Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (<i>Brassica napus</i> L.)
The leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. However, research on the leaf plastochron of crops remains limited. In this study, 2116C exhibited a rapid leaf plastochron com...
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2025-06-01
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| author | Mengfan Qin Xiang Liu Jia Song Feixue Zhao Yiji Shi Yu Xu Zhiting Guo Tianye Zhang Jiapeng Wu Jinxiong Wang Wu Li Keqi Li Shimeng Li Zhen Huang Aixia Xu |
| author_facet | Mengfan Qin Xiang Liu Jia Song Feixue Zhao Yiji Shi Yu Xu Zhiting Guo Tianye Zhang Jiapeng Wu Jinxiong Wang Wu Li Keqi Li Shimeng Li Zhen Huang Aixia Xu |
| author_sort | Mengfan Qin |
| collection | DOAJ |
| description | The leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. However, research on the leaf plastochron of crops remains limited. In this study, 2116C exhibited a rapid leaf plastochron compared to ZH18 during both rosette and bud periods. There were significant positive correlations among the leaf plastochron and primary branch number of the F<sub>2</sub> populations (<i>r</i> ranging from 0.395 to 0.635, <i>p</i> < 0.01). Genetic analyses over two years demonstrated that two equally dominant genes might govern the leaf plastochron. Through bulk segregant analysis sequencing (BSA-seq), three novel genomic intervals were identified on chromosomes A02 (9.04–9.48 Mb and 13.52–13.66 Mb) and A04 (19.84–20.14 Mb) of ZS11 and Darmor-<i>bzh</i> reference genomes. By gene functional annotations, single-nucleotide variation (SNV) analyses, transcriptome data from parents, genetic progeny, and natural accessions, we identified ten candidate genes within the intervals, including <i>FLOWERING LOCUS T</i>, <i>RGL1</i>, <i>MYB-like</i>, <i>CYP96A8</i>, <i>BLH3</i>, <i>NIT2</i>, <i>ASK6</i>, and three <i>CLAVATA3/ESR (CLE)-related</i> genes. These findings lay the molecular foundation for further exploration into the leaf plastochron and the implications in plastochron-related breeding in rapeseed. |
| format | Article |
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| institution | DOAJ |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj-art-c1ac27f42c1d42f49159fc748eefe74b2025-08-20T03:11:32ZengMDPI AGPlants2223-77472025-06-011411171910.3390/plants14111719Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (<i>Brassica napus</i> L.)Mengfan Qin0Xiang Liu1Jia Song2Feixue Zhao3Yiji Shi4Yu Xu5Zhiting Guo6Tianye Zhang7Jiapeng Wu8Jinxiong Wang9Wu Li10Keqi Li11Shimeng Li12Zhen Huang13Aixia Xu14College of Agronomy, Northwest A&F University, Yangling 712100, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaInstitute of Agricultural Sciences, Xizang Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850000, ChinaCrop Research Institute, Guangdong Academy of Agricultural Science, Guangzhou 510640, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaInstitute of Agricultural Sciences, Xizang Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850000, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, ChinaThe leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. However, research on the leaf plastochron of crops remains limited. In this study, 2116C exhibited a rapid leaf plastochron compared to ZH18 during both rosette and bud periods. There were significant positive correlations among the leaf plastochron and primary branch number of the F<sub>2</sub> populations (<i>r</i> ranging from 0.395 to 0.635, <i>p</i> < 0.01). Genetic analyses over two years demonstrated that two equally dominant genes might govern the leaf plastochron. Through bulk segregant analysis sequencing (BSA-seq), three novel genomic intervals were identified on chromosomes A02 (9.04–9.48 Mb and 13.52–13.66 Mb) and A04 (19.84–20.14 Mb) of ZS11 and Darmor-<i>bzh</i> reference genomes. By gene functional annotations, single-nucleotide variation (SNV) analyses, transcriptome data from parents, genetic progeny, and natural accessions, we identified ten candidate genes within the intervals, including <i>FLOWERING LOCUS T</i>, <i>RGL1</i>, <i>MYB-like</i>, <i>CYP96A8</i>, <i>BLH3</i>, <i>NIT2</i>, <i>ASK6</i>, and three <i>CLAVATA3/ESR (CLE)-related</i> genes. These findings lay the molecular foundation for further exploration into the leaf plastochron and the implications in plastochron-related breeding in rapeseed.https://www.mdpi.com/2223-7747/14/11/1719<i>Brassica napus</i> L.leaf plastochrongenetic analysisBSA-seqgene expressioncandidate gene |
| spellingShingle | Mengfan Qin Xiang Liu Jia Song Feixue Zhao Yiji Shi Yu Xu Zhiting Guo Tianye Zhang Jiapeng Wu Jinxiong Wang Wu Li Keqi Li Shimeng Li Zhen Huang Aixia Xu Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (<i>Brassica napus</i> L.) Plants <i>Brassica napus</i> L. leaf plastochron genetic analysis BSA-seq gene expression candidate gene |
| title | Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (<i>Brassica napus</i> L.) |
| title_full | Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (<i>Brassica napus</i> L.) |
| title_fullStr | Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (<i>Brassica napus</i> L.) |
| title_full_unstemmed | Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (<i>Brassica napus</i> L.) |
| title_short | Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (<i>Brassica napus</i> L.) |
| title_sort | genetic analyses bsa seq and transcriptome analyses reveal candidate genes controlling leaf plastochron in rapeseed i brassica napus i l |
| topic | <i>Brassica napus</i> L. leaf plastochron genetic analysis BSA-seq gene expression candidate gene |
| url | https://www.mdpi.com/2223-7747/14/11/1719 |
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