Genome-wide identification and analysis of the CNGC gene family in upland cotton under multiple stress conditions

Background The cyclic nucleotide-gated channel(CNGC)gene family plays a significant role in the uptake of both essential and toxic cations,and has a role in enhancing tolerance to various forms of abiotic stresses as well as the modulation of the heavy metal toxicity to plant through the absorption of heavy metals.Results A complete genome-wide identification and functional characterization of the cotton CNGC genes was carried out,in which 55,28,and 29 CNGC genes were identified in Gossypium hirsutum,G.raimondii,and G.arboreum,respectively.The protein encoded by the CNGC genes exhibited GRAVY value below zero,indicating their hydrophilic property.CNGC genes were unevenly distributed in 19 out of 26 chromosomes,in which the highest density were observed on Ah05,with 8 genes.High gene coverage was observed among the diploid cotton species,with CNGC genes mapped on all A chromosomes and on 11 out of 13 of D chromosomes.The majority of CNGC proteins were localized in the endoplasmic reticulum,nucleus,and plasma membrane.Gene expression analysis revealed the up-regulation of Gh_A01G0520(CNGC4)and Gh_D13G1974(CNGC5)across various forms of abiotic stresses.Moreover,down-regulation of Gh_A01G0520(CNGC4)and Gh_D13G1974(CNGC5)in CNGCs silenced plants caused the significantly reduced ability to tolerate drought and salt stresses.All CNGCs silenced plants were recorded to have significantly low content of antioxidants but relatively higher content of oxidant,including MDA and H_(2)O_(2).Furthermore,SPAD,CMS(cell membrane stability),ELWL(excised leaf water loss),SDW(shoot dry matter weight),and RDW(root dry matter weight)were all lower in CNGCs silenced plants compared with the wild type plants.Conclusion Significant reduction in antioxidant content and negative effects of physiological and morphological characters in CNGCs silenced plants has revealed the novel role of CNGC genes in enhancing cell integrity under abiotic stress conditions.These results provide vital information that will expand our understanding of the CNGC gene family in cotton and other plants,thus promoting the integration of these genes in the development of the environmental resilient plants.

Knockdown of 60S ribosomal protein L14‑2 reveals their potential regulatory roles to enhance drought and salt tolerance in cotton

Background:Cotton is a valuable economic crop and the main significant source of natural fiber for textile industries globally.The effects of drought and salt stress pose a challenge to strong fiber and large-scale production due to the ever-changing climatic conditions.However,plants have evolved a number of survival strategies,among them is the induction of various stress-responsive genes such as the ribosomal protein large(RPL)gene.The RPL gene families encode critical proteins,which alleviate the effects of drought and salt stress in plants.In this study,comprehensive and functional analysis of the cotton RPL genes was carried out under drought and salt stresses.Results:Based on the genome-wide evaluation,26,8,and 5 proteins containing the RPL14B domain were identified in Gossypium hirsutum,G.raimondii,and G.arboreum,respectively.Furthermore,through bioinformatics analysis,key cis-regulatory elements related to RPL14B genes were discovered.The Myb binding sites(MBS),abscisic acid-responsive element(ABRE),CAAT-box,TATA box,TGACG-motif,and CGTCA-motif responsive to methyl jasmonate,as well as the TCA-motif responsive to salicylic acid,were identified.Expression analysis revealed a key gene,Gh_D01G0234(RPL14B),with significantly higher induction levels was further evaluated through a reverse genetic approach.The knockdown of Gh_D01G0234(RPL14B)significantly affected the performance of cotton seedlings under drought/salt stress conditions,as evidenced by a substantial reduction in various morphological and physiological traits.Moreover,the level of the antioxidant enzyme was significantly reduced in VIGS-plants,while oxidant enzyme levels increased significantly,as demonstrated by the higher malondialdehyde concentration level.Conclusion:The results revealed the potential role of the RPL14B gene in promoting the induction of antioxidant enzymes,which are key in oxidizing the various oxidants.The key pathways need to be investigated and even as we exploit these genes in the developing of more stress-resilient cotton germplasms.

