Identification of microRNAs involved in drought stress responses in early-maturing cotton by high-throughput sequencing

다국어 초록 (Multilingual Abstract)

Drought stress is one of the most important abiotic stresses. Cotton is classified as drought tolerant crop but the regulatory mechanism is unknown. MicroRNAs (miRNAs) have been implicated important roles in stress responses in many plants.
However, the study of miRNAs in cotton responsive to drought stress is limited, especially in early-maturing cotton. In this study, we performed deep sequencing of small RNAs to identify known and novel miRNAs involved in the regulation of drought stress and understand the expression profile of miRNAs in early-maturing cotton. Three cotton small RNA libraries: non-stressed Shizao1 (early-maturing cotton variety) library (NSS), drought-stressed Shizao1 library (DSS) and non-stressed Jimian958 (medium-maturing cotton variety) library (NSJ) were constructed for deep sequencing. As a result, we identified a total of 64 known and 67 novel miRNAs in the 3 libraries and 88 of them were dramatically differentially expressed (greater than twofold) during drought stress. In addition, we found the expression of 41 miRNAs increased or reduced more than twofold in early-maturing cotton variety compared with that in medium-maturing cotton variety. Our results significantly increased the number of miRNAs in cotton and revealed for the first time the expression profile of miRNAs for early-maturing cotton.

참고문헌 (Reference)

1 Dai X, "psRNATarget: a plant small RNA target analysis server" 39 : 155-159, 2011

2 Gao P, "osa-MIR393: a salinity- and alkaline stress-related micro-RNA gene" 38 : 237-242, 2011

3 Wang JW, "miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana" 138 : 738-749, 2009

4 Valliyodan B, "Understanding regulatory networks and engineering for enhanced drought tolerance in plants" 9 : 189-195, 2006

5 Wu G, "The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis" 138 : 750-759, 2009

6 Shukla LI, "The role of microRNAs and other endogenous small RNAs in plant stress responses" 1779 : 743-748, 2008

7 Kidner CA, "The developmental role of microRNA in plants" 8 : 38-44, 2005

8 Lu S, "Stress-responsive micro-RNAs in Populus" 55 : 131-151, 2008

9 Schwab R, "Specific effects of microRNAs on the plant transcriptome" 8 : 517-527, 2005

10 Kidokoro S, "Soybean DREB1/CBF-type transcription factors function in heat and drought as well as cold stress-responsive gene expression" 81 : 505-518, 2015

11 Zhang D, "Soybean C2H2-type zinc finger protein GmZFP3 with conserved QALGGH motif negatively regulates drought responses in transgenic Arabidopsis" 7 : 325-, 2016

12 Wang Q, "Small RNA-mediated responses to low- and high-temperature stresses in cotton" 6 : 35558-, 2016

13 Li JB, "Simultaneous overexpression of the HhERF2 and PeDREB2a genes enhanced tolerances to salt and drought in transgenic cotton" 23 : 450-458, 2016

14 Nawrocki EP, "Rfam 12.0: updates to the RNA families database" 43 : 130-137, 2015

15 Mathieu J, "Repression of flowering by the miR172 target SMZ" 7 : e1000148-, 2009

16 Aukerman MJ, "Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes" 15 : 2730-2741, 2003

17 Chen C, "Real-time quantification of microRNAs by stem-loop RT-PCR" 33 : e179-, 2005

18 Xu K, "OsGRAS23, a rice GRAS transcription factor gene, is involved in drought stress response through regulating expression of stress-responsive genes" 15 : 141-, 2015

19 Sunkar R, "Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis" 16 : 2001-2019, 2004

20 Liu HH, "Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana" 14 : 836-843, 2008

21 Wang M, "MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development" 7 : 44454-, 2017

22 Zuker M, "Mfold web server for nucleic acid folding and hybridization prediction" 31 : 3406-3415, 2003

23 Price AH, "Linking drought-resistance mechanisms to drought avoidance in upland rice using a QTL approach: progress and new opportunities to integrate stomatal and mesophyll responses" 53 : 989-1004, 2002

24 Zhang Y, "Identification of miRNAs and their targets in cotton inoculated with Verticillium dahliae by high-throughput sequencing and degradome analysis" 16 : 14749-14768, 2015

25 Song QX, "Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing" 11 : 5-, 2011

26 Zhao B, "Identification of drought-induced microRNAs in rice" 354 : 585-590, 2007

27 Zhang B, "Identification of cotton microRNAs and their targets" 397 : 26-37, 2007

28 Lv S, "Identification and characterization of microRNAs from barley (Hordeum vulgare L.) by high-throughput sequencing" 13 : 2973-2984, 2012

29 Ni Z, "GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress" 82 : 113-129, 2013

30 Pang M, "Genomewide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L." 10 : R122-, 2009

31 Miao Q, "Genome-wide identification and characterization of microRNAs differentially expressed in fibers in a cotton phytochrome A1 RNAi line" 12 : e0179381-, 2017

32 Butt HI, "Functional characterization of cotton GaMYB62L, a novel R2R3 TF in transgenic Arabidopsis" 12 : e0170578-, 2017

33 Kwak PB, "Enrichment of a set of microRNAs during the cotton fiber development" 10 : 457-, 2009

34 Umezawa T, "Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future" 17 : 113-122, 2006

35 Sun R, "Differential expression of microRNAs during fiber development between fuzzless-lintless mutant and its wild-type allotetraploid cotton" 7 : 3-, 2017

36 Ding D, "Differential expression of miRNAs in response to salt stress in maize roots" 103 : 29-38, 2009

37 Yin Z, "Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity" 39 : 4961-4970, 2012

38 Xie F, "Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton" 66 : 789-804, 2015

39 Meyers BC, "Criteria for annotation of plant microRNAs" 20 : 3186-3190, 2008

40 Li H, "Characterization of the stress associated microRNAs in Glycine max by deep sequencing" 11 : 170-, 2011

41 Luo LJ, "Breeding for water-saving and drought-resistance rice (WDR) in China" 61 : 3509-3517, 2010

42 Ambros V, "A uniform system for microRNA annotation" 9 : 277-279, 2003

43 Yang Y, "A novel Ap2/ERF transcription factor from Stipa purpurea leads to enhanced drought tolerance in Arabidopsis thaliana" 35 : 2227-2239, 2016

44 Chen X, "A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development" 303 : 2022-2025, 2004

45 Wang ZM, "A comparative miRNAome analysis reveals seven fiber initiation-related and 36 novel miRNAs in developing cotton ovules" 5 : 889-900, 2012