Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium (original) (raw)
Related papers
Journal of Experimental Botany, 2008
Lipid modifying enzymes play a key role in the development of cold stress tolerance in cold-resistant plants such as cereals. However, little is known about the role of the endogenous enzymes in cold-sensitive species such as cotton. Delta 12 fatty acid desaturases (FAD2), known to participate in adaptation to low temperatures through acyl chain modifications were used in gene expression studies in order to identify parameters of plant response to low temperatures. The induction of microsomal delta 12 fatty acid desaturases at an mRNA level under cold stress in plants is shown here for first time. Quantitative PCR showed that though both delta 12 omega 6 fatty acid desaturase genes FAD2-3 and FAD2-4 identified in cotton are induced under cold stress, FAD2-4 induction is significantly higher than FAD2-3. The induction of both isoforms was light regulated, in contrast a third isoform FAD2-2 was not affected by cold or light. Stress tolerance and light regulatory elements were identified in the predicted promoters of both FAD2-3 and FAD2-4 genes. Di-unsaturated fatty acid species rapidly increased in the microsomal fraction isolated from cotton leaves, following cold stress. Expression analysis patterns were correlated with the observed increase in both total and microsomal fatty acid unsaturation levels suggesting the direct role of the FAD2 genes in membrane adaptation to cold stress.
BMC research notes, 2014
The most widely cultivated cotton (Gossypium hirsutum L., AD-genome) is derived from tetraploidization between A- and D-genome species. G. arboreum L. (A-genome) and G. raimondii Ulbr. (D-genome) are two of closely-related extant progenitors. Gene expression studies in allotetraploid cotton are complicated by the homoeologous loci of A- and D-genome origins. To develop genomic resources for gene expression and cotton breeding, we sequenced and assembled expressed sequence tags (ESTs) derived from G. arboreum and G. raimondii. Roche/454 FLX sequencing technology was employed to sequence normalized cDNA libraries prepared from leaves, roots, bolls, ovules, and fibers in G. arboreum and G. raimondii, respectively. Sequencing reads from two independent libraries in each species were combined to assemble high-quality EST contigs. The combined sequencing reads included 1,699,776 from A-genome and 1,464,815 from D-genome, which were clustered into 89,588 contigs in the A-genome and 65,542 ...
Identification of heat responsive genes in cotton
Biologia Plantarum, 2014
High summer temperature negatively affects cotton yield and better understanding of genetic mechanisms of heat stress responses in cotton may facilitate development of new heat tolerant cultivars. We attempted to determine heat responsive genes in cotton using tolerant (Stoneville 453, BA 119) and susceptible (Nazilli 84S) cultivars. Twenty five expressed sequence tags (ESTs) were sequenced and studied for gene homology. Sixteen ESTs were significantly similar to known genes, whereas eight ESTs were similar to not annotated cDNA clones and 1 EST did not show homology to any known gene. Expression of some ESTs was analyzed by quantitative real-time PCR and IAA-ala hydrolase (IAR3), folylpolyglutamate synthase (FPGS3), and two not annotated ESTs (GhHS126 and GhHS128) were consistently up-regulated under both short-and long-term heat stress. Since cotton is considered relatively more heat tolerant than most of the other crops, it can be suggested that these genes and ESTs could play a significant role in heat tolerance. In addition, GhHS126 and GhHS128 might be parts of the new candidate genes for heat tolerance.
Functional Plant Biology, 2014
Diurnal or prolonged exposure to air temperatures above the thermal optimum for a plant can impair physiological performance and reduce crop yields. This study investigated the molecular response to heat stress of two high-yielding cotton (Gossypium hirsutum L.) cultivars with contrasting heat tolerance. Using global gene profiling, 575 of 21854 genes assayed were affected by heat stress,~60% of which were induced. Genes encoding heat shock proteins, transcription factors and protein cleavage enzymes were induced, whereas genes encoding proteins associated with electron flow, photosynthesis, glycolysis, cell wall synthesis and secondary metabolism were generally repressed under heat stress. Cultivar differences for the expression profiles of a subset of heat-responsive genes analysed using quantitative PCR over a 7-h heat stress period were associated with expression level changes rather than the presence or absence of transcripts. Expression differences reflected previously determined differences for yield, photosynthesis, electron transport rate, quenching, membrane integrity and enzyme viability under growth cabinet and field-generated heat stress, and may explain cultivar differences in leaf-level heat tolerance. This study provides a platform for understanding the molecular changes associated with the physiological performance and heat tolerance of cotton cultivars that may aid breeding for improved performance in warm and hot field environments.
Functional characterization of the ABF gene family in upland cotton (Gossypium hirsutum L.)
