Nihar Ranjan Sahoo

Single nucleotide polymorphism mining and nucleotide sequence analysis of Mx1 gene in exonic regions of Japanese quail

Aim: An attempt has been made to study the Myxovirus resistant (Mx1) gene polymorphism in Japanese quail. Materials and Methods: In the present, investigation four fragments viz. Fragment I of 185 bp (Exon 3 region), Fragment II of 148 bp (Exon 5 region), Fragment III of 161 bp (Exon 7 region), and Fragment IV of 176 bp (Exon 13 region) of Mx1 gene were amplified and screened for polymorphism by polymerase chain reaction-single-strand conformation polymorphism technique in 170 Japanese quail birds. Results: Out of the four fragments, one fragment (Fragment II) was found to be polymorphic. Remaining three fragments (Fragment I, III, and IV) were found to be monomorphic which was confirmed by custom sequencing. Overall nucleotide sequence analysis of Mx1 gene of Japanese quail showed 100% homology with common quail and more than 80% homology with reported sequence of chicken breeds. Conclusion: The Mx1 gene is mostly conserved in Japanese quail. There is an urgent need of comprehensive analysis of other regions of Mx1 gene along with its possible association with the traits of economic importance in Japanese quail.

Immunomodulatory potential of β-glucan as supportive treatment in porcine rotavirus enteritis

A non-blinded randomized clinical trial was conducted to assess the immunomodulatory potential of β-glucan (BG) in piglet diarrhoea associated with type A rotavirus infection. A total of 12 rotavirus-infected diarrheic piglets were randomly divided into two groups: wherein six rotavirus-infected piglets were treated with supportive treatment (ST) and other six rotavirus-infected piglets were treated with BG along with ST (ST-BG). Simultaneously, six healthy piglets were also included in the study which served as control. In rotavirus-infected piglets, marked increase of Intestinal Fatty Acid Binding Protein-2 (I-FABP2), nitric oxide (NOx), Interferon-γ (IFN-γ) concentrations and decrease of immunoglobulin G (IgG) were noticed compared to healthy piglets. The faecal consistency and dehydration scores were significantly higher in rotavirus-infected piglets than healthy piglets. The ST-BG treatment progressively reduced the I-FABP2 and increased the IgG concentrations over the time in rotavirus-infected piglets compared to piglets received only ST. A pronounced enhancement of NOx and IFN-γ concentrations was observed initially on day 3 and thereafter the values reduced on day 5 in ST-BG treated piglets in comparison to piglets which received only ST. Additionally, ST-BG treatment significantly reduced faecal consistency and dehydration scores on day 3 compared to ST in rotavirus-infected piglets. These findings point that BG represents a potential additional therapeutic option to improve the health condition and reduce the piglet mortality from rotavirus associated diarrhoea where porcine rotavirus vaccine is not available.

Association of humoral response to classical swine fever vaccination with single nucleotide polymorphisms of swine leukocyte antigens

In present investigation genetic variability in humoral response to classical swine fever (CSF) vaccination was explored. The aim of the study was to find association of 14 single nucleotide polymorphisms (SNPs) (IL-1β, MX1, IRF3 and SLA genes) with humoral response measured in terms of percentage inhibition of E2 antibody by competitive enzyme-linked immunosorbent assay. The post-vaccination response of CSF vaccination was low to moderate in Desi piglets ranged from 25.29% to 92.23% whereas it was moderate to high in Desi × Landrace piglets ranged from 69.30% to 100%. The response to CSF vaccination was significantly (P < 0.0001) differing in Desi and Desi × Landrace piglets. The mean percentage inhibition in Desi piglets was 62.73% but in Desi × Landrace cross-bred it was 97.24%. None of the SNPs of present investigation was significantly associated with humoral immune response in Desi piglets. Two SNPs namely rs80937718 (SLA DQA1) and rs80929898 (SLA DQA1) were significantly (P < 0.01) affecting the humoral response of CSF vaccination in Desi × Landrace piglets.

Microsatellite and Mitochondrial Diversity Analysis of Native Pigs of Indo-Burma Biodiversity Hotspot

ABSTRACT Assessment of genetic diversity in indigenous animals is an important and essential task for animal genetic improvement studies as well as conservation decision-making. The genetic diversity and evolutionary relationships among geographically and phenotypically distinct three pig breeds/types native to Indo-Burma and Eastern Himalayan global biodiversity hotspots were determined by genotyping with a panel of 22 ISAG recommended microsatellite loci as well as sequencing partial MTRNR1gene. The mean number of alleles per locus, effective number of alleles and observed heterozygosity were found to be 11.27 ± 0.85, 5.29 ± 0.34, and 0.795 ± 0.01, respectively. The moderate FST value (0.115 ± 0.01) indicated a fair degree of genetic differentiation among the native breeds. The Nei’s unbiased genetic identity estimates indicated less genetic distance (0.2909) between Niang Megha and Tenyi Vo pigs than the both individually with Ghoongroo breed. The divergence time was also estimated from the microsatellite analysis. Analysis of MTRNR1gene revealed distinct clustering of native Indian pigs with Chinese pigs over European pigs. The study revealed the abundance of genetic variation within native Indian pigs and their relationships as well as genetic distances.

