Dr Ben Greyling, ARC-Animal Production Institute
Making sense of science
Albert Einstein once said, “A little knowledge is a dangerous thing, so is a lot”. One of our biggest challenges currently is how to make sense of all the information available and turn it into valuable knowledge.
Genomics, a DNA-based technology, is in all probability one of the fastest evolving technologies today, yielding an ever-increasing amount of information that relates to the genetic make-up of an individual. Simply put, genomics is the study of the association between the DNA profile of an individual and its phenotypic characteristics. It can be compared to your identity number: each unique number is associated or correlates with particular traits, and the more similar the numbers are between individuals (e.g. for relatives), the more similar their characteristics and vice versa. Genomics initially captured our imagination when it was applied to humans more than a decade ago. Some of the fascinating applications include how humans, as a result of their genetic make-up, respond to pharmaceutical drugs and their susceptibility to heritable diseases. Personalised medicine is thus understandably a hot research topic for pharmaceutical companies in their quest to design more cost-efficient and effective drugs. It wasn’t long before genomics appealed to animal scientists, and subsequent discoveries and developments revolutionised our understanding of how a mere DNA sequence can dictate many aspects of an animal’s performance and characteristics.
Genomics for farm animals
In less than six years since the entire bovine genome (complete DNA sequence) was analysed, genomics was applied to study the relationship between the genetic make-up (DNA sequence or SNP sequence) of cattle and their performance. The ultimate aim was to use the technology for the improvement of animal production by selecting superior performing animals based on their predicted genetic merit (expressed as a so-called genomic breeding value). In short, it means that animals with different DNA profiles, analogous to humans, will react differently to the same environmental conditions. An example for instance is that animals will perform differently under the same feeding regime. Other examples where DNA profiles are associated with phenotypic traits include meat tenderness, meat odour, fat content of meat and milk production, to name but a few. Genomics has also added a new dimension to conventional performance testing: We can now dramatically increase the accuracy with which we predict the genetic merit of an animal (especially young animals without progeny), depending on the type of trait and the heritability of the trait. Previously, animals had to be progeny tested to obtain accurate breeding values. By focusing on the traits of economic importance, for which generally many phenotypic records exist, it has become possible to select for top-performing animals. Genomics also has the potential that the more complex and difficult traits to measure, e.g. fertility, longevity and disease resistance, will be included in a breeding value.
Genomics for buffalo
Recently, a panel of DNA markers (called SNPs, pronounced “snips”) was developed for the African buffalo. The panel was developed by determining the DNA sequence of millions of small pieces of DNA from different individuals from all the different subspecies of the African buffalo. The interesting part is that the genome (the entire DNA sequence) of cattle was used as a reference or anchor to identify the specific locations on the DNA where individual buffalo differ from each other. This was possible since cattle and buffalo still share a lot of similarity in their DNA because the two species diverged from a common ancestor about 12 million years ago.
The SNP-panel consists of more than three thousand SNPs, meaning there are at least three thousand positions where the buffalo can potentially be distinguished from one another. This SNP panel was exclusively developed for population genetic studies, and will be a powerful tool to analyse genetic parameters, such as relatedness between individuals, how genes are exchanged between populations and the level to which populations are genetically differentiated. The panel will also be very useful for studying movement of animals between populations and subsequent disease transmission. With this high resolution tool, the effect of inbreeding (potentially affecting amongst others fertility, health status and disease sensitivity), effective population size (number of breeding individuals) and genetic drift (random allele [one member of a pair or series of genes that occupy a specific position on a specific chromosome] frequency fluctuations) in small populations, typically found on ranches, can be studied. Research outcomes on small populations can of course also serve as model systems for larger conservancy-based populations.
Considering the management practices on many buffalo ranches, genomics promise to make a significant contribution in the future towards genetic testing and evaluation with the aim of identifying genetically superior animals. This may be of particular relevance since selection of breeding animals is currently often based on market-desired traits of economic importance, e.g. horn length. Pedigrees of most ranched buffalo are also documented, whilst the recording of performance traits (e.g. body measurements, scrotal circumference, intercalving periods and horn size) is seemingly gaining momentum, setting the stage for genomic evaluation. The recently developed SNP-chip will most probably be upgraded and expanded in the near future in order to facilitate genomic studies on the African buffalo.
Requirements when investing in genomics
One of the foremost requirements of a genomics study is a well-defined reference population, individuals with detailed performance records and accurate pedigree links. Experience from research done on cattle has shown that an adequate reference population typically consists of at least a thousand animals. It is also desirable that the reference population should include animals with performance-tested relatives. Once a reference population has been established, all the individuals need to be DNA profiled and the profiles have to be linked to their performance records in order to establish the association between genotype and phenotype.
The next step is validation, whereby the associations are verified in a test population. Once verification has been confirmed, routine genomic analyses of performance-tested animals can proceed. In fact, genomic breeding values can even be predicted for individuals without any offspring or performance records.
Although these actions have been rigorously investigated in cattle, research is still on-going to refine the process and gain insights into factors that affect the final breeding value. Although research on buffalo genomics is still in its infancy, considering the priorities of industry and the pace at which the technology is progressing, it is envisaged that genomic selection of buffalo will become a reality in the foreseeable future.
What does the future hold?
The adoption of genomics by the buffalo-ranching industry will in all probability initially be slow, being motivated, amongst others, by cost factors and the needs of industry. The time elapsed between implementation and visible return on investment will also undoubtedly affect the rate of adoption. It is also vital that industry is well informed and motivated towards applying the technology. Studies on cattle have shown that despite the initial lag between research and impact, producers did eventually enhance their position among their clients and consumers. Taking all into consideration, it is believed that investments made in buffalo genomics will in the long term yield valuable results.
Article © Game & Hunt . Published Vol 19/01 January 2013 pp 57,58