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
s1_31070854s1_31070854genetic_marker
s1_31241811s1_31241811genetic_marker
s1_32726980s1_32726980genetic_marker
s1_33216138s1_33216138genetic_marker
s1_34231458s1_34231458genetic_marker
s1_34233251s1_34233251genetic_marker
s1_34386201s1_34386201genetic_marker
s1_34398105s1_34398105genetic_marker
s1_35437562s1_35437562genetic_marker
s1_35487570s1_35487570genetic_marker
s1_35674136s1_35674136genetic_marker
s1_36228350s1_36228350genetic_marker
s1_36420908s1_36420908genetic_marker
s1_36775180s1_36775180genetic_marker
s1_37097863s1_37097863genetic_marker
s1_37411927s1_37411927genetic_marker
s1_37551363s1_37551363genetic_marker
s1_38463002s1_38463002genetic_marker
s1_41520481s1_41520481genetic_marker
s1_42240643s1_42240643genetic_marker
s1_42284209s1_42284209genetic_marker
s1_42734131s1_42734131genetic_marker
s1_42792098s1_42792098genetic_marker
s1_45072148s1_45072148genetic_marker
s1_45265319s1_45265319genetic_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