Transcriptomic repertoires depict the initiation of lint and fuzz fibres in cotton (Gossypium hirsutum L.)

Abstract

SummaryCotton fibre is an important natural fibre for the textile industry. The number of fibre initials determines the lint percentage, which is an important factor for cotton fibre yield. Although fibre development has been described by transcriptomic analysis, the mechanism by which the long noncoding RNA manipulates the initiation of lint and fuzz fibres remains unknown. In this study, three lines with different lint percentages were developed by crossing Xu142 with its fibreless mutant Xu142 fl. We collected the epidermal cells from the ovules with attached fibres at 0 and 5 days post anthesis (DPA) from Xu142, the fibreless mutant Xu142 fl and the three lint percent diversified lines for deep transcriptome sequencing. A total of 2641 novel genes, 35 802 long noncoding RNAs (lncRNAs) and 2262 circular RNAs (circRNAs) were identified, of which 645 lncRNAs were preferentially expressed in the fibreless mutant Xu142 fl and 651 lncRNAs were preferentially expressed in the fibre‐attached lines. We demonstrated the functional roles of the three lncRNAs in fibre development via a virus‐induced gene silencing (VIGS) system. Our results showed that silencing XLOC_545639 and XLOC_039050 in Xu142 fl increased the number of fibre initials on the ovules, but silencing XLOC_079089 in Xu142 resulted in a short fibre phenotype. This study established the transcriptomic repertoires in cotton fibre initiation and provided evidence for the potential functions of lncRNAs in fibre development.

Updates on molecular mechanisms in the development of branched trichome in Arabidopsis and nonbranched in cotton

“…The lncRNAs and circular RNAs were identified, and of these, 645 and 651 lncRNAs were preferentially expressed in the fibreless and fibre‐attached lines, respectively. Via a virus‐induced gene silencing (VIGS) approach, down‐regulation of three lncRNAs increased the fibre initial numbers significantly (Hu et al ., ). Another study also identified more than 35 000 lncRNAs and showed their potential functions in fibre development of G. barbadense (Wang et al ., ,).…”

Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.)

“…In cotton, previous studies have shown that lncRNAs XLOC_063105-CotAD_37096 and XLOC_115463-CotAD_12502 probably function in cis-regulating responses to drought stress [32]. One lncRNA, TCONS_00061835-Gh_D06G1439 (GhMYB-like), regulates cotton fiber development [36] by complementary base pairing with the protein-coding gene, lncRNA, and the circRNA complex network, demonstrating that some lncRNAs are involved in biotic and abiotic stresses [31,33,34].…”

“…In cotton, lncRNAs participate in resistance to Verticillium dahliae [31], drought stress [32], salt stress [33], and other abiotic stresses [34]. LncRNAs also participate in regulating fiber development [5,35] and in lint initiation [36]. However, little is known about the mechanisms of lncRNA during the cytoplasmic male sterility (CMS) in cotton; therefore, it is necessary to identify novel lncRNA and analyze the lncRNA in the development of cotton anther.…”

Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum)

“…The availability of cotton genome G. raimondii (Paterson et al ., ; Wang et al ., ), G. arboreum (Li et al ., ) and upland G. hirsutum (Li et al ., ; Zhang et al ., ) sequences has enabled the use of RNA‐Seq for cotton transcriptomic studies. Previous studies have shown the efficacy of transcriptomic and proteomic data sets for understanding the molecular mechanisms of begomovirus and whitefly infestation on tomato and cultivated cotton G. hirsutum (Li et al ., ; Zhao et al ., ), cassava mosaic begomovirus infection on cassava (Allie et al ., ), tomato yellow leaf curl virus (TYLCV) infection on tomato (Chen et al ., ; Hasegawa et al ., ; Huang et al ., ), geminivirus infection on pepper (Gongora‐Castillo et al ., ) and other pathways related to begomovirus (Brustolini et al ., ) and cotton development (Hu et al ., ).…”