水稻根系盐胁迫响应miRNA和tRF的鉴定

doi:10.3864/j.issn.0578-1752.2020.04.001

Abstract

Abstract:

【Objective】 Rice (Oryza sativa L.) is the most important food crop in China. But as a salt sensitive plant, to study the expression pattern of salt stress responding genes in rice has theoretical and practical significance. The dissection of the molecular mechanism and regulatory network in response to salt stress will contribute to salt-tolerant rice breeding. 【Method】 The rice variety Nipponbare seeds were used as experimental materials. Samples were treated with 150 mmol·L ^-1 NaCl for 21 days in 1/2MS medium. Small RNAs were extracted from treated and non-treaded root samples for sequencing. Differentially expressed miRNAs and tRFs (tRNA-derived RNA fragments) were identified using the cut-off of log₂ fold change (log₂FC) >1 or ＜-1, and their predicted target genes were analyzed. The sequencing results and target genes were further verified by real-time quantitative PCRs.【Result】 RPM > 500 for at least one set of data and log₂ FC > 1 or ＜-1 were used as the cut-off threshold, and 31 differently expressed miRNAs were obtained. Among them, the expression of 8 miRNA were up-regulated and 23 miRNA were down-regulated under salt treatment. The differently expressed miRNAs belonged to 12 miRNA families. 8 of these miRNA families have been reported as salt responding ones in Arabidopsis, maize and wheat, including osa-miR397, osa-miR396, osa-miR156, osa-miR167, osa-miR1432, which were down-regulated miRNAs, and osa-miR159, osa-miR168, osa-miR164, which were up-regulated ones under salt treatment, The other 4 miRNA families, namely osa-miR1882, osa-miR1876, osa-miR1423 and osa-miR5077, have not yet been reported in relation to salt stress. 162 target genes of these 31 differentially expressed miRNAs were predicted. Under salt stress, the expression of 34-38nt tRFs were significantly enhanced in rice root, indicating these tRFs were not produced randomly, but induced by salt stress. RPM > 50 and log₂ FC > 1 or ＜-1 were used as the threshold, 3 tRFs were detected as 5' terminal tRFs and 3 tRFs were detected as 3' terminal tRFs. These tRFs are produced from 6 tRNAs. It is suggested that these tRFs function potentially response to salt stress in rice root. 【Conclusion】 In this study, 12 miRNA families responding to salt stress were detected in rice root. Most of their target genes are transcription factors. It is suggested that these miRNAs are involved in the salt response through post-transcriptional regulation of their target genes. In addition, 8 of them were conserved salt responsive miRNAs among plant species. Furthermore, the salt responsive tRFs of rice was examined in transcriptome level. 6 tRFs induced by salt stress were identified.

Key words: Oryza sativa L., salt stress, transcriptome, miRNAs, tRFs

ShuJun MENG, XueHai ZHANG, QiYue WANG, Wen ZHANG, Li HUANG, Dong DING, JiHua TANG. Identification of miRNAs and tRFs in Response to Salt Stress in Rice Roots[J].Scientia Agricultura Sinica, 2020, 53(4): 669-682.

Figures/Tables 10

Table 1

Fig. 1

Fig. 2

Table 2

Differentially expressed miRNAs in response to salt stress in rice"

