Jitendra Kumar

Biology and breeding of food legumes

1. History, Origin and Evolution 2. Biology and Floral Morphology 3. Domestication 4. Breeding for Improvement of Cool Season Food Legumes 5. Breeding for Improvement of Warm-season Food Legumes 6. Distant Hybridization and Alien Gene Introgression 7. Polyploidy 8. Cytology and Molecular Cytogenetics 9. Molecular Cytogenetics in Physical Mapping of Alien Introgressions 10. In vitro techniques 11. Microsporogenesis and Haploidy Breeding 12. Genetic Transformation 13. Male Sterility and Hybrid Production Technology 14. Mutagenesis 15. Breeding for Biotic Stresses 16. Breeding for Abiotic Stresses 17. Legume Improvement in the Acidic and less Fertile Soils 18. Genomic Approaches for Management of Abiotic Stresses 19. Molecular Breeding and Marker-assisted Selection 20. Underutilized Food Legumes 21. Legumes as a Model Plant Family 22. Plant Genetic Resources and Conservation of Biodiversity 23. Seed Dormancy and Viability 24. Post Harvest Technology 25. Value Addition and Trade.

Characterization of genetic structure of alfalfa ( Medicago sp.) from trans-Himalaya using RAPD and ISSR markers

Twenty five (25) accessions of Lucerne (Medicago sp.) collected from Leh valley of trans-Himalayan region of Ladakh (Jammu and Kashmir) were analyzed using inter simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD). The results of this study revealed that the level of genetic variation in the collected Medicago ecotypes were relatively high (P=96.54%, I=0.430, Ht=0.285). RAPD fingerprinting detected more polymorphic loci (97.96%) than ISSR fingerprinting (95.12%). Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the genotypes remained more or less the same in RAPD and combined data of RAPD + ISSR. The mean coefficient of differentiation (Gst) was 0.0584 indicating 30.23% of the genetic diversity within the populations. The overall value of mean estimated number of gene flow (Nm = 8.0682) revealed large gene exchanges among populations. Analysis of molecular variance (AMOVA) indicated that the distribution of genetic diversity was 49% among populations and 51% within populations. The plant is capable of reproducing by self-sowing, thus can influence population genetic structure. The pronounced genetic variation tells us that Medicago species is a proper plant for genetic research and that there is great potential of breeding this species for improved forage varieties. Key words : Genetic variation, ISSR, RAPD, Medicago species, population structure.

Inheritance and molecular tagging of MYMIV resistance gene in blackgram (Vigna mungo L. Hepper)

Yellow Mosaic disease (YMD) is one of the most destructive diseases of blackgram (Vigna mungo) causing heavy yield losses every year. Mungbean Yellow Mosaic India Virus (MYMIV) is one of the YMD causing begomoviruses prevalent in the major blackgram growing area (northern and central part) of India. Inheritance of MYMIV resistance gene was studied in blackgram using F1, F2 and F2:3 derived from cross DPU 88-31(resistant)× AKU 9904 (susceptible). The results of genetic analysis showed that a single dominant gene controls the MYMIV resistance in blackgram genotype DPU 88-31. The F2 population from the same cross was also used to tag and map the MYMIV resistance gene using SSR markers. Out of 361 markers, 31 were found polymorphic between the parents. However, marker CEDG 180 was found to be linked with resistance gene following the bulked segregant analysis. This marker was mapped in the F2 mapping population of 168 individuals at a map distance of 12.9xa0cm. The validation of this marker in nine resistant and seven susceptible genotypes has suggested its use in marker assisted breeding for developing MYMIV resistant genotypes in blackgram.

