Browsing by Author "Pradhan, S.K."
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ThesisItem Open Access Changes in spermiogram of breeding bulls affected by Lumpy Skin Disease(Department of Animal Reproduction, Gynaecology and Obstetrics, OUAT, Bhubaneswar, 2020) Beuria, Sangram Keshari; Biswal, S.S.; Mishra, P.C.; Sahoo, N.; Pradhan, S.K.; Mishra, C.; Rath, P.K.Lumpy skin disease (LSD) is an important viral disease caused by LSD virus belonging to family Poxviridae. The virus has much economic implication since it affects the fertility of bulls and cows alongwith decline in milk production and trade of animal products. The experiment aims to detect the changes in the spermiogram of breeding bulls affected by LSD and also to compare seminal parameters between different breeds. A total of 18 bulls of 3 different breeds were selected for study and they were divided into 3 groups on the basis of breeds with 6 bulls in each group i.e, 6 Cross bred Jersey (CBJ), 6 Jersey (JY) and 6 Cross bred Holstein Friesian (CBHF). In all the groups seminal parameters like post thaw motility, HOST, live sperm count, acrosomal integrity and Computer Assisted Semen Analysis (CASA) are studied before and after LSD virus infection. The mean post thaw motility, HOST, live sperm percent, acrosomal integrity values ranges from 52 to 60 (%), 53 to 58 (%), 86 to 88 (%), 78 to 81 (%) respectively before LSD and their corresponding value ranges from 40 to 47 (%), 36 to 45 (%), 67 to 68 (%), 58 to 64 (%) respectively after LSD. Similarly, CASA detected the mean progressive motility, VCL, VSL, VAP & wobble values ranges from 52 to 59 (%), 127 to 130 (µm/s), 92 to 94 (µm/s), 115 to 118 (µm/s) and 86 to 90 (%) respectively before LSD and their corresponding value ranges from 41 to 45 (%), 97 to 107 (µm/s), 74 to 82 (µm/s), 92 to 98 (µm/s) and 68 to 71 (%) respectively after LSD. It was found that all the seminal parameters including CASA values decreases significantly post LSD infection irrespective of breeds. When each parameter was compared individually between three breeds then there was no significant difference found for both before and after LSD virus infection which suggest that all the breeds produce semen of equal quality before infection and are equally affected after infection. Since, all the seminal parameters decreases post infection in all the bulls so the semen produced after LSD is of poor quality and should not be used for artificial insemination. Further research should be conducted on the fertility implication of LSD virus to produce semen of good quality and prevent the spread of disease.ThesisItem Open Access Comparative assessment of the adaptive capacity of goat to the heat stress based on genotype and phenotype(Department of Animal Breeding and Genetics, OUAT, Bhubaneswar, 2021) Venkatesh, K.M.; Mishra, Chinmoy; Nayak, G.D.; Behera, K.; Mishra, S.R.; Pradhan, S.K.Melanogenesis is primarily mediated by the melanocortin receptor type 1 gene. The present study was carried out to study the effect of polymorphism on animal coat colour and its association with heat stress indicators such as rectal temperature, skin temperature, respiration rate, heart rate, and cortisol level in goats under study. The genotyping (Dideoxy Sanger sequencing) result of the present study revealed three SNPs each in the Ganjam and Keonjhar goat populations and combinedly made four SNPs at 183rd (Y), 332nd (S), 748th (K) and 801st (S) positions. A novel SNP was observed at 332th (S) position in the Keonjhar goat population. Two amino acid changes (F250V and C267W) were observed due to the missense variation of nucleotides. Eight haplotypes were constructed from the unphased nucleotide sequences using the algorithm. The association between coat colour and the recorded traits revealed that white animals with the "CCTC" haplotype had significantly (P<0.05) less rectal temperature, skin temperature, respiration rate, and cortisol values as compared to black and brown animals. The principal component analysis revealed that