Identification and Characterization of Drought Stress- Responsive Novel microRNAs in Dongxiang Wild Rice

doi:10.1016/j.rsci.2018.06.001

Abstract

Abstract:

MicroRNAs (miRNAs) are non-coding small RNAs, which play important regulatory roles in response to biotic and abiotic stresses. Dongxiang wild rice (Oryza rufipogon, DXWR) can survive in extreme drought environment, but its molecular mechanism of drought resistance is still largely unknown. To further explore miRNA regulatory mechanisms involved in drought resistance, we identified 138 novel miRNAs in DXWR using small RNA sequencing and bioinformatics approaches, and found that the expression levels of 67 novel miRNAs were signiﬁcantly affected by drought stress. In total, 200 candidate target genes were predicted and annotated for the drought stress-responsive novel miRNAs. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways suggested that most of the target genes were related to metabolism. Stem-loop quantitative real-time PCR (qRT-PCR) results exhibited high concordance with sequencing data, which conﬁrmed that miRNA expression patterns based on small RNA sequencing in the present study were reliable. Meanwhile, qRT-PCR validated the inverse expression patterns between several miRNAs and their target genes. These results will enhance our understanding of miRNA regulatory mechanisms in response to drought stress in DXWR, and can serve as an important reference for the protection and utilization of this valuable genetic resource.

Key words: Dongxiang wild rice, drought stress, genetic resource, novel microRNA, small RNA sequencing

Fantao Zhang, Yuan Luo, Meng Zhang, Yi Zhou, Hongping Chen, Biaolin Hu, Jiankun Xie. Identification and Characterization of Drought Stress- Responsive Novel microRNAs in Dongxiang Wild Rice[J]. Rice Science, 2018, 25(4): 175-184.

Figures/Tables 5

References 54

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Name	DY-N-std	DY-D-std	log₂(DY-D-std/DY-N-std)	P-value	Up/down	Name	DY-N-std	DY-D-std	log₂(DY-D-std/DY-N-std)	P-value	Up/down
novel-mir-135	3.26	0.01	-8.35	2.77 × 10^-8	Down	novel-mir-68	0.01	1.07	6.75	2.00 × 10^-3	Up
novel-mir-96	2.79	0.01	-8.13	3.36 × 10^-7	Down	novel-mir-79	0.01	1.07	6.75	2.00 × 10^-3	Up
novel-mir-115	2.56	0.01	-8.00	1.17 × 10^-6	Down	novel-mir-82	0.01	1.07	6.75	2.00 × 10^-3	Up
novel-mir-125	2.33	0.01	-7.86	4.08 × 10^-6	Down	novel-mir-85	0.01	1.07	6.75	2.00 × 10^-3	Up
novel-mir-134	1.75	0.01	-7.45	9.23 × 10^-5	Down	novel-mir-12	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-94	1.51	0.01	-7.24	3.22 × 10^-4	Down	novel-mir-24	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-103	1.51	0.01	-7.24	3.22 × 10^-4	Down	novel-mir-29	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-111	1.51	0.01	-7.24	3.22 × 10^-4	Down	novel-mir-36	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-98	1.40	0.01	-7.13	6.00 × 10^-4	Down	novel-mir-38	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-114	1.40	0.01	-7.13	6.00 × 10^-4	Down	novel-mir-57	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-137	1.40	0.01	-7.13	6.00 × 10^-4	Down	novel-mir-66	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-88	1.28	0.01	-7.00	1.12 × 10^-3	Down	novel-mir-73	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-99	1.28	0.01	-7.00	1.12 × 10^-3	Down	novel-mir-4	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-116	1.28	0.01	-7.00	1.12 × 10^-3	Down	novel-mir-44	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-89	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-46	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-105	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-48	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-110	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-70	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-122	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-40	0.01	1.48	7.21	2.00 × 10^-4	Up
novel-mir-129	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-41	0.01	1.48	7.21	2.00 × 10^-4	Up
novel-mir-133	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-60	0.01	1.48	7.21	2.00 × 10^-4	Up
novel-mir-93	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-17	0.01	1.61	7.33	9.29 × 10^-5	Up
novel-mir-97	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-74	0.01	1.61	7.33	9.29 × 10^-5	Up
novel-mir-100	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-33	0.01	1.75	7.45	4.31 × 10^-5	Up
novel-mir-108	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-55	0.01	1.75	7.45	4.31 × 10^-5	Up
novel-mir-130	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-34	0.01	1.88	7.55	2.00 × 10^-5	Up
novel-mir-3	15.59	4.30	-1.86	3.27 × 10^-13	Down	novel-mir-26	0.01	2.01	7.65	9.29 × 10^-6	Up
novel-mir-69	38.63	18.80	-1.04	1.16 × 10^-13	Down	novel-mir-45	0.01	2.15	7.75	4.31 × 10^-6	Up
novel-mir-5	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-54	0.01	2.15	7.75	4.31 × 10^-6	Up
novel-mir-7	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-84	0.01	3.22	8.33	9.30 × 10^-9	Up
novel-mir-10	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-2	0.01	3.36	8.39	4.32 × 10^-9	Up
novel-mir-42	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-51	0.01	3.76	8.55	4.32 × 10^-10	Up
novel-mir-50	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-6	0.01	4.70	8.88	2.00 × 10^-12	Up
novel-mir-52	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-71	0.01	16.12	10.65	9.35 × 10^-41	Up
novel-mir-61	0.01	1.07	6.75	2.00 × 10^-3	Up

