BeanCAP snap bean diversity panel SNP data

Abstract

Genotype data consisting of 10,546 single nucleotide polymorphisms on the Illumina Infinium Genechip BARCBEAN6K_3 platform for 149 snap bean accessions.The accessions used to create the Snap Bean Diversity Panel were 149 snap bean accessions selected from North American and European germplasm. This panel was developed with support from the Common Bean Coordinated Agriculture Project (USDA-NIFA grant no. 2009-85606-05964). A modified CTAB procedure was used to extract genomic DNA and the resulting DNA samples were analyzed on an Illumina Infinium Genechip BARCBEAN6K_3 platform. The single nucleotide polymorphism (SNP) array utilized was composed of 10,546 allele-specific probes. The raw data was initially processed on GenomeStudio (v2.0.4) software (Illumina, San Diego, CA, USA). Two marker SNP positions contained greater than 20% missing data and were removed from the study. All missing data for the remaining SNPs was imputed using fastPHASE software (v1.4), including heterozygous SNPs which were treated as missing data. SNPs not assigned to a genomic position in Phytozome12 (Phaseolus vulgaris, version 2.1) were removed from the study resulting in 10,073 remaining SNPs