rectal temperature, skin temperature, respiration rate, and cortisol values were related to each other and contributed more to the variance components. The different gene flow and genetic differentiation parameters for the total population, Ganjam goat and Keonjhar goat populations were estimated. The histomorphology study of the skin of different coat-coloured goats supported the results of the present study that white animals were less heat-stressed as compared to black and brown goats. The presence of calcium ion, which plays a critical role in the ligand and receptor binding, doesn’t alter the confirmation and the complexes formed between the MC1R protein and α-MSH ligand during the docking study. In conclusion, according to the findings of the present study, the white coat colour of the animal may be the reason for the white animals' lower heat stress levels as compared to the black and brown coat colours of the animals. The haplotype CCTC, which was linked to the white coat colour of the animals, suggests an association between the haplotype and white animals' heat tolerance.Rearch HighlightItem Open Access CR Dhan 304 – Utpadan Kaushal (Odia)(Director, NRRI, Cuttack, 2021-08) Kar, M.K.; Bose, L.K.; Dash, S.K.; Pradhan, S.K.; Mishra, S.K.; Saha, Sanjaya; Mohanty, A.; Jena, M.Rearch HighlightItem Open Access CR Dhan 304 – Utpadan Kaushal (Odia)(Director, NRRI, Cuttack, 2021-08) Kar, M.K.; Bose, L.K.; Dash, S.K.; Pradhan, S.K.; Saha, S.; Mohanty, A.; Jena, M.Rearch HighlightItem Open Access CR Dhan 304 – Utpadan Kaushal (Odia)(Director, NRRI, Cuttack, 2021-08) Kar, M.K.; Bose, L.K.; Rath, P.C.; Pradhan, S.K.; Mishra, S.K.; Saha, Sanjaya; Mohanty, A.; Jena, M.Institutional PublicationsItem Open Access CR Dhan 801 and CR Dhan 802 Climate- Smart Rice Varieties of NRRI(Director, National Rice Research Institute , cuttack, 2019-04) Pradhan, S.K.; Pandit, E; Bose, L.K.; Reddy, J.N.; Pattanaik, SSC; Meher, J.; Behera, LResearch HighlightItem Open Access CRRI Rice Varieties for Diverse Ecologies(NRRI, Cuttack) Dash, S.K.; Pradhan, S.K.; Kar, M.K.; Patnaik, S.S.C.; Behera, L.; Meher, J.; Anandan, A.; Marandi, B.C.; Lenka, S.; Chattopadhyay, K.; Singh, O.N.; Mohapatra, T.; Director, NRRI, CuttackResearch HighlightItem Open Access Dhan Vhitika Fasal Parjjayare Unnat Pranalire Biri (Black Gram) Chasa (Odia)(The Director, ICAR-NRRI, Cuttack, 2015-12) Prasad, S.M.; Sethy, S.; Dash, S.K.; Pradhan, S.K.; Sarangi, D.R.; Chourasia, M.; Sahoo, T.R.; Mahanta, R.ThesisItem Open Access Genetic characterization of indigenous goats of Keonjhar district of Odisha(Department of Animal Breeding and Genetics, OUAT, Bhubaneswar, 2021) Sahoo, Pritiprasanna; Nayak, G.D.; Sahoo, N.; Sahoo, G.R.; Pradhan, S.K.; Karna, D.K.; Mishra, C.Data on different conformation, production and reproduction traits were collected from 120 indigenous Keonjhar goats after collecting weights and measurements of the body. The data that correspond were also collected from 120 Black Bengal and 120 Ganjam goats for comparison. The mean values of weight at birth in male Keonjhar, Black Bengal and Ganjam goats were 1.36±0.20, 1.41±0.20 and 2.68±0.22 kg, respectively. Correspondingf mean valuessin female goatsswere 1.28±0.22, 1.30±0.21 and 2.55±0.22 kg, respectively. At adult stage, the male Keonjhar, Black Bengal and Ganjam goats achieved 15.85±0.21, 24.40±0.23 and 41.39±0.20 kg of body weight, respectively. The values that correspond in case of female goats were found to be 14.90 ± 0.23, 22.31±0. 