Temporal regulation of alternative splicing events in rice memory under drought stress

doi:10.1016/j.pld.2020.11.004

Plant Diversity ›› 2022, Vol. 44 ›› Issue (01): 116-125.DOI: 10.1016/j.pld.2020.11.004

• Articles • 上一篇

Temporal regulation of alternative splicing events in rice memory under drought stress

Hong Yang^a,d, Ping Li^a, Guihua Jin^a,d, Daping Gui^a, Li Liu^a,b, Chengjun Zhang^a,c

a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China;
c Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China;
d University of Chinese Academy of Sciences, Beijing, 100049, China

收稿日期:2020-10-18 修回日期:2020-10-29 出版日期:2022-02-25 发布日期:2022-03-12
通讯作者: Li Liu, Chengjun Zhang
基金资助:
This study was funded by National Natural Science Foundation of China (31571311 to CZ and 31971410 to LL) and the CAS Pioneer Hundred Talents Program (CZ and LL).

Temporal regulation of alternative splicing events in rice memory under drought stress

Hong Yang^a,d, Ping Li^a, Guihua Jin^a,d, Daping Gui^a, Li Liu^a,b, Chengjun Zhang^a,c

a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China;
c Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China;
d University of Chinese Academy of Sciences, Beijing, 100049, China

Received:2020-10-18 Revised:2020-10-29 Online:2022-02-25 Published:2022-03-12
Contact: Li Liu, Chengjun Zhang
Supported by:
This study was funded by National Natural Science Foundation of China (31571311 to CZ and 31971410 to LL) and the CAS Pioneer Hundred Talents Program (CZ and LL).

摘要/Abstract

摘要： Plant adaptation to drought stress is essential for plant survival and crop yield. Recently, harnessing drought memory, which is induced by repeated stress and recovery cycles, was suggested as a means to improve drought resistance at the transcriptional level. However, the genetic mechanism underlying drought memory is unclear. Here, we carried out a quantitative analysis of alternative splicing (AS) events in rice memory under drought stress, generating 12 transcriptome datasets. Notably, we identified exon skipping (ES) as the predominant AS type (>80%) in differential alternative splicing (DAS) in response to drought stress. Applying our analysis pipeline to investigate DAS events following drought stress in six other plant species revealed variable ES frequencies ranging from 9.94% to 60.70% depending on the species, suggesting that the relative frequency of DAS types in plants is likely to be species-specific. The dinucleotide sequence at AS splice sites in rice following drought stress was preferentially GC-AG and AT-AC. Since U12-type splicing uses the AT-AC site, this suggests that drought stress may increase U12-type splicing, and thus increase ES frequency. We hypothesize that multiple isoforms derived from exon skipping may be induced by drought stress in rice. We also identified 20 transcription factors and three highly connected hub genes with potential roles in drought memory that may be good targets for plant breeding.

关键词: Alternative splicing, Drought memory, Exon skipping

Abstract: Plant adaptation to drought stress is essential for plant survival and crop yield. Recently, harnessing drought memory, which is induced by repeated stress and recovery cycles, was suggested as a means to improve drought resistance at the transcriptional level. However, the genetic mechanism underlying drought memory is unclear. Here, we carried out a quantitative analysis of alternative splicing (AS) events in rice memory under drought stress, generating 12 transcriptome datasets. Notably, we identified exon skipping (ES) as the predominant AS type (>80%) in differential alternative splicing (DAS) in response to drought stress. Applying our analysis pipeline to investigate DAS events following drought stress in six other plant species revealed variable ES frequencies ranging from 9.94% to 60.70% depending on the species, suggesting that the relative frequency of DAS types in plants is likely to be species-specific. The dinucleotide sequence at AS splice sites in rice following drought stress was preferentially GC-AG and AT-AC. Since U12-type splicing uses the AT-AC site, this suggests that drought stress may increase U12-type splicing, and thus increase ES frequency. We hypothesize that multiple isoforms derived from exon skipping may be induced by drought stress in rice. We also identified 20 transcription factors and three highly connected hub genes with potential roles in drought memory that may be good targets for plant breeding.

Key words: Alternative splicing, Drought memory, Exon skipping

Hong Yang, Ping Li, Guihua Jin, Daping Gui, Li Liu, Chengjun Zhang. Temporal regulation of alternative splicing events in rice memory under drought stress[J]. Plant Diversity, 2022, 44(01): 116-125.

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Temporal regulation of alternative splicing events in rice memory under drought stress

Temporal regulation of alternative splicing events in rice memory under drought stress

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