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_21497566s3_21497566genetic_marker
s3_4932471s3_4932471genetic_marker
s3_5631416s3_5631416genetic_marker
s3_6142674s3_6142674genetic_marker
s4_10363908s4_10363908genetic_marker
s4_13992214s4_13992214genetic_marker
s4_14704933s4_14704933genetic_marker
s4_21792166s4_21792166genetic_marker
s4_23719778s4_23719778genetic_marker
s4_5397947s4_5397947genetic_marker
s5_10631249s5_10631249genetic_marker
s5_17182064s5_17182064genetic_marker
s5_17226495s5_17226495genetic_marker
s5_17920734s5_17920734genetic_marker
s5_18370215s5_18370215genetic_marker
s6_1023095s6_1023095genetic_marker
s6_1063576s6_1063576genetic_marker
s6_1128067s6_1128067genetic_marker
s6_17636923s6_17636923genetic_marker
s6_1856492s6_1856492genetic_marker
s6_19812047s6_19812047genetic_marker
s6_24697767s6_24697767genetic_marker
s6_25216200s6_25216200genetic_marker
s6_25522796s6_25522796genetic_marker
s6_3789619s6_3789619genetic_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