Application of Nuclear and Genomic Tools to Enable for the Selection of Animals with Enhanced Productivity Traits

Summary

The World will be facing the challenge of manifolds increase in the production of food from animal origin to address the high demand that is expected to arise from population growth, income increases and urbanization. Breeding for robust animals with production systems optimised for exponential increase in productivity while retaining their adaptability to harsh environment and tolerance to tropical diseases could remain only option for the intensification of livestock productions with as minimum as possible environmental impacts. Crossbreeding zebu cattle with temperate taurine cattle has been tried in many countries for a rapid increase in the productivity but results were not always satisfactory. Lack of animal identification and not having a system in place for recording and analysing performance data to make appropriate breeding decision were identified to be main constraints that limited the enhancement of animal productivity by breeding, especially in developing countries.

This project at aims the application of nuclear and nuclear-derived molecular techniques to addresses two major issues prevailing in developing countries and are directly associated with food security and livelihood improvement. Firstly, it will generate genomic data of performance recorded animals, which will enable breeders and farmers relate production traits with parentage and genetic admixture of animals leading to identification and selection of superior (both genotypically and phenotypically) sires for breeding by using artificial insemination. Secondly, 60CO will be applied to develop a radiation hybrid panel of camel and use that for whole genome sequencing and identification of breeding markers that nobody has done yet for camel.

As outputs the project is expected to leave bind an animal identification system in place and 1000 phenotype recorded animals per breed/population from each country, develop a gene bank of phenotype recorded animals in participating countries (potentially available for future genotyping), validate genetic tool(s) for testing parentage, relationship and admixture level, develop whole genome radiation hybrid panels for camel, develop a set of performance data for different genetic groups in different production systems and deliver standard operating procedures (SOPs), protocols and guidelines for continued animal genetic research and application of results in animal breeding.

The project will be running five years and will involve 10 Research Contract (RC) holders from developing countries, three Technical Contract (TC) holders and four Research Agreement (RA) holders from laboratories engaged in high level animal genetics and breeding research and field application.

Background and Situation Analysis

A 70% increase in the consumption of animal-source protein as food is expected by 2050 due to population growth, income increases and urbanization. Consequently, the world will need to increase livestock production manifolds. This challenge has been compounded in tropical countries by poor productivity of indigenous animals and less tolerance of high producing exotic and crossbred animals to tropical diseases and hot and humid climates. Producers, breeders and scientists have continued their efforts to find a trade-off between the productivity and adaptability of animals for vertical increase of farm produces while addressing issues related to impacts of animal farming on the environment.

Current limitations in genetic improvement systems in developing countries are poor animal identification, lack of pedigree and performance data collection for sire and bull mother selection and unfocussed use of crossbreeding. There is therefore a strong need for improving the genetic evaluation system and the dissemination of superior genetics through artificial insemination (AI). A comprehensive storage and management of genomic and performance data would enable AI centres to establish a data flow system and increase interactions with farmers and thus compare and improve performance of sires they commercialise in different production systems.

Today science offers several opportunities whose concerted applications would bring positive changes in conventional animal breeding, especially in developing countries. For examples, (1) application of AI coupled with radioimmunoassay of hormones to ensure successful mating and thus to increase manifolds the dissemination of desired genetics, (2) nuclear and nuclear-derived molecular techniques for genetic characterization of animals and identification of marker(s) that drives favourable traits from parents to offspring, (3) radio-frequency identification (RFID) system for the identification of animals with high accuracy and reduced risk of duplications and facilitating data flow among laboratories, farms and breeders and (4) database applications and software to manage, analyse and make report from large datasets involving genomics, phenotypes and their possible interactions. Joint FAO/IAEA Centre in collaboration with the Technical Cooperation Department has been supporting implementation of AI programmes, animal identifications and genetic characterisation of animals for maximum production and adaptability, especially in developing Member States (MS). But these activities have been performed mostly on demand. Validation of genomic tools through adaptive research has been felt strongly during implementation of the IAEA TC projects.

New technologies permit the characterization of the genome with markers at a decreasing cost. In developed countries the use of genomic tools is rapidly increasing and resulting in efficient genetic improvement programmes. Now it is time to coalesce tested tools and methods for the validation of technologies through adaptive research to the needs of developing countries for a rapid, vertical growth in animal productivity. Low cost genomic tools for parentage testing are available and can be adapted for use in developing countries, and are required for genetic improvement programmes. It is possible to develop low cost genomic tools for measuring breed composition of crossbred animals, verify purity of purebred animals and match data with appropriate genetics to select superior stocks for breeding. Accurate parentage and breed composition can be combined with performance data to enhance the selection progress.

Along with cattle and buffalo, camel is an important animal for meat and milk in many countries and camel milk has been under increasing market demand. Understanding the camel genome and its genetic composition will drive its further development for increased productivity. A radiation hybrid panel will enable whole genome mapping and catalyse the development of DNA marker based tools to implement effective breeding programmes for genetic improvement in camels.

Nuclear Component

Nuclear technique involving Cobalt 60 will be used to construct radiation hybrid panel for camels, which will be eventually utilised for whole genome mapping of camel. Further, iodine 125 will be used in radioimmunoassay of hormones in milk or blood of cattle and buffaloes to monitor the efficiency of AI services whose improvement remains the major focus of the CRP.

CRP Overall Objective

To enable MS, especially developing countries to use genomic tools for enhancing the efficiency and effectiveness of genetic improvement of livestock.

Specific Objectives

  • To strengthen animal identification, pedigree and performance recording system in large ruminants under AI programmes and camels.
  • To characterize sires under AI programmes for whole genome variations, as a basis for future selection.
  • To implement parentage testing, performance recording and admixture analysis of females bred by AI sires.
  • To develop and characterize radiation hybrid panels for mapping camel genome.
  • Strengthen research capacity of animal scientists in developing countries.
  • Networking among animal scientists from developed and developing countries.

Expected Research Outcomes

  • Genomic tools are applied to improve livestock productivity.
  • Strengthened genetic improvement in AI systems.
  • Farmers improve productivity through better access to information about animals’ performance.
  • Standardized animal identification and data recording procedures are in place for implementation of genetic improvement programmes.
  • Improved genome sequence assembly to enhance genetic improvement of camels.

Expected Research Outputs

  • Animal identification system in place and 1000 phenotype recorded animals per breed from each country made available.
  • Gene bank of phenotype recorded animals established in participating countries (potentially available for future genotyping).
  • Genetic tool(s) for testing parentage, relationship and admixture level are made available.
  • Whole genome Radiation hybrid panels for camel are available.
  • Performance data are available for different genetic groups in different production systems.
  • SOPs, protocols and scientific papers are published on application of genomic tools for animal improvement.
  • Capacities are in place in MS to perform genomic data analyses.