Comparative Flower Transcriptome Network Analysis Reveals DEGs Involved in Chickpea Reproductive Success during Salinity

Salinity is increasingly becoming a significant problem for the most important yet intrinsically salt-sensitive grain legume chickpea. Chickpea is extremely sensitive to salinity during the reproductive phase. Therefore, it is essential to understand the molecular mechanisms by comparing the transcriptomic dynamics between the two contrasting genotypes in response to salt stress. Chickpea exhibits considerable genetic variation amongst improved cultivars, which show better yields in saline conditions but still need to be enhanced for sustainable crop production. Based on previous extensive multi-location physiological screening, two identified genotypes, JG11 (salt-tolerant) and ICCV2 (salt-sensitive), were subjected to salt stress to evaluate their phenological and transcriptional responses. RNA-Sequencing is a revolutionary tool that allows for comprehensive transcriptome profiling to identify genes and alleles associated with stress tolerance and sensitivity. After the first flowering, the whole flower from stress-tolerant and sensitive genotypes was collected. A total of ~300 million RNA-Seq reads were sequenced, resulting in 2022 differentially expressed genes (DEGs) in response to salt stress. Genes involved in flowering time such as FLOWERING LOCUS T (FT) and pollen development such as ABORTED MICROSPORES (AMS), rho-GTPase, and pollen-receptor kinase were significantly differentially regulated, suggesting their role in salt tolerance. In addition to this, we identify a suite of essential genes such as MYB proteins, MADS-box, and chloride ion channel genes, which are crucial regulators of transcriptional responses to salinity tolerance. The gene set enrichment analysis and functional annotation of these genes in flower development suggest that they can be potential candidates for chickpea crop improvement for salt tolerance

Development of EST derived microsatellite markers in chickpea and their validation in diversity analysis

55-58Microsatellites are widely used as genetic markers because they are co-dominant, multi-allelic, easily scorable and highly polymorphic. In order to enhance availability of genomic resources, microsatellite loci were identified from chickpea (Cicer arietinum L.), the third most important grain legume in the world. A total of 20 SSR markers were developed from EST clones of wilt resistant cultivar (JG 315) of chickpea. Chickpea varieties (15) were analyzed for genetic diversity with these markers, which produced a total of 35 alleles with a mean of 1.5 alleles per primer. About 5 markers were polymorphic in the selected genotypes and observed heterozygosity ranged from 0.12 to 0.87 with an average of 0.32. These microsatellite markers will be useful in diversity analysis, mapping agronomically important traits and marker assisted breeding in chickpea

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Not AvailablePaucity of polymorphic molecular markers in pigeonpea, Cajanus cajan (L.) Millsp., has been a major limiting factor in application of molecular tools for its genetic improvement. As the development of microsatellite markers requires considerable time, expertise and research infrastructure, transfer of markers from other related genera offers an alternative option to increase the number of available markers. Since microsatellite sequences are conserved across Fabaceae taxa, transferability of 100 chickpea (Cicer arietinum L.)-specific SSR markers was studied in two genotypes each of five wild and one cultivated species of Cajanus. The results revealed a significant transferability (46%) of chickpea microsatellites to Cajanus. In cultivated pigeonpea, chickpea-specific SSRs showed 38–39% transferability, while among wild Cajanus species, it ranged from 26% in Cajanus sericeus ICP 15760 to 40% in C. sericeus ICP 15761. The transferable primers exhibited extensive polymorphism in Cajanus with an average number of 4.11 alleles per marker. High level of polymorphism exhibited by chickpea microsatellite markers in the present study indicates their usefulness in diversity analysis, mapping agronomically important traits and marker-assisted breeding in pigeonpea.Not Availabl

Microbial Diversity and Characteristics of Kombucha as Revealed by Metagenomic and Physicochemical Analysis

Kombucha is a fermented tea made from a Symbiotic Culture of Bacteria and Yeast (SCOBY) with a long history of use as a health tonic. It is likely that most health benefits come from the tea and fermentation metabolites from specific microbial communities. Despite its growing importance as a functional health drink, the microbial ecosystem present in kombucha has not been fully documented. To characterize the microbial composition and biochemical properties of ‘The Good Brew’ original base kombucha, we used metagenomics amplicon (16S rRNA and ITS) sequencing to identify the microbial communities at the taxonomic level. We identified 34 genera with 200 microbial species yet described in kombucha. The dominance of organic acid producing microorganisms Acetobacter, Komagataeibacter and Starmerella are healthy for the human gut and their glucose metabolising activities have a putative role in preventing conditions such as diabetes and obesity. Kombucha contains high protein (3.31 µg/mL), high phenolic content (290.4 mg/100 mL) and low sugars (glucose: 1.87 g/L; sucrose 1.11 g/L; fructose: 0.05 g/L) as compared to green tea. The broad microbial diversity with proven health benefits for the human gut suggests kombucha is a powerful probiotic. These findings are important to improve the commercial value of kombucha and uncover the immense prospects for health benefits

