Expression of lncRNA SVR and adjacent <i>SAUR</i> genes in rice during seed germination under low temperature

LIU Jinzhao; PU Na; CHEN Chun; CHEN Weixiong; WANG Hui; XIAO Wuming

doi:10.7671/j.issn.1001-411X.202308015

Journal of South China Agricultural University > 2023 > 44(6): 896-905. > DOI: 10.7671/j.issn.1001-411X.202308015

LIU Jinzhao, PU Na, CHEN Chun, et al. Expression of lncRNA SVR and adjacent SAUR genes in rice during seed germination under low temperature[J]. Journal of South China Agricultural University, 2023, 44(6): 896-905. DOI: 10.7671/j.issn.1001-411X.202308015

Citation:

PDF (1946 KB)

Expression of lncRNA SVR and adjacent SAUR genes in rice during seed germination under low temperature

1.
National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
2.
Guangzhou Academy of Agricultural Sciences, Guangzhou 510338, China

More Information

Received Date: August 21, 2023
Available Online: November 12, 2023
Published Date: October 16, 2023

Graphical Abstract

Abstract

Abstract

Objective
Long non-coding RNA (lncRNA) is longer than 200 nt and generally does not code proteins. To explore the effect of lncRNA on the expression of neighbouring SAUR genes under low temperature, and provide a theoretical basis for studying the ability of rice seeds to germinate at low temperature.
Method
lncRNA SVR was investigated in response to cold stress in previous research of National Engineering Research Center of Plant Space Breeding, South China Agricultural University. The secondary structure of lncRNA SVR was analysed by bioinformatics, and the cold stress motifs within lncRNA SVR was searched. The expression characteristics of lncRNA SVR and SAUR genes were analysed by qRT-PCR.
Result
In this study, highly similar cold stress response motifs were found in the sequence of lncRNA SVR and at the stem-loop junction. Expression characterization showed that cold stress during seed germination continuously decreased the expression of lncRNA SVR, and the expression of some neighbouring SAUR genes was significantly higher under cold stress than that at room temperature, indicating that the neighbouring SAUR genes could respond to cold stress to some extent as well as lncRNA SVR. Expression correlation analysis showed that the expression relationship between lncRNA SVR and these SAUR genes in low temperature germination were all negatively correlated, and the expression of lncRNA SVR and OsSAUR55 showed a significant negative correlation. Further analysis of SAUR gene expression in low temperature seed germination in the lncRNA SVR knockout lines showed that the decrease of lncRNA SVR in the knockout lines was lower than that in the wild type, and the increase in expression of OsSAUR41, OsSAUR53, OsSAUR54 and OsSAUR55 was significantly lower than that in the wild type.
Conclusion
lncRNA SVR is able to negatively regulate the expression of OsSAUR55, further respond to low temperature stress.
- Oryza sativa L.,
- Long non-coding RNA,
- SAUR gene cluster,
- Low temperature stress,
- Transcription regulation,
- Seed germination

FullText(HTML)

References (27)

