Genetic Characterization of the Soybean Nested Association Mapping Population

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  • Qijian Song
    Soybean Genomics and Improvement Lab., USDA–ARS 10300 Baltimore Ave, Building 006 Beltsville MD 20705
  • Long Yan
    Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences Shijiazhuang 050035 China
  • Charles Quigley
    Soybean Genomics and Improvement Lab., USDA–ARS 10300 Baltimore Ave, Building 006 Beltsville MD 20705
  • Brandon D. Jordan
    Dep. of Crop Sciences Univ. of Illinois 268 National Soybean Research Center, 1101 West Peabody Drive Urban IL 61801
  • Edward Fickus
    Soybean Genomics and Improvement Lab., USDA–ARS 10300 Baltimore Ave, Building 006 Beltsville MD 20705
  • Steve Schroeder
    USDA–ARS, Animal Genomics and Improvement Laboratory Beltsville MD 20705
  • Bao‐Hua Song
    Dep. of Biological Sciences Univ. of North Carolina at Charlotte Charlotte NC 28223
  • Yong‐Qiang Charles An
    USDA–ARS, Plant Genetics Research Unit at Donald Danforth Plant Sciences Center Saint Louis Missouri
  • David Hyten
    Dep. of Agronomy and Horticulture Univ. of Nebraska Lincoln NE 68583
  • Randall Nelson
    USDA–ARS, Soybean/Maize Germplasm, Pathology and Genetics Research Unit and Dep. of Crop Sciences Univ. of Illinois Urbana IL 61801
  • Katy Rainey
    Dep. of Agronomy Purdue Univ. Lilly 2‐351 West Lafayette IN 47906
  • William D Beavis
    Dep. of Agronomy Iowa State Univ. Ames Iowa 50011
  • Jim Specht
    Dep. of Agronomy and Horticulture Univ. of Nebraska Lincoln NE 68583 USA
  • Brian Diers
    Dep. of Crop Sciences Univ. of Illinois 268 National Soybean Research Center, 1101 West Peabody Drive Urban IL 61801
  • Perry Cregan
    Soybean Genomics and Improvement Lab., USDA–ARS 10300 Baltimore Ave, Building 006 Beltsville MD 20705

Description

<jats:sec><jats:label /><jats:p>A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [<jats:italic>Glycine max</jats:italic> (L.) Merr.] genotypes to the common cultivar. The 41 parents were deeply sequenced for SNP discovery. Based on the polymorphism of the single‐nucleotide polymorphisms (SNPs) and other selection criteria, a set of SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 RILs from the 40 families. Analysis of the SNP profiles of the RILs showed a low average recombination rate. We constructed genetic linkage maps for each family and a composite linkage map based on recombinant inbred lines (RILs) across the families and identified and annotated 525,772 high confidence SNPs that were used to impute the SNP alleles in the RILs. The segregation distortion in most families significantly favored the alleles from the female parent, and there was no significant difference of residual heterozygosity in the euchromatic vs. heterochromatic regions. The genotypic datasets for the RILs and parents are publicly available and are anticipated to be useful to map quantitative trait loci (QTL) controlling important traits in soybean.</jats:p></jats:sec>

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