Skip to main content
ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Publications at this Location » Publication #315955

Research Project: Development and Characterization of Soybean Germplasm, Curation of Stored Accessions, and Regional Evaluations of New Genotypes

Location: Crop Genetics Research

Title: Genome-wide association analysis of diverse soybean genotypes reveals novel markers for nitrogen traits

Author
item Dhanapal, Arun
item Ray, Jeffery - Jeff
item Singh, Shardendu
item Hoyos-villegas, Valerio
item Smith, James - Rusty
item Purcell, Larry
item King, C
item Fritschi, Felix

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/2/2015
Publication Date: 9/25/2015
Citation: Dhanapal, A.P., Ray, J.D., Singh, S.K., Hoyos-Villegas, V., Smith, J.R., Purcell, L.C., King, C.A., Fritschi, F.B. 2015. Genome-wide association analysis of diverse soybean genotypes reveals novel markers for nitrogen traits. The Plant Genome. DOI: 10.3835/plantgenome2014.11.0086.

Interpretive Summary: Nitrogen is a primary plant nutrient that plays a major role in achieving the maximum economic yield. Insufficient nitrogen availability most often limits soybean crop growth. The accumulation of nitrogen in soybean plants can be highly sensitive to drought. The purpose of this research was to identify regions of soybean chromosomes associated with nitrogen. In this study we evaluated nitrogen components of 373 soybean lines in four environments (two years and two locations) and then analyzed the data to identify places in the soybean genome associated with differences in nitrogen components. As a result of the analysis, we identified specific regions of soybean chromosomes likely containing genes associated with various nitrogen components. This knowledge will be useful for improving soybean drought tolerance as well as for future studies.

Technical Abstract: Nitrogen is a primary plant nutrient that plays a major role in achieving maximum economic yield. Insufficient availability most often limits soybean crop growth. Symbiotic N2 fixation in soybean is highly sensitive to limited water availability, and breeding for reduced N2 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 nitrogen traits. A collection of 373 diverse soybean genotypes were grown in four field environments (two years and two locations) and characterized for nitrogen derived from atmosphere (Ndfa), nitrogen concentration ([N]) and carbon-nitrogen ratio (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 SNPs were identified by association analysis for each trait in only one of the four environments, 11, 18 and 17 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.