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Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)

BACKGROUND: Due to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple leaf gene using a backcross population and an F(2) population derived from t...

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Autores principales: Liu, Xiao-ping, Gao, Bao-zhen, Han, Feng-qing, Fang, Zhi-yuan, Yang, Li-mei, Zhuang, Mu, Lv, Hong-hao, Liu, Yu-mei, Li, Zhan-sheng, Cai, Cheng-cheng, Yu, Hai-long, Li, Zhi-yuan, Zhang, Yang-yong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348804/
https://www.ncbi.nlm.nih.gov/pubmed/28288583
http://dx.doi.org/10.1186/s12864-017-3613-x
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author Liu, Xiao-ping
Gao, Bao-zhen
Han, Feng-qing
Fang, Zhi-yuan
Yang, Li-mei
Zhuang, Mu
Lv, Hong-hao
Liu, Yu-mei
Li, Zhan-sheng
Cai, Cheng-cheng
Yu, Hai-long
Li, Zhi-yuan
Zhang, Yang-yong
author_facet Liu, Xiao-ping
Gao, Bao-zhen
Han, Feng-qing
Fang, Zhi-yuan
Yang, Li-mei
Zhuang, Mu
Lv, Hong-hao
Liu, Yu-mei
Li, Zhan-sheng
Cai, Cheng-cheng
Yu, Hai-long
Li, Zhi-yuan
Zhang, Yang-yong
author_sort Liu, Xiao-ping
collection PubMed
description BACKGROUND: Due to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple leaf gene using a backcross population and an F(2) population derived from two parental lines: W1827 (with white leaves) and P1835 (with purple leaves). RESULTS: Genetic analysis indicated that the purple leaf trait is controlled by a single dominant gene, which we named BoPr. Using markers developed based on the reference genome ‘02–12’, the BoPr gene was preliminarily mapped to a 280-kb interval of chromosome C09, with flanking markers M17 and BoID4714 at genetic distances of 4.3 cM and 1.5 cM, respectively. The recombination rate within this interval is almost 12 times higher than the usual level, which could be caused by assembly error for reference genome ‘02–12’ at this interval. Primers were designed based on ‘TO1000’, another B. oleracea reference genome. Among the newly designed InDel markers, BRID485 and BRID490 were found to be the closest to BoPr, flanking the gene at genetic distances of 0.1 cM and 0.2 cM, respectively; the interval between the two markers is 44.8 kb (reference genome ‘TO1000’). Seven annotated genes are located within the 44.8 kb genomic region, of which only Bo9g058630 shows high homology to AT5G42800 (dihydroflavonol reductase), which was identified as a candidate gene for BoPr. Blast analysis revealed that this 44.8 kb interval is located on an unanchored scaffold (Scaffold000035_P2) of ‘02–12’, confirming the existence of assembly error at the interval between M17 and BoID4714 for reference genome ‘02–12’. CONCLUSIONS: This study identified a candidate gene for BoPr and lays a foundation for the cloning and functional analysis of this gene. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3613-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-53488042017-03-14 Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala) Liu, Xiao-ping Gao, Bao-zhen Han, Feng-qing Fang, Zhi-yuan Yang, Li-mei Zhuang, Mu Lv, Hong-hao Liu, Yu-mei Li, Zhan-sheng Cai, Cheng-cheng Yu, Hai-long Li, Zhi-yuan Zhang, Yang-yong BMC Genomics Research Article BACKGROUND: Due to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple leaf gene using a backcross population and an F(2) population derived from two parental lines: W1827 (with white leaves) and P1835 (with purple leaves). RESULTS: Genetic analysis indicated that the purple leaf trait is controlled by a single dominant gene, which we named BoPr. Using markers developed based on the reference genome ‘02–12’, the BoPr gene was preliminarily mapped to a 280-kb interval of chromosome C09, with flanking markers M17 and BoID4714 at genetic distances of 4.3 cM and 1.5 cM, respectively. The recombination rate within this interval is almost 12 times higher than the usual level, which could be caused by assembly error for reference genome ‘02–12’ at this interval. Primers were designed based on ‘TO1000’, another B. oleracea reference genome. Among the newly designed InDel markers, BRID485 and BRID490 were found to be the closest to BoPr, flanking the gene at genetic distances of 0.1 cM and 0.2 cM, respectively; the interval between the two markers is 44.8 kb (reference genome ‘TO1000’). Seven annotated genes are located within the 44.8 kb genomic region, of which only Bo9g058630 shows high homology to AT5G42800 (dihydroflavonol reductase), which was identified as a candidate gene for BoPr. Blast analysis revealed that this 44.8 kb interval is located on an unanchored scaffold (Scaffold000035_P2) of ‘02–12’, confirming the existence of assembly error at the interval between M17 and BoID4714 for reference genome ‘02–12’. CONCLUSIONS: This study identified a candidate gene for BoPr and lays a foundation for the cloning and functional analysis of this gene. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3613-x) contains supplementary material, which is available to authorized users. BioMed Central 2017-03-14 /pmc/articles/PMC5348804/ /pubmed/28288583 http://dx.doi.org/10.1186/s12864-017-3613-x Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.
spellingShingle Research Article
Liu, Xiao-ping
Gao, Bao-zhen
Han, Feng-qing
Fang, Zhi-yuan
Yang, Li-mei
Zhuang, Mu
Lv, Hong-hao
Liu, Yu-mei
Li, Zhan-sheng
Cai, Cheng-cheng
Yu, Hai-long
Li, Zhi-yuan
Zhang, Yang-yong
Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)
title Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)
title_full Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)
title_fullStr Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)
title_full_unstemmed Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)
title_short Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)
title_sort genetics and fine mapping of a purple leaf gene, bopr, in ornamental kale (brassica oleracea l. var. acephala)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348804/
https://www.ncbi.nlm.nih.gov/pubmed/28288583
http://dx.doi.org/10.1186/s12864-017-3613-x
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