The Kintamani Dog: Genetic Profile of an Emerging Breed from Bali, Indonesia

Genetic Diversity of Bosnian and Herzegovinian Autochthonous Dog Breed Bosnian Broken-Haired Hound-Barak

Fédération Cynologique Internationale (FCI) classifies a group of hound dogs in the sixth FCI group divided into three sections and three subsections that include 76 dog breeds. With the Istrian wire-haired hound, the Bosnian broken-haired hound-Barak is one of the two internationally recognized and standardized broken-haired hound breeds from the Balkans. However, genotyping of this breed has not been the subject of study so far. A total of 30 dogs (22 males and eight females) from different breeders from 17 locations in Bosnia and Herzegovina were selected for genotyping. All selected individuals had a valid pedigree issued by the Kennel Club in Bosnia and Herzegovina to ensure dogs were unrelated. Hairs with follicles were used for DNA extraction. Ten microsatellite loci from the commercial StockMarks® for Canine Genotyping Kit were amplified. Estimated genetic indices showed that Bosnian broken-haired hound-Barak harbors a high genetic variability. Phylogenetic relationships between Barak and the other 15 dog breeds, including Tornjak, another indigenous breed from Bosnia and Herzegovina, were assessed. An analysis showed clear differentiation of Barak, with Tornjak as the closest one among analyzed breeds. The results suggest that Barak, as we know it today, was developed during the formation of most modern breeds. Although Barak cannot yet be considered an endangered breed thanks to enthusiasts and hunters, the declining population trends impose the urgent need to establish an animal gene bank and programs for in situ conservation to protect and preserve this autochthonous breed of hound dog for future generations.

What the dingo says about dog domestication

Worldwide, dogs (Canis familiaris) are certainly the most common domesticate (900 million according to the World Atlas) and are sometimes used as a proxy for human presence. Dogs were the first and therefore arguably most important species ever to be domesticated. It is widely accepted that the domestic dog is a descendent of Pleistocene gray wolves (Canis lupus), possibly of a population now extinct. How can an extant canid, the dingo (Canis dingo or Canis familiaris), whose status as a species and as a domesticate is controversial, improve our understanding of the ancient process of domesticating the dog? Here I review anatomical, behavioral, biogeographic, and molecular evidence on the appropriate status of dingoes in a historical context. Dingoes are now the major apex predator in Australia aside from humans. Different sources of evidence have suggested different times of arrival in Greater Australia for humans and canids and different degrees of intimacy or domestication between humans and canids. Just as domestic dogs are often accorded near‐human status, dingoes have special relationships with human families, but reproductively and behaviorally they remain independent. In sum, traits of the dingo reflect its lupine ancestry, a certain degree of accommodation to human company, and unique adaptations to the demands of its habitat. Emphasizing that domestication is a long‐term process, not an event, helps clarify the ambiguous status of dingoes.

Preservation of semen from Kintamani Bali dogs by freezing method

Objective:

To explore the effect of glycerol at different concentrations using different extenders on DNA fragmentation and motility of frozen-thawed Kintamani Bali dog spermatozoa.

Materials and Methods:

Sample was collected from four mature Kintamani Bali dogs. Each ejaculate was prepared for cryopreservation with two different semen extenders; egg yolk Tris extender and coconut water-based extender. For each extender, three different glycerol concentrations were used; 4%, 6%, and 8%. Each of the six aliquots was loaded into 0.5 ml cryotube, placed on a styrofoam box 5 cm over liquid nitrogen for 10 min, and immersed in liquid nitrogen up to 8 min. Then, the frozen cryotubes were transferred into liquid nitrogen container. The cryotubes were thawed in a water bath at 38.5°C for 120 sec. After equilibration and thawing, each sample was assessed for motility parameters and for DNA fragmentation.

Results:

The addition of 6% glycerol to extenders revealed the most effective addition of glycerol on motility and sperm DNA fragmentation after equilibrium and post-thawing.

Conclusion:

It is concluded that both extenders with the addition of 6% glycerol are safe to be used as an extender in Kintamani Bali dog semen preservation, and DNA fragmentation of Kintamani Bali dog spermatozoa was not influenced by the freezing procedure.