Phenomics in crop plants : trends, options and limitations

1. Plant Phenomics: An Overview.- 2. Traits for Phenotyping.- 3. High Precision Phenotyping under Controlled versus Natural Environments.- 4. Towards Digital and Image Based Phenotyping.- 5. Imaging Methods for Phenotyping of Plant Traits.- 6. Screening for Plant Features.- 7. Phenotyping Crop Plants for Drought and Heat Related Traits.- 8. Phenotyping for Root Traits.- 9. Phenotyping for Soil Problems.- 10. Phenotyping Methods of Fungal Diseases, Parasitic Nematodes and Weeds in Cool Season Food Legumes.- 11. Advances in Phenotyping of Functional Traits.- 12. Role of Fluorescence Approaches to Understand Functional Traits of Photosynthesis.- 13. Identification of Subcellular Structural and Metabolic Changes through NMR.- 14. Precision Nutrient Management and Crop Sensing.- 15. Phenotyping Nutritional and Anti-Nutritional Traits.- 16. Experimental Designs for Precision in Phenotyping.- 17. Biometrical Approaches for Analysis of Phenotypic Data of Complex Traits.- 18. Harnessing Genomics through Phenomics.- 19. High Throughput Plant Phenotyping Platforms.

Identification of New Alleles in Salt Tolerant Rice Germplasm Lines through Phenotypic and Genotypic Screening

The present study investigated eight rice lines (Rupsal, Nagalmutha, Polai, Ravana, Marishal, Talmugra, Kamini and Raspanjar) collected from coastal region of eastern India for salinity tolerance through phenotypic and genotypic screening. Among these, three rice lines as highly tolerant (Talmugra, Marishal and Kamini), three tolerant (Rupsal, Polai and Raspanjar) and two moderately tolerant (Ravana and Nagalmutha) to salt stress were identified in phenotypic screening. Pokkali was categorized as tolerant under salinity condition (12 EC dS m -1 ). In PCR screening using microsatellite (SSR) markers located within Saltol locus, we documented new allelic pattern in selected highly tolerant and tolerant genotypes with RM8094 marker as compared to Pokkali. Besides, another marker RM10694 was found to associate with selection of salinity tolerant genotypes similar to Pokkali. In gene expression studies, no significant difference linked with abscisic acid (ABA), calciumdependent proteins kinase (CDPK), ionic and osmotic signaling pathways in salinity tolerant genotypes was found as compared to sensitive line (IR29). Induction of AP37 gene expression differentiated Kamini and Marishal genotypes from other tolerant and sensitive lines. The chlorophyll and protein contents were maintained in highly tolerant genotypes (Marishal, Kamini and Talmugra) as compared to sensitive one (IR29). Among agronomic traits, selected rice lines recorded to have significant morphological features such as plant height, tiller number, leaf length and width in order to tolerate salt stress. Genetic diversity analysis revealed that, highly tolerant genotypes showed distant relationship with Pokkali at genetic level.

Insights into the structure–function relationship of brown plant hopper resistance protein, Bph14 of rice plant: a computational structural biology approach

Brown plant hopper (BPH) is one of the major destructive insect pests of rice, causing severe yield loss. Thirty-two BPH resistance genes have been identified in cultivated and wild species of rice Although, molecular mechanism of rice plant resistance against BPH studied through map-based cloning, due to non-existence of NMR/crystal structures of Bph14 protein, recognition of leucine-rich repeat (LRR) domain and its interaction with different ligands are poorly understood. Thus, in the present study, in silico approach was adopted to predict three-dimensional structure of LRR domain of Bph14 using comparative modelling approach followed by interaction study with jasmonic and salicylic acids. LRR domain along with LRR-jasmonic and salicylic acid complexes were subjected to dynamic simulation using GROMACS, individually, for energy minimisation and refinement of the structure. Final binding energy of jasmonic and salicylic acid with LRR domain was calculated using MM/PBSA. Free-energy landscape analysis revealed that overall stability of LRR domain of Bph14 is not much affected after forming complex with jasmonic and salicylic acid. MM/PBSA analysis revealed that binding affinities of LRR domain towards salicylic acid is higher as compared to jasmonic acid. Interaction study of LRR domain with salicylic acid and jasmonic acid reveals that THR987 of LRR form hydrogen bond with both complexes. Thus, THR987 plays active role in the Bph14 and phytochemical interaction for inducing resistance in rice plant against BPH. In future, Bph14 gene and phytochemicals could be used in BPH management and development of novel resistant varieties for increasing rice yield.

