RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton

Abstract

Background Cotton fiber is an important natural resource for textile industry and an excellent model for cell biology study. Application of glabrous mutant cotton and high-throughput sequencing facilitates the identification of key genes and pathways for fiber development and cell differentiation and elongation. LncRNA is a type of ncRNA with more than 200 nt in length and functions in the ways of chromatin modification, transcriptional and post-transcriptional modification, and so on. However, the detailed lncRNA and associated mechanisms for fiber initiation are still unclear in cotton. Results In this study, we used a novel glabrous mutant ZM24fl, which is endowed with higher somatic embryogenesis, and functions as an ideal receptor for cotton genetic transformation. Combined with the high-throughput sequencing, fatty acid pathway and some transcription factors such as MYB, ERF and bHLH families were identified the important roles in fiber initiation; furthermore, 3,288 lncRNAs were identified, and some differentially expressed lncRNAs were also analyzed. From the comparisons of ZM24_0 DPA vs ZM24_-2 DPA and fl_0 DPA vs ZM24_0 DPA, one common lncRNA MSTRG 2723.1 was found that function upstream of fatty acid metabolism, MBY25-mediating pathway, and pectin metabolism to regulate fiber initiation. In addition, other lncRNAs MSTRG 3390.1, MSTRG 48719.1, and MSTRG 31176.1 were also showed potential important roles in fiber development; and the co-expression analysis between lncRNAs and targets showed the distinct models of different lncRNAs and complicated interaction between lncRNAs in fiber development of cotton. Conclusions From the above results, a key lncRNA MSTRG 2723.1 was identified that might mediate some key genes transcription of fatty acid metabolism, MYB25-mediating pathway, and pectin metabolism to regulate fiber initiation of ZM24 cultivar. Co-expression analysis implied that some other important lncRNAs (e.g., MSTRG 3390.1, MSTRG 48719.1, and MSTRG 31176.1) were also showed the different regulatory model and interaction between them, which proposes some valuable clues for the lncRNAs associated mechanisms in fiber development.

Potential Roles of 1-Aminocyclopropane-1-carboxylic Acid Synthase Genes in the Response of Gossypium Species to Abiotic Stress by Genome-Wide Identification and Expression Analysis

“…The cotton histone 3 gene ( GhHistone3 ; AF024716) was used as the internal gene. The 2 −∆ Ct method was used to calculate the relative expression of each gene, with three technical repetitions and three biological repetitions [ 67 ]. Data are shown as mean ± SD.…”

Update on functional analysis of long non-coding RNAs in common crops

“…The salt-responsive lncRNAs TRABA and lncRNA354 serve as upstream regulators that control the expression of the salt stress response-related genes GhBGLU24 and GhARF , respectively ( Zhang X. et al, 2021 ; Cui et al, 2024 ) ( Figure 4D ). In cotton, MSTRG 2723.1 mediates the expression of key genes related to fatty acid metabolism, the MYB25-mediated pathway, and pectin metabolism to regulate fiber synthesis ( Zou et al., 2022 ). In addition to cotton, hemp is another major fiber crop.…”

Systematically and Comprehensively Understanding the Regulation of Cotton Fiber Initiation: A Review

“…This was the first functional identification of lncRNAs involved in fiber initiation, providing a basis for a deeper understanding of lncRNA functions during cotton fiber development [99]. Recently, 3288 lncRNAs were identified via high-throughput sequencing in a novel glabrous mutant ZM24fl, among them, a key lncRNA, MSTRG 2723.1, was isolated, which may activate the transcription of genes involved in pectin metabolism, the GhMYB25-mediating pathway, and the fatty acid metabolism to regulate fiber initiation in the ZM24 cultivar [100]. Taken together, the characterization and expression analysis of ncRNAs will contribute to future investigations of their roles in cotton fiber development.…”