Genetic Mapping of Soybean Seed Protein QTLs.

A quantitative trait locus (QTL) is the chromosomal location of a gene governing that trait. QTL identification is the first step towards using marker-assisted selection (MAS) to introgress desirable QTL alleles into elite high-yield cultivars.  Hundreds of high protein plant introductions (PIs) exist in the USDA germplasm collection, and are a source of high protein alleles, but only a few PIs have been characterized as to their allelic status at known (or unknown) protein QTLs.  Although 86 protein QTLs are listed in SoyBase, many are likely repeat discoveries of the same QTL(s), given the typical +/- 10cM confidence intervals associated with QTL positions.  The additive effect for these 86 QTLs were never greater than the respective 1.2% and 0.85% estimates obtained for the Chromosome 20 [Linkage Group (LG)-I] and Chromosome 15 (LG-E) QTLs.  All remaining QTLs had a smaller apparent additive effect (or even smaller true effect, given the Beavis Effect).  Discovery of protein QTLs different from the Chr 20 and Chr 15 QTLs, but still expressing a large additive effect, would be of great interest.  We have mated 51 high protein (48% or more) germplasm accessions to high-yield public cultivars with normal protein (42% or less) to generate 51 populations.  The 240 F₂ plants in each population produced F_2.3 seed progenies in 2008 that were phenotyped for seed protein content.  We used a technique called selective genotyping or phenotypic tail analysis to identify the lowest 10% the highest 10%. We have used a 1536-SNP locus assay panel to conduct a selective genotyping search for what might be completely new and heretofore unknown protein QTLs.  New protein QTLs could be great value, if the hi-protein alleles at these QTLs have less impact on yield than do the known QTLs on Chr 20 and Chr 15.