title: Fingerprinting Soybean Germplasm and Its Utility in Genomic Research.
abstract: The United States Department of Agriculture, Soybean Germplasm Collection includes 18,480 domesticated soybean and 1168 wild soybean accessions introduced from 84 countries or developed in the United States. This collection was genotyped with the SoySNP50K BeadChip containing greater than 50K single-nucleotide polymorphisms. Redundant accessions were identified in the collection, and distinct genetic backgrounds of soybean from different geographic origins were observed that could be a unique resource for soybean genetic improvement. We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the wild, landrace, and North American cultivar populations and identified candidate regions associated with domestication and selection imposed by North American breeding. We constructed the first soybean haplotype block maps in the wild, landrace, and North American cultivar populations and observed that most recombination events occurred in the regions between haplotype blocks. These haplotype maps are crucial for association mapping aimed at the identification of genes controlling traits of economic importance. A case-control association test delimited potential genomic regions along seven chromosomes that most likely contain genes controlling seed weight in domesticated soybean. The resulting dataset will facilitate germplasm utilization, identification of genes controlling important traits, and will accelerate the creation of soybean varieties with improved seed yield and quality.
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland 20705-2350 Qijian.Song@ars.usda.gov.
authors.forename: Qijian
authors.initials: Q
authors.lastname: Song
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland 20705-2350 Pioneer Hi-Bred International Inc, Johnston Iowa 50131-0184.
authors.forename: David L
authors.initials: DL
authors.lastname: Hyten
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland 20705-2350.
authors.forename: Gaofeng
authors.initials: G
authors.lastname: Jia
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland 20705-2350.
authors.forename: Charles V
authors.initials: CV
authors.lastname: Quigley
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland 20705-2350.
authors.forename: Edward W
authors.initials: EW
authors.lastname: Fickus
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Soybean/Maize Germplasm, Pathology and Genetics Research Unit and Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801-0000.
authors.forename: Randall L
authors.initials: RL
authors.lastname: Nelson
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland 20705-2350.
authors.forename: Perry B
authors.initials: PB
authors.lastname: Cregan
mesh_terms: D001947:Breeding; D016172:DNA Fingerprinting / Q000379:methods; D036281:Genetic Research; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D005838:Genotype; D006239:Haplotypes; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D012639:Seeds; D013025:Glycine max / Q000235:genetics*
keywords: SoySNP50K; genetic diversity; genotyping; germplasm; haplotype block map; soybean