Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits

Abstract

Soybean (Glycine max [L.] Merr.) is one of the most significant crops in the world in terms of oil and protein. Owing to the rising demand for soybean products, there is an increasing need for improved varieties for more productive farming. However, complex correlation patterns among quantitative traits along with genetic interactions pose a challenge for soybean breeding. Association studies play an important role in the identification of accession with useful alleles by locating genomic sites associated with the phenotype in germplasm collections. In the present study, a genome-wide association study was carried out for seven agronomic and yield-related traits. A field experiment was conducted in 2015/2016 at two locations that include 155 diverse soybean germplasm. These germplasms were genotyped using SoySNP50K Illumina Infinium Bead-Chip. A total of 51 markers were identified for node number, plant height, pods per plant, seeds per plant, seed weight per plant, hundred-grain weight, and total yield using a multi-locus linear mixed model (MLMM) in FarmCPU. Among these significant SNPs, 18 were putative novel QTNs, while 33 co-localized with previously reported QTLs. A total of 2,356 genes were found in 250 kb upstream and downstream of significant SNPs, of which 17 genes were functional and the rest were hypothetical proteins. These 17 candidate genes were located in the region of 14 QTNs, of which ss715580365, ss715608427, ss715632502, and ss715620131 are novel QTNs for PH, PPP, SDPP, and TY respectively. Four candidate genes, Glyma.01g199200, Glyma.10g065700, Glyma.18g297900, and Glyma.14g009900, were identified in the vicinity of these novel QTNs, which encode lsd one like 1, Ergosterol biosynthesis ERG4/ERG24 family, HEAT repeat-containing protein, and RbcX2, respectively. Although further experimental validation of these candidate genes is required, several appear to be involved in growth and developmental processes related to the respective agronomic traits when compared with their homologs in Arabidopsis thaliana. This study supports the usefulness of association studies and provides valuable data for functional markers and investigating candidate genes within a diverse germplasm collection in future breeding programs.

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

“…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.…”

Genomic Approaches for Enhancing Yield and Quality Traits in Mustard (Brassica spp.): A Review of Breeding Strategies

“…Functional characterization of these genes using transgenic approaches or gene editing technologies offers opportunities for targeted manipulation of yield-related traits in crops. Overall, the identification of yield-related genes and QTLs through genomic approaches provides a foundation for targeted breeding efforts aimed at enhancing crop productivity and resilience [39].…”