miRNA	染色体 Chr.	起始 Start	终止 End	长度 Length (bp)	序列 Sequence (5'-3')	NP-RPM 平均值 Average of NP-RPM	NP-Na-RPM 平均值 Average of NP-Na-RPM	Log₂ (NP-Na/NP)	表达差异 Differential expression
osa-miR397a	6	28489785	28489898	21	UCAUUGAGUGCAGCGUUGAUG	3385.00	273.09	-3.631709	下调Down
osa-miR397b	2	3280781	3280898	21	UUAUUGAGUGCAGCGUUGAUG	14209.57	1461.91	-3.280937	下调Down
osa-miR1882e-3p	10	10320904	10321044	24	GAAAUGAUCUUGGACGUAAUCUAG	3760.37	649.34	-2.533830	下调Down
osa-miR396f-5p	2	35636546	35636721	22	UCUCCACAGGCUUUCUUGAACU	1173.18	321.53	-1.867414	下调Down
osa-miR396e-5p	4	34436820	34437003	21	UCCACAGGCUUUCUUGAACUG	1173.18	321.53	-1.867414	下调Down
osa-miR156a	1	22524147	22524246	20	UGACAGAAGAGAGUGAGCAC	2155.81	688.99	-1.645684	下调Down
osa-miR156b-5p	1	4666341	4666516	20	UGACAGAAGAGAGUGAGCAC	2155.81	688.99	-1.645684	下调Down
osa-miR156c-5p	1	4665975	4666123	20	UGACAGAAGAGAGUGAGCAC	2155.81	688.99	-1.645684	下调Down
osa-miR156d	2	4512884	4513012	20	UGACAGAAGAGAGUGAGCAC	2155.81	688.99	-1.645684	下调Down
osa-miR156e	4	25026327	25026430	20	UGACAGAAGAGAGUGAGCAC	2155.81	688.99	-1.645684	下调Down
osa-miR156f-5p	8	21478230	21478415	20	UGACAGAAGAGAGUGAGCAC	2155.81	688.99	-1.645684	下调Down
osa-miR156g-5p	2	8412516	8412618	20	CGACAGAAGAGAGUGAGCAC	2155.81	688.99	-1.645684	下调Down
osa-miR156h-5p	8	21491232	21491417	20	UGACAGAAGAGAGUGAGCAC	2155.81	688.99	-1.645684	下调Down
osa-miR156i	2	24119995	24120084	20	UGACAGAAGAGAGUGAGCAC	2155.81	688.99	-1.645684	下调Down
osa-miR156j-5p	6	26554795	26554959	22	GCUCGCUCCUCUUUCUGUCAGC	2155.81	688.99	-1.645684	下调Down
osa-miR167d-5p	7	4166404	4166295	21	UGAAGCUGCCAGCAUGAUCUG	2924.08	1169.08	-1.322607	下调Down
osa-miR167e-5p	2	3742241	3742513	21	UGAAGCUGCCAGCAUGAUCUG	2924.08	1169.08	-1.322607	下调Down
osa-miR167f	10	14723044	14723156	21	UGAAGCUGCCAGCAUGAUCUG	2924.08	1169.08	-1.322607	下调Down
osa-miR167g	3	3347682	3347763	21	UGAAGCUGCCAGCAUGAUCUG	2924.08	1169.08	-1.322607	下调Down
osa-miR167h-5p	12	25480618	25480737	21	UGAAGCUGCCAGCAUGAUCUG	2924.08	1169.08	-1.322607	下调Down
osa-miR167i-5p	6	27674749	27674949	21	UGAAGCUGCCAGCAUGAUCUG	2924.08	1169.08	-1.322607	下调Down
osa-miR167j	1	32686068	32686227	21	UGAAGCUGCCAGCAUGAUCUG	2924.08	1169.08	-1.322607	下调Down
osa-miR1432-5p	7	23401702	23401810	21	AUCAGGAGAGAUGACACCGAC	485.58	219.53	-1.145259	下调Down
osa-miR159f	1	6693112	6693299	21	CUUGGAUUGAAGGGAGCUCUA	874.14	1817.05	1.055665	上调Up
osa-miR159a.1	1	17681923	17682194	21	UUUGGAUUGAAGGGAGCUCUG	15079.03	32657.51	1.114871	上调Up
osa-miR159b	1	1215030	1215217	21	UUUGGAUUGAAGGGAGCUCUG	15079.03	32657.51	1.114871	上调Up
osa-miR168a-5p	2	1553154	1553240	21	UCGCUUGGUGCAGAUCGGGAC	398.64	916.89	1.201650	上调Up
osa-miR1876	10	4833365	4833521	24	AUAAGUGGGUUUGUGGGCUGGCCC	1462.10	3609.01	1.303566	上调Up
osa-miR1423-5p	4	19715117	19715252	24	AGGCAACUACACGUUGGGCGCUCG	265.74	1720.74	2.694957	上调Up
osa-miR164e	3	10542157	10542288	21	UGGAGAAGCAGGGCACGUGAG	75.61	558.04	2.883783	上调Up
osa-miR5077	3	14094752	14094842	19	GUUCGCGUCGGGUUCACCA	93.53	856.96	3.195773	上调Up

Table 2

Fig. 3

Fig. 4

Table 3

Source tRNA of tRFs related to salt stress in rice"

