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

Shengyou Li; Yongqiang Cao; Changling Wang; Chunjuan Yan; Xugang Sun; Lijun Zhang; Wenbin Wang; Shuhong Song

doi:10.3389/fpls.2023.1265574

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

Front Plant Sci. 2023 Oct 9:14:1265574. doi: 10.3389/fpls.2023.1265574. eCollection 2023.

Authors

Shengyou Li¹, Yongqiang Cao¹, Changling Wang¹, Chunjuan Yan¹, Xugang Sun¹, Lijun Zhang¹, Wenbin Wang¹, Shuhong Song¹

Affiliation

¹ Institute of Crop Research, Liaoning Academy of Agricultural Sciences, Shenyang, China.

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.

Keywords: GWAS; drought stress; favorable haplotypes; soybean (Glycine max); yield-related traits.

Grants and funding

The authors declare financial support was received for the research, authorship, and/or publication of this article. The study was supported by the National Natural Science Foundation of China (32101795 and 32301782), Liaoning provincial Major Special Project of Agricultural Science and Technology (2022JH1/10200002 and 2021JH1/10400038), Key Research and Development Plan of Liaoning Science and Technology Department (2021JH2/1020027), and Shenyang Seed Industry Innovation Project (22-318-2-12).