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Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes

Theoretical and Applied Genetics volume 128, pages 73–91 (2015)Cite this article

An Erratum to this article was published on 10 January 2015

Abstract

Key message

Using genome-wide association studies, 39 SNP markers likely tagging 21 different loci for carbon isotope ratio (δ 13 C) were identified in soybean.

Abstract

Water deficit stress is a major factor limiting soybean [Glycine max (L.) Merr.] yield. Soybean genotypes with improved water use efficiency (WUE) may be used to develop cultivars with increased yield under drought. A collection of 373 diverse soybean genotypes was grown in four environments (2 years and two locations) and characterized for carbon isotope ratio (δ13C) as a surrogate measure of WUE. Population structure was assessed based on 12,347 single nucleotide polymorphisms (SNPs), and genome-wide association studies (GWAS) were conducted to identify SNPs associated with δ13C. Across all four environments, δ13C ranged from a minimum of −30.55 ‰ to a maximum of −27.74 ‰. Although δ13C values were significantly different between the two locations in both years, results were consistent among genotypes across years and locations. Diversity analysis indicated that eight subpopulations could contain all individuals and revealed that within-subpopulation diversity, rather than among-subpopulation diversity, explained most (80 %) of the diversity among the 373 genotypes. A total of 39 SNPs that showed a significant association with δ13C in at least two environments or for the average across all environments were identified by GWAS. Fifteen of these SNPs were located within a gene. The 39 SNPs likely tagged 21 different loci and demonstrated that markers for δ13C can be identified in soybean using GWAS. Further research is necessary to confirm the marker associations identified and to evaluate their usefulness for selecting genotypes with increased WUE.

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Acknowledgments

This work was supported by United States Department of Agriculture–Agriculture Research Service (USDA-ARS) project number 6402-21220-010-00D and United Soybean Board project numbers 9274 and 1274. We appreciate the assistance of Dr. Randall Nelson, curator of the USDA-ARS Germplasm Collection in selecting the genotypes evaluated in this study.

Conflict of interest

The authors have declared that no competing or conflicts of interest exist.

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Authors and Affiliations

  1. Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA

    Arun Prabhu Dhanapal & Felix B. Fritschi

  2. Crop Genetics Research Unit, USDA-ARS, 141 Experimental Station Road, Stoneville, MS, 38776, USA

    Jeffery D. Ray & James R. Smith

  3. Crop Systems and Global Change Lab, USDA-ARS, Beltsville, MD, USA

    Shardendu K. Singh

  4. Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA

    Valerio Hoyos-Villegas

  5. Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA

    Larry C. Purcell & C. Andy King

  6. USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, 20705, USA

    Perry B. Cregan & Qijian Song

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  1. Arun Prabhu Dhanapal
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  2. Jeffery D. Ray
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  9. Qijian Song
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  10. Felix B. Fritschi
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Correspondence to Felix B. Fritschi.

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Communicated by Jianbing Yan.

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Dhanapal, A.P., Ray, J.D., Singh, S.K. et al. Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes. Theor Appl Genet 128, 73–91 (2015). https://doi.org/10.1007/s00122-014-2413-9

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Keywords

  • Carbon isotope ratio
  • Genome wide association studies (GWAS)
  • SNPs
  • Water use efficiency (WUE)