Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton. Increased cotton production in the face of declining precipitation and availability of fresh water for agriculture use is the focus for breeders, cotton being the backbone of textile industries and a cash crop for many countries globally. In this work, a total of 242, 136 and 142 LEA genes were identified in G. hirsutum, G. arboreum and G. raimondii respectively. The identified genes were classified into eight groups based on their conserved domain and phylogenetic tree analysis. LEA 2 were the most abundant, this could be attributed to their hydrophobic character. Upland cotton LEA genes have fewer introns and are distributed in all chromosomes. Majority of the duplicated LEA genes were segmental. Syntenic analysis showed that greater percentages of LEA genes are conserved. Segmental gene duplication played a key role in the expansion of LEA genes. Sixty three miRNAs were found to target 89 genes, such as miR164, ghr-miR394 among others. Gene ontology analysis revealed that LEA genes are involved in desiccation and defense responses. Almost all the LEA genes in their promoters contained ABRE, MBS, W-Box and TAC-elements, functionally known to be involved in drought stress and other stress responses. Majority of the LEA genes were involved in secretory pathways. Expression profile analysis indicated that most of the LEA genes were highly expressed in drought tolerant cultivars Gossypium tomentosum as opposed to drought susceptible, G. hirsutum. The tolerant genotypes have a greater ability to modulate genes under drought stress than the more susceptible upland cotton cultivars. The finding provides comprehensive information on LEA genes in upland cotton, G. hirsutum and possible function in plants under drought stress.

Abiotic stresses have negative effects on plants growth and development. Plants, being sessile, have developed specific adaptive strategies that allow them to rapidly detect and respond to abiotic stress factors. The detoxification efflux carriers (DTX)/multidrug and toxic compound extrusion (MATE) transporters are of significance in the translocation of abscisic acid (ABA), a phytohormone with profound role in plants under various abiotic stress conditions. The ABA signaling cascades are the core regulators of abiotic stress responses in plants, triggering major changes in gene expression and adaptive physiological responses. We therefore carried out genome-wide analysis of the DTX/MATE gene family, transformed a DTX/MATE gene in Arabidopsis and carried out functional analysis under drought, salt, and cold stress conditions. We identified 128, 70, and 72 DTX/MATE genes in Gossypium hirsutum, Gossypium arboreum, and Gossypium raimondii, respectively. The proteins encoded by the DTX/MATE genes showed varied physiochemical properties but they all were hydrophobic. The Gh_D06G0281 (DTX/MATE) over-expressing Arabidopsis lines were highly tolerant under drought, salt, and cold stress with high production of antioxidant enzymes and significantly reduced levels of oxidants. Lipid peroxidation, as measured by the level of malondialdehyde concentrations was relatively low in transgenic lines compared to wild types, an indication of reduced oxidative stress levels in the transgenic plants. Based on physiological measurements, the transgenic plants exhibited significantly higher relative leaf water content, reduced excised leaf water loss and a significant reduction in ion leakage as a measure of the cell membrane stability compared to the wild types. Abiotic stress responsive genes, ABF4, CBL1, SOS1, and RD29B were highly expressed in the transgenic lines compared to the non-transformed wild type plants. The protein encoded by the Gh_D06G0281 (DTX/MATE) gene was predicted to be located within the plasma membrane. Since signals from extracellular stimuli are transmitted through the plasma membrane most of which are conducted by plasma membrane proteins it is possible the Gh_D06G0281 (DTX/MATE) gene product could be important for this process.

Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cytogenetics, and genomics. Here we update and provide a brief summary of the emerging picture of species relationships and diversification, and a set of the designations for individual genomes and chromosomes in Gossypium. This cytogenetic and genomic nomenclature will facilitate comparative studies worldwide, which range from basic taxonomic exploration to breeding and germplasm introgression.

The extrusion of toxins and substances at a cellular level is a vital life process in plants under abiotic stress. The multidrug and toxic compound extrusion (MATE) gene family plays a large role in the exportation of toxins and other substrates. We carried out a genome-wide analysis of MATE gene families in Gossypium raimondii and Gossypium arboreum and assessed their expression levels under salt, cadmium and drought stresses. We identified 70 and 68 MATE genes in G. raimondii and G. arboreum, respectively. The majority of the genes were predicted to be localized within the plasma membrane, with some distributed in other cell parts. Based on phylogenetic analysis, the genes were subdivided into three subfamilies, designated as M1, M2 and M3. Closely related members shared similar gene structures, and thus were highly conserved in nature and have mainly evolved through purifying selection. The genes were distributed in all chromosomes. Twenty-nine gene duplication events were detected, with segmental being the dominant type. GO annotation revealed a link to salt, drought and cadmium stresses. The genes exhibited differential expression, with GrMATE18, GrMATE34, GaMATE41 and GaMATE51 significantly upregulated under drought, salt and cadmium stress, and these could possibly be the candidate genes. Our results provide the first data on the genome-wide and functional characterization of MATE genes in diploid cotton, and are important for breeders of more stress-tolerant cotton genotypes.

Cotton (Gossypium spp.) is the number one crop cultivated for fiber production and the cornerstone of the textile industry. Drought and salt stress are the major abiotic stresses, which can have a huge economic impact on cotton production; this has been aggravated with continued climate change, and compounded by pollution. Various survival strategies evolved by plants include the induction of various stress responsive genes, such as cyclin dependent kinases (CDKs). In this study, we performed a whole-genome identification and analysis of the CDK gene family in cotton. We identified 31, 12, and 15 CDK genes in G. hirsutum, G. arboreum, and G. raimondii respectively, and they were classified into 6 groups. CDK genes were distributed in 15, 10, and 9 linkage groups of AD, D, and A genomes, respectively. Evolutionary analysis revealed that segmental types of gene duplication were the primary force underlying CDK genes expansion. RNA sequence and RT-qPCR validation revealed that Gh_D12G2017 (CDKF4) was strongly induced by drought and salt stresses. The transient expression of Gh_D12G2017-GFP fusion protein in the protoplast showed that Gh_D12G2017 was localized in the nucleus. The transgenic Arabidopsis lines exhibited higher concentration levels of the antioxidant enzymes measured, including peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) concentrations under drought and salt stress conditions with very low levels of oxidants. Moreover, cell membrane stability (CMS), excised leaf water loss (ELWL), saturated leaf weight (SLW), and chlorophyll content measurements showed that the transgenic Arabidopsis lines were highly tolerant to either of the stress factors compared to their wild types. Moreover, the expression of the stress-related genes was also significantly up-regulated in Gh_D12G2017 (CDKF4) transgenic Arabidopsis plants under drought and salt conditions. We infer that CDKF-4s and CDKG-2s might be the primary regulators of salt and drought responses in cotton.