来源tRNA基因编号 Gene ID of source tRNA	基因注释 Gene expression	位置 Loction	长度 Length (bp)	序列 Sequence (5'-3')	NP-RPM 平均值 NP-RPM average value	NP-Na-RPM 平均值 NP-Na-RPM average value	Log₂ (NP-Na/NP)
ENSRNA049444301	反密码子为UUC的谷氨酸 tRNA tRNA-Glu for anticodon UUC	12:25043392..25043429	38	GAAAGCCAGATAT CCTAACCGGACTA GACGACAATGGA	54.91457551	79.26862858	0.529560894
ENSRNA049444701	反密码子为UUC的谷氨酸 tRNA tRNA-Glu for anticodon UUC	12:2735598..2735634	37	GCCATTGTCGTCTA GTCCGGTTAGGAT ACCTGGCTTT	280.0756319	532.1395357	0.925988127
EPlORYSAT000373797	反密码子为UCC的谷氨酸 tRNA tRNA tRNA-Glu (UCC)	Pt:15650..15686	37	GCCCCTATCGTCTA GTGGTTCAGGACAT CTCTCTTTC	51.33846231	85.59087607	0.737416929
EPlORYSAT000373812	反密码子为GUG的组氨酸 tRNA tRNA-His (GUG)	Pt:81050..81087	38	GGCGGATGTAGC CAAGTGGATCAAG GCAGTGGATTGTG	27.04710805	62.75454797	1.214245673
EPlORYSAT000373840	反密码子为GUC的天门冬氨酸 tRNA tRNA-Asp (GUC)	Pt:16231..16267	37	GGGATTGTAGTTC AATTGGTCAGAGC ACCGCCCTGTC	45.81324826	183.8090975	2.004371412
ENSRNA049445145	反密码子为CGC的丙氨酸 tRNA tRNA-Ala for anticodon CGC	8:22194244..22194280	37	GGGGACGTAGCTCATATGGTAGAGCGCTCGCTTCGCA	3.948187725	64.83354259	4.037477913
ENSRNA049444418	反密码子为UUC的谷氨酸 tRNA tRNA-Glu for anticodon UUC	12:27018602..27018639	38	TCACCCAGACGACCCGGGTTCAAATCCCGGCAATGGAA	8.877923176	86.56822355	3.285543425
ENSRNA049446755	反密码子为GCC的甘氨酸 tRNA tRNA-Gly for anticodon GCC	3:25619176..25619211	36	ACGGTACAGACCC GGGTTCGATTCCC GGCTGGTGCA	5.511015306	72.72375321	3.722036619
EPlORYSAT000373797	反密码子为UCC的谷氨酸 tRNA tRNA-Glu(UCC)	Pt:15686..15722	37	CAAGGAGGCAGCG GGGATTCGACTTC CCCTGGGGGTA	24.28546159	47.55822306	0.969601905
EPlORYSAT000373840	反密码子为GUC的天门冬氨酸 tRNA tRNA-Asp(GUC)	Pt:16267..16304	38	CAAGGCGGAAGCT GCGGGTTCGAGCC CCGTCAGTCCCG	14.74937311	52.34254363	1.827330398

Table 3

Table 4

Predictive target genes for differential expression of tRFs in rice salt stress"

