|Hyten, David - Dupont Pioneer Hi-Bred|
|Jia, Gaofeng - Nanjing Forestry University|
|Quigley, Charles - Chuck|
|Cregan, Perry - Retired ARS Employee|
Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/22/2015
Publication Date: 7/29/2015
Publication URL: http://doi:10.1534/g3.115.019000
Citation: Song, Q., Hyten, D.L., Jia, G., Quigley, C.V., Fickus, E.W., Nelson, R.L., Cregan, P. 2015. Fingerprinting soybean germplasm and its utility in genomic research. G3, Genes/Genomes/Genetics. 5(9):1-17.
Interpretive Summary: More than 50,000 SNP DNA markers were used in the genetic analysis of the U.S. Department of Agriculture, Soybean Germplasm Collection including 18,480 domesticated and 1,168 wild soybeans. This represents the largest such genetic analysis to date in a plant species. The resulting dataset was used for a number of analyses including the similarity of the accessions in the collection and to compare diversity among wild, landrace and North America soybean cultivars. We identified genomic regions associated with domestication and subsequent breeding selection, and present a detailed analysis of the haplotype block structure of the chromosomes of the wild, landrace and N. Am. cultivars. These analyses provide a greatly improved understanding of the soybean genome and will be an important source of genetic information for further genetic improvement of soybean and development of new cultivars.
Technical Abstract: The annual accessions in the United States Department of Agriculture, Soybean Germplasm Collection including 18,480 domesticated and 1,168 wild soybeans introduced from 84 countries or developed in the U.S. were genotyped with the SoySNP50K BeadChip containing >50K single nucleotide polymorphism (SNP) DNA markers. We characterized the genetic diversity and genetic relationships of the accessions with their geographic origins. We observed that genetic diversity in the landrace and North American (N. Am.) cultivar populations was dramatically reduced by domestication and selection based on linkage disequilibrium and haplotype block size analyses. We constructed the first soybean haplotype map in the wild, landrace and N. Am. cultivar accessions, identified candidate regions associated with domestication and with selection imposed by N. Am. soybean breeding. We also confirmed that most recombination events occurred in the regions between haplotype blocks. Via genome-wide association analysis, we delimited potential genomic regions along seven chromosomes that most likely contain genes controlling seed weight. 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.