数字农科院2.0

Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus

文献类型： 外文期刊

作者： Zengdong Tan;Yan Peng;; Yao Xiong;; Feng Xiong;; Yuting Zhang;; Ning Guo ; Zhuo Tu ; Zhanxiang Zong ; Xiaokun Wu ; Jiang Ye; Chunjiao Xia; Tao Zhu; Yinmeng Liu; Hongxiang Lou ; Dongxu Liu; Shaoping Lu ; Xuan Yao; Rod J.Snowdon; Agnieszka A Golicz; Weibo Xie; Liang Guo and Hu Zhao

关键词： Brassica napus; eQTL; subgenome; machine learning; regulatory network; seed oil content

期刊名称： GENOME BIOLOGY

ISSN： 1474-760X

年卷期： 2022 年

页码：

收录情况： SCIE（2022版）

摘要： Background: Regulation of gene expression plays an essential role in controlling the phenotypes of plants. Brassica napus(B. napus) is an important source for the vegetable oil in the world, and the seed oil content is an important trait of B. napus. Results: We perform a comprehensive analysis of the transcriptional variability in the seeds of B. napus at two developmental stages, 20 and 40 days after flowering (DAF). We detect 53,759 and 53,550 independent expression quantitative trait loci (eQTLs) for 79,605 and 76,713 expressed genes at 20 and 40 DAF, respectively. Among them, the local eQTLs are mapped to the adjacent genes more frequently. The adjacent gene pairs are regulated by local eQTLs with the same open chromatin state and show a stronger mode of expression piggybacking. Inter-subgenomic analysis indicates that there is a feedback regulation for the homoeologous gene pairs to maintain partial expression dosage. We also identify 141 eQTL hotspots and find that hotspot87-88 co-localizes with a QTL for the seed oil content. To further resolve the regulatory network of this eQTL hotspot, we construct XGBoost model using 856 RNA-seq datasets and Basenji model using 59 ATAC-seq datasets. Using these two models, we predict the mechanisms affecting the seed oil content regulated by hotspot87-88, and experimentally validate that the transcription factors, NAC13 and SCL31, positively regulate the seed oil content. Conclusions: We comprehensively characterize the gene regulatory features in the seeds of B. napus and reveal the gene networks regulating the seed oil content of B. Manuscript Click here to access/download;Manuscript;20221007 eQTL_manuscript_clean.docx Click here to view linked Referencesus.

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