(2010) identified 7,108 SNPs between soybean and wild soybean ( Glycine soja Sieb. In soybean, SNP discovery on a large scale identified 5551 SNPs in five genotypes based on gene derived EST assembly ( Choi et al. This is due to their vast numbers identified with the most recent generation of sequencers. High-throughput genotyping platforms for SNPs can now overcome their biallelic nature and lower allele variability compared with SSR markers. However, the complexity of the evolutionary process requires estimates of genetic relationships without knowledge of the mutational properties of markers ( Ellegren 2004) while SNP markers based on nucleotide change would allow for more exact germplasm characterization. Simple sequence repeat (SSR) markers have been a conventional tool in soybean genetics because of their high allelic diversity. Technological advances in detecting and genotyping of single nucleotide polymorphisms (SNPs) by next generation sequencing and the high throughput genotyping systems has led to a decrease in genotyping cost and time. The recent sequencing of the soybean genome enables molecular tools to be developed for gene discovery, breeding and germplasm characterization. The knowledge and technologies of the newly available genome information are expected to broaden understanding the relationships between genes and agronomically important traits as well as assist in the better use of gene resources for soybean germplasm for breeding. The complex features in the soybean genome have been reviewed by Cannon and Shoemaker (2012) by comparing genomes across the related pulses. Soybean is known as palaeopolyploid species that have undergone whole genome duplication and simultaneous many rearrangements among chromosomes. A large proportion of the soybean genome, 975 Mb out of 1.1 Gb of the estimated size, is available as a chromosome-scale assembly of 20 soybean chromosomes from the phytozome web site ( Schmutz et al. Soybean is now regarded as a model legume crop owing to the availability of genome sequence information ( Schmutz et al. Soybean seeds contain a high percentage of protein and oil. Soybean has been used as a major source of nutritious feed for humans and livestock and is an important part of traditional foods in many Asian countries. Soybean, Glycine max (L.) Merr., is the most important legume globally and the fourth crop next to rice, wheat and maize in terms of global crop production. These selected sets of germplasm will provide an effective platform for enhancing soybean diversity studies and assist in finding novel traits for crop improvement. Based on the assessment of the SNP markers and several agro-morphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach a minimum of 12 accessions can represent the observed gene diversity a mini-core collection of 96 accession can represent a major proportion of both geographic origin and agro-morphologic trait variation. Nine hundred ninety eight Japanese accessions were separated to a certain extent into groups corresponding to their agro-morphologic characteristics such as photosensitivity and seed characteristics rather than their geographical origin. Although gene diversity of Japanese soybean germplasm was slight lower than that of exotic soybean germplasm, population differentiation and clustering analyses indicated clear genetic differentiation among Japanese cultivated soybeans, exotic cultivated soybeans and wild soybeans. Genetic variation and population structure among 1603 soybean accessions, consisted of 832 Japanese landraces, 109 old and 57 recent Japanese varieties, 341 landrace from 16 Asian countries and 264 wild soybean accessions, were characterized using 191 SNP markers.
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