Transcriptional regulation of transcription factor genes WRI1 and LAFL during Brassica napus seed development
The WRINKLED1 (WRI1) and LAFL [LEAFY COTYLEDON1 (LEC1), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2] transcription factors play essential roles in governing seed development and oil biosynthesis. To gain a comprehensive understanding of the transcriptional regulation of WRI1 and LAFL,...
| Main Authors: | , , , , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2024
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| Online Access: | https://hdl.handle.net/10356/179366 |
| _version_ | 1826112260997644288 |
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| author | Han, Xu Peng, Yan Yin, Sijie Zhao, Hu Zong, Zhanxiang Tan, Zengdong Zhang, Yuting Ma, Wei Guo, Liang |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Han, Xu Peng, Yan Yin, Sijie Zhao, Hu Zong, Zhanxiang Tan, Zengdong Zhang, Yuting Ma, Wei Guo, Liang |
| author_sort | Han, Xu |
| collection | NTU |
| description | The WRINKLED1 (WRI1) and LAFL [LEAFY COTYLEDON1 (LEC1), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2] transcription factors play essential roles in governing seed development and oil biosynthesis. To gain a comprehensive understanding of the transcriptional regulation of WRI1 and LAFL, we conducted genome-wide association studies for the expression profiles of WRI1 and LAFL in developing seeds at 20 and 40 days after flowering (DAF) using 302 rapeseed (Brassica napus) accessions. We identified a total of 237 expression quantitative trait nucleotides (eQTNs) and 51 expression QTN-by-environment interactions (eQEIs) associated with WRI1 and LAFL. Around these eQTNs and eQEIs, we pinpointed 41 and 8 candidate genes with known transcriptional regulations or protein interactions with their expression traits, respectively. Based on RNA-seq and ATAC-seq data, we employed the XGBoost and Basenji models which predicted 15 candidate genes potentially regulating the expression of WRI1 and LAFL. We further validated the predictions via tissue expression profile, haplotype analysis, and expression correlation analysis, and verified the transcriptional activation activity of BnaC03.MYB56 (R2R3-MYB transcription factor 56) on the expression of BnaA09.LEC1 by dual-luciferase reporter and yeast one-hybrid assays. BnaA10.AGL15 (AGAMOUS-LIKE 15), BnaC04.VAL1 (VIVIPAROUS1/ABSCISIC ACID INSENSITIVE3-LIKE 1), BnaC03.MYB56, and BnaA10.MYB56 were co-expressed with WRI1 and LAFL at 20 DAF in M35, a key module for seed development and oil biosynthesis. We further validated the positive regulation of MYB56 on seed oil accumulation using Arabidopsis (Arabidopsis thaliana) mutants. This study not only delivers a framework for future eQEI identification but also offers insights into the developmental regulation of seed oil accumulation. |
| first_indexed | 2024-10-01T03:04:05Z |
| format | Journal Article |
| id | ntu-10356/179366 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T03:04:05Z |
| publishDate | 2024 |
| record_format | dspace |
| spelling | ntu-10356/1793662024-07-29T15:32:15Z Transcriptional regulation of transcription factor genes WRI1 and LAFL during Brassica napus seed development Han, Xu Peng, Yan Yin, Sijie Zhao, Hu Zong, Zhanxiang Tan, Zengdong Zhang, Yuting Ma, Wei Guo, Liang School of Biological Sciences Medicine, Health and Life Sciences Brassica napus Expression genome-wide association study The WRINKLED1 (WRI1) and LAFL [LEAFY COTYLEDON1 (LEC1), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2] transcription factors play essential roles in governing seed development and oil biosynthesis. To gain a comprehensive understanding of the transcriptional regulation of WRI1 and LAFL, we conducted genome-wide association studies for the expression profiles of WRI1 and LAFL in developing seeds at 20 and 40 days