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

Reena Rani; Ghulam Raza; Hamza Ashfaq; Muhammad Rizwan; Muhammad Khuram Razzaq; Muhammad Qandeel Waheed; Hussein Shimelis; Allah Ditta Babar; Muhammad Arif

doi:10.3389/fpls.2023.1229495

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

Front Plant Sci. 2023 Aug 11:14:1229495. doi: 10.3389/fpls.2023.1229495. eCollection 2023.

Authors

Reena Rani¹, Ghulam Raza¹, Hamza Ashfaq¹, Muhammad Rizwan², Muhammad Khuram Razzaq³, Muhammad Qandeel Waheed⁴, Hussein Shimelis⁵, Allah Ditta Babar¹, Muhammad Arif¹

Affiliations

¹ Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan.
² Plant Breeding and Genetics Division, Nuclear Institute of Agriculture (NIA), Tando Jam, Pakistan.
³ Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China.
⁴ Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan.
⁵ School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa.

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.

Keywords: GWAS; candidate gene discovery; gene ontology; single nucleotide polymorphism; soybean.