来源tRNA基因编号 Gene ID of source tRNA	靶基因编号 Target gene ID	位置 Location	基因注释 Gene description
EPlORYSAT000373812	Os01g0810100	1:34412916..34416988	叶绿体核糖核酸酶III蛋白 Chloroplast ribonuclease III domain protein
	Os10g0119300	10:1234067..1241670	FH2结构域结合肌动蛋白 Actin-binding FH2 domain containing protein
	Os03g0301700	3:10621704..10625395	钙调蛋白结合蛋白磷酸酶 Calmodulin-binding protein phosphatase
	Os03g0435200	3:18355628..18365524	五肽重复蛋白 Pentatricopeptide repeat domain containing protein
EPlORYSAT000373840	Os04g0531300	4:26565544..26571685	tRNA -二氢吡啶合酶蛋白 tRNA-dihydrouridine synthase domain containing protein
	Os11g0593500	11:22604874..22606587	环状F-box蛋白 Cyclin-like F-box domain containing protein
	Os06g0128200	6:1485977..1490634	LMBR1膜内在蛋白 LMBR1 integral membrane protein
	Os03g0562200	3:20188178..20194997	环状F-box蛋白 Cyclin-like F-box domain containing protein
	Os03g0860700	3:36320679..36333253	肌球蛋白Myosin
	Os01g0850100	1:36540164..36545196	磷脂酸类磷脂 Phosphatidic acid phosphatase-like protein
ENSRNA049445145	Os08g0389300	8:18398361..18407618	UbiA-异戊二烯转移酶家族蛋白 UbiA prenyltransferase family domain containing protein
ENSRNA049445145	Os10g0464400	10:17133478..17137843	卤酸脱卤酶类水解酶蛋白 Haloacid dehalogenase-like hydrolase domain containing protein
ENSRNA049444418	Os08g0134900	8:1988346..1990818	保守假设蛋白Conserved hypothetical protein
	Os01g0267800	1:9192164..9193439	丝氨酸/苏氨酸蛋白激酶蛋白 Serine/threonine protein kinase domain containing protein
	Os03g0320100	3:11549564..11551862	α-N-阿拉伯呋喃糖苷酶 A Alpha-N-arabinofuranosidase A
	Os07g0484800	7:17787901..17801227	腺嘌呤磷酸核糖转移酶蛋白 Adenine phosphoribosyltransferase like protein
	Os09g0333600	9:10071433..10085739	多效性耐药蛋白4 Pleiotropic drug resistance protein 4
	Os09g0529700	9:20744838..20748509	液泡蛋白分选;内吞体分选转运复合体 Vacuolar protein sorting; endocyte sorting and transport complex
	Os02g0250700	2:8518506..8535685	表达蛋白Expressed protein
	Os12g0256600	12:8809699..8811919	保守假设蛋白Conserved hypothetical protein
	Os08g0226100	8:7698342..7699299	保守假设蛋白Conserved hypothetical protein
	Os05g0400200	5:19470226..19475222	逆转录转座子蛋白Ty1亚类 Retrotransposon protein Ty1-copia subclass
	Os05g0126200	5:1497942..1499638	保守假设蛋白Conserved hypothetical protein
ENSRNA049446755	Os08g0387300	8:18299461..18299571	膜蛋白质Membrane protein
	Os03g0320100	3:11549564..11551862	α-N-阿拉伯呋喃糖苷酶A Alpha-N-arabinofuranosidase A
	Os05g0400200	5:19470226..19475222	逆转录转座子蛋白Ty1亚类 Retrotransposon protein Ty1-copia subclass
EPlORYSAT000373840	Os03g0165300	3:3513371..3517214	保守假设蛋白Conserved hypothetical protein
	Os12g0274450	12:10072058..10075165	保守假设蛋白Conserved hypothetical protein
	Os04g0271700	4:11375483..11377317	玉米素葡萄糖基转移酶UDP-glycosyltransferase

Table 4

Fig. 5

Fig. 6

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名称 Name	引物序列 Primer sequence (5'-3')
osa-miR156a-F	TGACAGAAGAGAGTGAGCAC
osa-miR167f-F	TGAAGCTGCCAGCATGATCTG
osa-miR396e-5p-F	TCCACAGGCTTTCTTGAACTG
EPlORYSAT000373812-F	GCGGATGTAGCCAAGTGGATCA
EPlORYSAT000373840-F	GGATTGTAGTTCAATTGGTCAGAGC
T156-OsSPL11-F	ACCATGCAAACACCACTTCA
T156-OsSPL11-R	TTGGCAAGAGCTCATTTGTG
T156-OsSPL13-F	GTGCCAGGTGGAGAGGTG
T156-OsSPL13-R	GTCGAACTCCGTCAGCTCAT
T167-OsARF6-F	AGCCTGAGTACCTCCAGCAA
T167-OsARF6-R	GGTGTAGACTGAGGGGTGGA
T167-Os06g03830-F	GATGACCTTCGCCACAAACT
T167-Os06g03830-R	CGTCGGATCGTACGGTATCT
T396-OsGRF2-F	GTTGTCCAAGGAGCACTGC
T396-OsGRF2-R	GTGGGGATGGAGATGGAGAG
Os01g0810100-F	ATTCTGGGCACTGTTTGGAG
Os01g0810100-R	GCAACATCTTGCCATGTGAG
Os04g0531300-F	TGCCCACAAGAAAGGGATAG
Os04g0531300-R	GCTCCCATTCCACCACTAAG
Osβ-Actin-F	GGAAGTACAGTGTCTGGATTGGAG
Osβ-Actin-R	TCTTGGCTTAGCATTCTTGGGT

Identification of miRNAs and tRFs in Response to Salt Stress in Rice Roots

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