Bovine Herpesvirus Types 5 (BoHV5): A New and Emerging Threat in Indian Cattle

Bovine herpesvirus 5 (BoHV-5) belongs to the genus varicellovirus family herpesviridae and is a causative agent of meningo-encephalitis in cattle. BoHV-5 can replicates in the central nervous system (CNS) to cause encephalitis and establishes latency in the trigeminal ganglion of either naturally infected cattle or experimentally inoculated laboratory animals. BoHV 5 was first time reported in Australia in 1962 and subsequently reported in Latin Ameican countries Argentina, Brazil and Uruguay. Few cases of BoHV5 infection has also been reported in USA and Europe. Recently, the BoHV5 infection was reported in Indian cattle for the first time. The BoHV5 was isolated from aborted cattle and characterized as BoHV5 subtype A and this finding may necessitate inclusion of BoHV5 test protocol in testing of semen for sexually transmitted diseases. Because BoHV5 infection in cattle recently reported in India so, it is needed to explore the similarity of the isolates with earlier reported isolates and to check it’s pathogenicity to cause encephalitis in natural host and in experimental animals like rabbits, rat, guniea pig etc. Beside this, we have to explore the information about co-infection of BoHV5 with other viral, bacterial, fungal as well as parasitic agents.

Genetic diversity and effective population sizes of thirteen Indian cattle breeds

Background The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. Results Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. Conclusions The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

ABSTRACTThe present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately higher. A significantly strong negative correlation coefficient of −0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The phylogeny and genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

Comparitive Genome Sequence Analysis of Bovine Lymphocyte Antigen BoLA DRB3.2 Alleles in Deoni and Ongole (Bos indicus) Cattle Breeds of India

Background: India, a major livestock region of the Asian countries is rich in animal genetic resources having special qualities of hardy nature, resistance to many diseases and adopted to adverse climatic conditions. The cattle MHC, Bovine Lymphocyte Antigen DRB3 (BoLA-DRB3) is considered to be a major gene linked with disease resistance traits of Indian cattle. Methods: The present study was carried out to sequence the BoLA-DRB3.2 alleles in Deoni and Ongole breeds of Indian cattle. PCR RFLP analysis of the BoLA-DRB3.2 alleles in Deoni (n=51) and Ongole (n=60) cattle using three different restriction enzymes RsaI, BstYI and HaeIII to find out the possible restriction pattern. Based on the combined allelic patterns, each sample was further analyzed by PCR- SBT technique to detect the SNP variations present in BoLA-DRB3.2 alleles.Result: The PCR RFLP analysis revealed that the highest frequent alleles are *6 (0.216) and *15 (0.225) in Deoni and Ongole breeds of cattle, respectively. The second-highest frequency was observed for BoLA alleles *11 and *6 which were present at a frequency of 0.167 and 0.200 in Deoni and Ongole breeds of cattle, respectively. To get the complete picture of polymorphic pattern of BoLA-DRB3.2 allele direct sequencing was carried out for each plymorphic pattern. The interesting feature noticed in the Ongole breed was that at position 91 and 133 of the sequence, it had both A and G nucleotides in contrast to Bos taurus breed, which had only TT nucleotides. The sequence analysis of BoLA-DRB3 exon 2 between two breeds revealed that there are numerous variations in exon 2, whatever variation, that lead to different mobility shift and band pattern in gels. Deoni and Ongole breeds of cattle had similar variations at positions 94, 134, 211, 235 and 258noticed due to the unique nature of native breeds.