Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum

Background The dehydration responsive element-binding (DREB) gene family plays a crucial role as transcription regulators and enhances plant tolerance to abiotic stresses. Although the DREB gene family has been identified and characterized in many plants, knowledge about it in Solanum tuberosum (Potato) is limited. Results In the present study, StDREB gene family was comprehensively analyzed using bioinformatics approaches. We identified 66 StDREB genes through genome wide screening of the Potato genome based on the AP2 domain architecture and amino acid conservation analysis (Valine at position 14th). Phylogenetic analysis divided them into six distinct subgroups (A1–A6). The categorization of StDREB genes into six subgroups was further supported by gene structure and conserved motif analysis. Potato DREB genes were found to be distributed unevenly across 12 chromosomes. Gene duplication proved that StDREB genes experienced tandem and segmental duplication events which led to the expansion of the gene family. The Ka/Ks ratios of the orthologous pairs also demonstrated the StDREB genes were under strong purification selection in the course of evolution. Interspecies synteny analysis revealed 45 and 36 StDREB genes were orthologous to Arabidopsis and Solanum lycopersicum, respectively. Moreover, subcellular localization indicated that StDREB genes were predominantly located within the nucleus and the StDREB family’s major function was DNA binding according to gene ontology (GO) annotation. Conclusions This study provides a comprehensive and systematic understanding of precise molecular mechanism and functional characterization of StDREB genes in abiotic stress responses and will lead to improvement in Solanum tuberosum

Production and Salinity Tolerance of Fodder Beet (<em>Beta vulgaris</em> L. ssp. Maritima)

Fodder beet (Beta vulgaris L. ssp. maritima) belongs to the Amaranthaceae family. It was introduced first in the Europe and then to USA in 1800 and is currently being grown under cool environmental conditions of the world. It can be cultivated at temperature ranging from 8°C to 25°C. Both shoots and roots of fodder beet can be used as a feed for livestock. In the face of changing climate, there is a dire need to find out climate-resilient crops in new niches that can fulfill the growing needs of farming communities. In this context, fodder beet could be a good option for growers having sizable marginal as well as salt-affected soils. The chapter discusses in detail the efficient salinity-tolerance mechanism of fodder beet that enables it to survive under moderate salinity. Selective ion uptake mechanism, efficient antioxidant defensive mechanism and osmoregulation by accumulation of compatible solutes enable it to thrive well under saline environment. Hence, fodder beet is a relatively salt-tolerant crop that can be successfully grown on normal, marginal as well as salt-affected soils to fulfill the fodder requirements of livestock in fodder-scarce times and salinity amelioration

Expression Characterization of Flavonoid Biosynthetic Pathway Genes and Transcription Factors in Peanut Under Water Deficit Conditions

Drought is one of the hostile environmental stresses that limit the yield production of crop plants by modulating their growth and development. Peanut (Arachis hypogaea) has a wide range of adaptations to arid and semi-arid climates, but its yield is prone to loss due to drought. Other than beneficial fatty acids and micronutrients, peanut harbors various bioactive compounds including flavonoids that hold a prominent position as antioxidants in plants and protect them from oxidative stress. In this study, understanding of the biosynthesis of flavonoids in peanut under water deficit conditions was developed through expression analysis and correlational analysis and determining the accumulation pattern of phenols, flavonols, and anthocyanins. Six peanut varieties (BARD479, BARI2011, BARI2000, GOLDEN, PG1102, and PG1265) having variable responses against drought stress have been selected. Higher water retention and flavonoid accumulation have been observed in BARI2011 but downregulation has been observed in the expression of genes and transcription factors (TFs) which indicated the maintenance of normal homeostasis. ANOVA revealed that the expression of flavonoid genes and TFs is highly dependent upon the genotype of peanut in a spatiotemporal manner. Correlation analysis between expression of flavonoid biosynthetic genes and TFs indicated the role of AhMYB111 and AhMYB7 as an inhibitor for AhF3H and AhFLS, respectively, and AhMYB7, AhTTG1, and AhCSU2 as a positive regulator for the expression of Ah4CL, AhCHS, and AhF3H, respectively. However, AhbHLH and AhGL3 revealed nil-to-little relation with the expression of flavonoid biosynthetic pathway genes. Correlational analysis between the expression of TFs related to the biosynthesis of flavonoids and the accumulation of phenolics, flavonols, and anthocyanins indicated coregulation of flavonoid synthesis by TFs under water deficit conditions in peanut. This study would provide insight into the role of flavonoid biosynthetic pathway in drought response in peanut and would aid to develop drought-tolerant varieties of peanut

