Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry.

Publication Overview
TitleDevelopment and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry
AuthorsPeace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A
TypeJournal Article
Journal NamePloS one
Volume7
Issue12
Year2012
Page(s)e48305
CitationPeace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PloS one. 2012; 7(12):e48305.

Abstract

High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.

Features
This publication contains information about 582 features:
Feature NameUniquenameType
RosBREED_snp_sweet_cherry_Pp2_00217565RosBREED_snp_sweet_cherry_Pp2_00217565genetic_marker
RosBREED_snp_sweet_cherry_Pp2_00500420RosBREED_snp_sweet_cherry_Pp2_00500420genetic_marker
RosBREED_snp_sweet_cherry_Pp2_01221960RosBREED_snp_sweet_cherry_Pp2_01221960genetic_marker
RosBREED_snp_sweet_cherry_Pp2_01531563RosBREED_snp_sweet_cherry_Pp2_01531563genetic_marker
RosBREED_snp_sweet_cherry_Pp2_01653466RosBREED_snp_sweet_cherry_Pp2_01653466genetic_marker
RosBREED_snp_sweet_cherry_Pp2_01951353RosBREED_snp_sweet_cherry_Pp2_01951353genetic_marker
RosBREED_snp_sweet_cherry_Pp2_02164751RosBREED_snp_sweet_cherry_Pp2_02164751genetic_marker
RosBREED_snp_sweet_cherry_Pp2_02373744RosBREED_snp_sweet_cherry_Pp2_02373744genetic_marker
RosBREED_snp_sweet_cherry_Pp2_02840304RosBREED_snp_sweet_cherry_Pp2_02840304genetic_marker
RosBREED_snp_sweet_cherry_Pp2_03229768RosBREED_snp_sweet_cherry_Pp2_03229768genetic_marker
RosBREED_snp_sweet_cherry_Pp2_03396708RosBREED_snp_sweet_cherry_Pp2_03396708genetic_marker
RosBREED_snp_sweet_cherry_Pp2_04354053RosBREED_snp_sweet_cherry_Pp2_04354053genetic_marker
RosBREED_snp_sweet_cherry_Pp2_04953599RosBREED_snp_sweet_cherry_Pp2_04953599genetic_marker
RosBREED_snp_sweet_cherry_Pp2_05493845RosBREED_snp_sweet_cherry_Pp2_05493845genetic_marker
RosBREED_snp_sweet_cherry_Pp2_07280500RosBREED_snp_sweet_cherry_Pp2_07280500genetic_marker
RosBREED_snp_sweet_cherry_Pp2_09649536RosBREED_snp_sweet_cherry_Pp2_09649536genetic_marker
RosBREED_snp_sweet_cherry_Pp2_10930583RosBREED_snp_sweet_cherry_Pp2_10930583genetic_marker
RosBREED_snp_sweet_cherry_Pp2_11540955RosBREED_snp_sweet_cherry_Pp2_11540955genetic_marker
RosBREED_snp_sweet_cherry_Pp2_12407490RosBREED_snp_sweet_cherry_Pp2_12407490genetic_marker
RosBREED_snp_sweet_cherry_Pp2_12857631RosBREED_snp_sweet_cherry_Pp2_12857631genetic_marker
RosBREED_snp_sweet_cherry_Pp2_13301587RosBREED_snp_sweet_cherry_Pp2_13301587genetic_marker
RosBREED_snp_sweet_cherry_Pp2_15040326RosBREED_snp_sweet_cherry_Pp2_15040326genetic_marker
RosBREED_snp_sweet_cherry_Pp2_15084429RosBREED_snp_sweet_cherry_Pp2_15084429genetic_marker
RosBREED_snp_sweet_cherry_Pp2_15355971RosBREED_snp_sweet_cherry_Pp2_15355971genetic_marker
RosBREED_snp_sweet_cherry_Pp2_15624043RosBREED_snp_sweet_cherry_Pp2_15624043genetic_marker

Pages

Featuremaps
This publication contains information about 2 maps:
Map Name
Prunus-TE-6K cherry SNP-estimate
sweet cherry-consensus-map-2012-6K cherry SNP-estimate