Genetic characterization of indigenous chicken breeds in search for unique properties of immune-related genes

Domestic chicken (Gallus gallus domesticus) is one of the most important animal species worldwide because it provides a large proportion of animal protein in human diet. Chickens have also been used for ornamental purposes (e.g. silkie or bantams) and entertainment (e.g. gamecocks used for cockfighting). The contemporary chicken was most probably developed from its main wild ancestor, the red jungle fowl (Gallus gallus), after its domestication in Southeast Asia in 3,200 BC. Over the years, chicken evolved from the wild form to the multiple contemporary layers, broilers, bantams, game and fancy breeds, as well as the indigenous village chicken available today.

At first sight the diversity within domestic chicken is extensive, which should provide an excellent base for breeding animals that are well adapted to a variety of local environmental conditions. However, the industrialization and globalization of chicken production in the 20th century adversely affected the distribution of chicken genetic resources worldwide, practically limiting the breed composition to commercial stocks of broilers and egg-type, laying hens. Consequently, many chicken breeds have already become extinct or are seriously endangered with extinction.

Genetic characterization of indigenous chicken breeds in search for unique properties of immune-related genes Currently, the world poultry market is facing recurrent outbreaks of contagious diseases e.g. Avian Influenza or Salmonella which impose serious health and economic constraints due to several interrelated risk factors. First, commercially bred birds which constitute most of the genetic resources nowadays are likely to lose the genetic resistance to various diseases through the long-term process of one-sided selection for production traits. Additionally, extensive vaccination programmes can elicit incomplete immunity. Coupled with large flock sizes on commercial farms amounting to thousands of birds, this can result in very rapid transmission of pathogens. In case of the emergence of the highly contagious diseases like Highly Pathogenic Avian Influenza (HPAI), the whole flock in a given area can be endangered with infection requiring culling of the birds which would seriously threaten the livelihood of livestock farmers, jeopardize commercial poultry production, and seriously impede regional and international trade. Outbreaks of epidemic diseases in commercial flocks also pose a serious hazard to human health, especially in many developing countries where food hygiene needs to be drastically improved.

Immuno-competence can however be enhanced by using the already existing rich sources of genetic variation in chicken, i.e. those gene variants (alleles) that are associated with resistance to disease. However, the main obstacle preventing the direct application of modern molecular techniques in practical chicken breeding programmes is the lack of knowledge on which genes determine the fitness and robustness of the individual. This task is not easy given the complexity of the immune system, the multiple animal-pathogen interactions as well as the not fully understood genomic determination of physiological processes. However, the evolutionary mechanisms that followed the advent of chicken domestication and its distribution to all corners of the world have contributed to the adaptation of the birds to different environments. Since the process of adaptation of the indigenous chicken to often harsh and extreme environmental conditions demanded positive selection towards enhanced immune resistance; these birds are now more likely carrying fixed alleles determining their immuno-competence. However, this link has not been fully elucidated, but there are a number of papers that show existence of genotype × environment impact on the fitness traits including immuno-competence and thus on natural selection. Of course we need breed history and more data to draw any conclusions.

Genetic characterization of indigenous chicken breeds in search for unique properties of immune-related genes The search for beneficial mutations in the genomic DNA is therefore often sought in local, unselected breeds. This approach may eventually lead to better understanding of the evolutionary processes that resulted in adaptation of indigenous chicken and natural selection of immune-related genes. The first step in selection of a breed is to comprehensively characterize it, including the breed history, population size and distribution, physiological properties of the birds, as well as determining genetic polymorphisms within the loci that are specifically associated with relevant traits, such as immune resistance, that can be useful for studies on genetic resistance.

Since there are still a number of chicken breeds that could potentially carry desirable mutations within immune-related genes, a project was initiated by the Genetic Group at the Animal Production and Health Laboratory to undertake the genetic characterization of several indigenous chicken breeds and for that purpose, both breed information and DNA samples have been collected. Initially the project covered local breeds from Eastern European countries, including Poland, Bulgaria, Bosnia and Herzegovina, Macedonia and Montenegro but was lately extended to other parts of the world. Examples of the birds included in the study are the Green-legged Partridge, an indigenous Polish breed with characteristic green shanks that lays eggs with lower cholesterol content and Kadaknath – an Indian fowl with black coloured plumage whose meat is a rich source of iron.

Since the immune system has developed many divergent pathways to combat infection, characterization of the indigenous chickens included analysis of the polymorphism within loci engaged in different immune processes, primarily, the major histocompability complex (MHC). The MHC consists of a very gene-dense genomic region that encodes for a number of different molecules, which play a role in communicating between various components of the immune system and resistance to some contagious diseases (e.g. Marek’s disease) is strongly associated with variations in the MHC. Secondly, single nucleotide polymorphisms (SNPs) within some key immune response genes e.g. Myxovirus resistance gene (Mx) that has been reported to confer resistance to Avian Influenza Virus and interleukin 2 gene (Il-2), which is an immunoregulatory cytokine produced exclusively by Th1 cells (T helper 1 lymphocytes) and drives the immune system towards macrophage activation and antibody production. The third sequenced gene fragment included Toll-like Receptor 7 (TLR7), a member of a family of specialized receptors that recognize the invasion of a pathogen and subsequently trigger the immune response. The product of the TLR7 gene that has been analyzed can recognize single-stranded RNA fragments characteristic for several viruses including Avian Influenza Virus.

The results of the study will be made available both through a Genetic Repository Database and the publication of the results in a journal upon completion of the project. To sum up, the study carried out by IAEA to genetically characterize indigenous chicken breeds is crucial not only to manage genetic biodiversity within Farm Animal Genetic Resources (FAnGR), but also to provide information regarding evolutionary processes and genetic variation within avian immune-related genes. Even though local breeds are not considered highly productive and well-suited for commercial use, they possess many desired features due to their adaptation to the local environments where they are derived. It is therefore worthwhile to characterize the genetic potential of such breeds for better understanding of their uniqueness, since it could be helpful for future selection for poultry breeding.