Construction of High Density Sweet Cherry (Prunus avium L.) Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS)

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 methodo...

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Veröffentlicht in:PloS one 2015-05, Vol.10 (5), p.e0127750-e0127750
Hauptverfasser: Guajardo, Verónica, Solís, Simón, Sagredo, Boris, Gainza, Felipe, Muñoz, Carlos, Gasic, Ksenija, Hinrichsen, Patricio
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Solís, Simón
Sagredo, Boris
Gainza, Felipe
Muñoz, Carlos
Gasic, Ksenija
Hinrichsen, Patricio
description 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.
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Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-05-26</date><risdate>2015</risdate><volume>10</volume><issue>5</issue><spage>e0127750</spage><epage>e0127750</epage><pages>e0127750-e0127750</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26011256</pmid><doi>10.1371/journal.pone.0127750</doi><oa>free_for_read</oa></addata></record>
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subjects Bioinformatics
Breeding
Chromosome Mapping - methods
Chromosome Segregation - genetics
Construction
Cultivars
Density
Deoxyribonucleic acid
DNA
DNA methylation
Efficiency
Families & family life
Gene loci
Gene mapping
Gene sequencing
Genes, Plant
Genetic Linkage
Genetic markers
Genetics
Genomes
Genomics
Genotyping
Genotyping Techniques - methods
Germplasm
Haplotypes
Linearity
Markers
Microsatellite Repeats - genetics
Microsatellites
Next-generation sequencing
Physical Chromosome Mapping
Polymorphism
Polymorphism, Single Nucleotide - genetics
Population
Prunus avium
Prunus avium - genetics
Quantitative trait loci
Scaffolds
Sequence Analysis, DNA - methods
Single-nucleotide polymorphism
Synteny
title Construction of High Density Sweet Cherry (Prunus avium L.) Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS)
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