Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice

文献类型： 外文期刊

第一作者： Zhang, Hong

作者： Zhang, Hong;Chen, Wu;Zhu, De;Zhang, Bintao;Xu, Qiang;Shi, Chuanlin;He, Huiying;Dai, Xiaofan;Li, Yilin;He, Wenchuang;Lv, Yang;Yang, Longbo;Cao, Xinglan;Cui, Yan;Leng, Yue;Wei, Hua;Liu, Xiangpei;Zhang, Bin;Wang, Xianmeng;Guo, Mingliang;Zhang, Zhipeng;Li, Xiaoxia;Liu, Congcong;Yuan, Qiaoling;Wang, Tianyi;Yu, Xiaoman;Qian, Hongge;Zhang, Qianqian;Chen, Dandan;Hu, Guanjing;Qian, Qian;Shang, Lianguang;Zhang, Hong;Qian, Qian;Shang, Lianguang;Lv, Yang;Yu, Xiaoman;Qian, Qian;Hu, Guanjing;Shang, Lianguang

作者机构：

期刊名称：PLANT CELL （ 影响因子：10.0； 五年影响因子：11.1 ）

ISSN： 1040-4651

年卷期： 2024 年

页码：

收录情况： SCI

摘要： Alternative splicing (AS) plays crucial roles in regulating various biological processes in plants. However, the genetic mechanisms underlying AS and its role in controlling important agronomic traits in rice (Oryza sativa) remain poorly understood. In this study, we explored AS in rice leaves and panicles using the rice minicore collection. Our analysis revealed a high level of transcript isoform diversity, with approximately one-fifth of the potential isoforms acting as major transcripts in both tissues. Regarding the genetic mechanism of AS, we found that the splicing of 833 genes in the leaf and 1,230 genes in the panicle was affected by cis-genetic variation. Twenty-one percent of these AS events could only be explained by large structural variations. Approximately 77.5% of genes with significant splicing quantitative trait loci (sGenes) exhibited tissue-specific regulation, and AS can cause 26.9% (leaf) and 23.6% (panicle) of sGenes to have altered, lost, or gained functional domains. Additionally, through splicing-phenotype association analysis, we identified phosphate-starvation-induced RING-type E3 ligase (OsPIE1; LOC_Os01g72480), whose splicing ratio was significantly associated with plant height. In summary, this study provides an understanding of AS in rice and its contribution to the regulation of important agronomic traits. Genetic control of alternative splicing contributes to the regulation of agronomic traits in rice.

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