The AREB/ABF bZIP transcription factors play a pivotal role in abscisic acid-dependent abiotic stress-responsive gene expression. Despite the perennial damage and reduced productivity that result from water-deficit and unpredictable early season temperature fluctuations, these critical genes have not been previously examined in upland cotton (Gossypium hirsutum). Here, we report the isolation of the G. hirsutum ABF homologs, characterization of their expression patterns in response to abiotic stress treatments, and examination of their functions through heterologous ectopic expression in Arabidopsis. As expected for an allotetraploid, G. hirsutum ABF homologs are present in the genome as homeologous pairs. These genes are differentially expressed, both among the homologs and within the homeologous pairs, in response to exogenous abscisic acid (ABA) application, dehydration, and chilling temperatures. Furthermore, heterologous ectopic expression of many of the G. hirsutum ABF genes i...
In Silico Identification and Characterization of Rare Cold Inducible 2 (RCI2) Gene Family in Cotton
RCI2/PMP3s are involved in biotic and abiotic stresses and have an influence on the regulation of many genes. RCI2/PMP3 genes, which particularly encode small membrane proteins of the PMP3 family, are involved in abiotic stress responses in plants. In this work, in silico studies were used to investigate RCI2's potential function in stress tolerance and organogenesis. We conducted an extensive study of the RCI2 gene family and revealed 36 RCI2 genes from cotton species that were distributed over 36 chromosomes of the cotton genome. Functional and phylogenetic examination of the RCI2/PMP3 gene family has been studied in Arabidopsis, but in cotton, the RCI2/PMP3 genes have not yet been studied. Phylogenetic and sequencing studies revealed that cotton RCI2s are conserved, with most of them categorized into six distinct clades. A chromosome distribution and localization study indicated that cotton RCI2 genes were distributed unevenly on 36 chromosomes with segmental duplications, suggesting that the cotton RCI2 family is evolutionarily conserved. Many cis-elements related to stress responsiveness, development, and hormone responsiveness were detected in the promoter regions of the cotton RCI2. Moreover, the 36 cotton RCI2s revealed tissue-specific expression patterns in the development of cotton performed by transcriptome analysis. Gene structure analysis indicated that nearly all RCI2 genes have two exons and one intron. All of the cotton RCI2 genes were highly sensitive to drought, abscisic acid, salt, and cold treatments, demonstrating that they may be employed as genetic objects to produce stress-resistant plants.
Frontiers in Plant Science, 2021
Low temperature is a common biological abiotic stress in major cotton-growing areas. Cold stress significantly affects the growth, yield, and yield quality of cotton. Therefore, it is important to develop more robust and cold stress-resilient cotton germplasms. In response to climate change and erratic weather conditions, plants have evolved various survival mechanisms, one of which involves the induction of various stress responsive transcript factors, of which the C-repeat-binding factors (CBFs) have a positive effect in enhancing plants response to cold stress. In this study, genomewide identification and functional characterization of the cotton CBFs were carried out. A total of 29, 28, 25, 21, 30, 26, and 15 proteins encoded by the CBF genes were identified in seven Gossypium species. A phylogenetic evaluation revealed seven clades, with Clades 1 and 6 being the largest. Moreover, the majority of the proteins encoded by the genes were predicted to be located within the nucleus,...
Genetics and Molecular Research, 2011
Cotton (Gossypium hirsutum) is an important cash crop, but high temperature during its growing season is one of the major factors that limit its productivity. This problem compels plant breeders to breed for heat tolerance, which can help to overcome this challenge. It is very important to make a comprehensive screening of heat-tolerant genotypes so that only the best are chosen. Here we report the combined use of several techniques that can help breeders to screen their germplasm. Twelve cultivated cotton genotypes were evaluated for thermotolerance, using assays that included electrolyte leakage, chlorophyll accumulation and protein profiling, as well as RAPDs to assess genetic diversity. Two genotypes (B-557 and NIAB-78) showed tolerant behavior in three thermotolerance assays. RAPD analysis results showed maximum similarity in a range of 86.7-66.7% between the genotypes MNH-554 and CIM-443. We conclude that combined use should be made of relative electrolyte leakage, chlorophyll stability and differential display with SDS-PAGE to aid in screening for stress ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 10 (2): 1156-1167 (2011) Thermotolerance diversity in Gossypium hirsutum tolerance. RAPD-based diversity analysis will further help to improve the efficiency of breeding programs.
BMC genomics, 2018
Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family genes have been extensively studied under biotic and abiotic stresses, both in model and non-model plant species; however, information on their roles in cotton is still limited. A total of 64 putative LOX genes were identified in four cotton species (Gossypium (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii)). In the phylogenetic tree, these genes were clustered into three categories (9-LOX, 13-LOX type I, and 13-LOX type II). Segmental duplication of putative LOX genes was observed between homologues from A2 to A and D5 to D hinting at allopolyploidy in cultivated tetraploid species (G. hirsutum and G. barbadense). The structure and motif composition of GhLOX genes appears to be relatively conserved among the subfamilies. Moreover, many cis-acting elements related to g...