Han Xu, Peng Yan, Yin Sijie, Zhao Hu, Zong Zhanxiang, Tan Zengdong, Zhang Yuting, Ma Wei, Guo Liang
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
Yazhouwan National Laboratory, Sanya 572025, China.
Plant Physiol. 2025 Feb 7;197(2). doi: 10.1093/plphys/kiae378.
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-sequencing and assay for transposase-accessible chromatin with high-throughput sequencing data, we employed the Extreme Gradient Boosting 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 1-hybrid assays. BnaA10.AGL15 (AGAMOUS-LIKE 15), BnaC04.VAL1 (VIVIPAROUS1/ABSCISIC ACID INSENSITIVE3-LIKE 1), BnaC03.MYB56, and BnaA10.MYB56 were coexpressed 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.
皱叶1（WRINKLED1，WRI1）和LAFL（叶状子叶1 [LEAFY COTYLEDON1，LEC1]、脱落酸不敏感3 [ABSCISIC ACID INSENSITIVE3，ABI3]、FUSCA3 [FUS3]和LEC2）转录因子在调控种子发育和油脂生物合成中发挥着重要作用。为了全面了解WRI1和LAFL的转录调控，我们利用302份油菜（甘蓝型油菜）种质，对开花后20天和40天发育种子中WRI1和LAFL的表达谱进行了全基因组关联研究。我们共鉴定出237个表达数量性状核苷酸（eQTN）和51个与WRI1和LAFL相关的表达QTN-环境互作（eQEI）。围绕这些eQTN和eQEI，我们分别确定了41个和8个具有已知转录调控或与它们的表达性状存在蛋白质相互作用的候选基因。基于RNA测序和转座酶可及染色质高通量测序数据的分析，我们采用了极限梯度提升和巴森吉模型，预测了15个可能调控WRI1和LAFL表达的候选基因。我们通过组织表达谱、单倍型分析和表达相关性分析进一步验证了这些预测，并通过双荧光素酶报告基因和酵母单杂交试验验证了BnaC03.MYB56（R2R3-MYB转录因子56）对BnaA09.LEC1表达的转录激活活性。BnaA10.AGL15（AGAMOUS-LIKE 15）、BnaC04.VAL1（VIVIPAROUS1/ABSCISIC ACID INSENSITIVE3-LIKE 1）、BnaC03.MYB56和BnaA10.MYB56在种子发育和油脂生物合成的关键模块M35中，于开花后20天与WRI1和LAFL共表达。我们利用拟南芥突变体进一步验证了MYB56对种子油积累的正向调控作用。本研究不仅为未来eQEI的鉴定提供了一个框架，也为种子油积累的发育调控提供了见解。
