Genome-Wide Association Analysis of Hundred-Seed Weight in Soybean Using SNP Markers and The Development of Molecular Markers for Breeding
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Abstract
Soybean (Glycine max (L.) Merr.) is an important economic crop for food and feed industries. Hundred-seed weight (HSW) is a key trait influencing seed yield and quality. This study aimed to investigate the genome-wide associations of HSW and to develop DNA markers for soybean breeding. A panel of 101 soybean accessions was grown at the Chiang Mai Field Crops Research Center during the 2025 dry season, and HSW was measured. Genotyping was performed using low-pass whole genome sequencing, generating 1,076,102 SNPs for genome-wide association study (GWAS) using four statistical models: MLM, FarmCPU, SUPER, and MLMM. Nineteen missense SNPs significantly associated with HSW were identified across multiple chromosomes. Among them, SNPs within Glyma.03G094400 and Glyma.07G270000 were consistently detected by multiple models and selected for marker development. The SNP in Glyma.07G270000 was developed into a tetra-primer ARMS-PCR marker successfully, and the testing showed that it correctly classified genotypes in agreement with genomic data. Evaluation of the marker’s performance demonstrated an overall accuracy of 71.95% and a sensitivity of 98.1% to identify large-seeded accessions. These results indicate that the developed SNP marker is useful as a preliminary marker for enrichment of large-seeded genotypes to support breeding of soybean varieties with larger seeds and higher yield in the future.
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