Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data
Abstract Background High temperature during grape berry ripening impairs the quality of fruits and wines. Veraison time, which marks ripening onset, is a key factor for determining climatic conditions during berry ripening. Understanding its genetic control is crucial to successfully breed varieties...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-10-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-6124-0 |
| _version_ | 1818260258648227840 |
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| author | Pietro Delfino Sara Zenoni Zahra Imanifard Giovanni Battista Tornielli Diana Bellin |
| author_facet | Pietro Delfino Sara Zenoni Zahra Imanifard Giovanni Battista Tornielli Diana Bellin |
| author_sort | Pietro Delfino |
| collection | DOAJ |
| description | Abstract Background High temperature during grape berry ripening impairs the quality of fruits and wines. Veraison time, which marks ripening onset, is a key factor for determining climatic conditions during berry ripening. Understanding its genetic control is crucial to successfully breed varieties more adapted to a changing climate. Quantitative trait loci (QTL) studies attempting to elucidate the genetic determinism of developmental stages in grapevine have identified wide genomic regions. Broad scale transcriptomic studies, by identifying sets of genes modulated during berry development and ripening, also highlighted a huge number of putative candidates. Results With the final aim of providing an overview about available information on the genetic control of grapevine veraison time, and prioritizing candidates, we applied a meta-QTL analysis for grapevine phenology-related traits and checked for co-localization of transcriptomic candidates. A consensus genetic map including 3130 markers anchored to the grapevine genome assembly was compiled starting from 39 genetic maps. Two thousand ninety-three QTLs from 47 QTL studies were projected onto the consensus map, providing a comprehensive overview about distribution of available QTLs and revealing extensive co-localization especially across phenology related traits. From 141 phenology related QTLs we generated 4 veraison meta-QTLs located on linkage group (LG) 1 and 2, and 13 additional meta-QTLs connected to the veraison time genetic control, among which the most relevant were located on LG 14, 16 and 18. Functional candidates in these intervals were inspected. Lastly, taking advantage of available transcriptomic datasets, expression data along berry development were integrated, in order to pinpoint among positional candidates, those differentially expressed across the veraison transition. Conclusion Integration of meta-QTLs analysis on available phenology related QTLs and data from transcriptomic dataset allowed to strongly reduce the number of candidate genes for the genetic control of the veraison transition, prioritizing a list of 272 genes, among which 78 involved in regulation of gene expression, signal transduction or development. |
| first_indexed | 2024-12-12T18:28:29Z |
| format | Article |
| id | doaj.art-ccdd5dafdee94b6abb656221777a3091 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T18:28:29Z |
| publishDate | 2019-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-ccdd5dafdee94b6abb656221777a30912022-12-22T00:15:59ZengBMCBMC Genomics1471-21642019-10-0120111910.1186/s12864-019-6124-0Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic dataPietro Delfino0Sara Zenoni1Zahra Imanifard2Giovanni Battista Tornielli3Diana Bellin4Department of Biotechnology, University of VeronaDepartment of Biotechnology, University of VeronaDepartment of Biotechnology, University of VeronaDepartment of Biotechnology, University of VeronaDepartment of Biotechnology, University of VeronaAbstract Background High temperature during grape berry ripening impairs the quality of fruits and wines. Veraison time, which marks ripening onset, is a key factor for determining climatic conditions during berry ripening. Understanding its genetic control is crucial to successfully breed varieties more adapted to a changing climate. Quantitative trait loci (QTL) studies attempting to elucidate the genetic determinism of developmental stages in grapevine have identified wide genomic regions. Broad scale transcriptomic studies, by identifying sets of genes modulated during berry development and ripening, also highlighted a huge number of putative candidates. Results With the final aim of providing an overview about available information on the genetic control of grapevine veraison time, and prioritizing candidates, we applied a meta-QTL analysis for grapevine phenology-related traits and checked for co-localization of transcriptomic candidates. A consensus genetic map including 3130 markers anchored to the grapevine genome assembly was compiled starting from 39 genetic maps. Two thousand ninety-three QTLs from 47 QTL studies were projected onto the consensus map, providing a comprehensive overview about distribution of available QTLs and revealing extensive co-localization especially across phenology related traits. From 141 phenology related QTLs we generated 4 veraison meta-QTLs located on linkage group (LG) 1 and 2, and 13 additional meta-QTLs connected to the veraison time genetic control, among which the most relevant were located on LG 14, 16 and 18. Functional candidates in these intervals were inspected. Lastly, taking advantage of available transcriptomic datasets, expression data along berry development were integrated, in order to pinpoint among positional candidates, those differentially expressed across the veraison transition. Conclusion Integration of meta-QTLs analysis on available phenology related QTLs and data from transcriptomic dataset allowed to strongly reduce the number of candidate genes for the genetic control of the veraison transition, prioritizing a list of 272 genes, among which 78 involved in regulation of gene expression, signal transduction or development.http://link.springer.com/article/10.1186/s12864-019-6124-0GrapevinePhenologyQTLMeta-QTLTranscriptomicsVeraison |
| spellingShingle | Pietro Delfino Sara Zenoni Zahra Imanifard Giovanni Battista Tornielli Diana Bellin Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data BMC Genomics Grapevine Phenology QTL Meta-QTL Transcriptomics Veraison |
| title | Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data |
| title_full | Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data |
| title_fullStr | Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data |
| title_full_unstemmed | Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data |
| title_short | Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data |
| title_sort | selection of candidate genes controlling veraison time in grapevine through integration of meta qtl and transcriptomic data |
| topic | Grapevine Phenology QTL Meta-QTL Transcriptomics Veraison |
| url | http://link.springer.com/article/10.1186/s12864-019-6124-0 |
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