after flowering (DAF) using 302 rapeseed (Brassica napus) accessions. We identified a total of 237 expression quantitative trait nucleotides (eQTNs) and 51 expression QTN-by-environment interactions (eQEIs) associated with WRI1 and LAFL. Around these eQTNs and eQEIs, we pinpointed 41 and 8 candidate genes with known transcriptional regulations or protein interactions with their expression traits, respectively. Based on RNA-seq and ATAC-seq data, we employed the XGBoost and Basenji models which predicted 15 candidate genes potentially regulating the expression of WRI1 and LAFL. We further validated the predictions via tissue expression profile, haplotype analysis, and expression correlation analysis, and verified the transcriptional activation activity of BnaC03.MYB56 (R2R3-MYB transcription factor 56) on the expression of BnaA09.LEC1 by dual-luciferase reporter and yeast one-hybrid assays. BnaA10.AGL15 (AGAMOUS-LIKE 15), BnaC04.VAL1 (VIVIPAROUS1/ABSCISIC ACID INSENSITIVE3-LIKE 1), BnaC03.MYB56, and BnaA10.MYB56 were co-expressed with WRI1 and LAFL at 20 DAF in M35, a key module for seed development and oil biosynthesis. We further validated the positive regulation of MYB56 on seed oil accumulation using Arabidopsis (Arabidopsis thaliana) mutants. This study not only delivers a framework for future eQEI identification but also offers insights into the developmental regulation of seed oil accumulation. Ministry of Education (MOE) Submitted/Accepted version This work was supported by the National Key Research and Development Plan of China (grant no. 2023YFF1000700 to L.G.), National Natural Science Foundation of China (grant no. U2102217 to L.G.), the Ministry of Education (MOE) of Singapore Tier 2 (grant no. MOE-T2EP30220-0011 to W.M.), and MOE of Singapore Tier 1 (grant nos. RG89/21 and RG32/23 to W.M.). 2024-07-29T00:58:02Z 2024-07-29T00:58:02Z 2024 Journal Article Han, X., Peng, Y., Yin, S., Zhao, H., Zong, Z., Tan, Z., Zhang, Y., Ma, W. & Guo, L. (2024). Transcriptional regulation of transcription factor genes WRI1 and LAFL during Brassica napus seed development. Plant Physiology. https://dx.doi.org/10.1093/plphys/kiae378 0032-0889 https://hdl.handle.net/10356/179366 10.1093/plphys/kiae378 39041422 en MOE-T2EP30220-0011 RG89/21 RG32/23 Plant Physiology © 2024 The Author(s). Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. This article may be downloaded for personal use only. Any other use requires prior permission of the copyright holder. The Version of Record is available online at http://doi.org/10.1093/plphys/kiae378. application/pdf |
| spellingShingle | Medicine, Health and Life Sciences Brassica napus Expression genome-wide association study Han, Xu Peng, Yan Yin, Sijie Zhao, Hu Zong, Zhanxiang Tan, Zengdong Zhang, Yuting Ma, Wei Guo, Liang Transcriptional regulation of transcription factor genes WRI1 and LAFL during Brassica napus seed development |
| title | Transcriptional regulation of transcription factor genes WRI1 and LAFL during Brassica napus seed development |
| title_full | Transcriptional regulation of transcription factor genes WRI1 and LAFL during Brassica napus seed development |
| title_fullStr | Transcriptional regulation of transcription factor genes WRI1 and LAFL during Brassica napus seed development |
| title_full_unstemmed | Transcriptional regulation of transcription factor genes WRI1 and LAFL during Brassica napus seed development |
| title_short | Transcriptional regulation of transcription factor genes WRI1 and LAFL during Brassica napus seed development |
| title_sort | transcriptional regulation of transcription factor genes wri1 and lafl during brassica napus seed development |
| topic | Medicine, Health and Life Sciences Brassica napus Expression genome-wide association study |
| url | https://hdl.handle.net/10356/179366 |
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