Genome wide identification and characterization of light-harvesting Chloro a/b binding(LHC)genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

Background: Cotton is an important commercial crop for being a valuable source of natural fiber.Its production has undergone a sharp decline because of abiotic stresses,etc.Drought is one of the major abiotic stress causing significant yield losses in cotton.However,plants have evolved self-defense mechanisms to cope abiotic factors like drought,salt,cold,etc.The evolution of stress responsive transcription factors such as the trihelix,a nodule-inception-like protein(NLP),and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses.Results: Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding(LHC)genes were carried out in cotton under drought stress conditions.A hundred and nine proteins encoded by the LHC genes were found in the cotton genome,with 55,27,and 27 genes found to be distributed in Gossypium hirsutum,G.arboreum,and G.raimondii,respectively.The proteins encoded by the genes were unevenly distributed on various chromosomes.The Ka/Ks(Non-synonymous substitution rate/Synonymous substitution rate)values were less than one,an indication of negative selection of the gene family.Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues.Most genes were found to be highly expressed in MR-85,a relative drought tolerant germplasm.Conclusion: The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance,and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

Genetic map construction and functional characterization of genes within the segregation distortion regions(SDRs)in the F_(2:3) populations derived from wild cotton species of the D genome

Background:Segregation distortion(SD)is a common phenomenon among stable or segregating populations,and the principle behind it still puzzles many researchers.The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions(SDRs).A consensus map was developed between two maps from the four D genomes,map A derived from F2:3 progenies of Gossypium klotzschianum and G.davidsonii while Map B from G.thurberi and G.trilobum F2:3 generations.In each map,188 individual plants were used.Results:The consensus linkage map had 1492 markers across the 13 linkage groups with a map size of 1467.445 cM and an average marker distance of 1.0370 cM.Chromosome D502 had the highest percentage of SD with 58.6%,followed by Chromosome D507 with 47.9%.Six thousand and thirty-eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map.Within chromosome D502 and D507,2308 and 3730 genes were mined,respectively,and were found to belong to 1117 gourp out of which 622 groups were common across the two chromosomes.Moreover,genes within the top 9 groups related to plant resistance genes(R genes),whereas 188 genes encoding protein kinase domain(PF00069)comprised the largest group.Further analysis of the dominant gene group revealed that 287 miRNAs were found to target various genes,such as the gra-miR398,gramiR5207,miR164a,miR164b,miR164c among others,which have been found to target top-ranked stress-responsive transcription factors such as NAC genes.Moreover,some of the stress-responsive cis-regulatory elements were also detected.Furthermore,RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions,and also they were highly expressed at different stages of fiber development.Conclusion:The results indicated the critical role of the SDRs in the evolution of the key regulatory genes in plants.

The Signatures of Acid Concentration on the Optical Band Gap and Associated Band Tails of Chitosan from Shrimp for Application in Optoelectronic Devices

Over the recent years, the global increase of electronic wastes from electrical and electronic devices (e-wastes) has been on an alarming trend in quantity and toxicity and e-wastes are non-biodegradable resulting in its cumulative increase over time. Changes in technology and unrestricted regional movement of electrical devices have facilitated the generation of more e-wastes leading to high levels of air, soil and water pollution. To address these challenges, biodegradable organic components such as chitosan have been used to replace their inorganic counterparts for optoelectronic device applications. However, in-depth knowledge on how such materials can be used to tune the optical properties of their hybrid semiconductors is unrivaled. Thus, systematic studies of the interplay between the preparation methods and optical band gap and Urbach energy of such organic components are vital. This study has thus been dedicated to map out the effect of acid concentrations during chitosan extraction on the corresponding optical band gap and Urbach energy with a view to improving its applications in optoelectronic devices. The, 1.0 to 2.5 molar hydrochloric acid (HCl) was used for 12 hours at room temperature during demineralization and 2.0 molar sodium hydroxide (NaOH) during deprotonation processes. The absorbance spectrum of the samples was collected by UV-Vis spectrophotometer and band gap energies were analyzed by performing Tauc’s plot. This study revealed that the energy band gap of chitosan extracted from 1 M HCl, 1.5 M HCl, 2.0 M HCl and 2.5 M HCl were 3.72 eV, 3.50 eV, 3.45 eV and 3.36 eV respectively. Furthermore, the Urbach energy of chitosan extracted from 1 M HCl, 1.5 M HCl, 2.0 M HCl and 2.5 M HCl were 0.60496 eV, 0.5292 eV, 4724 eV and 0.2257 eV, respectively.

