Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a plant-specific serine/threonine kinase family involved in the abscisic acid (ABA) signaling pathway and responds to osmotic stress. A genome-wide analysis of this protein family has been conducted previously in some plant species, but little is known about SnRK2 genes in upland cotton (Gossypium hirsutum L.). The recent release of the G. hirsutum genome sequence provides an opportunity to identify and characterize the SnRK2 kinase family in upland cotton. We identified 20 putative SnRK2 sequences in the G. hirsutum genome, designated as GhSnRK2.1 to GhSnRK2.20. All of the sequences encoded hydrophilic proteins. Phylogenetic analysis showed that the GhSnRK2 genes were classifiable into three groups. The chromosomal location and phylogenetic analysis of the cotton SnRK2 genes indicated that segmental duplication likely contributed to the diversification and evolution of the genes. The gene structure and motif composition of the cotton SnRK2 genes were analyzed. Nine exons were conserved in length among all members of the GhSnRK2 family. Although the C-terminus was divergent, seven conserved motifs were present. All GhSnRK2s genes showed expression patterns under abiotic stress based on transcriptome data. The expression profiles of five selected genes were verified in various tissues by quantitative real-time RT-PCR (qRT-PCR). Transcript levels of some family members were up-regulated in response to drought, salinity or ABA treatments, consistent with potential roles in response to abiotic stress. This study is the first comprehensive analysis of SnRK2 genes in upland cotton. Our results provide the fundamental information for the functional dissection of GhSnRK2s and vital availability for the improvement of plant stress tolerance using GhSnRK2s.

The CONSTANS (CO)-like gene family has been well studied for its role in the regulation of plant flowering time. However, their role remains poorly understood in cotton. To better understand the possible roles of CO-like in cotton, we performed a comprehensive genome-wide analysis of CO-like genes in cotton. Phylogenetic tree analysis showed that CO-like genes naturally clustered into three groups. Segmental duplication and whole genome duplication (WGD), which occurred before polyploidy, were important contributors to its expansion within the At (“t” indicates tetraploid) and Dt subgenomes, particularly in Group III. Long-terminal repeat retroelements were identified as the main transposable elements accompanying 18 genes. The genotype of GhCOL12_Dt displayed low diversity; it was a candidate involved in domestication. Selection pressure analyses indicated that relaxed purifying selection might have provided the main impetus during the evolution of CO-like genes in upland cotton. In addition, the high expression in the torus and calycle indicated that CO-like genes might affect flowering. The genes from Group II, and those from Group III involved in segmental duplication or WGD, might play important roles in response to drought and salt stress. Overall, this comprehensive genome-wide study of the CO-like gene family would facilitate further detailed studies in cotton.

Plant terpenoid synthase (TPS) family genes participate in metabolite synthesis, hormones, gossypol, etc. Here, we genome-widely identified TPS family genes in 12 land plant species. Four hundred and thirty TPS-related genes were divided into seven subfamilies. The TPS-c in Bryophytes was suggested to be the earliest subfamily, followed by the TPS-e/f and TPS-h presence in ferns. TPS-a, the largest number of genes, was derived from monocotyledonous and dicotyledonous plants. Collinearity analysis showed that 38 out of the 76 TPS genes in G. hirsutum were collinear within G. arboreum and G. raimondii. Twenty-one GhTPS-a genes belong to the cadinene synthase (GhCDN) subfamily and were divided into five groups, A, B, C, D, and E. The special cis-elements in the promoters of 12 GhCDN-A genes suggested that the JA and ethylene signaling pathways may be involved in their expression regulation. When 12 GhCDN-A genes were simultaneously silenced through virus-induced gene silencing, the glandular color of GhCDN-A-silenced plants was lighter than that of the control, supported by a gossypol content decrease based on HPLC testing, suggesting that GhCDN-A subgroup genes participate in gossypol synthesis. According to RNA-seq analysis, gossypol synthesis-related genes and disease-resistant genes in the glandular variety exhibited upregulated expression compared to the glandless variety, whereas hormone signaling-related genes were downregulated. All in all, these results revealed plant TPS gene evolution rules and dissected the TPS subfamily, GhCDN-A, function in gossypol synthesis in cotton.

This paper systematically reviews breakthrough advances in research on cotton secondary cell wall (SCW) regulation and illustrates a novel four-tiered “MYB–NAC–MYB–structural gene” regulatory cascade orchestrated by GhMYB44. GhMYB44-interacting protein complexes sequentially activate key downstream genes related to fiber formation, establishing an efficient “initiation–amplification–execution” regulatory system, which represents an adaptive evolutionary module unique to Malvaceae. This review also discusses current research limitations and proposes future strategies that integrate multi-omics approaches and germplasm resource exploration.