Theoretical and Applied Genetics

, Volume 123, Issue 8, pp 1307–1317 | Cite as

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

  • Ming Li Wang
  • Sivakumar Sukumaran
  • Noelle A. Barkley
  • Zhenbang Chen
  • Charles Y. Chen
  • Baozhu Guo
  • Roy N. Pittman
  • H. Thomas Stalker
  • C. Corley Holbrook
  • Gary A. Pederson
  • Jianming Yu
Original Paper

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 R2 (RLR2) 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.

Supplementary material

122_2011_1668_MOESM1_ESM.doc (1.1 mb)
Supplementary material 1 (DOC 1.05 mb)
122_2011_1668_MOESM2_ESM.doc (36 kb)
Supplementary material 2 (DOC 35.5 kb)

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Copyright information

© Springer-Verlag (outside the USA) 2011

Authors and Affiliations

  • Ming Li Wang
    • 1
  • Sivakumar Sukumaran
    • 2
  • Noelle A. Barkley
    • 1
  • Zhenbang Chen
    • 3
  • Charles Y. Chen
    • 4
  • Baozhu Guo
    • 5
  • Roy N. Pittman
    • 1
  • H. Thomas Stalker
    • 6
  • C. Corley Holbrook
    • 7
  • Gary A. Pederson
    • 1
  • Jianming Yu
    • 2
  1. 1.USDA-ARS, PGRCUGriffinUSA
  2. 2.Department of AgronomyKansas State UniversityManhattanUSA
  3. 3.Crop and Soil Sciences DepartmentUniversity of GeorgiaGriffinUSA
  4. 4.USDA-ARS, National Peanut Research LaboratoryDawsonUSA
  5. 5.USDA-ARS, CPMRUTiftonUSA
  6. 6.Department of Crop ScienceNorth Carolina State UniversityRaleighUSA
  7. 7.USDA-ARS, CGBRUTiftonUSA

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