Genome-Wide Association Analysis of Diverse Soybean Genotypes Reveals Novel Markers for Nitrogen Traits

Abstract

Nitrogen is a primary plant nutrient that plays a major role in achieving maximum economic yield. Insufficient availability most often limits soybean [ (L.) Merr.] crop growth. Symbiotic N fixation in soybean is highly sensitive to limited water availability, and breeding for reduced N fixation sensitivity to drought is considered an important objective to improve yields under drought. The objective of this study was to identify single nucleotide polymorphism (SNP) markers associated with N traits. A collection of 373 diverse soybean genotypes were grown in four field environments (2 yr and two locations) and characterized for N derived from atmosphere (Ndfa), N concentration ([N]), and C/N ratio. The population structure of 373 soybean genotypes was assessed based on 31,145 SNPs and genome-wide association analysis using a unified mixed model identified SNPs associated with Ndfa, [N], and C/N ratio. Although the Ndfa, [N], and C/N ratio values were significantly different between the two locations in both years, results were consistent among genotypes across years and locations. While numerous SNPs were identified by association analysis for each trait in only one of the four environments, 17, 19, and 24 SNPs showed a significant association with Ndfa, [N], and C/N ratio, respectively, in at least two environments as well as with the average across all four environments. These markers represent an important resource for pyramiding favorable alleles for drought tolerance and for identifying extremes for comparative physiological studies.