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

Publication Overview
TitleThe cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies.
AuthorsVanderzande S, Zheng P, Cai L, Barac G, Gasic K, Main D, Iezzoni A and Peace C.
TypeJournal Article
Journal NameScientific Reports
Volume10
Year2020
Page(s)7613
CitationVanderzande 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

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.
Features
This publication contains information about 9,000 features:
Feature NameUniquenameType
scaffold_3:19478694scaffold_3:19478694genetic_marker
scaffold_3:19865904scaffold_3:19865904genetic_marker
scaffold_3:20074115scaffold_3:20074115genetic_marker
scaffold_3:2079170scaffold_3:2079170genetic_marker
scaffold_3:20897428scaffold_3:20897428genetic_marker
scaffold_3:20904236scaffold_3:20904236genetic_marker
scaffold_3:21080756scaffold_3:21080756genetic_marker
scaffold_3:21740379scaffold_3:21740379genetic_marker
scaffold_3:244595scaffold_3:244595genetic_marker
scaffold_3:2512240scaffold_3:2512240genetic_marker
scaffold_3:2519197scaffold_3:2519197genetic_marker
scaffold_3:274858scaffold_3:274858genetic_marker
scaffold_3:2761955scaffold_3:2761955genetic_marker
scaffold_3:3086189scaffold_3:3086189genetic_marker
scaffold_3:3319894scaffold_3:3319894genetic_marker
scaffold_3:3458486scaffold_3:3458486genetic_marker
scaffold_3:3522946scaffold_3:3522946genetic_marker
scaffold_3:374031scaffold_3:374031genetic_marker
scaffold_3:3821851scaffold_3:3821851genetic_marker
scaffold_3:3918927scaffold_3:3918927genetic_marker
scaffold_3:3957022scaffold_3:3957022genetic_marker
scaffold_3:4036946scaffold_3:4036946genetic_marker
scaffold_3:4038625scaffold_3:4038625genetic_marker
scaffold_3:4230079scaffold_3:4230079genetic_marker
scaffold_3:4238179scaffold_3:4238179genetic_marker

Pages

Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
Cherry 6+9K SNP arrayCherry 6+9K SNP arrayPrunus avium; cerasus
Featuremaps
This publication contains information about 1 maps:
Map Name
Sweet Cherry-RosBREED-3.8K-2020
Properties
Additional details for this publication include:
Property NameValue
URLhttps://www.nature.com/articles/s41598-020-64438-x