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_Pp6_20786682RosBREED_snp_sweet_cherry_Pp6_20786682genetic_marker
RosBREED_snp_sweet_cherry_Pp6_20982940RosBREED_snp_sweet_cherry_Pp6_20982940genetic_marker
RosBREED_snp_sweet_cherry_Pp6_22296379RosBREED_snp_sweet_cherry_Pp6_22296379genetic_marker
RosBREED_snp_sweet_cherry_Pp6_22578566RosBREED_snp_sweet_cherry_Pp6_22578566genetic_marker
RosBREED_snp_sweet_cherry_Pp6_22872838RosBREED_snp_sweet_cherry_Pp6_22872838genetic_marker
RosBREED_snp_sweet_cherry_Pp6_24430983RosBREED_snp_sweet_cherry_Pp6_24430983genetic_marker
RosBREED_snp_sweet_cherry_Pp6_24478883RosBREED_snp_sweet_cherry_Pp6_24478883genetic_marker
RosBREED_snp_sweet_cherry_Pp6_24914294RosBREED_snp_sweet_cherry_Pp6_24914294genetic_marker
RosBREED_snp_sweet_cherry_Pp6_25146440RosBREED_snp_sweet_cherry_Pp6_25146440genetic_marker
RosBREED_snp_sweet_cherry_Pp6_25429330RosBREED_snp_sweet_cherry_Pp6_25429330genetic_marker
RosBREED_snp_sweet_cherry_Pp6_25631852RosBREED_snp_sweet_cherry_Pp6_25631852genetic_marker
RosBREED_snp_sweet_cherry_Pp6_26417399RosBREED_snp_sweet_cherry_Pp6_26417399genetic_marker
RosBREED_snp_sweet_cherry_Pp6_28257046RosBREED_snp_sweet_cherry_Pp6_28257046genetic_marker
RosBREED_snp_sweet_cherry_Pp7_00926005RosBREED_snp_sweet_cherry_Pp7_00926005genetic_marker
RosBREED_snp_sweet_cherry_Pp7_01275199RosBREED_snp_sweet_cherry_Pp7_01275199genetic_marker
RosBREED_snp_sweet_cherry_Pp7_01392399RosBREED_snp_sweet_cherry_Pp7_01392399genetic_marker
RosBREED_snp_sweet_cherry_Pp7_01835696RosBREED_snp_sweet_cherry_Pp7_01835696genetic_marker
RosBREED_snp_sweet_cherry_Pp7_02481336RosBREED_snp_sweet_cherry_Pp7_02481336genetic_marker
RosBREED_snp_sweet_cherry_Pp7_02530796RosBREED_snp_sweet_cherry_Pp7_02530796genetic_marker
RosBREED_snp_sweet_cherry_Pp7_04261930RosBREED_snp_sweet_cherry_Pp7_04261930genetic_marker
RosBREED_snp_sweet_cherry_Pp7_05532720RosBREED_snp_sweet_cherry_Pp7_05532720genetic_marker
RosBREED_snp_sweet_cherry_Pp7_05729126RosBREED_snp_sweet_cherry_Pp7_05729126genetic_marker
RosBREED_snp_sweet_cherry_Pp7_07762587RosBREED_snp_sweet_cherry_Pp7_07762587genetic_marker
RosBREED_snp_sweet_cherry_Pp7_07884834RosBREED_snp_sweet_cherry_Pp7_07884834genetic_marker
RosBREED_snp_sweet_cherry_Pp7_09026518RosBREED_snp_sweet_cherry_Pp7_09026518genetic_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