Genotyping of major histocompatibility complex Class II DRB gene in Rohilkhandi goats by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing.

Aim: To study the major histocompatibility complex (MHC) Class II DRB1 gene polymorphism in Rohilkhandi goat using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and nucleotide sequencing techniques. Materials and Methods: DNA was isolated from 127 Rohilkhandi goats maintained at sheep and goat farm, Indian Veterinary Research Institute, Izatnagar, Bareilly. A 284 bp fragment of exon 2 of DRB1 gene was amplified and digested using BsaI and TaqI restriction enzymes. Population genetic parameters were calculated using Popgene v 1.32 and SAS 9.0. The genotypes were then sequenced using Sanger dideoxy chain termination method and were compared with related breeds/species using MEGA 6.0 and Megalign (DNASTAR) software. Results: TaqI locus showed three and BsaI locus showed two genotypes. Both the loci were found to be in Hardy–Weinberg equilibrium (HWE), however, population genetic parameters suggest that heterozygosity is still maintained in the population at both loci. Percent diversity and divergence matrix, as well as phylogenetic analysis revealed that the MHC Class II DRB1 gene of Rohilkhandi goats was found to be in close cluster with Garole and Scottish blackface sheep breeds as compared to other goat breeds included in the sequence comparison. Conclusion: The PCR-RFLP patterns showed population to be in HWE and absence of one genotype at one locus (BsaI), both the loci showed excess of one or the other homozygote genotype, however, effective number of alleles showed that allelic diversity is present in the population. Sequence comparison of DRB1 gene of Rohilkhandi goat with other sheep and goat breed assigned Rohilkhandi goat in divergence with Jamanupari and Angora goats.

Exploring the molecular basis of resistance/ susceptibility to mixed natural infection of Haemonchus contortus in tropical Indian goat breed

The present investigation was carried out with the objective to identify putative candidate genes / Quantitative trait loci for resistance / susceptibility towards Haemonchus infestation in tropical goat breed (Rohilkhandi goat) of India. The mean faecal egg count (FEC) and packed cell volume (PCV) of the population were 142.78 ± 22.54 epg (eggs per gram) and 31.73% ± 0.49, respectively. Grouping of animals as per dot ELISA test showed 41.33% (n = 124) positive and 58.66% (n = 176) negative for Haemonchus infestation. The microsatellite loci DYA and ODRB1.2 were significantly associated (P ≤ 0.05) to parasite resistance. The locus DYA showed significant association with log FEC and dot ELISA and the locus ODRB1.2 showed significant association with log FEC, PCV and dot ELISA at P ≤ 0.05. Real time expression profiling revealed that the susceptible group (high FEC group) had 11.1-fold more expression of IFNγ mRNA (Th1 cytokine) and 0.11-fold lower expression of IL-10 mRNA (Th2 cytokine), which was found to be statistically significant (P ≤ 0.05).

Comparative jejunal expression of MUC 13 in Indian native pigs differentially adhesive to diarrhoeagenic E. coli

ABSTRACT Escherichia coli are important pathogens among bacterial causes of neonatal piglet diarrhoea. Their adhesion to the intestinal epithelial cells is an essential prerequisite for incidence of diarrhoea, which makes certain animal innately resistant and this adhesion pattern is genetically controlled. Among the candidate genes associated with adhesion pattern, MUC13 is the most likely responsible gene examined in diverse outbred swine populations. The present investigation aimed to evaluate the native Indian (desi) pigs in terms of E. coli adhesion pattern (with Indian isolate) and MUC13 expression profile across adhesion phenotypes. Out of 80 pigs screened, 27 were found to be non-adhesive, 46 adhesive and 7 were weakly adhesive. Effect of sex was found to be significant (P<.05) with non-significant age effect. RT-PCR analysis revealed that although, porcine MUC13 mRNA expression was highest in adhesive (2.67±0.69 fold), moderate in weakly adhesive (1.22±0.35 fold) and low levels in non-adhesive (calibrator) phenotypes, differences were statistically non-significant (P<.05). While the availability of non-adhesive phenotypes among Indian desi pigs implicates abundance of input genetic resources to start a breeding programme against diarrhoea, the descending expression of MUC 13 in adhesive and weakly adhesive samples speculates its important role in adhesion of E. coli.

Comparative Jejunal Expression of TFRC gene in Pigs Differentially Adhesive to Diarrhoeagenic E. coli

1 Division of Animal Genetics, ICARIndian Veterinary Research Institute, Izatnagar, Bareilly, U.P-243122 India 2 Livestock Production & Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly U.P-243122, India 3 Department of Animal Genetics & Breeding, Col. of Vet. Sci. & A.H. Junagarh, Gujrat, India 4 Division of Animal Nutrition, ICARIndian Veterinary Research Institute, Izatnagar, Bareilly, U.P-243122, India