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
CBPbCBPbgenetic_marker
CBPcCBPcgenetic_marker
CBPc_2CBPc_2genetic_marker
CLFCLFgenetic_marker
CLF_2CLF_2genetic_marker
COL2COL2genetic_marker
COL2_2COL2_2genetic_marker
DDF1DDF1genetic_marker
DDL_2DDL_2genetic_marker
ELF8ELF8genetic_marker
ELF8_2ELF8_2genetic_marker
EMF2EMF2genetic_marker
EMF2_2EMF2_2genetic_marker
FAR1FAR1genetic_marker
FAR1_2FAR1_2genetic_marker
FIE1FIE1genetic_marker
FIE1_2FIE1_2genetic_marker
FIO1FIO1genetic_marker
FIO1_2FIO1_2genetic_marker
FL2_LFYFL2_LFYgenetic_marker
FL2_LFY_2FL2_LFY_2genetic_marker
FRIFRIgenetic_marker
FRS6FRS6genetic_marker
FRS6_2FRS6_2genetic_marker
FRS8FRS8genetic_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