Hinrichsen P. Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS).

Publication Overview
TitleConstruction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS).
AuthorsGuajardo V, Solís S, Sagredo B, Gainza F, Muñoz C, Gasic K, Hinrichsen P. Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). PLoS ONE 2015.
TypeJournal Article
Journal NamePLoS ONE
Volume10
Issue5
Year2015
Page(s)e0127750
CitationGuajardo V, Solís S, Sagredo B, Gainza F, Muñoz C, Gasic K, Hinrichsen P. Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). PLoS ONE 2015.

Abstract

Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs) and, recently, using single nucleotide polymorphism markers (SNPs) from a cherry 6K SNP array. Genotyping-by-sequencing (GBS), a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a 'Rainier' x 'Rivedel' (Ra x Ri) cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in 'Rainier', 'Rivedel' and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for 'Rainier', 'Rivedel' and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both 'Rainier' and 'Rivedel' maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.
Features
This publication contains information about 8,477 features:
Feature NameUniquenameType
s2_24581082s2_24581082genetic_marker
s2_24711542s2_24711542genetic_marker
s2_24987649s2_24987649genetic_marker
s2_24987690s2_24987690genetic_marker
s2_25114258s2_25114258genetic_marker
s2_25244162s2_25244162genetic_marker
s2_25362470s2_25362470genetic_marker
s2_25371101s2_25371101genetic_marker
s2_25390769s2_25390769genetic_marker
s2_25523698s2_25523698genetic_marker
s2_25553931s2_25553931genetic_marker
s2_25623458s2_25623458genetic_marker
s2_25755225s2_25755225genetic_marker
s2_25766562s2_25766562genetic_marker
s2_25780503s2_25780503genetic_marker
s2_26001307s2_26001307genetic_marker
s2_26013776s2_26013776genetic_marker
s2_26020798s2_26020798genetic_marker
s2_26020802s2_26020802genetic_marker
s2_26269439s2_26269439genetic_marker
s2_26288441s2_26288441genetic_marker
s2_26288476s2_26288476genetic_marker
s2_26293818s2_26293818genetic_marker
s2_26344024s2_26344024genetic_marker
s2_26552025s2_26552025genetic_marker

Pages

Featuremaps
This publication contains information about 4 maps:
Map Name
Sweet Cherry-Ra-F1
Sweet Cherry-Ri-F1
Sweet Cherry-RaxRi-F1
Sweet_cherry_RaxRi_F1-physical-Prunus-persicaV1.0