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
Pa1Cl_snp_sweet_cherry_Pp4_09145953Pa1Cl_snp_sweet_cherry_Pp4_09145953genetic_marker
Pa2Cl_snp_sweet_cherry_Pp4_12750612Pa2Cl_snp_sweet_cherry_Pp4_12750612genetic_marker
RosBREED_snp_sweet_cherry_Pp1_00348730RosBREED_snp_sweet_cherry_Pp1_00348730genetic_marker
RosBREED_snp_sweet_cherry_Pp1_00885553RosBREED_snp_sweet_cherry_Pp1_00885553genetic_marker
RosBREED_snp_sweet_cherry_Pp1_01176314RosBREED_snp_sweet_cherry_Pp1_01176314genetic_marker
RosBREED_snp_sweet_cherry_Pp1_01331155RosBREED_snp_sweet_cherry_Pp1_01331155genetic_marker
RosBREED_snp_sweet_cherry_Pp1_01450317RosBREED_snp_sweet_cherry_Pp1_01450317genetic_marker
RosBREED_snp_sweet_cherry_Pp1_01737374RosBREED_snp_sweet_cherry_Pp1_01737374genetic_marker
RosBREED_snp_sweet_cherry_Pp1_02115377RosBREED_snp_sweet_cherry_Pp1_02115377genetic_marker
RosBREED_snp_sweet_cherry_Pp1_02241751RosBREED_snp_sweet_cherry_Pp1_02241751genetic_marker
RosBREED_snp_sweet_cherry_Pp1_02441717RosBREED_snp_sweet_cherry_Pp1_02441717genetic_marker
RosBREED_snp_sweet_cherry_Pp1_02967004RosBREED_snp_sweet_cherry_Pp1_02967004genetic_marker
RosBREED_snp_sweet_cherry_Pp1_03438841RosBREED_snp_sweet_cherry_Pp1_03438841genetic_marker
RosBREED_snp_sweet_cherry_Pp1_04905651RosBREED_snp_sweet_cherry_Pp1_04905651genetic_marker
RosBREED_snp_sweet_cherry_Pp1_05878432RosBREED_snp_sweet_cherry_Pp1_05878432genetic_marker
RosBREED_snp_sweet_cherry_Pp1_05894052RosBREED_snp_sweet_cherry_Pp1_05894052genetic_marker
RosBREED_snp_sweet_cherry_Pp1_05962255RosBREED_snp_sweet_cherry_Pp1_05962255genetic_marker
RosBREED_snp_sweet_cherry_Pp1_07130958RosBREED_snp_sweet_cherry_Pp1_07130958genetic_marker
RosBREED_snp_sweet_cherry_Pp1_07328678RosBREED_snp_sweet_cherry_Pp1_07328678genetic_marker
RosBREED_snp_sweet_cherry_Pp1_07374161RosBREED_snp_sweet_cherry_Pp1_07374161genetic_marker
RosBREED_snp_sweet_cherry_Pp1_07824263RosBREED_snp_sweet_cherry_Pp1_07824263genetic_marker
RosBREED_snp_sweet_cherry_Pp1_08106269RosBREED_snp_sweet_cherry_Pp1_08106269genetic_marker
RosBREED_snp_sweet_cherry_Pp1_08240209RosBREED_snp_sweet_cherry_Pp1_08240209genetic_marker
RosBREED_snp_sweet_cherry_Pp1_08833408RosBREED_snp_sweet_cherry_Pp1_08833408genetic_marker
RosBREED_snp_sweet_cherry_Pp1_09597368RosBREED_snp_sweet_cherry_Pp1_09597368genetic_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