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Not AvailableProtease inhibitors are natural defense proteins that inhibit the proteolytic activity of proteases. Legume protease inhibitors are diverse in their molecular mechanism and many of them have successfully been deployed in crop plants to confer resistance against insect pests. Nine combinations of degenerated primers,designed, based on “multiple aligned” gene sequences from NCBI Gene bank database were used to amplify the protease inhibitor genes in of ten different legume crops (two varieties each)viz.fieldpea,chickpea, lentil, lathyrus, pigeonpea , frenchbean,mungbean ,clusterbean , horsegramand cowpea .The primer combination BBF2/BBR2 amplified the expectedamplicon of 800 bp invarities ofmungbean,horsegramand cowpea. These amplicons obtained from each genotype were further ligated to the pJET1.2/ blunt vector and transformed into XL1 blue strain of E.coli. Out of 41 clones sequenced, two clone sequences obtained from cowpea (DCS 6) showed homology with substilisin-like serine protease inhibitor of Desulfovibria vulgaris and serine/threonine protein kinase of Epichlocfastucae.These genes can be transformed into Agrobacterium based binary vectors and used for transformation of crops. Therefore these findings offer new genes for transgenic development against lepidopteron pests.Not Availabl

Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea

Abstract Salinity is a major constraint for intrinsically salt sensitive grain legume chickpea. Chickpea exhibits large genetic variation amongst cultivars, which show better yields in saline conditions but still need to be improved further for sustainable crop production. Based on previous multi-location physiological screening, JG 11 (salt tolerant) and ICCV 2 (salt sensitive) were subjected to salt stress to evaluate their physiological and transcriptional responses. A total of ~480 million RNA-Seq reads were sequenced from root tissues which resulted in identification of 3,053 differentially expressed genes (DEGs) in response to salt stress. Reproductive stage shows high number of DEGs suggesting major transcriptional reorganization in response to salt to enable tolerance. Importantly, cationic peroxidase, Aspartic ase, NRT1/PTR, phosphatidylinositol phosphate kinase, DREB1E and ERF genes were significantly up-regulated in tolerant genotype. In addition, we identified a suite of important genes involved in cell wall modification and root morphogenesis such as dirigent proteins, expansin and casparian strip membrane proteins that could potentially confer salt tolerance. Further, phytohormonal cross-talk between ERF and PIN-FORMED genes which modulate the root growth was observed. The gene set enrichment analysis and functional annotation of these genes suggests they may be utilised as potential candidates for improving chickpea salt tolerance

Comparative Flower Transcriptome Network Analysis Reveals <i>DEGs</i> Involved in Chickpea Reproductive Success during Salinity

Salinity is increasingly becoming a significant problem for the most important yet intrinsically salt-sensitive grain legume chickpea. Chickpea is extremely sensitive to salinity during the reproductive phase. Therefore, it is essential to understand the molecular mechanisms by comparing the transcriptomic dynamics between the two contrasting genotypes in response to salt stress. Chickpea exhibits considerable genetic variation amongst improved cultivars, which show better yields in saline conditions but still need to be enhanced for sustainable crop production. Based on previous extensive multi-location physiological screening, two identified genotypes, JG11 (salt-tolerant) and ICCV2 (salt-sensitive), were subjected to salt stress to evaluate their phenological and transcriptional responses. RNA-Sequencing is a revolutionary tool that allows for comprehensive transcriptome profiling to identify genes and alleles associated with stress tolerance and sensitivity. After the first flowering, the whole flower from stress-tolerant and sensitive genotypes was collected. A total of ~300 million RNA-Seq reads were sequenced, resulting in 2022 differentially expressed genes (DEGs) in response to salt stress. Genes involved in flowering time such as FLOWERING LOCUS T (FT) and pollen development such as ABORTED MICROSPORES (AMS), rho-GTPase, and pollen-receptor kinase were significantly differentially regulated, suggesting their role in salt tolerance. In addition to this, we identify a suite of essential genes such as MYB proteins, MADS-box, and chloride ion channel genes, which are crucial regulators of transcriptional responses to salinity tolerance. The gene set enrichment analysis and functional annotation of these genes in flower development suggest that they can be potential candidates for chickpea crop improvement for salt tolerance