ANTIFUNGAL ACTIVITY OF NICOTINE AND ITS CADMIUM COMPLEX

Nicotine and its metal complex; Cd(Il)-nicotine were isolated from leaves of Nicotiana tabacum using various metal ions by the reported techniques and studied for their antifungal activity against fourteen different species of fungi. For comparative study, pure sample of nicotine and metal salt used for complexation; cadmium(lI) iodide was also subjected to antifungal tests with the same species of fungus under similar conditions. Results indicated that nicotine is quite effective against the Rare pathogenic and Non pathogenic fungi but comparatively less effective against Pathogenic fungi. Nicotine was found to be completely ineffective against the selected species of Occasional pathogenic fungi. Cadmium(1I) iodide effectively inhibited Pathogenic and Non pathogenic fungi whereas relatively ineffective against the Occasional pathogenic and Rare pathogenic fungi. On the other hand, Cadmium(II) nicotine complex inhibited all the selected species of fungi except Fusarium solani

ANTIBACTERIAL ACTIVITY OF HARMINE, HgCl2 AND THEIR COMPLEX

Harmine and its mercury (II)-complex were isolated from seeds of Peganum harmala by an already reported method (Munir et al. 1995) and studied for their antibacterial activity against ten different species of gram positive and gram negative bacteria. For comparative studies, pure sample of mercury-(II)-chloride salt was also subected lo antibacterial tests with he same species of bacteria under similar conditions. Results indicated that harmine had no effect on all the bacteria tested. Mercury(II)-chloride and mercury-harmine complex were found to be effective towards all the ten species of bacteria at both the levels except Pseudomonas aeroginosa, which was resistant to mercury (II)-chloride. Results also indicated that both Mercury(II) chloride and mercurv-harmine complex were more effective at higher dose of 200 µg/100 µl, with mercury-harmine complex being two to three times more effective than mercury(ll)-chloride

Plant Glycomics

Glycomics is the comprehensive study of glycomes (the entire complement of sugars, whether free or present in more complex molecules of an organism), including genetic, physiologic, pathologic, and other aspects in living organisms. Carbohydrates being most abundant macromolecules are found in all organisms’ organs, tissues, and cells. They are present in almost every organelle of the cell in varying amounts depending on the type of organelle. Carbohydrates are not directly synthesized by genes; rather they are formed by gene products. Sometime carbohydrates are present in free form and also exist in the form of conjugates. Plants being the largest producer of carbohydrates on earth are of particular importance. Plants are rich in complex carbohydrates molecules. Complex biopolymers like cellulose, lignin, and hemicelluloses are being studied along with their structure and type of linkages present between them. The presence of these carbohydrates is somewhat linked to the survival of these plants under extreme conditions and stresses. Understanding these carbohydrates has allowed us to find answers on how plants survived severe climate changes in the past. These complex molecules form linkages with non-carbohydrate molecules and understanding the structure of these conjugates is a challenging task to the scientific community. Glycomics approach regarding the structural and functional analysis of these carbohydrates has been revolutionized by the modification in techniques like mass spectrophotometry, high pressure liquid chromatography, and capillary electrophoresis. Still some improvements are needed in these techniques to make glycomic approach less time-consuming and more specific and sensitive

Genome-Wide Identification of Stress-Associated Proteins (SAPs) Encoding A20/AN1 Zinc Finger in Almond (Prunus dulcis) and Their Differential Expression during Fruit Development

Stress-associated proteins (SAPs) are zinc finger proteins involved in the regulation of various stresses in a variety of plant species. A total of nine PdSAP genes were identified in Prunus dulcis. Phylogenetic and synteny analyses were performed to analyze the homology and evolutionary relationship of PdSAP genes. The functions of PdSAP genes were assessed by further analyses, including cis-regulatory elements, gene duplication, gene ontology, gene structure, subcellular localization, and motif pattern. This study found that PdSAP genes were unevenly distributed on chromosomes 2, 3, 6, and 7. Phylogenetic analysis of PdSAP genes with Arabidopsis thaliana and Oryza sativa suggested that six subgroups have a similar pattern of AN1 and A20 domains in each subgroup. PdSAP genes lacked duplicated blocks. The majority of PdSAP genes were localized in the nucleus region. Three hormonal and five stress cis-regulatory elements were found in the upstream promoter region of the PdSAP gene family. RNA-seq analysis revealed differential gene expression of PdSAP genes at days 12, 17, 22, 27, 32, and 37 of fruitlet development after flowering. This study identifies the SAP genes in P. dulcis and also provides insights into the expression of PdSAP genes in abnormal fruitlets with diapause atrophic growth at various developmental stages

Characterization of wheat cell wall invertase genes associated with drought tolerance in synthetic-derived wheat

