Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 4/29/2006
Publication Date: 4/29/2006
Citation: Hwang, E., Song, Q., Joseph, B., Shoemaker, R.C., Costa, J., Specht, J., Cregan, P.B. 2006. Genetic association analysis for the detection of genetic factors controlling seed protein concentration in soybean [abstract]. International Plant and Animal Genome IX Conference. January 13-17, 2006, San Diego, CA, p.167. Interpretive Summary:
Technical Abstract: Gene discovery using association analysis is reputed to have higher resolution and more power than conventional linkage or QTL analysis. Association analysis will narrow the genomic region in which an identified QTL is located and can detect previously undetected QTL. The goal of this study is to validate the application of association analysis for the detection of previously reported QTLs that control soybean seed protein concentration. A total of 327 soybean germplasm lines from the USDA-ARS, soybean germplasm collection were divided into two groups, those with ‘normal’ seed protein concentration (400-430 g kg-1) (control group) and those with high seed protein concentration (460-510 g kg-1) (case group). We developed SNP markers from BAC-ends associated with protein QTLs. SNPs were used to assay DNA marker allele frequencies in the case and control groups. We found a total of 38 SNPs in 12 BAC-ends associated with SSR marker Satt496 on linkage group I in which one of major seed protein QTL is located. Chi-square and ODDs ratio tests showed that three of 38 SNPs had significant (p < 0.05) marker allele frequency differences between the case and control groups. The limited association with protein content of SNPs in the region of Satt496 suggests relatively low linkage disequilibrium in this region and the need for further analysis of adjacent SNP loci.