Name	DY-N-std	DY-D-std	log₂(DY-D-std/DY-N-std)	P-value	Up/down	Name	DY-N-std	DY-D-std	log₂(DY-D-std/DY-N-std)	P-value	Up/down
novel-mir-135	3.26	0.01	-8.35	2.77 × 10^-8	Down	novel-mir-68	0.01	1.07	6.75	2.00 × 10^-3	Up
novel-mir-96	2.79	0.01	-8.13	3.36 × 10^-7	Down	novel-mir-79	0.01	1.07	6.75	2.00 × 10^-3	Up
novel-mir-115	2.56	0.01	-8.00	1.17 × 10^-6	Down	novel-mir-82	0.01	1.07	6.75	2.00 × 10^-3	Up
novel-mir-125	2.33	0.01	-7.86	4.08 × 10^-6	Down	novel-mir-85	0.01	1.07	6.75	2.00 × 10^-3	Up
novel-mir-134	1.75	0.01	-7.45	9.23 × 10^-5	Down	novel-mir-12	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-94	1.51	0.01	-7.24	3.22 × 10^-4	Down	novel-mir-24	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-103	1.51	0.01	-7.24	3.22 × 10^-4	Down	novel-mir-29	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-111	1.51	0.01	-7.24	3.22 × 10^-4	Down	novel-mir-36	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-98	1.40	0.01	-7.13	6.00 × 10^-4	Down	novel-mir-38	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-114	1.40	0.01	-7.13	6.00 × 10^-4	Down	novel-mir-57	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-137	1.40	0.01	-7.13	6.00 × 10^-4	Down	novel-mir-66	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-88	1.28	0.01	-7.00	1.12 × 10^-3	Down	novel-mir-73	0.01	1.21	6.92	9.29 × 10^-4	Up
novel-mir-99	1.28	0.01	-7.00	1.12 × 10^-3	Down	novel-mir-4	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-116	1.28	0.01	-7.00	1.12 × 10^-3	Down	novel-mir-44	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-89	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-46	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-105	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-48	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-110	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-70	0.01	1.34	7.07	4.31 × 10^-4	Up
novel-mir-122	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-40	0.01	1.48	7.21	2.00 × 10^-4	Up
novel-mir-129	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-41	0.01	1.48	7.21	2.00 × 10^-4	Up
novel-mir-133	1.16	0.01	-6.86	2.09 × 10^-3	Down	novel-mir-60	0.01	1.48	7.21	2.00 × 10^-4	Up
novel-mir-93	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-17	0.01	1.61	7.33	9.29 × 10^-5	Up
novel-mir-97	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-74	0.01	1.61	7.33	9.29 × 10^-5	Up
novel-mir-100	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-33	0.01	1.75	7.45	4.31 × 10^-5	Up
novel-mir-108	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-55	0.01	1.75	7.45	4.31 × 10^-5	Up
novel-mir-130	1.05	0.01	-6.71	3.90 × 10^-3	Down	novel-mir-34	0.01	1.88	7.55	2.00 × 10^-5	Up
novel-mir-3	15.59	4.30	-1.86	3.27 × 10^-13	Down	novel-mir-26	0.01	2.01	7.65	9.29 × 10^-6	Up
novel-mir-69	38.63	18.80	-1.04	1.16 × 10^-13	Down	novel-mir-45	0.01	2.15	7.75	4.31 × 10^-6	Up
novel-mir-5	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-54	0.01	2.15	7.75	4.31 × 10^-6	Up
novel-mir-7	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-84	0.01	3.22	8.33	9.30 × 10^-9	Up
novel-mir-10	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-2	0.01	3.36	8.39	4.32 × 10^-9	Up
novel-mir-42	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-51	0.01	3.76	8.55	4.32 × 10^-10	Up
novel-mir-50	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-6	0.01	4.70	8.88	2.00 × 10^-12	Up
novel-mir-52	0.01	1.07	6.75	2.00 × 10^-3	Up	novel-mir-71	0.01	16.12	10.65	9.35 × 10^-41	Up
novel-mir-61	0.01	1.07	6.75	2.00 × 10^-3	Up