Cell wall invertase (CWI) gene hydrolyzes sucrose into glucose and fructose that supports pollen development. Down regulation of CWI is responsible for drought induced pollen sterility which ultimately reduces grain yield by limiting grain numbers. In bread wheat, CWI gene has been localized on chromosomes 4A, 5B and 5D which have conserved WECPDF domain. In synthetic derived wheat (SYN-DER) diversity panel, 123 accessions had Hap-4A-C haplotype at TaCwi-Al which was significantly associated with 1000 grain weight (TGW) and other agronomic traits under both well-water and water-limited conditions. On the other hand, Hap-SD-C haplotype was fixed at TaCwi-D1 in synthetic derivatives. Previous studies identified high sequence conservation at TaCwi-B1, however sequencing of this gene in diverse SYN-DER identified several mutations putatively transferred from durum parents of synthetic hexaploid wheats. The non-synonymous substitutions observed in TaCwi-B1 in the conserved domain (WECPDF) were Glu372Lys, Glu372Gly, Pro374Gln, Asp375Thr, while Phe376Leu, Tyr377Thr, Val379Cys variants were observed in the neighboring region. In silico analysis revealed that these point mutations sequentially and structurally influenced the biological function of TaCwi-B1 protein. All the identified mutations caused poor hydrolysis of sucrose followed by improper pollen development which had implications in wheat drought adaptability. In addition, G320C allelic variant was found in high percentage (54%) in SYN-DERs. The association analysis confirmed that SNP TaCwi-B1-G enhanced TGW and grain yield in SYN-DERs. Our results significantly enhance the understanding of gene function affecting drought adaptability in wheat

Climate change and food security with emphasis on wheat /

Climate Change and Food Security with Emphasis on Wheat is the first book to present the full scope of research in wheat improvement, revealing the correlations to global issues including climate change and global warming which contribute to food security issues. Wheat plays a key role in the health of the global economy. As the world population continuously increases, economies modernize, and incomes rise, wheat production will have to increase dramatically to secure it as a reliable and sustainable food source. Since covering more land area with wheat crops is not a sustainable option, future wheat crops must have consistently higher yields and be able to resist and/or tolerate biotic and abiotic stresses that result from climate change. Addressing the biophysical and socioeconomic constraints of producing high-yielding, disease-resistant, and good quality wheat, this book will aid in research efforts to increase and stabilize wheat production worldwide. Written by an international team of experts, Climate Change and Food Security with Emphasis on Wheat is an excellent resource for academics, researchers, and students interested in wheat and grain research, especially as it is relevant to food security.Climate Change and Food Security with Emphasis on Wheat is the first book to present the full scope of research in wheat improvement, revealing the correlations to global issues including climate change and global warming which contribute to food security issues. Wheat plays a key role in the health of the global economy. As the world population continuously increases, economies modernize, and incomes rise, wheat production will have to increase dramatically to secure it as a reliable and sustainable food source. Since covering more land area with wheat crops is not a sustainable option, future wheat crops must have consistently higher yields and be able to resist and/or tolerate biotic and abiotic stresses that result from climate change. Addressing the biophysical and socioeconomic constraints of producing high-yielding, disease-resistant, and good quality wheat, this book will aid in research efforts to increase and stabilize wheat production worldwide. Written by an international team of experts, Climate Change and Food Security with Emphasis on Wheat is an excellent resource for academics, researchers, and students interested in wheat and grain research, especially as it is relevant to food security.Includes bibliographical references and index.Print version record.Elsevie

Karnal bunt resistance in synthetic hexaploid wheats (SH) derived from durum wheat × Aegilops tauschii combinations and in some SH × bread wheat derivatives

Bridge crosses utilizing the D genome synthetic hexaploids (SH), Triticum turgidum / Aegilops tauschii (2n = 6x = 42, AABBDD), are a potent means of improving bread wheat ( T. aestivum ) for biotic and abiotic stresses. The synthetic germplasm enables incorporation of the genetic diversity of T. turgidum cultivars together with the attributes of the Ae. tauschii accessions. In this research, SH wheats were screened for karnal bunt in Obregon, Mexico over six crop cycles and several SHs were earlier identified with an immune response. These SHs have unique Ae. tauschii accessions as parents. Phenologically descriptors and additional trait evaluations led us to develop a sub-set of the most desirable combinations for wheat breeding. The SH wheats are generally tall, late to mature, have good agronomic type, and are non-free threshing with a high 1000 kernel weight. All have a spring growth habit with several possessing multiple stress resistances. The resistance exhibited by SH wheats has been transferred into elite but KB susceptible bread wheat cultivars thus generating a new and unique genetic resource that can be readily exploited by conventional breeding programs