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Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers

The identification of genes involved in variation of peach fruit quality would assist breeders to create new cultivars with improved fruit quality. Peach is a genetic and genomic model within the Rosaceae. A large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphism...

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Autores principales: Font i Forcada, Carolina, Guajardo, Verónica, Chin-Wo, Sebastian Reyes, Moreno, María Ángeles
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344403/
https://www.ncbi.nlm.nih.gov/pubmed/30705685
http://dx.doi.org/10.3389/fpls.2018.02005
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author Font i Forcada, Carolina
Guajardo, Verónica
Chin-Wo, Sebastian Reyes
Moreno, María Ángeles
author_facet Font i Forcada, Carolina
Guajardo, Verónica
Chin-Wo, Sebastian Reyes
Moreno, María Ángeles
author_sort Font i Forcada, Carolina
collection PubMed
description The identification of genes involved in variation of peach fruit quality would assist breeders to create new cultivars with improved fruit quality. Peach is a genetic and genomic model within the Rosaceae. A large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from the peach genome sequence was used in this study. A set of 94 individuals from a peach germplasm collection was phenotyped and genotyped, including local Spanish and modern cultivars maintained at the Experimental Station of Aula Dei, Spain. Phenotypic evaluation based on agronomical, pomological and fruit quality traits was performed at least 3 years. A set of 4,558 out of a total of 8,144 SNPs markers developed by the Illumina Infinium BeadArray (v1.0) technology platform, covering the peach genome, were analyzed for population structure analysis and genome-wide association studies (GWAS). Population structure analysis identified two subpopulations, with admixture within them. While one subpopulation contains only modern cultivars, the other one is formed by local Spanish and several modern cultivars from international breeding programs. To test the marker trait associations between markers and phenotypic traits, four models comprising both general linear model (GLM) and mixed linear model (MLM) were selected. The MLM approach using co-ancestry values from population structure and kinship estimates (K model) identified a maximum of 347 significant associations between markers and traits. The associations found appeared to map within the interval where many candidate genes involved in different pathways are predicted in the peach genome. These results represent a promising situation for GWAS in the identification of SNP variants associated to fruit quality traits, potentially applicable in peach breeding programs.
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spelling pubmed-63444032019-01-31 Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers Font i Forcada, Carolina Guajardo, Verónica Chin-Wo, Sebastian Reyes Moreno, María Ángeles Front Plant Sci Plant Science The identification of genes involved in variation of peach fruit quality would assist breeders to create new cultivars with improved fruit quality. Peach is a genetic and genomic model within the Rosaceae. A large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from the peach genome sequence was used in this study. A set of 94 individuals from a peach germplasm collection was phenotyped and genotyped, including local Spanish and modern cultivars maintained at the Experimental Station of Aula Dei, Spain. Phenotypic evaluation based on agronomical, pomological and fruit quality traits was performed at least 3 years. A set of 4,558 out of a total of 8,144 SNPs markers developed by the Illumina Infinium BeadArray (v1.0) technology platform, covering the peach genome, were analyzed for population structure analysis and genome-wide association studies (GWAS). Population structure analysis identified two subpopulations, with admixture within them. While one subpopulation contains only modern cultivars, the other one is formed by local Spanish and several modern cultivars from international breeding programs. To test the marker trait associations between markers and phenotypic traits, four models comprising both general linear model (GLM) and mixed linear model (MLM) were selected. The MLM approach using co-ancestry values from population structure and kinship estimates (K model) identified a maximum of 347 significant associations between markers and traits. The associations found appeared to map within the interval where many candidate genes involved in different pathways are predicted in the peach genome. These results represent a promising situation for GWAS in the identification of SNP variants associated to fruit quality traits, potentially applicable in peach breeding programs. Frontiers Media S.A. 2019-01-17 /pmc/articles/PMC6344403/ /pubmed/30705685 http://dx.doi.org/10.3389/fpls.2018.02005 Text en Copyright © 2019 Font i Forcada, Guajardo, Chin-Wo and Moreno. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Font i Forcada, Carolina
Guajardo, Verónica
Chin-Wo, Sebastian Reyes
Moreno, María Ángeles
Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers
title Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers
title_full Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers
title_fullStr Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers
title_full_unstemmed Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers
title_short Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers
title_sort association mapping analysis for fruit quality traits in prunus persica using snp markers
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344403/
https://www.ncbi.nlm.nih.gov/pubmed/30705685
http://dx.doi.org/10.3389/fpls.2018.02005
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