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
s8_11284617s8_11284617genetic_marker
s8_12618983s8_12618983genetic_marker
s8_1338472s8_1338472genetic_marker
s8_13612599s8_13612599genetic_marker
s8_14281700s8_14281700genetic_marker
s8_16414948s8_16414948genetic_marker
s8_17263343s8_17263343genetic_marker
s8_17694886s8_17694886genetic_marker
s8_18085002s8_18085002genetic_marker
s8_18365429s8_18365429genetic_marker
s8_18534010s8_18534010genetic_marker
s8_20376775s8_20376775genetic_marker
s8_2737945s8_2737945genetic_marker
s8_5038726s8_5038726genetic_marker
s8_628498s8_628498genetic_marker
s1_10307853s1_10307853genetic_marker
s1_1035107s1_1035107genetic_marker
s1_11812518s1_11812518genetic_marker
s1_1238680s1_1238680genetic_marker
s1_13880573s1_13880573genetic_marker
s1_13940813s1_13940813genetic_marker
s1_14463799s1_14463799genetic_marker
s1_14557730s1_14557730genetic_marker
s1_16562957s1_16562957genetic_marker
s1_16668968s1_16668968genetic_marker

Pages

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