--- identifier: G19833.gnm1.mrk.BARCBean6K synopsis: "A core set of 6000 SNPs based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips." scientific_name: Phaseolus vulgaris taxid: 3885 scientific_name_abbrev: phavu genotype: - G19833 description: "A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad." publication_doi: 10.1534/g3.115.020594 publication_title: "SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean" contributors: "Qijian Song, Gaofeng Jia, David L Hyten, Jerry Jenkins, Eun-Young Hwang, Steven G Schroeder, Juan M Osorno, Jeremy Schmutz, Scott A Jackson, Phillip E McClean, Perry B Cregan" citation: "Qijian Song, Gaofeng Jia, David L Hyten, Jerry Jenkins, Eun-Young Hwang, Steven G Schroeder, Juan M Osorno, Jeremy Schmutz, Scott A Jackson, Phillip E McClean, Perry B Cregan, SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean, G3 Genes|Genomes|Genetics, Volume 5, Issue 11, 1 November 2015, Pages 2285–2290" data_curators: Steven Cannon public_access_level: public license: Open genotyping_platform: BARCBean6K