Identification and verification of pleiotropic QTL controlling multiple amino acid contents in soybean seed

Abstract

Soybean is important throughout the world due to its high seed protein and oil, while the quality and quantity of seed amino acids need to be improved. To improve the multiple amino acid concentrations in soybean simultaneously, detecting and utilizing the pleiotropic quantitative trait loci (QTL) and related genes become increasingly important. In view of this, a F6:7 recombinant inbred line population was genotyped using 1739 polymorphic SNP and 127 SSR markers in the present study and was phenotyped for seventeen types of amino acids simultaneously. In total, twelve co-located or overlapped pleiotropic additive QTL clusters, which explained 2.38–16.79% of the amino acid variation, were identified. Of them, one novel pleiotropic QTL cluster with a phenotypic variation explained ranging from 8.84 to 16.79% for ten kinds of amino acid contents (glycine, alanine, isoleucine, leucine, valine, methionine, aspartic acid, glutamic acid, lysine and phenylalanine), was located at the same position on linkage group D2, and the confidence interval was only 0.8 cM. Moreover, the individuals in this family-based population (345 lines) and another cultivar-based population (254 varieties) with different genotypes at the common flanking markers for this QTL cluster showed significantly different amino acid contents, which further validated the QTL mapping results. Additionally, some candidate genes that might participate in the amino acid biosynthesis process were found in these pleiotropic QTL regions. Thus, novel pleiotropic QTL clusters could be applied in marker-assisted selection breeding or map-based candidate gene cloning in soybean for multiple amino acid genetic improvements in seed in the future.