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Breeding: Exciting future predicted but there are pitfalls

By Dr Danie Visser (Part 2)
In this second of two articles, Dr Danie Visser, managing director of TOPIGS SA, takes a look at possible scenarios for pig breeding in future. Part 1 of the article appeared in the August/September issue of Porcus.In my opinion genomic selection will in future be the focus of most genetic improvement scenarios. Genomic selection is a complicated concept that basically means that the estimated effects of all genes or chromosomal positions are simultaneously estimated. This is called MEBV or Marker Estimated Breeding Values.
Simulation studies are being conducted to determine the accuracy of genomic selection, using three different statistical methods. They are LS, BLUP and Bayes.
The first research results indicate that genomic selection can achieve an accuracy of selection of marker-genotypes embryo’s that is comparable to that of a progeny test.
Studies also concluded that genetic gains from genomic selection methods in dairy bull evaluations are indeed promising. Van Raden et al concluded in 2009 that the reliability for predicted bulls was 50% for genomic predictions as only 27% for traditional methods. This is a 23% increase across traits – thus a major improvement.
Caution
Although these exciting improvements to selection and breeding promises a new era for pig breeding, one must always be cautious.
Experts believe that we have created more data than we now how to handle effectively. The reality is that technology is outpacing our abilities to use it.
Research in the future (some call it the “new renaissance animal breeding period”) will be expensive to conduct. It will require large and dedicated project teams and it will be laboratory intensive.
Issues such as intellectual property rights will be in the spotlight. What will producers’ financial contribution have to be in order to access the fruits of mind of many intensive hours of research? Will they have to pay for each pig on their farm using this new technology?
We will probably also see a reduction or even a termination of animal breeding programmes at state, semi-state and university levels.
The aging, classical or quantative researchers, living their dream, doing what they love for the sake of research and not for money, are likely to be something of the past.
But one the other hand, will the true animal breeders of the future be able to apply the so much needed systems approach to their way of thinking?
Animal breeding can’t be practiced in isolation. To stay competitive one must continuously borrow from other sciences, other disciplines, other (new) methods, other industries and other minds.
Closer to the consumer, closer to the plate
An issue that pork industries all over the world will have to face at some stage, is the issue of boar taint. The consumer is undoubtedly king and boar taint is a reality.
South Africa is changing with the rest of the world. Urbanisation happens to all countries, especially those belonging to the third world.
Urbanisation means a better life for all and a higher per capita income.
More money in the consumers’ pocket will mean a shift from buying cereals to buying animal protein. Many surveys however indicate that consumers do experience boar taint when buying pork. A study conducted in South Africa in 1997 indicated that almost 50% of the consumers participating in the study had a strange experience with pork (boar taint). To be part of the growing meat protein market, pork producers will have to address this issue.
Solutions to combat and eliminate boar taint
The following may be solutions to make boar taint something of the past:

  • Castration: Yes, but up till now not cost effective for the producer.
  • Improvac vaccination
  • Sex splitting is an option, but very expensive. More research is required.
  • Genotype selection
  • Feeding and housing strategies can play an important role
  • Marketing strategies
  • On-line detection in processing plants
  • Selection against boar taint
  • Genomic selections
  • Selection against boar taint is a viable option, but:
  • Correlation with female fertility will require careful selection in dam lines.
  • Trait has a non-linear distribution. Genetic markers are therefore limited.
  • Indirect genetic effects are to be expected for age at puberty and back fat
  • Validation of boar taint for animals at risk (especially AI boars) are important.

Some scientists believe the problem can be solved genetically within the next five to six years.
Conclusion
Miniaturisation, molecular genetics, robotics and nanotechnology will set the scene for the creation of new gendres of life. This will not only be applicable to animal breeding but will also apply to engineering, drugs and synthetic materials. The rapid growth in high throughput genotyping platforms has two major advantages:

  • It becomes cost effective to genotype large numbers of markers (SNP Markers) in a single run.
  • It simultaneously provide diagnostics of multiple traits of economic interest, parentage ID, individual ID and traceability, and genetic effects of importance. In short, everything in one genetic basket.

The cost and time of genomic analysis will be reduced in future and associated technologies will also improve.
New genomic and improved AI technologies will create a new world of genome enabled genetic improvement and precision animal management.
The efficiency and accuracy of the traditional pig selection schemes and genetic evaluations will improve sustainability by the addition of molecular data into pig breeding programmes.
Selecting an animal, based on the genes it carries, is likely to become the norm in animal breeding. Gene catalogue auctions could also be possible.
To conclude: Breeding objectives of the future will have to take the following into account: Biosecurity and health protocols, product safety, a welfare and environmental code, a trustworthy and practical traceability system, quality assurance, product quality and worker rights.

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