Expression pattern of wheat miRNAs under salinity stress and prediction of salt-inducible miRNAs targets

doi:10.1007/s11703-011-1133-z

Front Agric Chin

0, Vol.

Issue () : 413-422 https://doi.org/10.1007/s11703-011-1133-z

RESEARCH ARTICLE

Expression pattern of wheat miRNAs under salinity stress and prediction of salt-inducible miRNAs targets

Wenjing LU², Jincai LI³, Fangpeng LIU², Juntao GU², Chengjin GUO¹, Liu XU², Huiyan ZHANG², Kai XIAO¹(

)

1. College of Agronomy, Agricultural University of Hebei, Baoding 071001, China; 2. College of Life Sciences, Agricultural University of Hebei, Baoding 071001, China; 3. Science and Technology Management Office, Agricultural University of Hebei, Baoding 071001, China

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Abstract

MicroRNAs (miRNAs) are non-coding small RNAs that regulate gene expression by translational repression or transcript degradation. Thus far, a large number of miRNAs have been identified from model plant species and the quantity of miRNAs has been functionally characterized in diverse plants. However, the molecular characterizations of the conserved miRNAs are still largely elusive in wheat. In this study, 32 wheat miRNAs (TaMIRs) currently released in the Sanger miRBase (the microRNA database) were selected to evaluate the expression patterns under conditions of non-stress (CK) and salt stress treatment. Based on the analysis of semiquantitative RT-PCR and quantitative real qRT-PCR, TaMIR159a, TaMIR160, TaMIR167, TaMIR174, TaMIR399, TaMIR408, TaMIR11124 and TaMIR1133 were found to have responses to salinity stress, with an upregulated pattern under salt stress treatment. Based on a BLAST search against the NCBI GenBank database, the potential targets of the salt-inducible wheat miRNAs were predicted. Except for TaMIR399 not being identified to have the putative target genes, other salt-inducible TaMIRs were found to possess 2 to 7 putative target genes. Together, our results suggest that a subset of miRNAs are involved in the mediation of salt stress signaling responses in wheat via their roles on the regulation of acted target genes at post-transcriptional and translation levels.

Keywords wheat (Triticum aestivum L.) microRNA expression target gene salinity stress

Corresponding Author(s): XIAO Kai,Email:xiaokai@hebau.edu.cn

Issue Date: 05 December 2011

Cite this article:

Wenjing LU,Jincai LI,Fangpeng LIU, et al. Expression pattern of wheat miRNAs under salinity stress and prediction of salt-inducible miRNAs targets[J]. Front Agric Chin, 0, (): 413-422.

URL:

https://academic.hep.com.cn/fag/EN/10.1007/s11703-011-1133-z
https://academic.hep.com.cn/fag/EN/Y0/V/I/413

