@article{b62e493f761a4b9194c5bf26b3980ffc,
title = "Genetic characterization of the soybean nested association mapping population",
abstract = "A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [Glycine max (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.",
author = "Song, \{Qi Jian\} and Long Yan and Charles Quigley and Jordan, \{Brandon D.\} and Edward Fickus and Steve Schroeder and Song, \{Bao Hua\} and An, \{Yong Qiang Charles\} and David Hyten and Randall Nelson and Katy Rainey and Beavis, \{William D.\} and Jim Specht and Brian Diers and Perry Cregan",
note = "We thank Rob Parry and Chris Pooley at USDA–ARS, Beltsville, MD, for their technical support in assembling the necessary hardware and software required for the data analysis; David Grant at USDA–ARS, Ames, IA, for making the dataset available at the Soybase. This research was supported with funding from the United Soybean Board Project 2241. The support of the United Soybean Board is greatly appreciated. B.D. and J.S. built consensus among public soybean breeders to conduct a coordinated NAM project. B.D., W.D.B., K.R. and J.S. designed the SoyNAM to minimize the confounding impact of maturity on yield and other agronomic traits in the primary soybean growing region of North America. R.N. selected and provided lines for parents, J.S., and B.D. created NAM populations and provided RILs, Q.S., D.H., J.S., B.D. and P.C. provided planning and coordination for genotyping, C.Q. and E.F. prepared DNA sequence libraries and performed molecular genotyping, Q.S. and S.S. performed DNA sequence analysis, Q. S. and Y.A. performed annotation analysis, Q.S., L.Y., B.D.J., B.S., W.D.B., K.R., J.S., B.D. and P.C. performed data analyses. Q.S. and P.C. designed the BeadChip and prepared the manuscript.",
year = "2017",
doi = "10.3835/plantgenome2016.10.0109",
language = "English (US)",
volume = "10",
journal = "Plant Genome",
issn = "1940-3372",
publisher = "John Wiley \& Sons, Ltd.",
number = "2",
}