Technical information - selection

“Know your Genes” workshops a success



by Philip Mann TROPICAL BEEF TECHNOLOGY SERVICES (TBTS)

BRAHMAN NEWS SEPTEMBER 2009 Issue #164

The Tropical Beef Technology Services (TBTS) and Southern Beef Technology Services (SBTS) team recently completed a national workshop series titled “Know Your Gene – An update on DNA technology for the Seedstock producer”.

A total of 20 workshops were run across Australia with each state visited except for the Northern Territory. The workshops were well attended with 374 people benefiting from the information provided during the half day workshops.

There have been rapid advancements in the field of DNA technology for the beef industry in recent times. As such, the “Know Your Genes” workshop was developed to help producers better understand this technology and answer some of the questions surrounding it - how can it be used in my herd, what are the advantages and disadvantages of using it, what questions should I ask before investing in this technology and what direction will it go in the future? While there was sponsorship of the workshops by the Beef CRC, the workshops provided a completely independent assessment of the of the DNA technology that is available as no funding was received from the genomics companies or DNA testing laboratories.

The workshop commenced with a short questionnaire to gauge participants understanding of DNA technology before moving into a theory session where some of the terminology surrounding this technology e.g. DNA (Deoxyribonucleic acid), SNP (Single nucleotide polymorphism), Alleles, Genes and Gene markers, was defined.

The uses of DNA technology for beef cattle were explained in depth to workshop participants. DNA technology currently has many uses in the beef industry and has the potential to have a much greater impact in the future. Some of the current uses of DNA technology include parent verification, identification of carriers of genetic diseases (refer table 1), identification of animals possessing favourable genes for type traits such as coat colour e.g. homozygous black or horn/polled e.g homozygous polled and the identification of animals carrying genes that are superior for a number of production traits (refer table 2). While genetic diseases and type traits are controlled by one or two genes, production traits are controlled by 100’s or 1000’s of genes. As such, DNA tests for genetic diseases and type traits provide a high level of accuracy while the DNA tests for production traits currently only identify a small proportion of the genes responsible for controlling the trait and therefore offer a lower level of accuracy in identifying animals with superior genetics for that trait.

Pfizer animal genetics is the only company currently providing DNA tests for production traits in Australia with their 56 marker panel (a marker is a difference in the DNA sequence at a known location along the bovine genome that is associated with genes responsible for influencing the trait of interest). These production traits include Marbling, Feed Efficiency and Tenderness. A DNA test using the 56 marker panel provides a prediction of an animal’s genetic merit or breeding value for each of these traits and is expressed as a Molecular Value Prediction (MVP). This is also known as a Molecular Breding Value (MBV). Whereas a BREEDPLAN Estimated Breeding Value (EBV) is derived from performance and pedigree records, a MVP or MBV is derived directly from a measure of the animal’s genes. The ability to predict the performance of an animal from its DNA is potentially one of the greatest advantages of this technology over current methods for genetic improvement of production traits. DNA can be collected very early in an animal’s life and allow selection and management decisions to be made at an early age rather than waiting to evaluate an animal’s genetic merit based on performance measurements on itself and relatives much later in life. This is particularly important where these performance measurements are expensive or difficult to measure e.g feed efficiency and tenderness.

TABLE 1: DNA TESTS AVAILABLE FOR GENETIC DISEASES

Genetic Defect Breed(s)
Alpha - Mannosidosis Angus, Red Angus, Murray Grey, Galloway
Beta - Mannosidosis Salers
Cardiomyopathy & woolly haircoat syndrome (CWH) Poll Hereford
Factor VII Deficiency Hereford
Inherited Congenital Myoclonus (ICM) Poll Hereford
Maple Syrup Urine Disease (MSUD) Hereford, Poll Hereford, Shorthorn
Congenital Myasthenic Syndrome (CMS) Brahman
Pompes Disease Brahman, Shorthorn
Protoporphyria Limousin, Blonde d’ Aquitaine
Myophosphorylase Deficiency Charolais
Arthrogryposis Multiplex (AM) Angus
Neuropathic Hydrocephalus (NH) Angus


