Senescence-associated genes (SAGs) in cotton: Genome-wide identification, phylogenetic, and expression analyses provide insight into their role in development and stress response

Abstract

Senescence-associated genes (SAGs) are identified in Arabidopsis and other plants according to their function. Herein, we identified 23 SAGs containing the senescence domain (PF06911) across four cotton species: G. arboreum (4 GaSAG), G. raimondii (4 GrSAG), G. hirsutum (8 GhSAG), and G. barbadense (7 GbSAG). They were phylogenetically classified into four clades, each with similar motif composition and gene structure. The gene distribution and phylogenetic analysis showed the gain and loss of genes from chromosomes during evolution. Additionally, the GhSAGs (Gh_D12G034100, Gh_A12G040600) are expressed at high levels in tissue and developmental stages, while showing low expression in abiotic stress conditions such as cold, drought, heat, and salt. Gh_A02G203200 and Gh_D08G268900 show high expression in stress conditions. Two GhSAG, Gh_A06G075500 and Gh_D06G073900 are predicted to be localized in cell membranes and show low expression under abiotic stress conditions, developmental stages, and tissues, and high expression under biotic stress. We have identified 73 cis-regulatory elements out of which 43 cis-regulatory elements in GhSAGs that belong to different functional categories, viz. Growth and conditional responses, biotic and abiotic stresses, hormonal responses, and other regulatory pathways. AlphaFold's 3-D model of the SAG domain shows that one face has a more positive charge and the other has a more negative charge. The functional enrichment and protein-protein interactions of GhSAG genes reveal their roles in protein transport and stress response processes. The qRT-PCR analysis of selected five GhSAG treated with MeJA, SA, NaCl, and PEG for different time intervals shows that GhSAG expression is relatively downregulated, with unique upregulated expression patterns under SA treatments. Overall, it has been suggested that SAG genes might have a crucial role in tissue functioning, development, and plant survival under stressful conditions. This study will lay the groundwork for future investigations into the detailed function of each gene.