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Identification and characterization of miRNAs during flag leaf senescence in rice by high-throughput sequencing.

ABSTRACT: Senescence is the ultimate stage of plant development. Among the different levels of senescence processes, flag leaf senescence plays a crucial role in determining grain quality in rice. In the present study, efforts are made to identify the possible involvement of miRNAs in flag leaf senescence. Four small RNA libraries were generated from different stages of flag leaf senescence and sequenced by Illumina deep sequencing. A total of 29 known miRNA families and 494 novel miRNAs were identified in the senescing flag leaves. 21 known and 116 novel miRNAs exhibited differential expression pattern. Computational prediction and analysis of putative targets of detected miRNAs revealed that miRNAs regulate the flag leaf senescence mainly by regulating transcription factors and hormone metabolism genes. The present study gives a clue about the senescence-associated miRNAs which can be used as a tool for manipulating flag leaf senescence in rice and other crops.

ORGANISM(S): Oryza sativa

PROVIDER: GSE123171 | GEO | 2021/11/30

REPOSITORIES: GEO

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Project description:Enhancing grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human being. One approach to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. microRNAs (miRNAs) are key regulators for aging and cellular senescence in eukayotes. However, miRNAs and their roles in rice leaf senescence remain unexplored. Here, 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). Totally 372 known miRNAs and 162 miRNA candidates were identified, 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. [miRNA] sample 1:The flag leaves at early stage of grain-filling of N2Y6 rice; sample 2: The flag leaves at middle stage of grain-filling of N2Y6 rice;sample 3:The flag leaves at late stage of grain-filling of N2Y6 rice; sample 4:The flag leaves at early stage of grain-filling of LYP9 rice; sample 5: The flag leaves at middle stage of grain-filling of LYP9 rice;sample 6:The flag leaves at late stage of grain-filling of LYP9 rice. [DGE]: samples 7-12 [degradome (targets)]: samples 13:The flag leaves at mixed stages of grain-filling of N2Y6 rice; sample 14:The flag leaves at mixed stages of grain-filling of LYP9 rice

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Identification and characterization of miRNAs during flag leaf senescence in rice by high-throughput sequencing.

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