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The SPL gene family (for Squamosa Promoter-binding like Proteins) represents specific transcription factors that have significant roles in abiotic stress tolerance, development and the growth processes of different plants, including initiation of the leaf, branching and development of shoot and fruits. The SPL gene family has been studied in different plant species; however, its role is not yet fully explored in pigeon pea (Cajanus cajan). In the present study, 11 members of the CcSPL gene family were identified in C. cajan. The identified SPLs were classified into nine groups based on a phylogenetic analysis involving SPL protein sequences from C. cajan , Arabidopsis thaliana , Cicer arietinum , Glycine max , Phaseolus vulgaris , Vigna unguiculata and Arachis hypogaea. Further, the identification of gene structure, motif analysis, domain analysis and presence of cis -regulatory elements in the SPL family members were studied. Based on RNA-sequencing data, gene expression analysis was performed, revealing that CcSPL2.1, 3 and 13A were significantly upregulated for salt-tolerance and CcSPL14 and 15 were upregulated in a salt-susceptible cultivar. Real-time qPCR validation indicated that CcSPL3, 4, 6 and 13A were upregulated under salt stress conditions. Therefore, molecular docking was performed against the proteins of two highly expressed genes (CcSPL3 and CcSPL14) with three ligands: abscisic acid, gibberellic acid and indole-3-acetic acid. Afterward, their binding affinity was obtained and three-dimensional structures were predicted. In the future, our study may open avenues for harnessing CcSPL genes in pigeon pea for enhanced abiotic stress resistance and developmental traits. The pigeon pea (Cajanus cajan) is a diploid legume, grown in humid and subtropic regions around the world. The gene family of Squamosa Promoter-binding like Proteins has been studied in different plant species, but is not yet fully explored in pigeon pea. The identified genes were classified into nine groups based on a phylogenetic analysis. Gene expression analysis using RNA sequencing revealed that CcSPL2.1, 3 and 13A were significantly upregulated in salt-tolerant cultivars, which could be further explored. This article belongs to the Collection Functional Genomics for Developing Climate Resilient Crops. [ABSTRACT FROM AUTHOR]

Drought is a major threat to wheat production worldwide and development of drought-tolerant wheat genotypes may improve the production of this cereal crop in drought affected regions. In the present study, 24 mutant lines were developed by treating a wheat variety 'NN-Gandum-1(NN-1) with ethyl methane sulfonate (EMS). The M5, M6, and M7 generations were evaluated for quantitative traits under well irrigated and rainfed conditions. Furthermore, best performing mutants of M6 and M7 generations were examined for biochemical parameters. A substantial correlation was found among the quantitative traits (plant height, spike length, tillers per plant, number of spikelets per spike and thousand grain weight) which confirmed their high heritability and relative relation. Principal component analysis (PCA) showed that the first two PCs with eigenvalues >1 had more than 50% of the total variability among the mutant lines under normal and water limited conditions. Cluster analysis depicted that considerable variations existed among all mutant lines. Among these mutant lines, some mutants showed significant variation consistently larger than corresponding values of wild type in multigeneration replication. Using drought tolerance indices (Stress tolerance index and geometric mean productivity), high yielding mutant lines under drought stress were selected. Across all these three-mutant generations, mutant lines NN1-M-363, NN1-M-506, NN1-M-700, NN1-M-701, and NN1-M-1621 showed significant improvement as compared to wild type in response to stress conditions. The selected five drought tolerant mutants showed increased accumulation of proline contents, total soluble sugars, total free amino acids, while decreased total chlorophyll content, carotenoids, and total soluble proteins. Results suggested that the morphological traits and yield attributes along with biochemical parameters could be utilized for the evaluation of wheat cultivars under drought stress. [ABSTRACT FROM AUTHOR]

Coronavirus Disease 2019 (COVID-19) is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARSCOV-2). It started from Wuhan city of China and now has become a pandemic all over the world, affecting the majority of countries. COVID-19 has caused 71.6 million cases worldwide till now, out of which 46.8 million recovered and 1.6 million died. In Pakistan, it affected 429 thousand population till now, out of which 374 thousand recovered and 8796 precious lives were lost, making fatality rate at 2%. The spectrum of coronavirus disease continues to unfold as time passes. It has created health and economic crisis all over the world. Being a new virus means less information on behavior and a lot to learn for its immunity. It was assumed initially that reinfection was less likely. Once exposed, we will develop antibodies and will be safe. But now we have a case of Covid-19 reinfection, depicting that despite exposure and having IgG Antibody titer, reinfection occurred within 6 months. [ABSTRACT FROM AUTHOR]

