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
s3_6856537s3_6856537genetic_marker
s3_6856571s3_6856571genetic_marker
s3_6868479s3_6868479genetic_marker
s3_7077511s3_7077511genetic_marker
s3_8498134s3_8498134genetic_marker
s3_9029530s3_9029530genetic_marker
s3_9504364s3_9504364genetic_marker
s3_9633733s3_9633733genetic_marker
s3_9633969s3_9633969genetic_marker
s3_972706s3_972706genetic_marker
s4_12924888s4_12924888genetic_marker
s4_13896593s4_13896593genetic_marker
s4_14119071s4_14119071genetic_marker
s4_16119556s4_16119556genetic_marker
s4_17986946s4_17986946genetic_marker
s4_18375803s4_18375803genetic_marker
s4_1899472s4_1899472genetic_marker
s4_19790956s4_19790956genetic_marker
s4_21029933s4_21029933genetic_marker
s4_21030275s4_21030275genetic_marker
s4_21793861s4_21793861genetic_marker
s4_21883890s4_21883890genetic_marker
s4_2247727s4_2247727genetic_marker
s4_2271127s4_2271127genetic_marker
s4_2285693s4_2285693genetic_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