SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

Publication 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 Article
Journal NameG3 (Bethesda, Md.)
Volume5
Issue11
Year2015
Page(s)2285-90
CitationSong Q, Jia G, Hyten DL, Jenkins J, Hwang EY, Schroeder SG, Osorno JM, Schmutz J, Jackson SA, McClean PE, Cregan PB. SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean. G3 (Bethesda, Md.). 2015 Aug 28; 5(11):2285-90.

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.

Stocks
This publication contains information about 3 stocks:
Stock NameUniquenameType
StampedeStampedeaccession
Red HawkRed Hawkaccession
Stampede/RedHawk-F2Stampede/RedHawk-F2population
Features
This publication contains information about 12,360 features:
Feature NameUniquenameType
BARC-PV_1.0_Chr07_32194300_C_TBARC-PV_1.0_Chr07_32194300_C_Tgenetic_marker
BARC-PV_1.0_Chr07_32219222_T_CBARC-PV_1.0_Chr07_32219222_T_Cgenetic_marker
BARC-PV_1.0_Chr07_32223875_G_ABARC-PV_1.0_Chr07_32223875_G_Agenetic_marker
BARC-PV_1.0_Chr07_32312429_C_TBARC-PV_1.0_Chr07_32312429_C_Tgenetic_marker
BARC-PV_1.0_Chr07_32326140_C_TBARC-PV_1.0_Chr07_32326140_C_Tgenetic_marker
BARC-PV_1.0_Chr07_32347603_G_ABARC-PV_1.0_Chr07_32347603_G_Agenetic_marker
BARC-PV_1.0_Chr07_32353906_A_GBARC-PV_1.0_Chr07_32353906_A_Ggenetic_marker
BARC-PV_1.0_Chr07_32404969_C_TBARC-PV_1.0_Chr07_32404969_C_Tgenetic_marker
BARC-PV_1.0_Chr07_32411740_G_ABARC-PV_1.0_Chr07_32411740_G_Agenetic_marker
BARC-PV_1.0_Chr07_32443930_A_GBARC-PV_1.0_Chr07_32443930_A_Ggenetic_marker
BARC-PV_1.0_Chr07_32493624_G_ABARC-PV_1.0_Chr07_32493624_G_Agenetic_marker
BARC-PV_1.0_Chr07_32502502_A_GBARC-PV_1.0_Chr07_32502502_A_Ggenetic_marker
BARC-PV_1.0_Chr07_32571960_G_TBARC-PV_1.0_Chr07_32571960_G_Tgenetic_marker
BARC-PV_1.0_Chr07_32587214_G_ABARC-PV_1.0_Chr07_32587214_G_Agenetic_marker
BARC-PV_1.0_Chr07_32595931_A_GBARC-PV_1.0_Chr07_32595931_A_Ggenetic_marker
BARC-PV_1.0_Chr07_32605550_G_TBARC-PV_1.0_Chr07_32605550_G_Tgenetic_marker
BARC-PV_1.0_Chr07_32668769_C_TBARC-PV_1.0_Chr07_32668769_C_Tgenetic_marker
BARC-PV_1.0_Chr07_32675523_C_TBARC-PV_1.0_Chr07_32675523_C_Tgenetic_marker
BARC-PV_1.0_Chr07_32719716_C_TBARC-PV_1.0_Chr07_32719716_C_Tgenetic_marker
BARC-PV_1.0_Chr07_32732628_A_GBARC-PV_1.0_Chr07_32732628_A_Ggenetic_marker
BARC-PV_1.0_Chr07_32751695_C_ABARC-PV_1.0_Chr07_32751695_C_Agenetic_marker
BARC-PV_1.0_Chr07_32788732_C_TBARC-PV_1.0_Chr07_32788732_C_Tgenetic_marker
BARC-PV_1.0_Chr07_32820278_T_CBARC-PV_1.0_Chr07_32820278_T_Cgenetic_marker
BARC-PV_1.0_Chr07_32866878_T_CBARC-PV_1.0_Chr07_32866878_T_Cgenetic_marker
BARC-PV_1.0_Chr07_32961172_A_GBARC-PV_1.0_Chr07_32961172_A_Ggenetic_marker

Pages

Libraries
This publication contains information about 3 libraries:
Library NameUnique NameOrganism
BARCBean6K_1BARCBean6K_1N/A N/A
BARCBean6K_2BARCBean6K_2N/A N/A
BARCBean6K_3BARCBean6K_3N/A N/A
Featuremaps
This publication contains information about 1 maps:
Map Name
Bean-Stampede/RedHawk-F2
Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic
ISSN2160-1836
eISSN2160-1836
Publication Date2015 Aug 28
Journal AbbreviationG3 (Bethesda)
DOI10.1534/g3.115.020594
Elocation10.1534/g3.115.020594
CopyrightCopyright © 2015 Song et al.
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryUnited States
Publication TypeResearch Support, U.S. Gov't, Non-P.H.S.