Genome-Wide Association Mapping for Seed Weight in Soybean with Black Seed Coats and Green Cotyledons

Abstract

The yield of soybean (Glycine max (L.) Merr.) is based on several components, such as the number of plants per unit area, pod number per plant, number of nodes, and seed weight. Additionally, the hundred-seed weight (HSW) is an important component affecting soybean yield. The HSW trait can determine soy products meant for human consumption. In this study, we conducted genome-wide association studies with 470 accessions of black seed coats with green cotyledons and applied an online tool with publicly available genome sequencing data. The objective of the study was to identify the genomic regions in the soybean genome associated with seed weight and to identify the candidate genes in linkage disequilibrium blocks where the most significant SNPs were located. This study identified significant SNPs for seed weight on chromosomes 2 and 16. Furthermore, this study indicated that GmCYP78A57 (Glyma.02G119600) encoded a cytochrome P450 monooxygenase may be a possible candidate gene for controlling the seed size in soybean. We assumed that another gene on chromosome 16 may play the important role of a small additive genetic effect to reduce seed size along with GmCYP78A57. An online tool was used to identify 12 allelic variations of GmCYP78A57 with publicly available genomic sequence data. The HSW of 45 accessions having a missense mutation from the Germplasm Resources Information Network ranged from 4.4 to 17.6 g. In addition, 19 accessions were shown to be less than 10.0 g of HSW. This information can provide for the development of molecular markers to use in soybean breeding programs to release new cultivars with increased or decreased seed weight.