Overview
TitleSNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean
AuthorsSong Q, Jia G, Hyten DL, Jenkins J, Hwang EY, Schroeder SG, Osorno JM, Schmutz J, Jackson SA, McClean PE, Cregan PB
TypeJournal
Media TitleG3: Genes, Genomes, Genetics
Volume5
Issue11
Year2015
Page(s)2285-2290
CitationSong Q, Jia G, Hyten DL, Jenkins J, Hwang EY, Schroeder SG, Osorno JM, Schmutz J, Jackson SA, McClean PE, Cregan PB. (2015). SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean. G3: Genes, Genomes, Genetics. 5:11 2285-2290

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 14x 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 x 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.
Maps
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Pages

Properties
Additional details for this publication include:
Property NameValue
Publication Speciesphavu
URLhttp://www.g3journal.org/content/5/11/2285.abstract
KeywordsPhaseolus vulgaris, SNP, Molecular markers, BARCBean6K BeadChip, Linkage map
Cross References
This publication is also available in the following databases:
DatabaseAccession
DOI: Document Object IdentifierDOI:10.1534/g3.115.020594
PMID: PubMedPMID:26318155
Stocks
This publication contains information about 1 stocks:
Stock NameUniquenaemType
Stampede_x_RedHawk_F2_aStampede_x_RedHawk_F2_aMapping Population