Genus cotton has total 50 species, diploid species fall into 8 genomic groups (A-G, and K). To the extent of our knowledge, frequency of single nucleotide polymorphisms (SNPs) has not been calculated in genes of multiple genomes of the genus Gossypium. Here we present the frequency of SNPs in the transcribed regions of the multiple genes, and their utility in resolving phylogenies among 11 diploid species representing five of the eight diploid genomes of the genus Gossypium. We explored the expressed sequence tags (ESTs) data set of G. arboreum showing homology with genes encoding for mitochondrial small heat shock protein (MT-sHSP), histone H2B1, S-adenosyl methionine synthetase, cytochrome p450, actin-depolymerizing factor 2, C-terminal domain of helicases and histone H2B3 for designing primers. The resultant PCR products amplifying partial gene sequences were sequenced. In total, 61 SNPs were detected in cotton genomes which include 53 substitutions and 8 Indels in the total 1920 bp genome length. Phylogenetic analysis using this data revealed grouping of genomes comparable with previous studies. A1 and A2 genomes were most similar (98.0%) while D9 and Oryza genomes were least similar (31.2%). Oryza was most distantly related with other genomes. In conclusion SNPs are potent markers to delineate cotton genomes according to their evolutionary positions. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) is among the most important food crops that provide a staple food for nearly half of the world’s population. Rice crops are prone to various types of stresses, both biotic and abiotic. Biotic stresses include insect pests, fungus, bacteria, viruses, and herbicide toxicity. Among abiotic stresses, drought, cold, and salinity are also well studied in rice. Various genes have been identified, cloned, and characterized to combat these stresses and protect rice crops. The identified genes are successfully transformed into rice plants to produce transgenic plants. These transgenic rice plants are being evaluated under field conditions in different countries. Genetic engineering has a very positive impact on improvement of rice crops. The development of rice with improved traits of biotic and abiotic stress tolerance is discussed in this review article. The objective of this review is to provide an overview of recent research and development in the field of rice biotechnology. [ABSTRACT FROM AUTHOR]

Drought and salinity are causing significant loss in crop yield worldwide. Genetically engineered salt and drought tolerant crop varieties can be a potential remedy for the recovery of lost uncultivated saline and low rain fall areas. In eukaryotes, transcription factors are involved in gene expression which activate or repress the transcription under specific conditions. Hence, the present study has been designed to characterize a fully modified synthetic hsr1 gene. This gene encodes for a transcription factor of heat shock family and has been found to be involved in drought and salinity tolerance in yeast. The synthetic hsr1 gene was cloned under double 35S promoter and caMV terminator for high level of expression in the transgenic plants. Initially the gene was cloned into pJIT163 and then into expression vector pGreen0029. Agrobacterium tumefaciens strain GV was used as a vector for transformation into tobacco. In three different experiments about 34.5% transformation efficiency was observed. Putative transgenic plants were confirmed by PcR analysis using hsr1 gene specific primers. Further screening of these putative transgenic plants against different salinity levels and drought stress showed that transgenic plants were tolerant to drought and salinity conditions. Transformation in the model plant paves the way to genetically engineer vital crops for the development of drought and salinity resistant genotypes. © 2015 Friends Science Publishers [ABSTRACT FROM AUTHOR]

This study explains the construction of an intraspecific genetic linkage map of the A-genome diploid cotton with simple sequence repeat (SSR) and randomly amplified polymorphic DNA (RAPD) markers, using 180 F2 plants derived from the cross of 2 Gossypium arboreum cotton cultivars (Ravi x Entry-17). Polymorphisms between the 2 parents were detected using 1089 pairs of SSR primers and 520 RAPD primers. In total, 34 pairs of SSR primer-amplified and 18 RAPD primer-amplified polymorphic loci were selected to survey the F2 population. In total, 52 polymorphic DNA fragments were generated and used to construct a linkage map with JoinMap 3.0. A total of 45 loci and 5 phenotypic traits were mapped at a logarithm of odds ratio of ≥3.0 on 10 linkage groups. The total length of the map was 346 cM, and the average distance between adjacent markers was 7.7 cM. Chromosome assignments were made according to previous studies. In total, 7 quantitative trait loci (QTLs), including 5 for productivity traits and 2 for fibre traits, were mapped. Identification of these QTLs will set the stage for initiating marker-assisted selection and map-based cloning in cotton. [ABSTRACT FROM AUTHOR]