Genetic diversity and population structure of African village dogs based on microsatellite and immunity-related molecular markers

The village and street dogs represent a unique model of canine populations. In the absence of selective breeding and veterinary care, they are subject mostly to natural selection. Their analyses contribute to understanding general mechanisms governing the genetic diversity, evolution and adaptation. In this study, we analyzed the genetic diversity and population structure of African village dogs living in villages in three different geographical areas in Northern Kenya. Data obtained for neutral microsatellite molecular markers were compared with those computed for potentially non-neutral markers of candidate immunity-related genes. The neutral genetic diversity was similar to other comparable village dog populations studied so far. The overall genetic diversity in microsatellites was higher than the diversity of European pure breeds, but it was similar to the range of diversity observed in a group composed of many European breeds, indicating that the African population has maintained a large proportion of the genetic diversity of the canine species as a whole. Microsatellite marker diversity indicated that the entire population is subdivided into three genetically distinct, although closely related subpopulations. This genetical partitioning corresponded to their geographical separation and the observed gene flow well correlated with the communication patterns among the three localities. In contrast to neutral microsatellites, the genetic diversity in immunity-related candidate SNP markers was similar across all three subpopulations and to the European group. It seems that the genetic structure of this particular population of Kenyan village dogs is mostly determined by geographical and anthropogenic factors influencing the gene flow between various subpopulations rather than by biological factors, such as genetic contribution of original migrating populations and/or the pathogen-mediated selection. On the other hand, the study of oldest surviving dogs suggested a biological mechanism, i.e. a possible advantage of the overal heterozygosity marked by the the microsatellite loci analyzed.

Studies of modern Italian dog populations reveal multiple patterns for domestic breed evolution

Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves, and an established dataset of 161 globally recognized dog breeds, applying multiple genetic methods to characterize the modes by which breeds are formed within a single geographic region. Our consideration of each of five genetic analyses reveals a series of development events that mirror historical modes of breed formation, but with variations unique to the codevelopment of early dog and human populations. Using 142,840 genome-wide SNPs and a dataset of 1,609 canines, representing 182 breeds and 16 wild canids, we identified breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.

The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease

BACKGROUND

Sebaceous adenitis (SA) and Addison's disease (AD) increased rapidly in incidence among Standard Poodles after the mid-twentieth century. Previous attempts to identify specific genetic causes using genome wide association studies and interrogation of the dog leukocyte antigen (DLA) region have been non-productive. However, such studies led us to hypothesize that positive selection for desired phenotypic traits that arose in the mid-twentieth century led to intense inbreeding and the inadvertent amplification of AD and SA associated traits.

RESULTS

This hypothesis was tested with genetic studies of 761 Standard, Miniature, and Miniature/Standard Poodle crosses from the USA, Canada and Europe, coupled with extensive pedigree analysis of thousands more dogs. Genome-wide diversity across the world-wide population was measured using a panel of 33 short tandem repeat (STR) loci. Allele frequency data were also used to determine the internal relatedness of individual dogs within the population as a whole. Assays based on linkage between STR genomic loci and DLA genes were used to identify class I and II haplotypes and disease associations. Genetic diversity statistics based on genomic STR markers indicated that Standard Poodles from North America and Europe were closely related and reasonably diverse across the breed. However, genetic diversity statistics, internal relatedness, principal coordinate analysis, and DLA haplotype frequencies showed a marked imbalance with 30 % of the diversity in 70 % of the dogs. Standard Poodles with SA and AD were strongly linked to this inbred population, with dogs suffering with SA being the most inbred. No single strong association was found between STR defined DLA class I or II haplotypes and SA or AD in the breed as a whole, although certain haplotypes present in a minority of the population appeared to confer moderate degrees of risk or protection against either or both diseases. Dogs possessing minor DLA class I haplotypes were half as likely to develop SA or AD as dogs with common haplotypes. Miniature/Standard Poodle crosses being used for outcrossing were more genetically diverse than Standard Poodles and genetically distinguishable across the genome and in the DLA class I and II region.

CONCLUSIONS

Ancestral genetic polymorphisms responsible for SA and AD entered Standard Poodles through separate lineages, AD earlier and SA later, and were increasingly fixed by a period of close linebreeding that was related to popular bloodlines from the mid-twentieth century. This event has become known as the midcentury bottleneck or MCB. Sustained positive selection resulted in a marked imbalance in genetic diversity across the genome and in the DLA class I and II region. Both SA and AD were concentrated among the most inbred dogs, with genetic outliers being relatively disease free. No specific genetic markers other than those reflecting the degree of inbreeding were consistently associated with either disease. Standard Poodles as a whole remain genetically diverse, but steps should be taken to rebalance diversity using genetic outliers and if necessary, outcrosses to phenotypically similar but genetically distinct breeds.

On dogs, people, and a rabies epidemic: results from a sociocultural study in Bali, Indonesia

Background

Previously free of rabies, Bali experienced an outbreak in 2008, which has since caused a large number of human fatalities. In response, both mass dog culling and vaccination have been implemented. In order to assess potential community-driven interventions for optimizing rabies control, we conducted a study exploring the relationship between dogs, rabies, and the Balinese community. The objectives of this study were to: i) understand the human-dog relationship in Bali; ii) explore local knowledge, attitudes, and practices (KAPs) relating to rabies; and iii) assess potential community-driven activities to optimize rabies control and surveillance.

