Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L
Abstract 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) pop...
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5356-8 |
| _version_ | 1818290918881492992 |
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| author | Hongju Jian Aoxiang Zhang Jinqi Ma Tengyue Wang Bo Yang Lan Shuan Shuang Min Liu Jiana Li Xinfu Xu Andrew H. Paterson Liezhao Liu |
| author_facet | Hongju Jian Aoxiang Zhang Jinqi Ma Tengyue Wang Bo Yang Lan Shuan Shuang Min Liu Jiana Li Xinfu Xu Andrew H. Paterson Liezhao Liu |
| author_sort | Hongju Jian |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-13T02:35:49Z |
| format | Article |
| id | doaj.art-b19b3cdf3a2d4bd19224dff651856e91 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T02:35:49Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b19b3cdf3a2d4bd19224dff651856e912022-12-22T00:02:24ZengBMCBMC Genomics1471-21642019-01-0120111410.1186/s12864-018-5356-8Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus LHongju Jian0Aoxiang Zhang1Jinqi Ma2Tengyue Wang3Bo Yang4Lan Shuan Shuang5Min Liu6Jiana Li7Xinfu Xu8Andrew H. Paterson9Liezhao Liu10Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural SciencesChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural SciencesChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural SciencesChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural SciencesChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural SciencesPlant Genome Mapping Laboratory, University of GeorgiaPlant Genome Mapping Laboratory, University of GeorgiaChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural SciencesChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural SciencesPlant Genome Mapping Laboratory, University of GeorgiaChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural SciencesAbstract 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.http://link.springer.com/article/10.1186/s12864-018-5356-8Flowering timeQTLGene expressionRNA-SeqBrassica napus |
| spellingShingle | Hongju Jian Aoxiang Zhang Jinqi Ma Tengyue Wang Bo Yang Lan Shuan Shuang Min Liu Jiana Li Xinfu Xu Andrew H. Paterson Liezhao Liu Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L BMC Genomics Flowering time QTL Gene expression RNA-Seq Brassica napus |
| 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 | Flowering time QTL Gene expression RNA-Seq Brassica napus |
| url | http://link.springer.com/article/10.1186/s12864-018-5356-8 |
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