88 and 30.31±0.52 kg, respectively. All the body morphometric traits were positively correlated among each other in this study. Females of Keonjhar, Black Bengal and Ganjam goats came to heat at 229.18±1.88, 279.89±2.15 and 440.46±1.79 days, respectively and dropped their first kids at 395.25±1.45, 469.73±2.68 and 618.68±1.84 days, respectively. The average size of litter in female Keonjhar, Black Bengal and Ganjam goats were found as 1.77±0.47, 1.97±0.73 and 1.02±0.14, respectively. All the conformation and reproductive traits varied significantly (p<0.05) among the three goat populations. However, Keonjhar and Black Bengal goats didn’t show any significant difference with regard to tail length and gestation length. Keonjhar goats showed significantly lower estimates for all the conformation traits than other two goat populations with satisfactory reproductive performance. DNA isolation was carried out from the buccal swab samples of Keonjhar goats and the complete coding region of the Nerve Growth Factor (NGF) gene was amplified using the specified primers. Sequence alignment with the reference sequence confirmed the presence of a synonymous mutation (C291A) in this population. The gene frequencies of C and A allele were found to be 0.74 and 0.26. The does with CA genotypes showed higher litter size than CC genotype (p<0.05). The findings indicate that NGF gene can be put to use as a candidate gene for the improvement of the size of the litter in these population of goat. The nucleotide sequence of NGF gene in goat is in close similarity with sheep, cattle, buffalo and wild yak. The value of theoretical isoelectric point (PI), instability index, aliphatic index and GRAVY value for NGF protein were predicted as 9.81, 45.73, 74.90 and -0.287, respectively. The secondary and tertiary structure of NGF protein were predicted as well. Ten putative interacting proteins of goat NGF protein were predicted.ThesisItem Open Access Genome wide association analysis for tolerance to iron-toxicity in rice(Department of Agricultural Biotechnology, OUAT, Bhubaneswar, 2021) Saha, Debanjana; Mohanty, Iswar Chandra; Rout, G.R.; Pradhan, S.K.; Panda, S.; Bastia, D.N.; Garnayak, L.MRice is one of the main staple food crops and a prominent source of calories for billions of people worldwide. Iron toxicity is a root related abiotic stress; affect the yield of rice in lowland production systems. High concentration of reduced iron (Fe2+) leads to iron toxicity and yield losses due to this varied from 15% to 100% depending on the genotype of rice, growth stage of plant, soil fertility and stress severity. The production of resistant rice genotypes through breeding programs is one of the most promising ways to increase yield under iron toxicity conditions. A powerful way to classify novel loci involved in complex phenotypic characteristics, is Genome-Wide Association Studies (GWASs).The most important aspect is morphological and genotyping characterization, according to this genome mapping method. In this present study, 150 germplasm lines of rice were screened in iron toxicity a hot spot and in control condition as well. Germplasm lines like Ganjamgedi, Kusuma, Pratikhsya, Ranidhan, Lalat etc are found iron toxicity tolerant by LBI scoring (IRRI 2013). Based on the morphological characterization, 120 panel populations have been created for the molecular characterization with 70 SSR markers. A total of 238 alleles were amplified with the 70 SSR markers and average alleles per locus were 4. The highest number of allele was 6 in the marker RM296. Minimum allele frequency was present in RM335 and lowest in RM174.The PIC value was maximum in RM335 and minimum value in RM339. Gene diversity (He) or expected heterozygosity was lowest in RM339 and highest observed in RM335. Estimation of K = 2 based on the ΔK determined by structure harvester, the entire population can be grouped into two sub groups (SP1 and SP2). While considering both the model GLM and MLM, RM346, RM492, RM293, RM201 and RM258 markers are strongly associated with leaf bronzing score. Significant association of RM293 present on chromosome 3 (193.4 cM) designated as qFeTox3.1and RM346 present on chromosome 7 (78.3 cM) designated as qFeTox7.1 was detected as novel QTL for Fe-toxicity tolerance.Research HighlightItem Open Access High Yielding and Water Saving NRRI Aerobic Rice Varieties(The Director, ICAR-NRRI, Cuttack, 2016) Anandan, A.; Pradhan, S.K.; Mohapatra, S.D.; Saha, S.; Panneerselvam, P.; Singh, O.N.ThesisItem Open Access Physiological basis of growth and yield of low land rice cultivars grown