Indigenous Knowledge on Production and Utilisation of Termite(Isoptera)in Western Kenya

The study sought to assess the level of knowledge on the utilization of termites,harvesting methods and characterise local edible termite species.Focus group discussion with key informants was used to collect data that was analysed using SPSS Version 21.0 to generate descriptive statistics.Results indicated different levels of termites’utilisation where 45%of farmers use alates as food,35%as feed for chicks and quails,while 20%use the queen to fatten young bulls.Majority of farmers(40%)prefer the use of termites as feed because it is readily available,followed with 20%that use it because of nutritive value,10%relate its use with better taste of poultry products,5%associate termite use in enhancing early maturity weight while 5%said it improves growth and strength of bulls.On harvesting,three methods are commonly used with most farmers(45%)using underground trapping method,(35%)use above ground trapping method but 20%use mound excavation.Varied plant materials are used as attractants and the effect is more when combined with dry cow dung.Farmers further characterised species based on time of emergence of alates and habitat’s physical features.Most respondents(45%)associated:big mounds with Macrotermes bellicosus(Mafendete);small mount to Macrotermes subhyalinus(Kitunda);presence of open big tunnels with Coptotermes millitaris(Riamke)while seasonal gallaries and small tunnels was a confirmatory feature of either Pseudocanthotermes militaris(Chiisiisi)and Pseudocanthotermes spiniger(Maburi).The study demonstrates the richness in indigenous knowledge on techniques of termite production and utilization.

Environmental and Management Factors That Influence Commelina Species in Selected Agro-Ecological Zones in Western Kenya

Commelina species are plant resources full of promise as future food and feed that thrive in diverse ecosystems. They are medicinal plants, leafy vegetables, forage for ruminants, feed for cricket insects, crop protection, and fuel. However, information regarding factors driving Commelina in agro-ecological zones in Western Kenya is lacking. Therefore, we investigated the diversity of Commelina species, the composition of associated weed species as well as environmental and management factors affecting their diversity and distribution based on 22 variables from 12 production sites. In the survey, 115 species belonging to 30 families were recorded of which 11 Commelina species were identified. Among Commelina species, Commelina diffusa and Commelina benghalensis var. benghalensis (non-hybrid variant) had higher relative density. Multiple linear regressions revealed that the environment (exchangeable sodium percentage, magnesium, soil pH, and total nitrogen) and management (agriculture system type) variables exert a stronger effect on the diversity of Commelina species. Detrended Correspondence Analysis detected different ecological conditions for Commelina species and the composition of associated weed species. The forward selection based on Canonical Correspondence Analysis indicated that the distribution of Commelina species responded significantly to soil pH, available phosphorous, total nitrogen, fertility, and crop spacing. Partitioning variation showed the great importance to the environment than management (10.57% versus 5.97%). The low shared variance (environment × management) was -0.4%, indicating that the two factors have a more individualistic than interactive nature. However, the 83.86% that remained unexplained was attributed to stochastic variation or unmeasured variables. This study suggests that the identified five important variables affecting the distribution of Commelina species will certainly contribute to the prioritization of ecological aspects leading to the growth condition of Commelina species.