title: Development, validation and genetic analysis of a large soybean SNP genotyping array.
abstract: Cultivated soybean (Glycine max) suffers from a narrow germplasm relative to other crop species, probably because of under-use of wild soybean (Glycine soja) as a breeding resource. Use of a single nucleotide polymorphism (SNP) genotyping array is a promising method for dissecting cultivated and wild germplasms to identify important adaptive genes through high-density genetic mapping and genome-wide association studies. Here we describe a large soybean SNP array for use in diversity analyses, linkage mapping and genome-wide association analyses. More than four million high-quality SNPs identified from high-depth genome re-sequencing of 16 soybean accessions and low-depth genome re-sequencing of 31 soybean accessions were used to select 180,961 SNPs for creation of the Axiom(®) SoyaSNP array. Validation analysis for a set of 222 diverse soybean lines showed that 170,223 markers were of good quality for genotyping. Phylogenetic and allele frequency analyses of the validation set data indicated that accessions showing an intermediate morphology between cultivated and wild soybeans collected in Korea were natural hybrids. More than 90 unanchored scaffolds in the current soybean reference sequence were assigned to chromosomes using this array. Finally, dense average spacing and preferential distribution of the SNPs in gene-rich chromosomal regions suggest that this array may be suitable for genome-wide association studies of soybean germplasm. Taken together, these results suggest that use of this array may be a powerful method for soybean genetic analyses relating to many aspects of soybean breeding.
authors: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea; Department of Bioinformatics, University of Science and Technology, Daejeon, 305-806, Korea.
authors: Yun-Gyeong
authors: YG
authors: Lee
authors: Namhee
authors: N
authors: Jeong
authors: Ji Hong
authors: JH
authors: Kim
authors: Kwanghee
authors: K
authors: Lee
authors: Kil Hyun
authors: KH
authors: Kim
authors: Ali
authors: A
authors: Pirani
authors: Bo-Keun
authors: BK
authors: Ha
authors: Sung-Taeg
authors: ST
authors: Kang
authors: Beom-Seok
authors: BS
authors: Park
authors: Jung-Kyung
authors: JK
authors: Moon
authors: Namshin
authors: N
authors: Kim
authors: Soon-Chun
authors: SC
authors: Jeong
mesh_terms: D055106:Genome-Wide Association Study; D060005:Genotyping Techniques; D006824:Hybridization, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D013025:Glycine max / Q000235:genetics*
keywords: Glycine max; SNP array; genome-wide association study; genotyping; hybrid; unanchored scaffold; validation