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

Hyun Jo,Jeong-Dong Lee,Ji Yun Lee

doi:10.3390/agronomy12020250

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.

Highlights

Soybean (Glycine max (L.) Merr.) is one of the most economically and nutritionally important crops worldwide because it contains 40% protein, 20% oil, and 15% soluble carbohydrates in the seed
Due to the to the health benefits of black seed coats with green cotyledons (BLG) soybean, consumers prefer to use it to cook with rice and health benefits of BLG soybean, consumers prefer to use it to cook with rice and other side dishes in Korea
This study investigated the phenotypic variation of hundred-seed weight (HSW) in BLG accessions, ranging from 9.1 to 49.3 g, with a mean value of 33.9 g

Summary

Introduction

Soybean (Glycine max (L.) Merr.) is one of the most economically and nutritionally important crops worldwide because it contains 40% protein, 20% oil, and 15% soluble carbohydrates in the seed. The seed weight is an important component affecting the soybean yield, and a determinant of soy products for human consumption [4,5,6,7]. Small-seed soybeans are used for the production of high-quality soybean sprouts and natto, whereas large-seed soybeans are preferred to produce tofu, soybean paste, edamame, and miso soup [8]. It is important to understand the genetic basis of hundred-seed weight (HSW) in improving the potential of soybean yield and the associated soybean food quality. This understanding will provide helpful information in the soybean breeding program to develop a new cultivar

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Conclusion