Genome-Wide Association Study for Earliness in Soybean (Glycine max).

Abstract

Soybean (Glycine max) is a vital legume globally, valued for its high protein (~40%) and oil (~20%) content, contributing to human and livestock nutrition. Earliness traits, including days to flowering, reproductive period, and days to maturity, are crucial for adaptation and yield but are complex, and regulated by multiple genes and environmental interactions. Understanding their genetic basis is key to developing climate-resilient varieties. This study aimed to (i) evaluate phenotypic variability in early maturity traits among 308 soybean genotypes in Uganda and (ii) identify associated SNP markers using a genome-wide association study (GWAS). Field trials were conducted at MUARIK, Nakabango, and Ngetta ZARDI during the 2024A season. Genotyping was performed using Diversity Arrays Technology (DArT) sequencing at SEQART AFRICA, ILRI-Nairobi. Phenotypic variability was assessed using ANOVA in R, and Best Linear Unbiased Predictors (BLUPs) were derived using “lme4” package in R statistical software. GWAS was conducted using the FARMCPU model in GAPIT-R after quality control in TASSEL v5.73. Days to 50% flowering ranged from 27 to 49 days after planting (DAP), with genotypes Carsoy 79, Ux990-086B, and Ux990-017 being earliest (27 DAP), and Pan9 and NGDT 3.15-10 latest (49 DAP). The reproductive period varied from 40 to 59 days, with genotype Pan 3-1 having the shortest reproductive period (40 days) while Spike had the longest (59 days). Days to maturity ranged from 70 to 97 DAP, with Ux990-079A and Ux990-086 maturing earliest (70 DAP) and Pan 32 latest (97 DAP). GWAS identified six significant SNPs (-log[P] > 5) for flowering time (chromosomes 9, 10, 14, 18), four for reproductive period (chromosomes 1, 5, 16, 17), and nine for maturity (chromosomes 9, 10, 11, 12, 15, 19). Novel loci were detected on chromosomes 1 and 16. Candidate gene annotation linked these loci to photoperiod regulation, flowering time, and hormonal signalling. A pleiotropic SNP on chromosome 9 (Ps: 1142493) influenced both flowering and maturity, highlighting shared genetic control. These findings provide key genomic insights for breeding early-maturing soybean varieties for tropical environments. Identified SNP markers can enhance marker-assisted selection, expediting breeding cycles. Further validation through multi-environment trials is recommended.