Identification of QTNs Controlling Seed Protein Content in Soybean Using Multi-Locus Genome-Wide Association Studies.

Kaixin Zhang,Xiaocui Tian,Shiping Liu,Zhixi Tian,Zhongying Qi,Shulin Liu,Hailong Ning,Wenbin Li,Jun Zhang,Xiyu Li,Wen-Xia Li,Jianan Zhang,Shichao Xu,Jie Song,Yanlong Fang,Yue Wang

doi:10.3389/fpls.2018.01690

Abstract

Protein content (PC), an important trait in soybean (Glycine max) breeding, is controlled by multiple genes with relatively small effects. To identify the quantitative trait nucleotides (QTNs) controlling PC, we conducted a multi-locus genome-wide association study (GWAS) for PC in 144 four-way recombinant inbred lines (FW-RILs). All the FW-RILs were phenotyped for PC in 20 environments, including four locations over 4 years with different experimental treatments. Meanwhile, all the FW-RILs were genotyped using SoySNP660k BeadChip, producing genotype data for 109,676 non-redundant single-nucleotide polymorphisms. A total of 129 significant QTNs were identified by five multi-locus GWAS methods. Based on the 22 common QTNs detected by multiple GWAS methods or in multiple environments, pathway analysis identified 8 potential candidate genes that are likely to be involved in protein synthesis and metabolism in soybean seeds. Using superior allele information for 22 common QTNs in 22 elite and 7 inferior lines, we found higher superior allele percentages in the elite lines and lower percentages in the inferior lines. These findings will contribute to the discovery of the polygenic networks controlling PC in soybean, increase our understanding of the genetic foundation and regulation of PC, and be useful for molecular breeding of high-protein soybean varieties.

Highlights

Soybean [Glycine max (L.) Merr.] is a globally important high-protein crop, with protein accounting for about 40% of the seed’s dry weight
We measured the Protein content (PC) phenotypes of the parents and the 144 four-way recombinant inbred lines (FW-RILs) in 20 environments, which are presented in Supplementary Table S2 and Supplementary Figure S1
We found a high coefficient of variation in PC across all the environments

Summary

Introduction

Soybean [Glycine max (L.) Merr.] is a globally important high-protein crop, with protein accounting for about 40% of the seed’s dry weight. Soybean is one of humans’ main sources of dietary protein; breeding high-protein varieties of soybean is an ongoing, important objective of plant breeders. Detecting Soybean Protein Content QTNs. Breeders and molecular geneticists have routinely used populations derived from biparental crosses for development of new varieties and mapping quantitative trait loci (QTLs) for traits of interest. The richness of allelic and phenotypic variation in biparental inter-mated populations is somewhat limited. To overcome this limitation, animal breeders have developed the multi-parental inter-mated population design, for example by using a population descended from eight mouse strains (Yalcin et al, 2005). The four-way cross population, is easier to obtain while providing some of the same benefits as an eight-way cross population

Methods

Results

Discussion

Conclusion