Abstract
INTRODUCTION: A key objective of soybean breeding programs is to enhance nutritional quality for human and animal consumption, with improved fatty acid (FA) composition for health benefits, and expand soybean use for industrial applications. METHODS: We conducted a metabolite genome-wide association study (mGWAS) to identify genomic regions associated with changes in FA composition and FA ratios in soybean seeds influenced by environmental factors. This mGWAS utilized 218 soybean plant introductions (PIs) grown in two field locations in Virginia over two years. RESULTS: The mGWAS revealed that 20 SNPs were significantly associated with 21 FA ratios, while additional suggestive SNPs were found for 36 FA ratios, highlighting potential quantitative trait loci linked to FA composition. DISCUSSION: Many of these SNPs are located near or within the genes related to phytohormone-mediated biotic and abiotic stress responses, suggesting the involvement of environmental factors in modulating FA composition in soybean seeds. Our findings provide novel insights into the genetic and environmental factors influencing FA composition in oilseeds. This research also lays the foundation for developing stable markers to develop soybean cultivars with tailored FA profiles for different practical applications under variable growth conditions.