Bulk RNA-Seq Analysis Reveals Differentially Expressed Genes Associated with Lateral Branch Angle in Peanut

文献类型： 外文期刊

第一作者： Ahmad, Naveed

作者： Ahmad, Naveed;Hou, Lei;Ma, Junjie;Xia, Han;Zhao, Shuzhen;Tian, Ruizheng;Pan, Jiaowen;Li, Changsheng;Li, Aiqin;Wang, Xingjun;Zhao, Chuanzhi;Hou, Lei;Zhou, Ximeng;Wang, Mingxiao;Wang, Xingjun;Zhao, Chuanzhi;Leal-Bertioli, Soraya;Bertioli, David;Leal-Bertioli, Soraya;Bertioli, David

作者机构：

关键词： bulk RNA-sequencing (BR-seq); branch angle; gravitropism; plant hormones; alternative splicing; peanut

期刊名称：GENES （ 影响因子：4.141； 五年影响因子：4.474 ）

ISSN：

年卷期： 2022 年 13 卷 5 期

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收录情况： SCI

摘要： Lateral branch angle (LBA), or branch habit, is one of the most important agronomic traits in peanut. To date, the underlying molecular mechanisms of LBA have not been elucidated in peanut. To acquire the differentially expressed genes (DEGs) related to LBA, a TI population was constructed through the hybridization of a bunch-type peanut variety Tifrunner and prostrate-type Ipadur. We report the identification of DEGs related to LBA by sequencing two RNA pools, which were composed of 45 F-3 lines showing an extreme opposite bunch and prostrate phenotype. We propose to name this approach Bulk RNA-sequencing (BR-seq) as applied to several plant species. Through BR-seq analysis, a total of 3083 differentially expressed genes (DEGs) were identified, including 13 gravitropism-related DEGs, 22 plant hormone-related DEGs, and 55 transcription factors-encoding DEGs. Furthermore, we also identified commonly expressed alternatively spliced (AS) transcripts, of which skipped exon (SE) and retained intron (RI) were most abundant in the prostrate and bunch-type peanut. AS isoforms between prostrate and bunch peanut highlighted important clues to further understand the post-transcriptional regulatory mechanisms of branch angle regulation. Our findings provide not only important insights into the landscape of the regulatory pathway involved in branch angle formation but also present practical information for peanut molecular breeding in the future.

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