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Population structure and marker–trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection

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Abstract

Peanut (Arachis hypogaea L.) is one of the most important oilseed and nutritional crops in the world. To efficiently utilize the germplasm collection, a peanut mini-core containing 112 accessions was established in the United States. To determine the population structure and its impact on marker–trait association, this mini-core collection was assessed by genotyping 94 accessions with 81 SSR markers and two functional SNP markers from fatty acid desaturase 2 (FAD2). Seed quality traits (including oil content, fatty acid composition, flavonoids, and resveratrol) were obtained through nuclear magnetic resonance (NMR), gas chromatography (GC), and high-performance liquid chromatography (HPLC) analysis. Genetic diversity and population structure analysis identified four major subpopulations that are related to four botanical varieties. Model comparison with different levels of population structure and kinship control was conducted for each trait and association analyses with the selected models verified that the functional SNP from the FAD2A gene is significantly associated with oleic acid (C18:1), linoleic acid (C18:2), and oleic-to-linoleic (O/L) ratio across this diverse collection. Even though the allele distribution of FAD2A was structured among the four subpopulations, the effect of FAD2A gene remained significant after controlling population structure and had a likelihood-ratio-based R 2 (R 2 LR ) value of 0.05 (oleic acid), 0.09 (linoleic acid), and 0.07 (O/L ratio) because the FAD2A alleles were not completely fixed within subpopulations. Our genetic analysis demonstrated that this peanut mini-core panel is suitable for association mapping. Phenotypic characterization for seed quality traits and association testing of the functional SNP from FAD2A gene provided information for further breeding and genetic research.

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Acknowledgments

The authors gratefully thank Drs. Paul Raymer, Weibo Dong, and Peggy Ozias-Akins for giving useful comments and suggestions to improve the quality of this manuscript, Mr. Brandon Tonnis for his excellent technical assistance on chemical analysis, and Ms. Jessica Norris for her assistance in gel electrophoresis and DNA extraction.

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Authors and Affiliations

  1. USDA-ARS, PGRCU, Griffin, GA, 30223, USA

    Ming Li Wang, Noelle A. Barkley, Roy N. Pittman & Gary A. Pederson

  2. Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA

    Sivakumar Sukumaran & Jianming Yu

  3. Crop and Soil Sciences Department, University of Georgia, Griffin, GA, 30223, USA

    Zhenbang Chen

  4. USDA-ARS, National Peanut Research Laboratory, Dawson, GA, 39842, USA

    Charles Y. Chen

  5. USDA-ARS, CPMRU, Tifton, GA, 31793, USA

    Baozhu Guo

  6. Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA

    H. Thomas Stalker

  7. USDA-ARS, CGBRU, Tifton, GA, 31793, USA

    C. Corley Holbrook

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  1. Ming Li Wang
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  2. Sivakumar Sukumaran
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  3. Noelle A. Barkley
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Correspondence to Ming Li Wang or Jianming Yu.

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Communicated by J. Wang.

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Wang, M.L., Sukumaran, S., Barkley, N.A. et al. Population structure and marker–trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection. Theor Appl Genet 123, 1307–1317 (2011). https://doi.org/10.1007/s00122-011-1668-7

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