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_Pp5_04755463RosBREED_snp_sweet_cherry_Pp5_04755463genetic_marker
RosBREED_snp_sweet_cherry_Pp5_07711329RosBREED_snp_sweet_cherry_Pp5_07711329genetic_marker
RosBREED_snp_sweet_cherry_Pp5_08194627RosBREED_snp_sweet_cherry_Pp5_08194627genetic_marker
RosBREED_snp_sweet_cherry_Pp5_08344028RosBREED_snp_sweet_cherry_Pp5_08344028genetic_marker
RosBREED_snp_sweet_cherry_Pp5_08714232RosBREED_snp_sweet_cherry_Pp5_08714232genetic_marker
RosBREED_snp_sweet_cherry_Pp5_10237059RosBREED_snp_sweet_cherry_Pp5_10237059genetic_marker
RosBREED_snp_sweet_cherry_Pp5_10500237RosBREED_snp_sweet_cherry_Pp5_10500237genetic_marker
RosBREED_snp_sweet_cherry_Pp5_10734088RosBREED_snp_sweet_cherry_Pp5_10734088genetic_marker
RosBREED_snp_sweet_cherry_Pp5_12036633RosBREED_snp_sweet_cherry_Pp5_12036633genetic_marker
RosBREED_snp_sweet_cherry_Pp5_12348189RosBREED_snp_sweet_cherry_Pp5_12348189genetic_marker
RosBREED_snp_sweet_cherry_Pp5_12646495RosBREED_snp_sweet_cherry_Pp5_12646495genetic_marker
RosBREED_snp_sweet_cherry_Pp5_12750950RosBREED_snp_sweet_cherry_Pp5_12750950genetic_marker
RosBREED_snp_sweet_cherry_Pp5_12868715RosBREED_snp_sweet_cherry_Pp5_12868715genetic_marker
RosBREED_snp_sweet_cherry_Pp5_13064758RosBREED_snp_sweet_cherry_Pp5_13064758genetic_marker
RosBREED_snp_sweet_cherry_Pp5_13473331RosBREED_snp_sweet_cherry_Pp5_13473331genetic_marker
RosBREED_snp_sweet_cherry_Pp5_13715106RosBREED_snp_sweet_cherry_Pp5_13715106genetic_marker
RosBREED_snp_sweet_cherry_Pp5_15559243RosBREED_snp_sweet_cherry_Pp5_15559243genetic_marker
RosBREED_snp_sweet_cherry_Pp5_15817487RosBREED_snp_sweet_cherry_Pp5_15817487genetic_marker
RosBREED_snp_sweet_cherry_Pp5_16228253RosBREED_snp_sweet_cherry_Pp5_16228253genetic_marker
RosBREED_snp_sweet_cherry_Pp5_16375840RosBREED_snp_sweet_cherry_Pp5_16375840genetic_marker
RosBREED_snp_sweet_cherry_Pp5_16416089RosBREED_snp_sweet_cherry_Pp5_16416089genetic_marker
RosBREED_snp_sweet_cherry_Pp5_16642695RosBREED_snp_sweet_cherry_Pp5_16642695genetic_marker
RosBREED_snp_sweet_cherry_Pp5_16741368RosBREED_snp_sweet_cherry_Pp5_16741368genetic_marker
RosBREED_snp_sweet_cherry_Pp5_16857681RosBREED_snp_sweet_cherry_Pp5_16857681genetic_marker
RosBREED_snp_sweet_cherry_Pp5_17158315RosBREED_snp_sweet_cherry_Pp5_17158315genetic_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