Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice
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 p...
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| Veröffentlicht in: | The Plant cell 2024-10, Vol.36 (10), p.4372-4387 |
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| container_title | The Plant cell |
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| creator | 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 |
| description | 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 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. |
| doi_str_mv | 10.1093/plcell/koae181 |
| format | Article |
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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 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.</description><identifier>ISSN: 1040-4651</identifier><identifier>ISSN: 1532-298X</identifier><identifier>EISSN: 1532-298X</identifier><identifier>DOI: 10.1093/plcell/koae181</identifier><identifier>PMID: 38916914</identifier><language>eng</language><publisher>England</publisher><ispartof>The Plant cell, 2024-10, Vol.36 (10), p.4372-4387</ispartof><rights>The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c180t-17dddb7e2edb9f0dcb30a1ef361bd5ee8d2058c4de5e173332eec459fb76a75e3</cites><orcidid>0000-0001-5640-3421 ; 0000-0003-4212-1073 ; 0000-0001-8547-2944 ; 0000-0003-4776-1942 ; 0009-0000-7087-3462 ; 0009-0009-1463-3259 ; 0000-0001-6744-2418 ; 0000-0003-4844-9870 ; 0000-0002-6373-0145 ; 0000-0002-9307-0504 ; 0009-0006-8342-4213 ; 0000-0003-0503-1482 ; 0009-0001-2247-5627 ; 0009-0009-5336-1946 ; 0000-0002-7558-2987 ; 0000-0002-1272-428X ; 0000-0002-0349-4937 ; 0000-0001-8140-6712 ; 0000-0001-5568-7215 ; 0000-0002-4606-2800 ; 0009-0002-6414-3417 ; 0000-0002-1335-6239 ; 0000-0002-3567-1782 ; 0009-0005-1834-4965 ; 0000-0002-8499-1985 ; 0000-0001-9664-6794 ; 0009-0005-2349-4618 ; 0000-0002-5091-173X ; 0000-0002-7525-5564 ; 0009-0004-2525-4194 ; 0009-0000-8514-094X ; 0000-0001-8552-7394 ; 0000-0002-5847-9750 ; 0009-0000-2491-1851</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,777,781,27905,27906</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38916914$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Hong</creatorcontrib><creatorcontrib>Chen, Wu</creatorcontrib><creatorcontrib>Zhu, De</creatorcontrib><creatorcontrib>Zhang, Bintao</creatorcontrib><creatorcontrib>Xu, Qiang</creatorcontrib><creatorcontrib>Shi, Chuanlin</creatorcontrib><creatorcontrib>He, Huiying</creatorcontrib><creatorcontrib>Dai, Xiaofan</creatorcontrib><creatorcontrib>Li, Yilin</creatorcontrib><creatorcontrib>He, Wenchuang</creatorcontrib><creatorcontrib>Lv, Yang</creatorcontrib><creatorcontrib>Yang, Longbo</creatorcontrib><creatorcontrib>Cao, Xinglan</creatorcontrib><creatorcontrib>Cui, Yan</creatorcontrib><creatorcontrib>Leng, Yue</creatorcontrib><creatorcontrib>Wei, Hua</creatorcontrib><creatorcontrib>Liu, Xiangpei</creatorcontrib><creatorcontrib>Zhang, Bin</creatorcontrib><creatorcontrib>Wang, Xianmeng</creatorcontrib><creatorcontrib>Guo, Mingliang</creatorcontrib><creatorcontrib>Zhang, Zhipeng</creatorcontrib><creatorcontrib>Li, Xiaoxia</creatorcontrib><creatorcontrib>Liu, Congcong</creatorcontrib><creatorcontrib>Yuan, Qiaoling</creatorcontrib><creatorcontrib>Wang, Tianyi</creatorcontrib><creatorcontrib>Yu, Xiaoman</creatorcontrib><creatorcontrib>Qian, Hongge</creatorcontrib><creatorcontrib>Zhang, Qianqian</creatorcontrib><creatorcontrib>Chen, Dandan</creatorcontrib><creatorcontrib>Hu, Guanjing</creatorcontrib><creatorcontrib>Qian, Qian</creatorcontrib><creatorcontrib>Shang, Lianguang</creatorcontrib><title>Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice</title><title>The Plant cell</title><addtitle>Plant Cell</addtitle><description>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 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. 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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 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. 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| identifier | ISSN: 1040-4651 |
| ispartof | The Plant cell, 2024-10, Vol.36 (10), p.4372-4387 |
| issn | 1040-4651 1532-298X 1532-298X |
| language | eng |
| recordid | cdi_proquest_miscellaneous_3072001410 |
| source | Oxford University Press Journals All Titles (1996-Current) |
| title | Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice |
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