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_20486124s2_20486124genetic_marker
s2_206335s2_206335genetic_marker
s2_206350s2_206350genetic_marker
s2_20921620s2_20921620genetic_marker
s2_21483227s2_21483227genetic_marker
s2_21629421s2_21629421genetic_marker
s2_21662414s2_21662414genetic_marker
s2_21695836s2_21695836genetic_marker
s2_21900771s2_21900771genetic_marker
s2_22033331s2_22033331genetic_marker
s2_22040051s2_22040051genetic_marker
s2_22345474s2_22345474genetic_marker
s2_22407394s2_22407394genetic_marker
s2_22505376s2_22505376genetic_marker
s2_22505538s2_22505538genetic_marker
s2_2251791s2_2251791genetic_marker
s2_22765536s2_22765536genetic_marker
s2_22784889s2_22784889genetic_marker
s2_22860625s2_22860625genetic_marker
s2_22947360s2_22947360genetic_marker
s2_2301347s2_2301347genetic_marker
s2_2301353s2_2301353genetic_marker
s2_2301387s2_2301387genetic_marker
s2_23061020s2_23061020genetic_marker
s2_23065474s2_23065474genetic_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