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Genome-wide analysis of microRNAs and their target genes related to leaf senescence of rice.

Xu X, Bai H, Liu C, Chen E, Chen Q, Zhuang J, Shen B - PLoS ONE (2014)

Bottom Line: Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively.Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways.These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding.

View Article: PubMed Central - PubMed

Affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.

ABSTRACT
Grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human beings. One of the approaches to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. MicroRNAs (miRNAs) are key regulators of aging and cellular senescence in eukaryotes. Here, to help understand their biological role in rice leaf senescence, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). In total 372 known miRNAs, 162 miRNA candidates and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding.

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Expression validation of miRNAs in the leaves of N2Y6 and LYP9 by qRT-PCR.The amount of expression was normalized by the level of OsU6_snRNA in qRT-PCR. All reactions of qRT-PCR were repeated three times for each sample. The left indicates the miRNA relative expression tested by qRT-PCR, and the right indicates the miRNA relative expression generated from the high-throughput sequencing.
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pone-0114313-g005: Expression validation of miRNAs in the leaves of N2Y6 and LYP9 by qRT-PCR.The amount of expression was normalized by the level of OsU6_snRNA in qRT-PCR. All reactions of qRT-PCR were repeated three times for each sample. The left indicates the miRNA relative expression tested by qRT-PCR, and the right indicates the miRNA relative expression generated from the high-throughput sequencing.

Mentions: To validate the sequencing results and the expression level of miRNAs, the differential expression pattern of five miRNAs, osa-miR1320-5p, osa-miR164a, osa-miR167c-5p_R-1, osa-miR2871a-5p_L+1R-4 and osa-miR530-3p, which showed significant changes by sequencing in the two rice, were randomly selected for qRT-PCR analysis. As shown in Fig. 5, qRT-PCR results were consistent with the data from high-throughput sequencing for all the five miRNAs in all the three stages.


Genome-wide analysis of microRNAs and their target genes related to leaf senescence of rice.

Xu X, Bai H, Liu C, Chen E, Chen Q, Zhuang J, Shen B - PLoS ONE (2014)

Expression validation of miRNAs in the leaves of N2Y6 and LYP9 by qRT-PCR.The amount of expression was normalized by the level of OsU6_snRNA in qRT-PCR. All reactions of qRT-PCR were repeated three times for each sample. The left indicates the miRNA relative expression tested by qRT-PCR, and the right indicates the miRNA relative expression generated from the high-throughput sequencing.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257594&req=5

pone-0114313-g005: Expression validation of miRNAs in the leaves of N2Y6 and LYP9 by qRT-PCR.The amount of expression was normalized by the level of OsU6_snRNA in qRT-PCR. All reactions of qRT-PCR were repeated three times for each sample. The left indicates the miRNA relative expression tested by qRT-PCR, and the right indicates the miRNA relative expression generated from the high-throughput sequencing.
Mentions: To validate the sequencing results and the expression level of miRNAs, the differential expression pattern of five miRNAs, osa-miR1320-5p, osa-miR164a, osa-miR167c-5p_R-1, osa-miR2871a-5p_L+1R-4 and osa-miR530-3p, which showed significant changes by sequencing in the two rice, were randomly selected for qRT-PCR analysis. As shown in Fig. 5, qRT-PCR results were consistent with the data from high-throughput sequencing for all the five miRNAs in all the three stages.

Bottom Line: Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively.Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways.These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding.

View Article: PubMed Central - PubMed

Affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.

ABSTRACT
Grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human beings. One of the approaches to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. MicroRNAs (miRNAs) are key regulators of aging and cellular senescence in eukaryotes. Here, to help understand their biological role in rice leaf senescence, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). In total 372 known miRNAs, 162 miRNA candidates and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding.

Show MeSH