Genome-wide identification, characterization and expression profiles of FORMIN gene family in cotton (Gossypium Raimondii L.)

Abstract

Background

Gossypium raimondii serves as a widely used genomic model cotton species. Its genetic influence to enhance fiber quality and ability to adapt to challenging environments both contribute to increasing cotton production. The formins are a large protein family that predominately consists of FH1 and FH2 domains. The presence of the formin domains highly regulates the actin and microtubule filament in the cytoskeleton dynamics confronting various abiotic stresses such as drought, salinity, and cold temperatures.

Results

In this study, 26 formin genes were analyzed and characterized in G. raimondii and mostly were found in the nucleus and chloroplast. According to the evolutionary phylogenetic relationship, GrFH were dispersed and classified into seven different groups and shared an ancestry relationship with MtFH. The GrFH gene structure prediction revealed diverse intron-exon arrangements between groups. The FH2 conserved domain was found in all the GrFH distributed on 12 different chromosomes. Moreover, 11 pairs of GrFH transpired segmental duplication. Among them, GrFH4-GrFH7 evolved 35 million years ago (MYA) according to the evolutionary divergence time. Besides, 57 cis-acting regulatory elements (CAREs) motifs were found to play a potential role in plant growth, development, and in response to various abiotic stresses, including cold stress. The GrFH genes mostly exhibited biological processes resulting in the regulation of actin polymerization. The ERF, GATA, MYB, and LBD, major transcription factors (TFs) families in GrFH, regulated expression in abiotic stress specifically salt as well as defense against certain pathogens. The microRNA of GrFH unveiled the regulatory mechanism to regulate their gene expression in abiotic stresses such as salt and cold. One of the most economic aspects of cotton (G.raimondii) is the production of lint due to its use in manufacturing fabrics and other industrial applications. The expression profiles of GrFH in different tissues particularly during the conversion from ovule to fiber (lint), and the increased levels (up-regulation) of GrFH4, GrFH6, GrFH12, GrFH14, and GrFH26 under cold conditions, along with GrFH19 and GrFH26 in response to salt stress, indicated their potential involvement in combating these environmental challenges. Moreover, these stress-tolerant GrFH linked to cytoskeleton dynamics are essential in producing high-quality lint.

Conclusions

The findings from this study can contribute to elucidating the evolutionary and functional characterizations of formin genes and deciphering their potential role in abiotic stress such as cold and salt as well as in the future implications in wet lab.