Functional examination of lncRNAs in allotetraploid Gossypium hirsutum

BMC Genomics

Ting Zhao¹  Xiaoyuan Tao¹  Jin Han¹  Zeyi Cao¹  Xueying Guan²  Quanjia Chen³  Luyao Wang⁴  Menglin Li⁵  Kening Lu⁵  Xue Chen⁵  Mengtao Gao⁵ 

[1] College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China;College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China;Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Building 11, Yonyou Industrial Park, Yazhou District, 572025, Sanya, Hainan Province, China;Engineering Research Centre of Cotton, Ministry of Education / College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, China;Engineering Research Centre of Cotton, Ministry of Education / College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, China;State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China;College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China;State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China;

关键词: lncRNA function;    Conservation;    Abiotic stress;   

DOI  :  10.1186/s12864-021-07771-3

来源: Springer

【 摘 要 】

BackgroundAn evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown.ResultsWe employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses.ConclusionsLow-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.

【 授权许可】

CC BY