Cherry 6+9K SNP array

SNP Chip Overview
Array NameCherry 6+9K SNP array
OrganismPrunus avium; cerasus (sweet cherry; tart cherry)
TypeSNP_chip

The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies

Publication

Vanderzande S, Zheng P, Cai L, Barac G, Gasic K, Main D, Iezzoni A and Peace C.(2020) The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies. Scientific Reports 10, 7613 https://doi.org/10.1038/s41598-020-64438-x

Abstract

Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb cherry whole genome sequence. For sweet cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet cherry, the fruticosa subgenome of sour cherry, and cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet cherry and the avium and the fruticosa subgenomes of sour cherry, respectively. For sweet cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in cherry.

Publications
YearPublication
2020Vanderzande S, Zheng P, Cai L, Barac G, Gasic K, Main D, Iezzoni A and Peace C. The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies. Scientific Reports 10, 7613 (2020). https://doi.org/10.1038/s41598-020-64438-x
Download
Download SNP data
File Description File
List of 9000 SNPs submitted to Illumina for inclusion on the +9K add-on Vanderzande_2020_Supplementary_Table_S1.xlsx
Physical position in the sweet cherry whole genome sequence for all SNPs of the 6+9K SNP array Vanderzande_2020_Supplementary_Table_S2.xlsx
Estimated sweet cherry genetic map positions of polymorphic reliable SNPs on the cherry 6+9K SNP array Vanderzande_2020_Supplementary_Table_S3.xlsx