References

[1]	杨贺, 张楠, 刘自广, 等. 低温胁迫下结球甘蓝BoNR8 lncRNA过表达对拟南芥种子萌发的影响[J]. 植物研究, 2020, 40(3): 441-446.
[2]	FU X D. Non-coding RNA: A new frontier in regulatory biology[J]. National Science Review, 2014, 1(2): 190-204. doi: 10.1093/nsr/nwu008
[3]	WASEEM M, LIU Y, XIA R. Long non-coding RNAs, the dark matter: An emerging regulatory component in plants[J]. International Journal of Molecular Sciences, 2020, 22(1): 86. doi: 10.3390/ijms22010086.
[4]	KAPRANOV P, CHENG J, DIKE S, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription[J]. Science, 2007, 316(5830): 1484-1488. doi: 10.1126/science.1138341
[5]	SHI X, SUN M, LIU H, et al. Long non-coding RNAs: A new frontier in the study of human diseases[J]. Cancer Letters, 2013, 339(2): 159-166. doi: 10.1016/j.canlet.2013.06.013
[6]	MA L, BAJIC V B, ZHANG Z. On the classification of long non-coding RNAs[J]. RNA Biology, 2013, 10(6): 925-934.
[7]	KOPP F, MENDELL J T. Functional classification and experimental dissection of long noncoding RNAs[J]. Cell, 2018, 172(3): 393-407. doi: 10.1016/j.cell.2018.01.011
[8]	王彬, 陈敏氡, 白昌辉, 等. 长链非编码RNA在植物生长发育和逆境胁迫响应中的研究进展[J]. 中国细胞生物学学报, 2023, 45(1): 153-163.
[9]	郑佳秋, 吴永成, 王薇薇, 等. 植物逆境相关长链非编码RNA的研究进展[J]. 江苏农业科学, 2020, 48(4): 19-23.
[10]	张楠, 刘自广, 孙世臣, 等. 拟南芥AtR8 lncRNA对盐胁迫响应及其对种子萌发的调节作用[J]. 植物学报, 2020, 55(4): 421-429.
[11]	WANG Y, LUO X, SUN F, et al. Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice[J]. Nature Communications, 2018, 9: 3516. doi: 10.1038/s41467-018-05829-7.
[12]	蔡晶晶. 长链非编码RNA13853调控拟南芥干旱胁迫应答机制研究[D]. 南昌: 南昌大学, 2020.
[13]	张晓佩. 陆地棉长链非编码RNAs-lncRNA354和lncRNA973的功能和作用机制研究[D]. 泰安: 山东农业大学, 2022.
[14]	WANG P, DAI L, AI J, et al. Identification and functional prediction of cold-related long non-coding RNA (lncRNA) in grapevine[J]. Scientific Reports, 2019, 9: 6638. doi: 10.1038/s41598-019-43269-5.
[15]	CAO Z, ZHAO T, WANG L, et al. The lincRNA XH123 is involved in cotton cold-stress regulation[J]. Plant Molecular Biology, 2021, 106(6): 521-531. doi: 10.1007/s11103-021-01169-1
[16]	MOISON M, PACHECO J M, LUCERO L, et al. The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold[J]. Molecular Plant, 2021, 14(6): 937-948. doi: 10.1016/j.molp.2021.03.008
[17]	PACHECO J M, MANSILLA N, MOISON M, et al. The lncRNA APOLO and the transcription factor WRKY42 target common cell wall EXTENSIN encoding genes to trigger root hair cell elongation[J]. Plant Signaling & Behavior, 2021, 16(8): 1920191. doi: 10.1080/15592324.2021.1920191.
[18]	GAO Q, LIU J, WENG H, et al. A long noncoding RNA derived from lncRNA-mRNA networks modulates seed vigor[J]. International Journal of Molecular Sciences, 2022, 23(16): 9472. doi: 10.3390/ijms23169472.
[19]	管健. 应用Real Time PCR法进行mRNA表达量相对定量分析方法的探讨[J]. 现代园艺, 2014(5): 4-5.
[20]	DI C, YUAN J, WU Y, et al. Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features[J]. The Plant Journal, 2014, 80(5): 848-861. doi: 10.1111/tpj.12679
[21]	朱宇斌, 孔莹莹, 王君晖. 植物生长素响应基因SAUR的研究进展[J]. 生命科学, 2014, 26(4): 407-413.
[22]	CHAE K, ISAACS C G, REEVES P H, et al. Arabidopsis SMALL AUXIN UP RNA63 promotes hypocotyl and stamen filament elongation[J]. The Plant Journal, 2012, 71(4): 684-697. doi: 10.1111/j.1365-313X.2012.05024.x
[23]	吴春梅. 拟南芥生长素响应基因SAUR6、SAUR14和SAUR16对抗冻的作用和机理研究[D]. 兰州: 兰州大学, 2021.
[24]	翟立升. 水稻OsSAUR10的表达和功能研究及水稻胚芽特异表达基因的生物信息学分析[D]. 贵阳: 贵州师范大学, 2019.
[25]	李明发. SAUR15在种子萌发中的功能及分子机理研究[D]. 兰州: 兰州大学, 2022.
[26]	宋松泉, 刘军, 唐翠芳, 等. 生长素代谢与信号转导及其调控种子休眠与萌发的分子机制[J]. 科学通报, 2020, 65(34): 3924-3943.
[27]	SUN Y, HAO P, LV X, et al. A long non-coding apple RNA, MSTRG. 85814.11, acts as a transcriptional enhancer of SAUR32 and contributes to the Fe-deficiency response[J]. The Plant Journal, 2020, 103(1): 53-67. doi: 10.1111/tpj.14706

Cited By

Cited by

Periodical cited type(0)

Other cited types(2)

Get Citation

PDF

XML

Article views (595) PDF downloads (20) Cited by(2)

Turn off MathJax

Article Contents

Abstract

References

Expression of lncRNA SVR and adjacent SAUR genes in rice during seed germination under low temperature

Abstract

References

Cited by

Periodical cited type(0)

Other cited types(2)

Catalog

Export File

Citation

Format

Content