Detection of Soybean Seed Protein QTLs Using Selective Genotyping.

Quantitative trait locus (QTL) identification is the first step towards using marker-assisted selection (MAS) to introgress desirable QTL alleles into elite high-yield soybean cultivars. Hundreds of high protein plant introductions (PIs) exist in the USDA germplasm collection, and are potential sources of high protein genes. There are 86 protein QTLs listed in SoyBase, but most are repeat discoveries of existing QTLs, and most have only small effects, except for two QTLs on Chromosome 20 [Linkage Group (LG)-I] and Chromosome 15 (LG-E), which have large additive effects of 1.2 and 0.85 percentage points. Discovery of new protein QTLs with additive effects similar to these two QTLs, but with lesser pleiotropic effects on seed oil and yield, would be of great interest. Forty-eight high seed protein (48% or more) germplasm accessions representing maturity groups (MGs) 000 to V were mated to a high-yielding cultivar with normal seed protein (42% or less) of the same MG to generate 48 populations. The 240 individual plants in each population produced F2:3 seed progenies that were phenotyped for seed protein content. We used a technique called selective genotyping or phenotypic tail analysis to identify the lowest 10% and the highest 10% which were then genotyped with a 1536-SNP locus assay chip to conduct a search for what might be completely new and heretofore unknown protein QTLs. Thus far, 48 populations have been genotyped. Parental genotype analysis indicated that 13 PI parents from MGs 000 and 00 were identical to each other, and that four PIs from MG 0 were also identical to each other, but not to these 13 PI parents. Lastly, two PI parents from MG I were also identical to each other, but not to the others. QTL analysis has been completed on 48 populations detected 63 protein QTLs with LOD scores greater than 3.0 that mapped on 13 linkage groups. We detected significant QTLs on chromosomes 2, 7, 10, 14, 16 and 18 that are not currently listed in SoyBase.