New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data.

The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.

Identification of tamaraw (Bubalus mindorensis) from natural habitat-derived fecal samples by PCR-RFLP analysis of cytochrome b gene.

Fecal DNA analysis is a useful tool for the investigation of endangered species. Tamaraw (Bubalus mindorensis) is endemic to the Philippine island of Mindoro but knowledge of its genetic and ecological information is limited. In this study, we developed a species identification method for tamaraw by fecal DNA analysis. Eighteen feces presumed to be from tamaraw were collected in Mount Iglit-Baco National Park and species-known feces from domestic buffaloes and cattle were obtained from a farm. Additionally, one species-unknown fecal sample was obtained in Mount Aruyan Preserve, where the sighting of tamaraw has not been reported in recent years. Based on DNA sequence data previously reported, the genus Bubalus- and tamaraw-specific primers for PCR of cytochrome b gene were newly designed. The Bubalus-specific primer yielded a 976 bp fragment of cytochrome b for all fecal samples from tamaraw and domestic buffaloes, but not for cattle, whereas the tamaraw-specific primer yielded a 582 bp fragment for all tamaraw fecal samples and for one of the four domestic buffalo samples. PCR-RFLP (restriction fragment length polymorphism) analysis of the 976 bp PCR fragment with AvrII or BsaXI provided distinct differences between tamaraw and domestic buffalo. PCR-RFLP analysis also showed that the species-unknown sample obtained in Mount Aruyan Preserve, originates from tamaraw.

Possible use of RNA isolate from inactivated vaccine for external positive control in reverse transcription-based detection of foot-and-mouth disease virus in bull semen.

This study has demonstrated the novel use of inactivated and purified vaccine against FMD virus for detection and analysis. RNA isolate was efficiently generated from the vaccine for an external positive control for reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays. The target DNA fragment sequences from the 2B region and 3D RNA polymerase gene of the virus for RT-PCR and RT-LAMP respectively were successfully amplified using the RNA template. Laboratories lacking complex equipment may not be feasible to handle high-risk viruses for conventional methods such as the isolation and culture of live viruses. Here, with the use of these molecular tools, novel use of RNA isolate from inactivated, purified vaccine proved to be an effective external positive control for the assays. Therefore, with these methods, the derived RNA control template aids in a safe method for screening FMD virus for diagnostic laboratories. And by using the same technique, it is then possible to generate a standard for diagnosing any other infectious viral diseases.

Development and application of a quantitative real-time PCR for the diagnosis of Surra in water buffaloes.

Trypanosoma evansi (T. evansi) causes the disease called Surra in domestic animals, which is of great economic importance in South Asian countries. In order to improve the diagnosis of Surra, we endeavored to develop a real-time PCR assay for the detection and quantification of parasites in water buffaloes using specific primers for the T. evansi Rode Trypanozoon antigen type (RoTat) 1.2 Variable Surface Glycoprotein (VSG) gene, which is a known diverse DNA region in trypanosomes. The quantitative detection limit of the assay was 10(2) trypanosomes per mL of blood, and the identity of the amplicon was confirmed in all assays by melting curve analysis. To evaluate the clinical applicability of this procedure, detection and estimation of parasitemia in blood samples obtained from water buffaloes and horses were conducted. T. evansi was detected in 17/607 (2.8%) blood samples, with parasitemia levels ranging from >10(1) to 10(7) parasites per mL of blood. Interestingly, out of the 17 PCR positive animals, 3 had previously received trypanocidal treatment and 1 had abortion history. These data indicate that real-time PCR for the estimation of putative parasitemia levels is a quantitatively and objectively applicable technique for clinical diagnosis of Surra, and could help to understand disease stage and risk of transmission of T. evansi.

Comparative moleculo-immunological analysis of swamp- and riverine-type water buffaloes responses.

