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
FRS8_2FRS8_2genetic_marker
FYPP3FYPP3genetic_marker
FYPP3_2FYPP3_2genetic_marker
GH17GH17genetic_marker
GH17_2GH17_2genetic_marker
GH17-101GH17-101genetic_marker
GH17-101_2GH17-101_2genetic_marker
GH17-61GH17-61genetic_marker
GH17-61_2GH17-61_2genetic_marker
GIGIgenetic_marker
GI_2GI_2genetic_marker
LHYLHYgenetic_marker
LHY_2LHY_2genetic_marker
MBF1CMBF1Cgenetic_marker
MBF1C_2MBF1C_2genetic_marker
NUANUAgenetic_marker
NUA_2NUA_2genetic_marker
PHYCPHYCgenetic_marker
PHYC_2PHYC_2genetic_marker
SUF4SUF4genetic_marker
SVPSVPgenetic_marker
SWNSWNgenetic_marker
SWN_2SWN_2genetic_marker
TUB2TUB2genetic_marker
VEL1VEL1genetic_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