TABLE 2: DNA TESTS AVAILABLE FOR PRODUCTION TRAITS

Company Tests
University of Queensland, Animal Genetics Lab or Elizabeth Macarthur Agricultural Institute (EMAI) Myostatin* : 7 variants
Pfizer Animal Genetics (MVPs) GeneSTAR Tenderness GeneSTAR Marbling GeneSTAR Feed Efficiency
IGENITY (Merial) (Molecular Breeding Values (MBVs) & 1 - 10 score) Carcase Composition (3), Carcase Quality (3), Female Traits (3), Average Daily Gain (1), Feed Efficiency (1), Docility (1), Myostatin* : 9 variants
METAMORPHIX (MGVs) Tru-Marbling Tru-Tenderness


While DNA technology offers potential for distinct advantages over current methods of genetic improvement for production traits, workshop participants were also made aware of some of the disadvantages. Current DNA tests for production traits account for a very small proportion of the genetic variation (< 10%) of individual traits and offer limited scope for genetic improvement as a stand alone selection tool. DNA markers used for DNA tests may have a different relationship with trait of interest both across and within breeds i.e. a DNA test that is associated with identifying cattle for favourable genes for a particular trait may work in one breed or production system but may not necessarily work in another breed or production system within the same breed . The potential for genetic improvement is also limited by the frequency of the favourable genes in the population you are testing e.g Brahmans as a breed already have a very high frequency of the favourable genes identified for feed efficiency and selecting Brahmans on high feed efficiency values to cross with other Brahmans will have no impact on genetic improvement of this trait. Additionally, DNA tests are presently very expensive for identifying superior genetics for traits that are easily measured by other methods e.g growth identified through weighing cattle.

Participants were also advised of the various organisations that provided independent assessment of the DNA tests to identify if they worked in relevant cattle populations. The National Beef Cattle Evaluation Consortium (http://www.ansci.cornell.edu/nbcec/) provides independent assessment of DNA tests on North American cattle populations while the Beef CRC (http://www.beefcrc.com.au/) through the Animal Genetics and Breeding Unit (AGBU) provide assessment on Australian cattle populations.

It was strongly advised that producers identify if an independent assessment of the DNA test had been conducted on a population of cattle that was relevant to their own breed and production system and to ensure they understood what the results meant before investing in the test. By having this information, a cost/benefit analysis could be performed to determine if the genetic gain that could potentially be achieved outweighed the cost of performing the tests.

The workshop concluded with an insight to the future direction of DNA technology. It is likely that other genomics companies e.g Igenity, will enter the Australian market with the benefit of reduced prices for DNA tests through additional competition.

Many more DNA markers will be identified and included in DNA tests for production traits which in turn should explain more of the genetic variation of specific traits than current tests and provide a higher level of accuracy. It is envisaged that DNA tests will also be available for a wider range of traits.

It was also advised that the best way for information from DNA tests for production traits to be used in the future will be to incorporate it with performance and pedigree data to produce Marker assisted EBVs providing an EBV of higher accuracy at a younger age. This has already been achieved with the release of the marker assisted Trial Shear Force (Tenderness) EBV for Brahmans in 2008. This EBV incorporates results from DNA tests for tenderness, performance measurements of shear force and flight time and pedigree details to determine an animal’s genetic merit for this trait.

In summary, workshop participants where provided with some key questions they needed to ask of DNA tests before deciding to utilize it to achieve genetic improvement

1. How big of an effect (phenotypic & genetic) does the MBV have on the trait of interest (for my breed)?
2. Does the effect provide a cost-benefit?
3. What level of accuracy will the MBV provide (relative to an EBV)?
4. Has the effect of the MBV been independently assessed and published?
5. Has the MBV information been incorporated into BREEDPLAN EBVs?

Before departing, participants were asked to complete the same questionnaire they answered before the start of the workshop. Once analysed, it was revealed that the overall understanding of DNA technology by workshop participants had improved by 80% from the start of the workshop and this illustrated a successful learning outcome for the workshop series.

For information regarding DNA technology, please contact Philip Mann at TBTS (philip@tbts.une.edu.au, ph 4927 6066.