title: SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean.
abstract: 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.
authors: USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705 Qijian.Song@ars.usda.gov.
authors: Qijian
authors: Q
authors: Song
authors: USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705.
authors: Gaofeng
authors: G
authors: Jia
authors: USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705.
authors: David L
authors: DL
authors: Hyten
authors: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806.
authors: Jerry
authors: J
authors: Jenkins
authors: Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742.
authors: Eun-Young
authors: EY
authors: Hwang
authors: USDA-ARS, Bovine Functional Genomics Laboratory, Animal and Natural Resources Institute, Beltsville, Maryland 20705.
authors: Steven G
authors: SG
authors: Schroeder
authors: Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102.
authors: Juan M
authors: JM
authors: Osorno
authors: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598.
authors: Jeremy
authors: J
authors: Schmutz
authors: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602.
authors: Scott A
authors: SA
authors: Jackson
authors: Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102.
authors: Phillip E
authors: PE
authors: McClean
authors: USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705.
authors: Perry B
authors: PB
authors: Cregan
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D008040:Genetic Linkage; D018745:Genome, Plant; D020641:Polymorphism, Single Nucleotide; D013025:Glycine max / Q000235:genetics*
keywords: BARCBean6K BeadChip; Phaseolus vulgaris; SNP; linkage map; molecular markers