In silico identification and characterization of differential expressed genes (DEGs) associated with grain and panicle number in rice

Grain number is an important trait for yield in rice. Several genes have been identified controlling grain and panicle number, which has direct or indirect effect on yield. Some genes play a key role for panicle formation and number of panicles per plant. The number of panicles per plant is directly regulating the grain number per plant. In present study, in silico approach was adopted for identifying differentially expressed genes associated with grain number and panicle number. Further, pathway enrichment analysis of these genes performed. The microarray data, GSE51616, downloaded from the GEO database originally submitted by Wang et al. (2014).Young leaves in vegetative stage (35-days old) and developing panicles (0.1cm) from fieldgrown OX-Ghd7HJ19 transgenic and wild-type plants with two biological replicates were used to isolate RNA for chip analysis. Background correction and normalization of raw microarray data was carried out using the Robust Multichip Averaging (RMA) method of affy packages of R (v. 3.1.3). The linear regression model package, limma was utilized to classify chips into two groups. The Bayes method (Benjamini and Hochberg) was used to correct for multiple testing. Adjusted P-value < 0.01 and |logFC| > 2 was used as a cut-off to identify differentially expressed genes. We identified 393 differentially expressed genes, which mainly belongs to either Phosphatidylethanolamine-binding protein family or DUF3778 domain family. Proteins of these two families regulate formation of high grain number as well as panicle number. These genes like Ghd7, Ehd1, Dep1, Os10g0463400, Os03g0752800, Os03g0215400, Os06g0157700 and Os06g0157500 function to integrate the dynamic environmental inputs with phase transition, architecture regulation, and stress response to maximize the reproductive success of the rice plant. Thus, these genes can act as potential target protein for increasing grain and panicle number in rice plant, which will lead to increase in yield of rice grain. Citation: Gouda, G., Gupta, M.K., Vadde, R., Donde, R., Kumar, J., Nayak, S., Behera, L. and Mohapatra, T. In silico identification and characterization of differential expressed genes (DEGs) associated with grain and panicle number in rice [Abstract]. In: Abstracts of the NGBT conference; Oct 02-04, 2017; Bhubaneswar, Odisha, India: Can J biotech, Volume 1, Special Issue, Page 38. https://doi.org/10.24870/cjb.2017a25

In Vitro Callus Induction and Plantlet Regeneration of Saussurea lappa (Clarke.) from Ladakh Region of India

In vitro propagation protocol was developed for Saussurea lappa (Clarke.) species threatened by over exploitation due to medicinal importance and habitat destruction in Ladakh region of India. The aim of the present study was to examine the main aspects of in vitro callus induction (CI) and plantlet regeneration of S. lappa. Explants were cultured on Murashige and Skoog (MS) basal medium supplemented with various concentrations and combinations of auxins and cytokinins for in vitro CI and plantlets regeneration. Callus initiation and induction was observed within eight and fifteen days after inoculation. 3xa0mg/L 2, 4-Dichlorophenoxyacetic acid (2, 4-D) and 5xa0mg/L Kinetin (Kin) was found to be more effective for CI frequencies in all the explants as compared to other combinations. Root (79.6xa0±xa00.8) and stem (76.4xa0±xa00.6) explants were found with better callus frequencies and early response as compared to other explants. Maximum number of shoots (11.8xa0±xa00.7), highest shoot length (9.2xa0±xa00.6xa0cm), maximum root number (6.2xa0±xa00.7) and highest root length (6.6xa0±xa00.8xa0cm) were found on MS medium with 2xa0mg/L Kinetin (Kin) and 2xa0mg/L Indole-3-butyric-acid in root derived callus explant. Plantlets with 3–5 shoots were transferred to potting mixture containing sand: soil: perlite (1:1:1) for acclimatization to field conditions and further multiplication. For the first time, protocol has been developed in S. lappa for in vitro CI and plantlet regeneration that holds robust potential for metabolite production and large-scale propagation.