Methods

Conducted between February and June 2011, the study combined a questionnaire (n = 300; CI = 95 %; error margin = 5 %) and focus group discussions (FGDs) in 10 villages in the Denpasar, Gianyar, and Karangasem regencies. The questionnaire included a Likert scale to assess community knowledge and attitudes. For the knowledge assessment, three points were given for a correct answer, while wrong answers and uncertain answers were given zero points. For the attitudes assessment, three points were given for a positive answer, two points for a neutral answer, and one point for a negative answer. Respondent knowledge was categorized as good (score >40), fair (score 20–40), or poor (score <20), based on a maximum total score 60. Respondent attitudes were categorized as positive (score >26), neutral (score 13–26), or negative (score <13), based on a maximum total score of 39. Mixed-gender FGDs in each sub-village (banjar) were conducted, each involving 7–15 participants to complement the questionnaire results. On a follow-up research trip in mid-2013, the data analysis was triangulated and validated using semi-structured interviews. Questionnaire data were analyzed descriptively using SPSS 17.0, while qualitative data from interviews and FGDs were analyzed manually according to accepted methods of coding and memo writing. The chi-square test was then used to analyze the statistical relationships between knowledge and attitudes of the respondents.

Results

Out of the total 300 respondents, most were predominantly male (82 %), Hindu (99 %), married (96 %), older than 30 years of age (92 %), and owned dogs (72 %). Dog ownership was motivated by culture, personal taste, and function, with dogs was being used as guards (85 %) and companion animals (27 %), and was sometimes related to religious or traditional obligations (2 %). Relating to their culture and local beliefs, and eventually becoming their way of life, 79 % of respondents kept free-roaming dogs. With the rabies outbreak in Bali and Western breeds becoming more popular, more responsible dog ownership (leashing, confining, regular feeding) became more acceptable and changed community perceptions on keeping dogs, even though the sustainability of this practice cannot be gauged. In addition, the economic situation posed major problems in rural areas. The level of community knowledge about rabies and its associated control programs were generally fair and community attitudes were positive. However, community KAPs still need to be improved. A total of 74 % respondents reported to have vaccinated their dogs in 2011, but only few were found to report rabid animals to livestock officers (12 %) and a significant number believed that washing a bite wound was not important (62 %). Moreover, free-roaming dog practices and discarding of unwanted female puppies still continue and possibly create difficulties for rabies elimination as these practices potentially increase the stray dog population. We identified three major sociocultural aspects with potential for community-driven interventions to optimize current rabies elimination efforts: integrating local notions of ahimsa (non-violence) into education campaigns, engaging communities through the local banjar sociopolitical system, and working with traditional legal structures to increase local compliance with rabies control.

Conclusion

The human-dog relationship in Bali is multifaceted. Due to the uniqueness of the culture and the local beliefs, and encouraged by a socioeconomic aspect, a number of local practices were found to be constituting risk factors for continued rabies spread. Community knowledge and attitudes, which can consequently result in behavioral changes, needs to be improved across different genders, ages, educational backgrounds, and roles in the community, regardless of the individual village’s experiences with rabies. Furthermore, community-driven activities based on sociocultural conditioning and community capacity at the banjar and village levels, such as public awareness activities, vaccination, dog registration, dog population management, and rapid response to dog bites, were identified as being able to complement the rabies control program in Bali. The program also needs recognition or acknowledgement from governments, especially local government as well as regular mentoring to improve and sustain community participation.

Electronic supplementary material

The online version of this article (doi:10.1186/s40249-015-0061-1) contains supplementary material, which is available to authorized users.

Microsatellite characterization of Cimarron Uruguayo dogs

Various genetic markers, including microsatellites, have been used to analyze the genetic polymorphism and heterozygosity in canine breeds. In this work, we used nine microsatellite markers to investigate the genetic variability in Cimarron Uruguayo dogs, the only officially recognized native canine breed in Uruguay. DNA from 30 Cimarron Uruguayo dogs from northeastern and southern Uruguay was analyzed. The allelic frequencies for each microsatellite, the genetic variability and the consanguinity were calculated, as were the polymorphic information content (PIC) and the probability of exclusion (PE). All of the microsatellites studied were polymorphic. FH 2361, FH 2305 and PEZ 03 were the most informative, with PIC values > 0.7, in agreement with results for other canine breeds. The PE values for the markers were within the ranges previously described and were generally greater for microsatellites with higher PIC values. The heterozygosity value (0.649) was considered high since only nine microsatellites were analyzed. Compared with data for other breeds, the results obtained here indicate that Cimarron Uruguayo dogs have high genetic diversity.