Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.
Zalingei University, Central Darfur, Sudan.
BMC Genomics. 2019 Aug 19;20(1):661. doi: 10.1186/s12864-019-5978-5.
Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood. In order to investigate the function of LncRNAs in cotton fiber development, it is necessary and important to identify LncRNAs and their potential roles in fiber cell development.
In this work, we identified 18,333 LncRNAs, with the proportion of long intergenic noncoding RNAs (LincRNAs) (91.5%) and anti-sense LncRNAs (8.5%), all transcribed from Ligon-lintless-1 (Li1) and wild-type (WT). Expression differences were detected between Ligon-lintless-1 and wild-type at 0 and 8 DPA (day post anthesis). Pathway analysis and Gene Ontology based on differentially expressed LncRNAs on target genes, indicated fatty acid biosynthesis and fatty acid elongation being integral to lack of fiber in mutant cotton. The result of RNA-seq and RT-qPCR clearly singles out two potential LncRNAs, LNC_001237 and LNC_017085, to be highly down-regulated in the mutant cotton. The two LncRNAs were found to be destabilized or repressed by ghr-miR2950. Both RNA-seq analysis and RT-qPCR results in Ligon-lintless-1 mutant and wild-type may provide strong evidence of LNC_001237, LNC_017085 and ghr-miR2950 being integral molecular elements participating in various pathways of cotton fiber development.
The results of this study provide fundamental evidence for the better understanding of LncRNAs regulatory role in the molecular pathways governing cotton fiber development. Further research on designing and transforming LncRNAs will help not only in the understanding of their functions but will also in the improvement of fiber quality.
长非编码 RNA（LncRNA）是基因的一部分，不翻译成蛋白质，在植物生长和发育中起着至关重要的作用。然而，LncRNA 的存在以及它们在 Ligon-lintless-1 突变体中棉花纤维早期发育停止时的功能仍未得到很好的理解。为了研究 LncRNA 在棉花纤维发育中的功能，有必要也很重要去鉴定 LncRNA 及其在纤维细胞发育中的潜在作用。
在这项工作中，我们鉴定了 18333 个 LncRNA，其中长基因间非编码 RNA（LincRNA）（91.5%）和反义 LncRNA（8.5%）的比例均转录自 Ligon-lintless-1（Li1）和野生型（WT）。在 Ligon-lintless-1 和野生型之间，在 0 和 8 DPA（开花后天数）时检测到表达差异。基于差异表达 LncRNA 的靶基因的通路分析和基因本体论表明，脂肪酸生物合成和脂肪酸延伸对于突变体棉花中纤维的缺失至关重要。RNA-seq 和 RT-qPCR 的结果清楚地表明，两个潜在的 LncRNA，LNC_001237 和 LNC_017085，在突变体棉花中高度下调。发现这两个 LncRNA 被 ghr-miR2950 不稳定或抑制。Ligon-lintless-1 突变体和野生型的 RNA-seq 分析和 RT-qPCR 结果都可能为 LNC_001237、LNC_017085 和 ghr-miR2950 作为参与棉花纤维发育的各种途径的完整分子元素提供有力证据。
本研究结果为更好地理解 LncRNA 在调控棉花纤维发育的分子途径中的作用提供了基础证据。进一步研究设计和转化 LncRNA 将不仅有助于理解它们的功能，而且有助于提高纤维质量。