Microsatellite regions in DNA fragments of Gossypium arboreum were explored and PCR products 500-800 bp long were analyzed for genomic simple sequence repeats (gSSRs). From 39 segments, 23 short gSSRs were identified; on average they occurred every 1.6 kb. Primers were used to amplify fragments from 18 diploid species representing 6 diploid genomes and 1 tetraploid species, G. hirsutum (AD). The phylogeny of diploid genomes was subsequently determined. No primer amplified the DNA from all genotypes; however, amplification occurred in 59% of 437 PCR events. All genomes were grouped into 2 clusters (a and b). The obtained phylogeny of the species parallels previous reports. The strategy adopted here is an efficient method of identifying new gSSRs from species not extensively explored. [ABSTRACT FROM AUTHOR]

MicroRNAs are small non-coding RNA molecules that are produced in a cell endogenously. They are made up of 18 to 26 nucleotides in strength. Due to their evolutionary conserved nature, most of the miRNAs provide a logical basis for the prediction of novel miRNAs and their clusters in plants such as sunflowers related to the Asteraceae family. In addition, they participate in different biological processes of plants, including cell signaling and metabolism, development, growth, and tolerance to (biotic and abiotic) stresses. In this study profiling, conservation and characterization of novel miRNA possessing conserved nature in various plants and their targets annotation in sunflower (Asteraceae) were obtained by using various computational tools and software. As a result, we looked at 152 microRNAs in Arabidopsis thaliana that had already been predicted. Drought tolerance stress is mediated by these 152 non-coding RNAs. Following that, we used local alignment to predict novel microRNAs that were specific to Helianthus annuus. We used BLAST to do a local alignment, and we chose sequences with an identity of 80% to 100%. MIR156a, MIR164a, MIR165a, MIR170, MIR172a, MIR172b, MIR319a, MIR393a, MIR394a, MIR399a, MIR156h, and MIR414 are the new anticipated miRNAs. We used MFold to predict the secondary structure of new microRNAs. We used conservation analysis and phylogenetic analysis against a variety of organisms, including Gossypium hirsutum, H. annuus, A. thaliana, Triticum aestivum, Saccharum officinarum, Zea mays, Brassica napus, Solanum tuberosum, Solanum lycopersicum, and Oryza sativa, to determine the evolutionary history of these novel non-coding RNAs. Clustal W was used to analyze the evolutionary history of discovered miRNAs. [ABSTRACT FROM AUTHOR]

Since 6000 BC, cotton has been cultivated for lint fiber, which now dominates the natural textile industry worldwide. Common resources such as an integrated web database, a microsatellite database, and comparative quantitative trait loci (QTL) resources for Gossypium have accelerated the progress towards quantifying the impact of repeated human dispersals and selection regimes on various gene pools of the genus Gossypium. Out of 50 Gossypium species, four have been domesticated-two diploids and two tetraploids-for elimination of hard seed coat, improvement in lint percentage of about 40% and fiber length of 22%, larger boll size, and day-neutral reproductive habit. The major drawback of domestication is the lack of genetic diversity. This lack of genetic diversity is observed more in Gossypium hirsutum L. cultivars characterizing upland cotton than in Gossypium barbadense, typical of Pima and Egyptian cotton. Much of the genetic diversity among G. barbadense cultivars is attributed to the introgression of G. hirsutum alleles. This process highlights the importance of introgression of new alleles from accessions of all the Gossypium species into cultivated cotton species. Among the genomic resources, about 16,162 publicly available SSRs and 312 mapped cotton RFLP sequences containing simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), and random amplified polymorphic DNA (RAPD) markers have been surveyed on numerous mapping populations, and developed about 26 linkage maps (SSR, RFLP, AFLP, and RAPD). Reports show the identification of DNA markers associated with over 29 important traits or QTLs such as fiber quality and yield, leaf and flower morphology, trichome density and their distribution, and disease resistance. In comparative mapping studies, 432 QTLs mapped on 11 different mapping populations were aligned on a high-density reference map containing 3,475 loci. In a meta-analysis study of over 1,000 QTLs obtained from backcross population and recombinant inbred line populations derived from the same parents, most consistent meta-clusters were reported for fiber color, fineness, and length. For exploring the function of genes, the targeting induced local lesions in genomes (TILLING) approach-avoiding gene transfer process was used for identifying a brassino steroid receptor gene that is involved in fiber development. Lastly, cotton genome has been enriched with genes isolated from distantly related organisms using various transformation methods. For example, Cry1Ac, Cry1Ab, and herbicide-resistant genes were transformed in cotton that covered a vast majority of cotton acreage worldwide. Here the authors discuss investigations for improving the efficacy of transformation and regeneration systems, and for searching new genes or silencing the unwanted cotton genes using RNAi technology. We suggest initiating projects on sequencing the diploid and tetraploid genomes for exploring the extent of genetic variations, developing TILLING populations, initiating nested association mapping studies, and developing third generation genetically modified cotton, collectively setting the stage for sustaining cotton production under continually changing production conditions, climates, and human needs. [ABSTRACT FROM AUTHOR]