This moleculo-epidemiological and immunological study through cytokine response assessment was done to know the dynamics of cytokines in the initiation, persistence and association to physiological changes of a particular pathogen in water buffaloes. This is important to understand the magnitude and behavior of disease progression. Water buffalo blood samples gathered from different places in the Philippines revealed a 9.4%, 27.6%, 10.3% and 4.4% prevalence of bovine viral diarrhea virus (BVDV), bovine leukemia virus (BLV), Anaplasma marginale and Babesia bigemina infection, respectively. This was the first surveillance study of BVDV and BLV in the country. Furthermore, cytokine expression of these naturally infected animals was also quantified. BVDV-infected animals had up-regulated expressions of TNFalpha, IL-2 and IL-4; and down-regulated expressions of IFNgamma and IL-12p40 while BLV positive animals had an up-regulated IL-4 and IL-6, and highly expressed IL-10 and IL-12p40 with unchanged IFNgamma expression. Meanwhile, animals infected with A. marginale had all interleukins and IFNgamma up-regulated with significant expression of IL-10 and IL-12p40 similar to the BLV positive animals. Since it was also observed that swamp-type buffaloes were more disease tolerant than riverine-type buffaloes based on the gathered infection rate of each examined pathogen, further assessment was done focusing on the two vital cytokines, IFNgamma and TNFalpha. We quantified IFNgamma and TNFalpha expressions in ConA-stimulated PBMC from both swamp and riverine buffaloes by real-time PCR. Cytokine expression from ConA-stimulated PBMC revealed that both IFNgamma and TNFalpha were more highly expressed in swamp than in riverine buffalo. To further examine the probable cause of expression differences, the proximal promoter region of these two cytokines were sequenced for the presence of nucleotide polymorphism followed by luciferase assay to analyze the effect of these polymorphisms in gene transcription. A single nucleotide polymorphism was found in the IFNgamma (-299) while eight polymorphisms in the TNFalpha promoter (-541, -553, -562, -596, -609, -655, -659, -688). Luciferase assay showed that both IFNgamma promoter and TNFalpha promoter in swamp-type water buffalo had higher transcription activity compared to riverine-type water buffalo. These findings confirm that IFNgamma and TNFalpha transcriptions in these animals were highly affected by the disparity in the cytokine promoter region. This suggests that disease tolerance or susceptibility of these buffaloes could be due to the differences in their relative cytokine transcription and may relate to pathogen-host specific pathogenesis.

A survey of abortifacient infectious agents in livestock in Luzon, the Philippines, with emphasis on the situation in a cattle herd with abortion problems.

In the Philippines, insufficient consideration has been given to the implementation of systematic control measures against major abortifacient infectious agents in livestock. To elucidate the epidemiology of abortifacient infectious agents in livestock, the prevalence of four abortifacient agents was assessed. Initially, a total of 96 cattle including 17 cows with history of abortion were examined in a herd in Luzon at the request of the farm owner. Six (35.3%) of the 17 aborting cows were found to be serologically positive for Neospora caninum (N. caninum), whereas the seroprevalence in non-aborting cows was 15.9% (10/63). Four of the 6 serologically positive aborting cows were also RT-PCR-positive for bovine viral diarrhea virus (BVDV). Two (12.5%) of the 16 bulls examined were also found to be infected with BVDV, suggesting a putative risk factor of transmission via semen. Based on sequence analysis, the isolates detected belong to BVDV type 1b group. Furthermore, an epidemiological survey of abortifacient infectious agents was conducted with various species of livestock from herds located in Luzon. Out of the 105 water buffalo samples collected, 4 (3.8%) were indicated positive to N. caninum, 2 (1.9%) to Toxoplasma gondii (T. gondii) and 2 (1.9%) to Trypanosoma evansi (T. evansi). The overall seroprevalence of N. caninum in goat and sheep were 23.6% (21/89) and 26.3% (10/38), respectively. BVDV was not detected in these herds. The findings of this exploratory study indicate a relationship between infection and bovine abortion and that a lager study is required to statistically confirm this relationship.

Post-warming hatching and birth of live calves following transfer of in vitro-derived vitrified water buffalo (Bubalus bubalis) embryos.

Viability of in vitro-derived vitrified-warmed preimplantation stage buffalo embryos were assessed in vitro and in vivo. Oocytes were collected from ovaries of slaughtered riverine buffaloes, matured and fertilized in vitro with frozen semen from riverine buffalo bull and cultured on cumulus cell monolayers. Resultant preimplantation stage embryos were cryopreserved by vitrification with ethylene glycol, ficoll and sucrose. Seventy-one frozen embryos were warmed in 0.5M sucrose and were further cultured in vitro for 72 h to assess hatching rate. On the other hand, 95 embryos were transferred non-surgically to riverine buffalo recipients to assess development competence in vivo through detection of pregnancy and birth of live calves. Hatching rate of 83.10% (59/71) was noted among embryos cultured in vitro. Pregnancy rate was 16.36% (9/55) while calving rate was 10.91% (6/55) after transfer of in vitro-derived vitrified-warmed embryos to recipient animals. Six healthy and normal calves with average birth weight of 38.75+/-3.55 kg were born from the transferred embryos. These results indicate the viability of vitrified in vitro-derived buffalo embryos and the potential application of in vitro embryo production and vitrification techniques for production and transport of buffalo embryos from germplasm-rich sources to guarantee genetic improvement in many parts of the world.