Transcriptome analysis in Indian buffalo and the genetics of innate immunity

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute


India is home to almost half of the world's domesticated water buffalo. Buffalo are used as draft, meat, and dairy animals. Their dung is used as a fertilizer, and as a fuel when dried. Buffalo milk has the lowest water content and highest fat content amongst farm animals, and the butterfat is a major source of ghee used in cooking. A number of major breeds of buffalo have been generated, but there has been relatively little systematic study of their disease resistance. The buffalo population of India is afflicted by a wide range of diseases with substantial mortality and morbidity, which have a massive impact on small holders' livelihoods and in many cases are also zoonotic. Some of these afflict cattle and buffalo equally, others such as pasteurellosis, are far more likely to cause death to buffalo than to cattle. In order to understand the molecular basis of disease susceptibility, and to build capacity for buffalo improvement, we propose a three-pronged project. We will carry out a survey of two major diseases of buffalo: tuberculosis and brucellosis. These diseases are both present at estimated percentages of at least 10% in adult animals and substantially greater in some villages. They represent significant sources of zoonotic infections of humans with whom they share close quarters. Where possible, and opportunistically in the case of significant outbreaks, we will also screen animals for other common pathogens such as pasteurella (haemorhagic septiceamia) black quarter (chlostridia) and leptospirosis, which tend to be seasonal, theileria spp and FMDV. In every case, we will collect DNA and we will seek to understand why some animals are infected and others are resistant. There are several major breeds of buffalo in India, but we know little of their genetic diversity. A second focus of the project is to understand how these breeds differ from each other. Finally, and building upon recent data from mouse, human and pig, and a parallel Roslin project on sheep, we proposed to create a gene expression atlas for the water buffalo. This will involve collection of a wide range of tissues from young adult animals. This information will underpin efforts to understand how genetic diversity leads to differences in infectious disease resistance between breeds and between animals. An important outcome of this project will be the transfer of molecular genetic skills and knowledge between the UK and India; in both directions because the diseases of interest are also economically important in the UK.

Technical Summary

This project combined two major arms. The first is a combination of large scale genomic and transcriptomic sequencing that aims to improve the draft sequence of the water buffalo, survey genetic diversity amongst breeds, annotate genes, and create an expression atlas that provides an indication of gene function to enable comparison with ruminants and other mammals. The second is a genetic epidemiology study that builds upon the transcriptomic and genomic information. We will collect DNA from around 1000 animals in Indian villages, with a definitive diagnosis of tuberculosis or brucellosis. We will identify allelic variation that correlates with susceptibility to infection. The final stage of the project will attempt to link genetic association to inferred gene functions within loci of interest.

Planned Impact

The water buffalo (Bubalus bubalis) contributes immensely to the agricultural economy through milk, meat, hides and draught power. A larger part of the human population depends on domestic water buffalo than on any other livestock species in the world (FAO & UNEP 2000). Buffalo is the mainstay of the dairy industry in India, this country being home to 57% of world buffalo population and most of the famous buffalo breeds. Although buffalo constitute 35.6% of total bovine population in India, they contribute to 55% of milk production. In addition buffalo production is a major source of employment to the landless and marginal farmers in several part of rural India. Buffalo milk is known for its whitening properties and contains higher levels of protein and fat, and thus this species is more economical as compared to cattle for production of several dairy products. Similarly, buffalo carcasses have less fat and higher proportions of muscle.
Brucellosis and Tuberculosis are very prevalent diseases amongst Indian buffalo, with serious and demonstrated zoonotic potential. Both diseases are also prevalent in cattle in developing countries and the latter is a major source of current economic losses in the UK. By contrast to the UK, where infected animals are culled, the Indian buffalo population is largely unselected and the prevalence is so high that one can assume that uninfected adult animals are resistant. The Indian buffalo therefore provides a unique opportunity to identify genetic variation that controls the pathology of these important pathogens, potentially also extending to insights into human disease resistance.
This proposal falls clearly within the FADH Initiative priority area of 'Genetics of Host Disease Resistance'. As highlighted in the BBSRC-DBT FADH Call for Proposals India has a wide variety of native breeds and immense genetic diversity and the UK has major expertise in genomics and host genetics. Roslin exemplifies the latter and CCMB and BAIF provide a portal to the former combined with critical domain expertise in respect of buffalo. This proposal addresses identified research needs within the 'Genetics of Host Disease Resistance' priority specifically directed towards understanding the molecular basis and mechanisms of genetic resistance to disease, and understanding species and strain difference in disease resistance and distinguishing resistant genotypes and potential for SNP marker discovery to support breed improvement through selection. It will enable academic research teams within India and the UK to develop a collaborative research framework that links the expertise of Roslin in ruminant genomics with application in the buffalo. The benefit is mutual, because the diseases of specific focus (tuberculosis and brucellosis) are also significant issues in the UK cattle population. Furthermore, the detailed information gathered will be relevant to annotation of other ruminant genomes, sheep, goat and cattle, that are economically important in both countries. It will use resources provided by BBSRC and DBT in a coordinated manner to provide access to skills, expertise, existing equipment and infrastructure, including, for example, the resources of ARK Genomics which is supported by a BBSRC National Capacity Grant. The project will foster close relationship between The Roslin Institute, which receives BBSRC support as a National Institute of Bioscience, and the National Institute for Animal Biotechnology in Hyderabad, on which Professor Hume serves as a member of the Scientific Advisory Board.
The major translatable outcomes of this project is the identification of molecular markers that could provide the basis for breeding for disease resistance in buffalo, and might also be translated to cattle and to assessment of disease risk and prevention strategies in humans. Implementation of this information may proceed via BAIF, and also major breeding companies such as Genus Plc.
Description We have almost completed a transcriptional atlas of the water buffalo which will be placed in the public domain. We are also involved in producing a much better water buffalo genome
Exploitation Route We are developing genotyping platforms and will also provide a comparative platform to support understanding ruminant immune systems
Sectors Agriculture, Food and Drink

Description Oral Presentation FAANG Session Plant and Animal Genomes Conference 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The functional annotation of animal genomes consortium (FAANG) is an international consortium dedicated to improving the livestock genomes and linking genotype to phenotype. This was the first year that there was a half day dedicated session organised by the FAAAG consortium at the international plant and animal genomes conference in San Diego, January 2018. Emily Clark was invited to present an overview of the water buffalo and sheep transcriptome work to members of the consortium in this session. There were interesting questions raised and the opportunity to present the work to an audience of 50+ livestock genomics researchers both raised the profile of the atlas projects as a resource for the community to use and highlighted the potential for further related activity.
Year(s) Of Engagement Activity 2018