Panigrahy Madhusmita, Panigrahi Kishore Chandra Sekhar, Poli Yugandhar, Ranga Aman, Majeed Neelofar
Biofuel & Bioprocessing Research Centre, Institute of Technical Education and Research, Siksha 'O' Anusandhan University, Bhubaneswar 751002, India.
National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India.
Biology (Basel). 2022 May 23;11(5):798. doi: 10.3390/biology11050798.
Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be - and - for enhanced panicle size, - for grain formation, miR6245- for decreased stem mechanical strength, - and - for better pollen development, and - for hyponasty under shade.
生殖阶段的长期遮荫会导致水稻产量大幅损失。在本研究中，我们利用小RNA和降解组测序，并结合微阵列和qRT-PCR进行表达分析，阐明了耐荫水稻品种Swarnaprabha（SP）在生殖阶段的microRNA在耐长期遮荫（约20天遮荫）中的作用。本研究表明，miRNA（miR）对耐荫性的调控主要包括miR自身的失活，导致其靶标的上调。基于所涉及的功能和途径，上调和下调的差异表达miR（DEm）在靶标类别上呈现出巨大差异。此外，中性调控和独特表达的miR也通过改变其靶标的差异表达对耐荫性反应做出贡献，这可能是由于它们不同的结合亲和力。上调的DEm大多靶向细胞壁、膜、细胞骨架和纤维素合成相关的转录本，而下调的DEm靶向光合作用、碳和糖代谢、能量代谢以及氨基酸和蛋白质代谢的转录本。我们鉴定出16个miRNA及其21个靶标对，它们的作用可能对SP的耐荫表型和可持续产量有显著贡献。其中最显著的是——用于增加穗大小，——用于籽粒形成，miR6245用于降低茎的机械强度，——和——用于更好的花粉发育，以及——用于遮荫下的叶片下弯。