Tab.1 The molecular characterization of wheat TaMIRs

Name of TaMIR	Forward primer	Reverse primer	Length of product (bp)
TaMIR159a	5′-GGTTCCCACTATCCTATC CC A	5′-TGCAGAGCTCCCTTCAATCCA	112
TaMIR159b	5′-AAAAAGGGGTGTTGCTGTG	5′-ATGCAGAGCTCCCTTCAATCC	238
TaMIR160	5′-GATATGCCTGGCTCCCTGTATG	5′-AGACGGTCATGCTTGGCTCCTC	103
TaMIR164	5′-GGTGGAGAAGCAGGGCACGT	5′-GGTGGAGAAGAAAGGCACAT	156
TaMIR167	5′-CTGCCCAAGGGAACGAGTGA	5′-AGAAGTAGTTGAGCCCAACG	108
TaMIR174	5′-GATGTTGGCTCGACTCACTCAG	5′-CTGAGATATTGGCACGGCTCA	89
TaMIR399	5′-CGTGTGTGAATCACAGGGC	5′-GGGCAATTTCCTTTGGCA	125
TaMIR408	5′-AAGGGATGAGGCAAGCAACAAAA	5′-GGAGGGGAGCCAGGGAAGAG	119
TaMIR444	5′-CAAGGCGCAAAATTAATAGAAGAT	5′-ACCTGCCAGTAGATGAAAACA	310
TaMIR1117	5′-AAAATGGGACCTTTAGTACC	5′-GCGACTAAAGCTCCTCCCT	113
TaMIR1118	5′-AAGCACGTGGATAGAGGAAG	5′-CGAACCAAACATAAAAAAAAGG	139
TaMIR1119	5′-AGCGTCAGCGTGTGAGGCG	5′-CGCATAGCACTCCCACTCC	158
TaMIR1120	5′-GGGCAGGTACTCCCTCCGT	5′-GTGATTCAGGAGCTGGGAA	109
TaMIR1121	5′-TATATATGTACTCCCTCTGT	5′-TACAGTACTCCCTCCGTAA	98
TaMIR1122	5′-CTCCCTCCGTCCCAAAAA	5′-ACGAAGTAAAATGAGTGAATCTA	211
TaMIR1123	5′-CCAGGTCTCATATAAATCAGGT	5′-AATTCTATGAGACCAGGTCTCA	196
TaMIR1124	5′-ATTACATGACTCAAAGGAACG	5′-AGTACCGAGTCTAGCTTCC	129
TaMIR1125	5′-TTTGGCCGTAAATTTAACCA	5′-GACCGGTAAATTTAACCAAC	138
TaMIR1126	5′-GTACTCTCTCCGTTCCTAAA	5′-ATACTCCCTCCGTTTCTAA	164
TaMIR1127	5′-ACATTAGATCTCAACTAC	5′-ATCCACATTAGAATATACTCCC	149
TaMIR1128	5′-ATATGAGAGCATGGGTGAG	5′-ACATAAACGCCAAGCCAGAA	190
TaMIR1129	5′-GCCATTCAGCCAGAAGAA	5′-ATGGTGGACGGAGGGAGTT	269
TaMIR1130	5′-AAATGTCTTATACTCCCTCC	5′-CGTTGCAAATACTACCACTC	122
TaMIR1131	5′-CATTAGTACCGGTTCGTGG	5′-CCCAGACTGACAACATCC	91
TaMIR1132	5′-TACTCCCTCCGTTTCACAAT	5′-TACTCCTTCCGTTCCATAAT	154
TaMIR1133	5′-ACTTCTTAGTGATAGTGGTCA	5′-TAGCAACTTCAGTGAGTATATC	180
TaMIR1134	5′-ACGCGTCCGGCATTCTTCT	5′-TACATGTTGTTGCAGCTGCA	178
TaMIR1135	5′-CTACTCCCTCCATTCGGAA	5′-TACTCCCTCCGTTCGGAAT	108
TaMIR1136	5′-TACTCCCTCCGTTCCGAAT	5′-TACTCCCTCCGTTTCAAATT	107
TaMIR1137	5′-CACGATGACGACGATTAGA	5′-GATTTTCCTTATCACTAGCAA	148
TaMIR1138	5′-ATCTTGTATAGGTCTGTCTA	5′-CAGTTTGTTTAATTCACATCTAG	189
TaMIR1139	5′-GCCACAGTGGAGAGTAACAT	5′-AGTGGGAGTAACTTCAATAGT	216

Tab.2 Primers used for detection of the precursor transcripts of the wheat TaMIRs

Fig.1 Semiquantitative RT-PCR results of 32 wheat TaMIR transcripts under conditions of non-stress (CK) and salt stress treatment.

Fig.2 qRT-PCR results of 32 wheat TaMIR transcripts under conditions of non-stress (CK) and salt stress treatment.