under low light environment(Department of Plant Physiology, OUAT, Bhubaneswar, 2021-11-15) Dey, Prajjal; Baig, M.J; Rout, G.R.; Samal, K.C.; Panda, R.K.; Pradhan, S.K.Rice is the major food crop in the world. It ensures livelihood security of millions of people around the world especially in economically weaker section people of Asia. Abiotic stress including salinity, drought, high and low temperature, high and low light majorly affect the yield of rice in plants. Among the abiotic stresses affecting rice productivity, low light stress is one of the most persistent in India, mostly in Eastern and North Eastern states, where it has a significant impact on agricultural productivity. Low light conditions damage rice production and strongly influences not only duration but physiological and agronomic traits of rice. Keeping in view the increasing threat, efforts have been made to understand the mechanism (molecular, biochemical and physiological) underlying low light stress. Against this background, the present investigation entitled “Physiological basis of growth and yield of low land rice cultivars grown under low light environment” was carried out with the major objectives of screening and characterization (physiological, biochemical and molecular) of rice genotypes under low light stress. The entire experiment was conducted at the National Rice Research Institute, Cuttack, Odisha. The experiment was laid out in randomized block design. Ten rice genotypes were selected out of the fifty genotypes screened in a previous experiment (Kharif 2016 and 2017) of the same lab under NASF funded project. Selected genotypes were grown during Kharif 2018 and 2019. Experiment was conducted with three replications during Kharif season under Normal Light, 75% light intensity (25% light cut off) and 50% light intensity (50% light cut off). The low light treatment was imposed by putting agro-shade net of different light intensities mounted on a hardwood frame. The treatment was imposed at 30 DAT. Swarnaprabha and IR-8 were used as tolerant and susceptible checks respectively. The observations for agronomic and morphological traits i.e. tiller m-2 , panicle m-2 , specific leaf area (SLA). Specific leaf weight (SLW), root length, root weight, plant height, shoot weight, yield attributing parameters were recorded during flowering and harvest stages. Correspondingly, physiological parameters (Net assimilation Rate, Stomatal Conductance, Transpiration rate, Fv/Fm, A/Ci, WUE) and biochemical parameters (total chlorophyll content, chl a, chl b, starch content, total Soluble Sugar content, Superoxide Dismutase, Catalase, Peroxidase) were recorded. Among the ten rice genotypes, Panindra, PS-3 along with Swarnaprabha performed better and were found to be tolerant than other genotypes for low light conditions. Swarnaprabha and Panindra performed better for yield attributing traits (grain yield, thousand grain weight, Harvest Index) among all the varieties. For studying the possible mechanism behind, we targeted and studied the expression of genes responsible for photosynthesis and starch synthesis i.e “SourceSink concept”. The expression analysis revealed non-significant down regulation of selected genes in Panindra and PS-3 along with Swarnaprabha whereas susceptible genotypes HKR-126 and IR-8 reported significant down regulation under low light stress. These results clearly indicate the light modulated activity of photosynthetic and starch biosynthetic genes. Though the exact pathway underlying is not clearly understood, the results indicate the potential of exploring the selected tolerant genotypes (Panindra, PS-3 and Swarnaprabha) as model plant for understanding low light stress in crop plants.Research HighlightItem Open Access SATYABHAMA(NRRI, Cuttack) Pradhan, S.K.; Barik, S.R.; Meher, J.; Anandan, A; Sadangi, B.N.; Singh, O.N.; Mohapatra, T.; Director, NRRI, CuttackThesisItem Open Access STRESSOME : A public database and webserver to understand role of stress in disease and physiology: A note to Gene