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:
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RosCOS1919-113_snp_sweet_cherry_Pp8_01569566RosCOS1919-113_snp_sweet_cherry_Pp8_01569566genetic_marker
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RosCOS2354-264_snp_sweet_cherry_Pp1_30895488RosCOS2354-264_snp_sweet_cherry_Pp1_30895488genetic_marker
RosCOS2370-108_snp_sweet_cherry_Pp2_26346122RosCOS2370-108_snp_sweet_cherry_Pp2_26346122genetic_marker
RosCOS2378-113_snp_sweet_cherry_Pp5_16803595RosCOS2378-113_snp_sweet_cherry_Pp5_16803595genetic_marker
RosCOS2386-454_snp_sweet_cherry_Pp3_03792552RosCOS2386-454_snp_sweet_cherry_Pp3_03792552genetic_marker
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RosCOS2612-347_snp_sweet_cherry_Pp5_18375738RosCOS2612-347_snp_sweet_cherry_Pp5_18375738genetic_marker
RosCOS2622-075_snp_sweet_cherry_Pp1_33117964RosCOS2622-075_snp_sweet_cherry_Pp1_33117964genetic_marker
RosCOS2633-111_snp_sweet_cherry_Pp6_14662633RosCOS2633-111_snp_sweet_cherry_Pp6_14662633genetic_marker
RosCOS2753-188_snp_sweet_cherry_Pp1_32621488RosCOS2753-188_snp_sweet_cherry_Pp1_32621488genetic_marker
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RosCOS3729-417_snp_sweet_cherry_Pp7_04467254RosCOS3729-417_snp_sweet_cherry_Pp7_04467254genetic_marker
RosCOS3732-078_snp_sweet_cherry_Pp8_16350869RosCOS3732-078_snp_sweet_cherry_Pp8_16350869genetic_marker
RosCOS3738-215_snp_sweet_cherry_Pp1_42355743RosCOS3738-215_snp_sweet_cherry_Pp1_42355743genetic_marker
RosCOS3782-122_snp_sweet_cherry_Pp5_12355943RosCOS3782-122_snp_sweet_cherry_Pp5_12355943genetic_marker
RosCOS3802-247_snp_sweet_cherry_Pp1_30725127RosCOS3802-247_snp_sweet_cherry_Pp1_30725127genetic_marker
PavPHYCPavPHYCgenetic_marker
PavGH17-61PavGH17-61genetic_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