Genetic Variation on the Control of Resistance to Infectious Diseases in Small Ruminants for Improving Animal Productivity (D3.10.26)


Small ruminants, mainly sheep and goats, constitute an important livestock resource in most developing countries and are essential for the livelihood of millions of small farmers. Infectious diseases, such as gastrointestinal nematodes impose severe constraints on animal production in pastoral systems worldwide. Losses occur through mortalities, reduced production due to sub clinical diseases and direct costs associated with pest control. Widespread and indiscriminative use of drugs to alleviate parasite infestation has resulted in the emergence of strains which are resistant to them in many cases. There are also increasing environmental concerns about chemical residues in meat, milk, and pasture resulting from the use of these drugs.

There is well-documented evidence for within and between breed genetic variation in resistance to infectious diseases, namely gastrointestinal nematode infections, diseases due to mycotoxins, bacterial diseases including foot root and mastitis, ectoparasites such as flies and lice, and scrapie, the small ruminant transmissible spongiform encephalopathy.

Due to this document within-breed variation, in many cases disease resistance is a heritable trait. This offers the opportunity to select animals for enhanced resistance to the disease. The feasibility of this approach has been experimentally demonstrated and in other cases, breeding programmes selecting commercial animals for enhanced resistance are being successfully established, especially for sheep as compared to goats. There are concerted efforts to find genetic markers associated with resistance to infections, potentially allowing selection for increased resistance in the absence of infection, especially for scrapie and nematode parasitism.

Genetic disease resistance is particularly relevant in developing countries, as indigenous breeds usually display enhanced resistance to local diseases as compared to exotic ones reared in the same environment. However, little is known on the genetic composition controlling this condition. The rapid and growing knowledge on genes and genomes in livestock such as the assessment of a large number of DNA markers in phenotypic recorded populations could be used to localize and further characterize candidate genes of economic interest. The analysis of mutations (SNPs) is in essence the discovery and exploitation of the natural variation existing in the biological machinery with the aim of increasing the frequency of favourable alleles to the benefit of livestock breeding strategies.

Many gaps still exist in the understanding of adaptation and disease resistance traits, as well as the genes controlling these traits. Disease resistance and adaptation traits are not sufficiently characterized, they are underutilized in conventional breeding programmes, and there is insufficient research on the ways to select breeds or individuals carrying the most advantageous traits. The characterization and mapping of genes controlling such traits – “quantitative trait loci” (QTL) and the subsequent use of this information in selection and breeding programmes, should make it possible to facilitate significant increases in small ruminant productivity. Almost certainly this will be achieved through the use of SNP markers.

The IAEA, through Seibersorf’s Laboratories has been providing a series of facilities for enabling Member States (MS) access to the detailed genetic knowledge available in various databases for improving the genetic potential of local and indigenous livestock. It has also transferred to several MS the technical capacity for DNA analysis and Marker Assisted Selection (MAS).

The CRP D3.10.25 on “Gene-based Technologies in Livestock Breeding: Characterization of Small Ruminant Genetic Resources in Asia”, has provided relevant information on which this CRP project proposal is building up. Through this CRP, technical capacity within the eight Asian countries was notoriously improved and many scientists from the region were trained on the use of radio-isotopic micro-satellite methods and related technologies for genotype characterization of ruminants and equipment for the laboratories was procured through the project. Genotypic and phenotypic information was collected and partially analyzed from 40 sheep breeds and 60 goat breeds. The new CRP will use much of the collected data.

Overall objectives:

The objective of this CRP is to improve productivity in smallholder livestock systems using gene based and related technologies.

Specific research objectives:

  • To develop capacity in developing countries in the use of molecular and related technologies and create opportunities for international research collaboration.
  • To establish or improve programmes for animal identification and data recording for small ruminants in developing countries, allowing for the monitoring of production, reproduction and health traits and generating populations suitable for molecular genetic studies.
  • To collect phenotypic data and DNA samples from goat and sheep breeds or populations within-breeds with history of infectious disease resistance.
  • To develop expertise on the use and development of bioinformatic tools for the analysis of large datasets if genomic data related to parasite resistance in various breeds.
  • To provide valid data for the identification of genetic markers associated to infectious disease resistance and to initiate the development of tools for molecular diagnostics and assisted breeding.
  • To contribute on the development and use of nuclear technology for genomic research in small ruminants, including radiation hybrid map, Southern Blot with radioactive [a-³²P]ATP labelling in genetic marker analysis, and PCR-RFLP.

Expected outputs:

  • Sequenced analysis of genes associated to infectious disease resistance.
  • Identification of genetic markers associated to infectious disease resistance in small ruminants.
  • Standardised and validated protocols and SOPs for DNA analysis and genetic studies on small ruminants.
  • Standardised procedures and methods for phenotypic characterization of indigenous livestock breeds.
  • An improved animal identification programme for local populations of small ruminants.
  • Established programmes for identifying and selecting superior productive animals, including those resistant to gastrointestinal parasitism.
  • Research groups in developing countries with enhanced capacity for phenotypic characterization with emphasis on infectious diseases resistance.
  • Laboratories in developing countries with enhanced expertise on DNA analysis.
  • Scientific publications for dissemination of research results.

Implementation procedure:

Organisation of the CRP network

Up to 14 research contracts will be awarded to Member States submitting appropriate research proposals. Institutions willing to participate in the CRP must be engaged in programmes of national importance in genetics and breeding of livestock, have access to basic laboratory facilities for studies on molecular genetics, have local support and facilities for phenotypic data collection, and be recipients of collateral financial support from national, bilateral, or international sources.