Networking(2017-09) Nayak, Ananya; Pradhan, S.K.Stress is the feeling we have when under pressure, while stressors are the things we respond to in our environment. The present prospective is the collection of microarray data of stress genes. For identification of those genes, we store them in a database for further analysis. Then those genes enriched for network analysis. We created an interface for the analysis using cytoscape. I have input the secondary micro-array gene dataset into the cytoscape and getting the network structures as an output. These networks can be analyzed and enriched through various platforms like KEGG pathway analysis, GO annotation analysis, etc. For the future prospective, the database-cum-webserver is to mining the data of different prospective of stress genes like its disease, physiology and mechanism which is a future study and tointerface Cytoscape to the web-server for associative gene networkingThesisItem Open Access Studies on Genome wide analysis of AP2 gene family sequences of Vigna radiata and its comparative Phylogenetic relationship with other crop plants(2017-09) Singh, Deepak; Pradhan, S.K.The genus Vigna is a potentially valuable new model system for studying plant adaptation to stressful environments. Recently, wild relatives of crop species have received a great deal of attention in research communities as potential genetic resources for crop improvement through harnessing the desirable traits of wild species and by adopting new breeding concepts such as ‘neo-domestication’ and ‘reverse breeding’, Transcription factors belonging to the APETALA2/Ethylene Responsive Factor (AP2/ERF) family are conservatively widespread in the plant kingdom. These regulatory proteins are involved in the control of primary and secondary metabolism, growth and developmental programs, as well as responses to environmental stimuli. Due to their plasticity and to the specificity of individual members of this family, AP2/ERF transcription factors represent valuable targets for genetic engineering and breeding of crops. The AP2/ERF super family is defined by the AP2/ERF domain, which consists of about 60 to 70 amino acids and is involved in DNA binding. The AP2 family proteins contain two repeated AP2/ERF domains, the ERF family proteins contain a single AP2/ERF domain, and the RAV family proteins contain a B3 domain, which is a DNA-binding domain conserved in other plant-specific transcription factors, in addition to the single AP2/ERF domain. Genes in the AP2 family have been shown to participate in the regulation of developmental processes, e.g. flower development, spikelet meristem determinacy, leaf epidermal cell identity, and embryo development. Considering their significance in plant growth and development, whole genome search was carried out in the present study to identify AP2 genes in many plants like Arabidopsis thaliana (30), Soyabean (99), Common bean (31), Chickpea (35), Red gram (25). There are 21 AP2 family members of genes and proteins belonging to Vigna radiata were retrieved from plant TFDB database. It was observed that protein length varied from 191 to 664 amino acids where as gene length varied from 573 to 1992 base pairs. Three domain viz. smart00380, cd00018, pfam00847 were identified in AP2 protein of Vigna radiata. These domains are DNA-binding domain and act as transcription regulators in plants. Three motifs viz. ‘GNKYLYLGTYATQEEAAAAYDMAAIEYRGANAVTNFDVSRY’ (Red Color), ‘KEEYIGSLRRKSSGFSRGVSKYRGVAR’ (Blue Color) and ‘QSKKGRQGAYDDEEAAARAYDLAALKYWGQDTILNFPLTNY’ (Green Color) were identified in all AP2 proteins of Vigna radiata.. The phylogenetic analysis of 21 AP2 genes of Vigna radiata were clustered into two subgroups and vradi04g02560.1 was found to be distantly related to vradi05g12030.1 Maximum likelihood phylogenetic analysis had been carried out to understand AP2 proteins divergence pattern and here 21 AP2 proteins were clustered into two different groups. The AP2 proteins viz. vardi03g01560.1 and vradi08g06840.1 were diverged from the rest of 19 proteins.