Uncloaking lncRNA-meditated gene expression as a potential regulator of CMS in cotton (Gossypium hirsutum L.)

• Published in: Genomics (San Diego, Calif.) Calif.), 2020-09, Vol.112 (5), p.3354-3364
• Main Authors: Hamid, Rasmieh, Jacob, Feba, Marashi, Hassan, Rathod, Visha, Tomar, Rukam S.
• Format: Article
• Language: English
• Subjects: Cotton; Long non-coding RNAs; Male sterility; Micro RNA
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2020.06.027

Cytoplasmic male sterility is a well-proven mechanism for cotton hybrid production. Long non-coding RNAs belong to a class of transcriptional regulators that function in multiple biological processes. The cDNA libraries from the flower buds of the cotton CGMS, it's restorer (Rf) and maintainer lines were sequenced using high throughput NGS technique. A total of 1531 lncRNAs showed significant differential expression patterns between these three lines. Functional analysis of the co-expression network of lncRNA-mRNA using gene ontology vouchsafes that, lncRNAs play a crucial role in cytoplasmic male sterility and fertility restoration through pollen development, INO80 complex, development of anther wall tapetum, chromatin remodeling, and histone modification. Additionally, 94 lncRNAs were identified as putative precursors of 49 miRNAs. qRT-PCR affirms the concordance of expression pattern to RNA-seq data. These findings divulge the lncRNA driven miRNA-mediated regulation of gene expression profiling superintended for a better understanding of the CMS mechanisms of cotton. •A total of 1531 lncRNAs showed significant differential expression patterns between these three lines•94 lncRNAs were identified as putative precursors of 49 miRNAs.•lncRNAs regulate miR-156, miR-167 and miR-159 families that are important for sterility and fertility restoration in cotton.•These findings reveal how lncRNA driven miRNAs mediate regulation of gene expression which leads to CMS