Publications at this Location » Publication #330072
Title: Genome-wide association mapping of qualitatively inherited traits in a germplasm collection

Author
item BANDILLO, NONOY - University Of Nebraska
item LORENZ, AARON - University Of Nebraska
item GRAEF, GEORGE - University Of Nebraska
item JARQUIN, DIEGO - University Of Nebraska
item HYTEN, DAVID - University Of Nebraska
item Nelson, Randall
item SPECHT, JAMES - University Of Nebraska

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2017
Publication Date: 7/13/2017
Citation: Bandillo, N., Lorenz, A., Graef, G., Jarquin, D., Hyten, D., Nelson, R.L., Specht, J. 2017. Genome-wide association mapping of qualitatively inherited traits in a germplasm collection. The Plant Genome. 10(2):1-18.

Interpretive Summary: Knowing the genes that control differences in soybean is an important first step in understanding the genetic variation of the species. Having extensive descriptive data for more the 13,000 soybean accessions in the USDA Soybean Germplasm Collection that have also been characterized with 50,000 DNA markers provides the necessary resources to identify the chromosomal locations of the genes responsible for 10 commonly used soybean traits. Using a procedure called genome-wide association analysis, we linked DNA markers with these common soybean traits. In cases where the genes had already been cloned and their precise location was known, our confirmation of those genes was evidence of the power of this technique. For some known genes that have not been cloned, we identifed their location with sufficient precision that these data could be used to identify candidate genes from reference genome. We also identified strong associations with some regions which are likely to contain previously unknown genes controlling classical soybean descriptive traits. These results confirm this technique could be used in other germplasm collections to identify the genetic location of genes controlling simply inherited traits and will be of use to breeders and geneticists in many crops.

Technical Abstract: Genome-wide association (GWA) has been used as a tool for dissecting the genetic architecture of quantitatively inherited traits. We demonstrate here that GWA can also be highly useful for detecting the genomic locations of major genes governing categorically defined phenotype variants that exist for qualitatively inherited traits in a germplasm collection. GWA mapping was applied to categorical phenotypic data available for ten descriptive traits in a collection of ~13,000 Glycine max (L.) Merr. accessions that had been genotyped with a 50K SNP chip. A GWA on a panel of accessions of this magnitude offered substantial statistical power and mapping resolution, and we found that GWA mapping resulted in the identification of strong SNP signals for 23 known genes as well as several heretofore unknown genes controlling the phenotypic variants in those traits. Because some of those genes had been cloned, we were able to show that the narrow SNP signal regions we detected for the phenotypic variants had chromosomal bp spans that, with few exceptions, bracketed the bp region of the cloned gene coding sequences, despite variation in SNP number/distribution of chip SNP set. Our GWA results identified very narrow regions that likely contained the trait-governing candidate genes, and we provide insights on how to deal with digenic traits for which linkage or epistasis can influence the outcome. In essence, GWA mapping aimed at qualitatively inherited traits can provide a convenient path for rapidly generating high-resolution positioning of many yet to be mapped genes on the soybean genomic sequence map.