MicroRNAs are small non-coding RNA molecules that are produced in a cell endogenously. They are made up of 18 to 26 nucleotides in strength. Due to their evolutionary conserved nature, most of the miRNAs provide a logical basis for the prediction of novel miRNAs and their clusters in plants such as sunflowers related to the Asteraceae family. In addition, they participate in different biological processes of plants, including cell signaling and metabolism, development, growth, and tolerance to (biotic and abiotic) stresses. In this study profiling, conservation and characterization of novel miRNA possessing conserved nature in various plants and their targets annotation in sunflower (Asteraceae) were obtained by using various computational tools and software. As a result, we looked at 152 microRNAs in Arabidopsis thaliana that had already been predicted. Drought tolerance stress is mediated by these 152 non-coding RNAs. Following that, we used local alignment to predict novel microRNAs that were specific to Helianthus annuus. We used BLAST to do a local alignment, and we chose sequences with an identity of 80% to 100%. MIR156a, MIR164a, MIR165a, MIR170, MIR172a, MIR172b, MIR319a, MIR393a, MIR394a, MIR399a, MIR156h, and MIR414 are the new anticipated miRNAs. We used MFold to predict the secondary structure of new microRNAs. We used conservation analysis and phylogenetic analysis against a variety of organisms, including Gossypium hirsutum, H. annuus, A. thaliana, Triticum aestivum, Saccharum officinarum, Zea mays, Brassica napus, Solanum tuberosum, Solanum lycopersicum, and Oryza sativa, to determine the evolutionary history of these novel non-coding RNAs. Clustal W was used to analyze the evolutionary history of discovered miRNAs. [ABSTRACT FROM AUTHOR]

Genomic technologies have been used to improve cultivated crop species. For example, Bt genes such as Cry1Ac, Cry2Ab, Cry1F and Cry3Bb1 are derived from Bacillus thuringiensis, a soil bacterium. Such genes provide protection against lepidopteran insect pests. Bt genes have been introduced in corn, cotton, soybean, rice, potato and canola. Genetically modified (GM)-cotton, containing the Cry1Ac gene, was released for cultivation in the mid-1990s in the USA and later in 28 countries including China and India. Potential harmful effects of the Bt-crops on non-targets were assessed before release into the environment. Most commonly, cultivation of the Bt-crops was found safe. Safety was tested using various experiments including: the insertional impact of transgene and its regulatory elements on plant phenotype and agronomic performance; effect on non-target organisms; and nutritional impacts on multiple experimental models, albeit the studies were conducted for limited durations. However, skeptics always claim for conducting extensive clinical as well as field trials and also cast doubt on methods and procedures of calculating the ecological risks. This debate got further momentum especially after the publication of reports on substantial reduction in monarch butterfly caterpillars when exposed to Bt-maize pollen-though later nullified-and detection of traces of transgene in various tissues of experimental animals. It is generally accepted that procedures, methods and protocols for evaluating the potential risks of GM-crops and foods should be standardized for building confidence of all stakeholders. Efforts should be exerted in deploying genes of interest, marker genes and regulatory sequences invoking no or little issues of potential risks to the ecosystem. [ABSTRACT FROM AUTHOR]

