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_Pp8_17467401RosBREED_snp_sweet_cherry_Pp8_17467401genetic_marker
RosBREED_snp_sweet_cherry_Pp8_17492237RosBREED_snp_sweet_cherry_Pp8_17492237genetic_marker
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RosCOS0502-212_snp_sweet_cherry_Pp1_35635315RosCOS0502-212_snp_sweet_cherry_Pp1_35635315genetic_marker
RosCOS0519-218_snp_sweet_cherry_Pp4_13606903RosCOS0519-218_snp_sweet_cherry_Pp4_13606903genetic_marker
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RosCOS0546-209_snp_sweet_cherry_Pp4_06464070RosCOS0546-209_snp_sweet_cherry_Pp4_06464070genetic_marker
RosCOS0547-123_snp_sweet_cherry_Pp1_19104586RosCOS0547-123_snp_sweet_cherry_Pp1_19104586genetic_marker
RosCOS0548-123_snp_sweet_cherry_Pp6_25325607RosCOS0548-123_snp_sweet_cherry_Pp6_25325607genetic_marker
RosCOS0921-061_snp_sweet_cherry_Pp7_20819981RosCOS0921-061_snp_sweet_cherry_Pp7_20819981genetic_marker
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RosCOS1124-244_snp_sweet_cherry_Pp6_22953307RosCOS1124-244_snp_sweet_cherry_Pp6_22953307genetic_marker
RosCOS1148-321_snp_sweet_cherry_Pp7_16283834RosCOS1148-321_snp_sweet_cherry_Pp7_16283834genetic_marker
RosCOS1154-267_snp_sweet_cherry_Pp8_12227080RosCOS1154-267_snp_sweet_cherry_Pp8_12227080genetic_marker
RosCOS1169-212_snp_sweet_cherry_Pp1_37078592RosCOS1169-212_snp_sweet_cherry_Pp1_37078592genetic_marker
RosCOS1201-071_snp_sweet_cherry_Pp1_00450381RosCOS1201-071_snp_sweet_cherry_Pp1_00450381genetic_marker
RosCOS1252-088_snp_sweet_cherry_Pp4_18584595RosCOS1252-088_snp_sweet_cherry_Pp4_18584595genetic_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
Cross References
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DatabaseAccession
PMID: PubMedPMID:23284615