Four Research Agreements will be awarded to institutes that have expertise in specific areas of importance to the CRP.

Two technical contracts will be awarded for A) Direct sequencing of 25 genes in nearly 200 animals, and B) Development of a database for hosting all generated gene information and sequence that will be integrated with the Domestic Animal Diversity Information System (DAD-IS) of the FAO and the Science Satellite system of the IAEA Collaborating Centre on Animal Genomics and Bioinformatics in Brazil. The latter will also contribute with the development of bioinformatic tools.

Selection of participating institutes will be done in consultation with FAO and ILRI, and will consider the importance of the country and the target sheep and goat population in relation to the FAO Programme on Global Animal Genetic Resources (AnGR), and potential for future applications in generating and using populations with resistance to gastro-intestinal helminth parasites.

Applicants to research contracts are expected to work with a minimum of two breeds or populations within-breeds of goats or sheep where one of them has recorded data or anecdotal history of parasite infection resistance; however, working with both species or with four groups within ones species would be desirable. Also, a minimum of 25 unrelated animals per breed or group will need to be sampled for SNP verification. Phenotypic data, including parasite disease resistance, for each breed or population, if not available, will need to be collected during the first two years of the project using funds others than the CRP.

First Research Coordination Meeting (RCM)

The first RCM will be held in early 2011. All CRP participants and an FAO representative from the animal genetic resources group will be invited to attend the meeting. Research Contract holders (RCH) will present an outline of the small ruminant production systems in their countries and existent information related to infectious disease resistance. Agreement holders will present up-to-date laboratory techniques, methodologies, and available sources for identifying, evaluating, and monitoring gene markers. The IAEA, through the Technical Officer will present the existing resources (optimized genes, DNA-markers, sequencing procedures, and nuclear techniques) that have been developed or optimized at Seibersorf’s Laboratories. The RCM will focus on evaluating and agreeing on the details of standardize work plans and protocols of work for the next 18 months, and on general activities for the whole period of the CRP; including criteria for selecting “resistant” and “susceptible” populations, phenotypic data collection and parasite monitoring. Training on FAMACHA scoring, DNA quality, phenotype collection, and experimental design will be provided.

First Phase of Programme of Work

The first phase will last approximately 2.5 years. It comprises the phenotypical evaluation of the resistance to gastrointestinal parasites of sheep and goat breeds and DNA sample collection for genomic association studies.

The first step it the identification of (at least) two breeds of sheep or goats, where one is suspected of being “resistant” to gastrointestinal parasites. Animals should be of 4-6 months of age at the time of data collection and sampling. The second step is the quantification of the relative resistance to gastrointestinal parasites of sheep and goat breeds using an artificial challenge protocol and then a natural field challenge.

The “Artificial Challenge” trial will consist of a minimum of 20 animals per breed of equal sex distribution that are brought to a common location and dewormed. Then, 4-6 weeks later a blood sample for DNA extraction will be collected and animals challenged with 5000 infective L3 larvae. Body weight, fecal egg counts (FEC), packed cell volume (PCV), and FAMACHA scores taken at 28, 35, and 42 days after artificial infection. This trial can be omitted if samples and data exist from previous studies.

The “Field” trial will require a relative large numbers (several hundreds) of animals to determine genetic associations between DNA markers and parasite resistance, but these data can be accumulated across several farms and years. The trial can be done using only one breed (500 animals or more) or using two or more breeds (200 animals or more per breed in a common grazing environment). Animals will be dewormed and 28 days later body weight, FEC, PCV, and FAMACHA scores will be taken twice, one week apart. A blood sample for DNA extraction will be collected at the first sampling time. The size of individual flocks should be large enough to monitor and sample no less than 20 lambs/kids of each breed per year (the ideal situation is only one large flock).

DNA samples will be sent to the IAEA Seibersdorf Laboratories (preferably) or at least to a commercial service provider for SNP genotyping. IAEA will also evaluate and advise on the quality of DNA purification done by each participant.

Second RCM

The second RCM will be held in 2012 to review the preliminary results in relation to the identification of selected candidate genes and results of selected SNP markers in sheep and goats, to review available information published elsewhere, to reconsider the status of tools like the 60K chip, SNPs, and the RH map, and to advice on individual breeding programmes; and based on that to devise detailed activities for the second part of the CRP within a time schedule for each research contract.

Second Phase of Programme of Work

Activities related to the 2nd phase (2013-2015) as genotyping strategies, validation of SNP markers and data analysis will be discussed at the 2nd RCM (2013). Also, training on genomic analysis and bioinformatics will be provided during the meeting. SNP genotyping will be outsourced after the 2nd RCM. A workshop of genomic data analysis will be organized after receiving the genotyping results to perform SNP x phenotype association studies. Some of the activities in the last two years might also include validation, gene sequencing, use of a low density SNP panel and other tools that may be available.

Final RCM 2014

The meeting will be held in 2015 to review the results from the CRP, and to make recommendations for future directions, strategies, and activities related to genetics studies for improving animal productivity in developing countries. Final reports will be peer reviewed, edited, and prepared for publication as an Agency TECDOC or for external publication in 2015-2016.


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  • Report of the First RCM, Vienna from 21 to 25 February 2011. [Download pdf]