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
s2_24581082s2_24581082genetic_marker
s2_24711542s2_24711542genetic_marker
s2_25362470s2_25362470genetic_marker
s2_26293818s2_26293818genetic_marker
s2_26572434s2_26572434genetic_marker
s2_26687741s2_26687741genetic_marker
s2_3867998s2_3867998genetic_marker
s2_4907835s2_4907835genetic_marker
s3_13417026s3_13417026genetic_marker
s3_13767131s3_13767131genetic_marker
s3_1440110s3_1440110genetic_marker
s3_15472030s3_15472030genetic_marker
s3_15681482s3_15681482genetic_marker
s3_15681566s3_15681566genetic_marker
s3_15691821s3_15691821genetic_marker
s3_17988256s3_17988256genetic_marker
s3_1870731s3_1870731genetic_marker
s3_19894677s3_19894677genetic_marker
s3_208499s3_208499genetic_marker
s3_21639696s3_21639696genetic_marker
s3_446641s3_446641genetic_marker
s3_4879172s3_4879172genetic_marker
s3_4988156s3_4988156genetic_marker
s3_5616597s3_5616597genetic_marker
s3_615587s3_615587genetic_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