Name of TaMIRs	Contig hit	Identity between TaMIR and contig	E-value between TaMIR and contig	Pairing position between TaMIR and contig	Accession number of target gene	Putative function of target gene	E-value between target gene and contig
TaMIR159a	Contig4672	13/13 (100%)	1.0	Query: 8-20 corresponding to Subject: 907-895	AF332874	phosphoinositide-specific phospholipase C [Oryza sativa]	0.0
	Contig2035	13/13 (100%)	1.0	Query: 4-16 corresponding to Subject: 640-628	BAA96769.1	putative pyruvate decarboxylase [Oryza sativa]	0.0
	Contig1341	13/13 (100%)	1.0	Query: 7-19 corresponding to Subject: 2392-2380	BAD53266.1	putative disease resistance protein RPS2 [Oryza sativa]	0.0
	tp1b0004 g13	13/13 (100%)	0.92	Query: 9-21 corresponding to Subject: 1419-1407		No hit
TaMIR160	tp1b005m02	20/20 (100%)	6e-05	Query: 1-20 corresponding to Subject: 1743-1724	AAP54297.2	Auxin response factor 16 [Oryza sativa]	0.0
	Contig1937	13/13 (100%)	1.0	Query: 4-16 corresponding to Subject: 1227-1215	BAA07785.3	plastid omega-3 fatty acid desaturase [Triticum aestivum]	0.0
	tp1b0011d04	13/13 (100%)	1.0	Query: 1-13 corresponding to Subject: 670-658	NP_001056613.1	putative 60S ribosomal protein L13E [Oryza sativa]	2e-84
TaMIR167	Contig4774	17/18 (94)	0.27	Query: 3-20 corresponding to Subject: 3131-3114	BAD25169.1	putative auxin response transcription factor(ARF6) [Oryza sativa]	0.0
tp1b0010k14	13/13 (100%)	0.92	Query: 5-17 corresponding to Subject: 362-350	ABF93706.1	oxidoreductase, 2OG-Fe oxygenase family protein, expressed [Oryza sativa]	0.0
TaMIR174	tp1b0006d11	21/21 (100%)	2e-05	Query: 1-21 corresponding to Subject: 1172-1152	AT4G00150.1	scarecrow-like transcription factor 6 (SCL6)[Arabidopsis thaliana]	e-68
Contig548	13/13 (100%)	1.0	Query: 2-14 corresponding to Subject: 509-497	AT4G23180.1	RLK4, CRK10 (CYSTEINE-RICH RLK10); kinase [Arabidopsis thaliana]	2e-37
TaMIR399				No hit
TaMIR408	Contig750	20/20 (100%)	7e-05	Query: 1-20 corresponding to Subject: 136-117	AAO20055.1	putative basic blue copper protein [Oryza sativa]	6e-38
	Contig3888	20/21 (95%)	4e-03	Query: 1-21 corresponding to Subject: 513-493	BAD17097.1	putative Blue copper protein precursor [Oryza sativa]	6e-29
	Contig628	13/13 (100%)	1.0	Query: 6-18 corresponding to Subject: 293-281	CAA55482.1	ORF1 [Hordeum vulgare]	7e-06
	tp1b0009j01	13/13 (100%)	0.92	Query: 4-16 corresponding to Subject: 1601-1589	AT4G35740.1	RecQl3 (Recq-like 3); ATP binding / ATP-dependent helicase [Arabidopsis thaliana]	0.0
	tp1b0002i21	13/13 (100%)	0.92	Query: 3-15 corresponding to Subject: 642-630	AAZ23777.1	plastid division regulator MinD [Sorghum bicolor]	1e-82
TaMIR1124	Contig5386	15/15 (100%)	7.6-e3	Query: 3-17 corresponding to Subject: 1376-1362	ABF94408.1	Serine carboxypeptidase family protein, expressed [Oryza sativa]	1e-175
	tp1b0008m03	13/13 (100%)	1.0	Query:10-22 corresponding to Subject: 347-335	AAA63164.1	ribulose 1,5-bisphosphate carboxylase activase isoform 2 [Hordeum vulgare]	0.0
	tp1b0005i18	13/13 (100%)	1.0	Query: 10-22 corresponding to Subject: 347-335	AAC97932.3	ribulose-1,5-bisphosphate carboxylase/oxygenase activase precursor [Zea mays]	0.0
	tp1b0004o15	13/13 (100%)	1.0	Query: 10-22 corresponding to Subject: 541-529	AT5G10770.1	chloroplast nucleoid DNA binding protein [Arabidopsis thaliana]	4e-78
	tp1b0004111	13/13 (100%)	1.0	Query: 1-13 corresponding to Subject: 103-91	BAA28942.1	endonuclease [Hordeum vulgare subsp. vulgare]	e-151
	tp1b0002p14	13/13 (100%)	1.0	Query: 7-193 corresponding to Subject: 879-867		No hit
	tp1b0002 g24	13/13 (100%)	1.0	Query: 10-22 corresponding to Subject: 337-325	AAA63164.1	ribulose 1,5-bisphosphate carboxylase activase isoform 2 [Hordeum vulgare]	0.0
TaMIR1133	Contig2331	22/22 (100%)	5e-06	Query: 10-22 corresponding to Subject: 337-325	AT1G30270.1	SnRK3.23, ATCIPK23, CIPK23 (CBL-INTERACTING PROTEIN KINASE 23); kinase [Arabidopsis thaliana]	9e-08
	Contig6025	18/18 (100%)	1e-3	Query: 5-22 corresponding to Subject: 3354-3440	AT1G63130.1	pentatricopeptide (PPR) repeat-containing protein [Arabidopsis thaliana]	2e-84
	Contig4016	18/18 (100%)	1e-3	Query: 2-19 corresponding to Subject: 3327-3510	AAK63878.1	Putative salt-inducible protein [Oryza sativa]	0.0
	tp1b0009d21	16/16 (100%)	1.7e-3	Query: 4-19 corresponding to Subject: 923-908		No hit
	tp1b0016j06	15/15 (100%)	6.6e-03	Query: 4-18 corresponding to Subject: 3406-3392	AAX95848.1	NB-ARC domain, putative [Oryza sativa]	0.0

Tab.3 Features of the target genes putatively interfered by the salt-inducible TaMIRs

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