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Not AvailableTo study the conservation of microsatellite regions, a set of 137 microsatellite markers developed from Phaseolus, Cajanus, Lens and Cicer genera of Leguminosae family were tested for their transferability across 16 genotypes of Phaseolus belonging to diverse collections from South America and Asia. Considerable transferability was observed with markers derived from Cajanus (60%), Lens (46%) and Cicer (28%). Of the total 122 loci were amplified, 82 cross-species polymorphic amplicons were obtained. Maximum number of alleles per marker was six (Cicer markers). Polymorphism information content values ranged from 0.12 to 0.96 with Cajanus, 0.13 to 0.74 with Lens and 0.30 to 0.93 with Cicer markers. Unweighted pair group method employing arithmetic averages cluster analysis of Phaseolus genotypes showed clear demarcation between the commercial cultivars falling in separate cluster with respect to their seed size and maturity. Transferability of genomic SSRs was different from that of expressed sequence tag-derived genic microsatellite markers.Not Availabl

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Not AvailableMolecular markers have emerged as useful tools to assess the genetic diversity across crops. In lentil, molecular markers are limited. The objective of the study was to explore cross-genera transferability of sequence tagged microsatellite site (STMS) markers from related legumes and assess their utility in lentils. Thirty lentil (Lens culinaris Medik. subsp. culinaris) accessions were evaluated for genetic similarity analysis using cross-genera STMS markers. Thirty-nine STMS markers amplified 68 alleles with an average of 1.74 alleles per locus. Twenty lentil-specific STMS markers produced a total of 36 amplicons, of which 90% (18) markers were polymorphic. A maximum of four alleles were obtained with primers SSR13 and SSR19. Of 47 STMS markers from other legume genera, only 19 markers produced 32 scorable amplicons, and only 58% (11) of the amplified markers exhibited polymorphism. The polymorphism information content values observed with lentil specific markers ranged from 0.02 to 0.99, while for transferrable markers it ranged from 0.06 to 0.84. Maximum genetic similarity was observed between ‘NDL1’ and ‘LH84-8’ (0.942) and minimum between ‘PL234’ and ‘Precoz’ (0.709). The dendrogram based on Jaccard's similarity coefficients showed limited genetic variability among the cultivars included in the present study. A combination of lentil-specific and transferrable STMS markers was successfully used for identification of genetic similarity in lentil germplasm.Not Availabl

Proteo-Molecular Investigation of Cultivated Rice, Wild Rice, and Barley Provides Clues of Defense Responses against Rhizoctonia solani Infection

Rhizoctonia solani is a soil-borne fungus causing sheath blight disease in cereal crops including rice. Genetic resistance to sheath blight disease in cereal crops is not well understood in most of the host(s). Aside from this, a comparative study on the different hosts at the biochemical and proteomic level upon R. solani infection was not reported earlier. Here, we performed proteomic based analysis and studied defense pathways among cultivated rice (cv. Pusa Basmati-1), wild rice accession (Oryza grandiglumis), and barley (cv. NDB-1445) after inoculation with R. solani. Increased levels of phenol, peroxidase, and &beta;-1, 3-glucanase were observed in infected tissue as compared to the control in all of the hosts. Wild rice accession O. grandiglumis showed a higher level of biochemical signals than barley cv. NDB 1445 and cultivated rice cv. Pusa Basmati-1. Using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS), differently expressed proteins were also studied in control and after inoculation with R. solani. Wild rice accession O. grandiglumis induced a cysteine protease inhibitor and zinc finger proteins, which have defense functions and resistance against fungal pathogens. On the other hand, barley cv. NDB-1445 and cultivated rice cv. Pusa Basmati-1 mainly induce energy metabolism-related proteins/signals after inoculation with R. solani in comparison to wild rice accession O. grandiglumis. The present comprehensive study of R. solani interaction using three hosts, namely, Pusa Basmati-1 (cultivated rice), O. grandiglumis (wild rice), and NDB-1445 (barley) would interpret wider possibilities in the dissection of the protein(s) induced during the infection process. These proteins may further be correlated to the gene(s) and other related molecular tools that will help for the marker-assisted breeding and/or gene editing for this distressing disease among the major cereal crops