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High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing

BACKGROUND: Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In this study, grapevine interspecific hybridisation was carried out with the matern...

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Autores principales: Su, Kai, Xing, Huiyang, Guo, Yinshan, Zhao, Fangyuan, Liu, Zhendong, Li, Kun, Li, Yuanyuan, Guo, Xiuwu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310074/
https://www.ncbi.nlm.nih.gov/pubmed/32571215
http://dx.doi.org/10.1186/s12864-020-06836-z
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author Su, Kai
Xing, Huiyang
Guo, Yinshan
Zhao, Fangyuan
Liu, Zhendong
Li, Kun
Li, Yuanyuan
Guo, Xiuwu
author_facet Su, Kai
Xing, Huiyang
Guo, Yinshan
Zhao, Fangyuan
Liu, Zhendong
Li, Kun
Li, Yuanyuan
Guo, Xiuwu
author_sort Su, Kai
collection PubMed
description BACKGROUND: Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In this study, grapevine interspecific hybridisation was carried out with the maternal parent ‘Cabernet sauvignon’ and paternal parent ‘Zuoyouhong’. A total of 181 hybrid offspring and their parents were used as samples for restriction-site associated DNA sequencing (RAD). Grapevine cane phloem and xylem cold hardiness of the experimental material was detected using the low-temperature exotherm method in 2016, 2017 and 2018. QTL mapping was then conducted based on the integrated map. RESULTS: We constructed a high-density genetic linkage map with 16,076, 11,643, and 25,917 single-nucleotide polymorphism (SNP) markers anchored in the maternal, paternal, and integrated maps, respectively. The average genetic distances of adjacent markers in the maps were 0.65 cM, 0.77 cM, and 0.41 cM, respectively. Colinearity analysis was conducted by comparison with the grape reference genome and showed good performance. Six QTLs were identified based on the phenotypic data of 3 years and they were mapped on linkage group (LG) 2, LG3, and LG15. Based on QTL results, candidate genes which may be involved in grapevine cold hardiness were selected. CONCLUSIONS: High-density linkage maps can facilitate grapevine fine QTL mapping, genome comparison, and sequence assembly. The cold hardiness QTL mapping and candidate gene discovery performed in this study provide an important reference for molecular-assisted selection in grapevine cold hardiness breeding.
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spelling pubmed-73100742020-06-23 High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing Su, Kai Xing, Huiyang Guo, Yinshan Zhao, Fangyuan Liu, Zhendong Li, Kun Li, Yuanyuan Guo, Xiuwu BMC Genomics Research Article BACKGROUND: Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In this study, grapevine interspecific hybridisation was carried out with the maternal parent ‘Cabernet sauvignon’ and paternal parent ‘Zuoyouhong’. A total of 181 hybrid offspring and their parents were used as samples for restriction-site associated DNA sequencing (RAD). Grapevine cane phloem and xylem cold hardiness of the experimental material was detected using the low-temperature exotherm method in 2016, 2017 and 2018. QTL mapping was then conducted based on the integrated map. RESULTS: We constructed a high-density genetic linkage map with 16,076, 11,643, and 25,917 single-nucleotide polymorphism (SNP) markers anchored in the maternal, paternal, and integrated maps, respectively. The average genetic distances of adjacent markers in the maps were 0.65 cM, 0.77 cM, and 0.41 cM, respectively. Colinearity analysis was conducted by comparison with the grape reference genome and showed good performance. Six QTLs were identified based on the phenotypic data of 3 years and they were mapped on linkage group (LG) 2, LG3, and LG15. Based on QTL results, candidate genes which may be involved in grapevine cold hardiness were selected. CONCLUSIONS: High-density linkage maps can facilitate grapevine fine QTL mapping, genome comparison, and sequence assembly. The cold hardiness QTL mapping and candidate gene discovery performed in this study provide an important reference for molecular-assisted selection in grapevine cold hardiness breeding. BioMed Central 2020-06-22 /pmc/articles/PMC7310074/ /pubmed/32571215 http://dx.doi.org/10.1186/s12864-020-06836-z Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Su, Kai
Xing, Huiyang
Guo, Yinshan
Zhao, Fangyuan
Liu, Zhendong
Li, Kun
Li, Yuanyuan
Guo, Xiuwu
High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing
title High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing
title_full High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing
title_fullStr High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing
title_full_unstemmed High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing
title_short High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing
title_sort high-density genetic linkage map construction and cane cold hardiness qtl mapping for vitis based on restriction site-associated dna sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310074/
https://www.ncbi.nlm.nih.gov/pubmed/32571215
http://dx.doi.org/10.1186/s12864-020-06836-z
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