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Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L

BACKGROUND: Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QTL) analysis of flowering time in a recombinant inbred line (RIL) population,...

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Autores principales: Jian, Hongju, Zhang, Aoxiang, Ma, Jinqi, Wang, Tengyue, Yang, Bo, Shuang, Lan Shuan, Liu, Min, Li, Jiana, Xu, Xinfu, Paterson, Andrew H., Liu, Liezhao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325782/
https://www.ncbi.nlm.nih.gov/pubmed/30626329
http://dx.doi.org/10.1186/s12864-018-5356-8
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author Jian, Hongju
Zhang, Aoxiang
Ma, Jinqi
Wang, Tengyue
Yang, Bo
Shuang, Lan Shuan
Liu, Min
Li, Jiana
Xu, Xinfu
Paterson, Andrew H.
Liu, Liezhao
author_facet Jian, Hongju
Zhang, Aoxiang
Ma, Jinqi
Wang, Tengyue
Yang, Bo
Shuang, Lan Shuan
Liu, Min
Li, Jiana
Xu, Xinfu
Paterson, Andrew H.
Liu, Liezhao
author_sort Jian, Hongju
collection PubMed
description BACKGROUND: Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QTL) analysis of flowering time in a recombinant inbred line (RIL) population, including lines with extreme differences in flowering time, in six environments, along with RNA-Seq analysis. RESULTS: We detected 27 QTLs distributed on eight chromosomes among six environments, including one major QTL on chromosome C02 that explained 11–25% of the phenotypic variation and was stably detected in all six environments. RNA-Seq analysis revealed 105 flowering time-related differentially expressed genes (DEGs) that play roles in the circadian clock/photoperiod, autonomous pathway, and hormone and vernalization pathways. We focused on DEGs related to the regulation of flowering time, especially DEGs in QTL regions. CONCLUSIONS: We identified 45 flowering time-related genes in these QTL regions, eight of which are DEGs, including key flowering time genes PSEUDO RESPONSE REGULATOR 7 (PRR7) and FY (located in a major QTL region on C02). These findings provide insights into the genetic architecture of flowering time in B. napus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-5356-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-63257822019-01-11 Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L Jian, Hongju Zhang, Aoxiang Ma, Jinqi Wang, Tengyue Yang, Bo Shuang, Lan Shuan Liu, Min Li, Jiana Xu, Xinfu Paterson, Andrew H. Liu, Liezhao BMC Genomics Research Article BACKGROUND: Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QTL) analysis of flowering time in a recombinant inbred line (RIL) population, including lines with extreme differences in flowering time, in six environments, along with RNA-Seq analysis. RESULTS: We detected 27 QTLs distributed on eight chromosomes among six environments, including one major QTL on chromosome C02 that explained 11–25% of the phenotypic variation and was stably detected in all six environments. RNA-Seq analysis revealed 105 flowering time-related differentially expressed genes (DEGs) that play roles in the circadian clock/photoperiod, autonomous pathway, and hormone and vernalization pathways. We focused on DEGs related to the regulation of flowering time, especially DEGs in QTL regions. CONCLUSIONS: We identified 45 flowering time-related genes in these QTL regions, eight of which are DEGs, including key flowering time genes PSEUDO RESPONSE REGULATOR 7 (PRR7) and FY (located in a major QTL region on C02). These findings provide insights into the genetic architecture of flowering time in B. napus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-5356-8) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-09 /pmc/articles/PMC6325782/ /pubmed/30626329 http://dx.doi.org/10.1186/s12864-018-5356-8 Text en © The Author(s). 2019 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
Jian, Hongju
Zhang, Aoxiang
Ma, Jinqi
Wang, Tengyue
Yang, Bo
Shuang, Lan Shuan
Liu, Min
Li, Jiana
Xu, Xinfu
Paterson, Andrew H.
Liu, Liezhao
Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L
title Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L
title_full Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L
title_fullStr Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L
title_full_unstemmed Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L
title_short Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L
title_sort joint qtl mapping and transcriptome sequencing analysis reveal candidate flowering time genes in brassica napus l
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325782/
https://www.ncbi.nlm.nih.gov/pubmed/30626329
http://dx.doi.org/10.1186/s12864-018-5356-8
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