Genome-wide association mapping for yield-related traits in soybean (Glycine max) under well-watered and drought-stressed conditions

Abstract

Soybean (Glycine max) productivity is significantly reduced by drought stress. Breeders are aiming to improve soybean grain yields both under well-watered (WW) and drought-stressed (DS) conditions, however, little is known about the genetic architecture of yield-related traits. Here, a panel of 188 soybean germplasm was used in a genome wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers linked to yield-related traits including pod number per plant (PN), biomass per plant (BM) and seed weight per plant (SW). The SLAF-seq genotyping was conducted on the population and three phenotype traits were examined in WW and DS conditions in four environments. Based on best linear unbiased prediction (BLUP) data and individual environmental analyses, 39 SNPs were significantly associated with three soybean traits under two conditions, which were tagged to 26 genomic regions by linkage disequilibrium (LD) analysis. Of these, six QTLs qPN-WW19.1, qPN-DS8.8, qBM-WW1, qBM-DS17.4, qSW-WW4 and qSW-DS8 were identified controlling PN, BM and SW of soybean. There were larger proportions of favorable haplotypes for locus qPN-WW19.1 and qSW-WW4 rather than qBM-WW1, qBM-DS17.4, qPN-DS8.8 and qSW-DS8 in both landraces and improved cultivars. In addition, several putative candidate genes such as Glyma.19G211300, Glyma.17G057100 and Glyma.04G124800, encoding E3 ubiquitin-protein ligase BAH1, WRKY transcription factor 11 and protein zinc induced facilitator-like 1, respectively, were predicted. We propose that the further exploration of these locus will facilitate accelerating breeding for high-yield soybean cultivars.

Genome-Wide Association Analysis for Yield-Related Traits and Candidate Genes in Vegetable Soybean

“…Besides, in the process of population analysis, the acceptable distance between candidate genes and markers were determined by LD, the variation of LD was varies with different populations [29]. And the LD decay distance of 188 vegetable soybean varieties in this study was 150.00 kb (r 2 = 0.375), within the previously reported range (90 kb to 574 kb) [30][31][32] . Therefore, it is sufficient for a valid GWAS analysis.…”

“…In the previously reported, the QTL region related to plant height was located in Chr13:21,937,082-23,937,081 [31,32]. In this paper, a SNP (Chr13:22150035) identified from plant height trait, is also located in this interval, and Glyma.13G109100 is located at 154.23kb away from chr13:22150035.…”

“…Among them, Glyma.09G102300 mainly encodes F-box related protein and F-box proteins are a family of proteins that exist widely in eukaryotes and contain the F-box domain. It plays an important role in cell cycle regulation, transcription regulation, apoptosis, cell signal transduction, growth and development [39,40]. In addition, studies have shown that F-box proteins OsFBX206, OsFBK12 can regulate the synthesis of ethylene and boisterousness for improving the grain size and yield in rice [41][42][43] .Besides, we found that NADH dehydrogenase1 alpha sub-complex was predicted to be an interacting protein of the fresh pod weight candidate gene Glyma.09G102300.…”

Genome-Wide Association Analysis of Yield-Related Traits and Candidate Genes in Vegetable Soybean

“…In a recent report, 294 seed weight-related SNPs were identified in soybean chromosomes ( ) [ 16 , 38 ]. In addition, some identified SNP S have been identified to correlate with yield traits, such as seed size, maturity, flowering time, and plant height [ 39 ].…”