Sunflower is the fourth most important oil seed crop of the world. Drought is a major limiting factor severely influencing the production sunflower. Cuticular wax is the outermost defensive layer which protect the plants from abiotic stress. In present investigation, ten sunflower genotypes were grown in growth chambers along with their controls. At the age of thirty days, drought stress was applied to these genotypes for ten days to study the impact of dehydration stress on different drought tolerance traits. Further, we studied the association of epicuticular wax load on drought-related traits, i.e., morpho-physiological traits, photosynthetic pigments, osmolyte contents and enzymatic activities both under stress and normal conditions. It was observed that sunflower genotypes subjected to drought stress enhanced wax load compared to normal plants. However, drought stress reduced leaf area, relative water contents, leaf water potential, osmotic adjustment and chlorophyll contents. In addition, proline, glycine betaine contents and antioxidant enzymatic activities of SOD, POD and CAT increased when plants were subjected to drought condition. Regression analysis indicated that osmolytes and antioxidant enzymatic activities showed positive correlation with wax quantity, whereas physiological traits showed negative correlation with wax load indicating elevation in wax quantity, reduced transpiration rate, leaf water potential and residual transpiration under drought condition. Based on findings, it can be concluded role of wax quantity can be exploited to develop genotypes with enhanced wax content to tolerate the drought stress and identification of drought resistant sunflower genotypes. [ABSTRACT FROM AUTHOR]

The damaging potential of Alternaria alternata on different mungbean genotypes was accessed and its management was done under in vitro and in vivo conditions through suitable fungicides. Seeds of fifty different mungbean genotypes were sown in lines. There were fifteen replications for each line. The data on disease incidence and percent disease intensity were accessed on all the genotypes. Infection was observed on all genotypes, none of them were found to be immune. Fourteen lines were found to be the most susceptible (14114, 14117, 14128, 14198, 14203, 14205, 14250, 14265, 14266, 14295, 14305, 14306, 14368, 14438). Infection was observed on all genotypes, none of them were found to be immune. The maximum PDI (Percent Disease Intensity) was recorded 35.30% while minimum was 2.43%. For detached leaf assay, the conidial suspension of 105 conidia/mLwas prepared and sprayed on detached leaves. The results revealed that maximum infection percentage was observed in 14306, 14198 genotypes while minimum was observed in 14128, 14203. The lesion area was found to be maximum in 14306, 14198 (0.23, 0.22) while minimum in 14128 (0.12) respectively. For management experiments, different fungicides; Propiconazole (Tilt), Propineb (Antracol), Difenconazole (Score), Thiophanate methyl (Topsin M), Mancozeb (Dithane M-45) were tested under in vitro and in vivo conditions. Significant decrease in mycelial growth with the increase in concentration of fungicides was observed. Percent inhibition of mycelial growth was maximum in Propiconazole at its highest concentration (1000 ppm) under in vitro conditions. A significant decline in disease incidence was observed as compared to control treatment. The minimum percent disease incidence was recorded in Propiconazole (10.34) with PDC (67.31) while the maximum percent disease incidence was observed in Thiophanate methyl (25.46). So, Propiconazole could be used successfully for the management of A. alternata under field conditions. [ABSTRACT FROM AUTHOR]

The present study was designed to evaluate genetic diversity among twenty cotton genotypes by employing thirty one SSR markers that were reported from Brookheaven National Laboratories. Out of thirty-one primers, six SSR primers were found polymorphic at different SSR loci. Maximum number of loci (33), were amplified by MNH-93, while minimum (22) by 238-F. Total percentage of informative loci was 36.8%. Genetic diversity matrix of these genotypes was calculated by NTSYS-pc 2.2 software. Genetic similarity coefficients ranged from 0.474 to 0.974. The highest dissimilarity (0.474) was observed between genotype 298-F and CIM-496. Cluster analysis as performed using un-weighted pair group method of arithmetic average algorithm showed that Nei and Li's coefficients ranged from 0.63 to 0.97. The dendrogram of cotton lines showed two major clusters except 238-F forming an out-group from other genotypes, thus showing maximum dissimilarity. Genotypes MNH-93 and K-68/9 showed maximum similarity coefficient of 0.97. Information obtained from the present study can be used to select divergent parents for future breeding programs. [ABSTRACT FROM AUTHOR]