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Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers

Tomato (Solanum lycopersicum) fruit weight (FW), soluble solid content (SSC), fruit shape and fruit color are crucial for yield, quality and consumer acceptability. In this study, a 192 accessions tomato association panel comprising a mixture of wild species, cherry tomato, landraces, and modern var...

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Autores principales: Liu, Xiaoxi, Geng, Xiaolin, Zhang, Hongchi, Shen, Huolin, Yang, Wencai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515879/
https://www.ncbi.nlm.nih.gov/pubmed/28769968
http://dx.doi.org/10.3389/fpls.2017.01269
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author Liu, Xiaoxi
Geng, Xiaolin
Zhang, Hongchi
Shen, Huolin
Yang, Wencai
author_facet Liu, Xiaoxi
Geng, Xiaolin
Zhang, Hongchi
Shen, Huolin
Yang, Wencai
author_sort Liu, Xiaoxi
collection PubMed
description Tomato (Solanum lycopersicum) fruit weight (FW), soluble solid content (SSC), fruit shape and fruit color are crucial for yield, quality and consumer acceptability. In this study, a 192 accessions tomato association panel comprising a mixture of wild species, cherry tomato, landraces, and modern varieties collected worldwide was genotyped with 547 InDel markers evenly distributed on 12 chromosomes and scored for FW, SSC, fruit shape index (FSI), and color parameters over 2 years with three replications each year. The association panel was sorted into two subpopulations. Linkage disequilibrium ranged from 3.0 to 47.2 Mb across 12 chromosomes. A set of 102 markers significantly (p < 1.19–1.30 × 10(−4)) associated with SSC, FW, fruit shape, and fruit color was identified on 11 of the 12 chromosomes using a mixed linear model. The associations were compared with the known gene/QTLs for the same traits. Genetic analysis using F(2) populations detected 14 and 4 markers significantly (p < 0.05) associated with SSC and FW, respectively. Some loci were commonly detected by both association and linkage analysis. Particularly, one novel locus for FW on chromosome 4 detected by association analysis was also identified in F(2) populations. The results demonstrated that association mapping using limited number of InDel markers and a relatively small population could not only complement and enhance previous QTL information, but also identify novel loci for marker-assisted selection of fruit traits in tomato.
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spelling pubmed-55158792017-08-02 Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers Liu, Xiaoxi Geng, Xiaolin Zhang, Hongchi Shen, Huolin Yang, Wencai Front Plant Sci Plant Science Tomato (Solanum lycopersicum) fruit weight (FW), soluble solid content (SSC), fruit shape and fruit color are crucial for yield, quality and consumer acceptability. In this study, a 192 accessions tomato association panel comprising a mixture of wild species, cherry tomato, landraces, and modern varieties collected worldwide was genotyped with 547 InDel markers evenly distributed on 12 chromosomes and scored for FW, SSC, fruit shape index (FSI), and color parameters over 2 years with three replications each year. The association panel was sorted into two subpopulations. Linkage disequilibrium ranged from 3.0 to 47.2 Mb across 12 chromosomes. A set of 102 markers significantly (p < 1.19–1.30 × 10(−4)) associated with SSC, FW, fruit shape, and fruit color was identified on 11 of the 12 chromosomes using a mixed linear model. The associations were compared with the known gene/QTLs for the same traits. Genetic analysis using F(2) populations detected 14 and 4 markers significantly (p < 0.05) associated with SSC and FW, respectively. Some loci were commonly detected by both association and linkage analysis. Particularly, one novel locus for FW on chromosome 4 detected by association analysis was also identified in F(2) populations. The results demonstrated that association mapping using limited number of InDel markers and a relatively small population could not only complement and enhance previous QTL information, but also identify novel loci for marker-assisted selection of fruit traits in tomato. Frontiers Media S.A. 2017-07-19 /pmc/articles/PMC5515879/ /pubmed/28769968 http://dx.doi.org/10.3389/fpls.2017.01269 Text en Copyright © 2017 Liu, Geng, Zhang, Shen and Yang. 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) or licensor 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
Liu, Xiaoxi
Geng, Xiaolin
Zhang, Hongchi
Shen, Huolin
Yang, Wencai
Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers
title Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers
title_full Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers
title_fullStr Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers
title_full_unstemmed Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers
title_short Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers
title_sort association and genetic identification of loci for four fruit traits in tomato using indel markers
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515879/
https://www.ncbi.nlm.nih.gov/pubmed/28769968
http://dx.doi.org/10.3389/fpls.2017.01269
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