DCS - Bulletin article - Spring 2014 Andrew Sheppy (1)
Dec 19, 2014 2:16:33 GMT
lonecowhand likes this
Post by jamshundred on Dec 19, 2014 2:16:33 GMT
The following is an article which appeared in the spring issue of the Dexter Cattle Society publication. There is a follow up article in the current issue which is now hitting the mailboxes and there is also permission to print it and it will be added shortly. Reprinted by permission of the author; Andrew Sheppy
The Marvels of modern Genetics for cattle breeders
Recent advances in genetics make possible many more informed choices by cattle breeders. When I started in the conservation breeding of livestock, genetics was more or less limited to Mendelian character driven selection. After all, the actual structure of the DNA (Deoxyribonucleic acid) which makes up the genes had only been discovered in 1953 and that knowledge had barely started to be used in teaching, let alone practical breeding situations.
It had always been my assumption that this type of genetics would be all that I needed to know to allow me to work effectively in breeding and conserving livestock. By the early 1990s it had become clear to me that genetics was moving on very fast and developing new techniques and tools which would have a profound influence on the world of animal breeding. This prompted me to bite the bullet and take a course in Molecular Genetics at Bristol University, a decision which soon proved its worth in all manner of circumstances in later work. Incidentally, another reason I am glad I did that is that unexpectedly, I actually found it fascinating, totally absorbing in fact.
Among the techniques which we studied was the one which we now routinely use to verify the parentage of animals and their relationships. The Dexter Cattle Society has already made good use of this DNA technology to introduce parent verification on all bulls put forward for registration. Several times anomalies have been detected and usually resolved by a bit of pat detective work. A breed advisor for Holstein-Friesians told a meeting some years ago that there were intentional or unintentional errors in 12-13% of the recorded parentages within their animals. There is no reason to think that the situation in our breed is any different. The new scheme of testing Dexter females at regular intervals may well produce some valuable insights into the relationships within the breed and Council is to be commended for this initiative.
We now have the tools to test for many genetic defects, in our breed, notably Chondrodysplasia, many of which could previously only be detected by test matings and progeny testing. These methods are time consuming and expensive but their biggest drawback is that they cannot be guaranteed to detect the presence of the defective gene concerned. Once such a gene is identified, it can always be detected in a simple and immediate laboratory test. The DCS has made wise use of this technology in testing for chondrodysplasia in bulls before they are used, especially for A.I. bulls.
These techniques are based on the differences which can be detected in fragments of DNA, quite large chunks in molecular terms. In general, we look at 20-30 of these fragments which is usually quite enough to do what we need. In recent years a new technology has been developed, commonly pronounced ‘snip’, this is SNP (Single Nucleotide Polymorphism) which looks at differences at the level of the individual units which make up the DNA.
The speed of development of some of these techniques is breathtaking. Two or three years ago, Prof. John Woolliams was talking in a Farm Animal Genetic Resources Committee about a computer chip which could read 50,000 SNP. Recently we were talking about this and he told me that they no longer use it, as they now had a 700,000 ‘snip chip’.
It has long been known that the modern Dexter has a complicated mixture of breeds in its ancestry. Alderson concluded this in his paper to the 1st World Congress on Dexter Cattle (Alderson 1998). Studies of the blood and genetic polymorphisms have shown that the modern Dexter breed is a multiple composite of influences from many other breeds (Royle 1983; Buys & Chiperzak 1992; Blott 1997). These studies were on the generality of the breed of the day, no attempt was made to separate animals with known recent introgression from any which might be free of such influences.
Alderson also commented that, ‘The appearance in a breed, which has been selected for whole colour for many generations, of calves with significant white markings suggests that illicit introgression may have occurred’ (Alderson 1998). The standard text on pedigree breed management (Sponenberg & Bixby 2007) gives three specific tests for the authenticity of animals within a specific breed. ‘The three most useful investigations into animals presented as members of a breed include phenotype, history and finally genetic analysis, Any of the three, if used alone, can lead to a wrong conclusion. In contrast, when all three are used in concert, it is rare to misclassify animals.’ (Sponenberg & Bixby 2007).
The phenotype test is an assessment of visible and measurable characteristics of the animal itself, but often more significantly, their descendents. This has to be on the basis of ‘if it looks right, it could be right, but if it looks wrong it is wrong’
The history test takes into account any information on an animal from sources such as written records and interviews with breeders. In the case of an animal which is questionable because of the phenotypes, is their any evidence to suggest a possible reason for the atypical appearance of the animal or its offspring. However, ‘Historical investigation can be quite difficult because many of the people involved have a vested interest in the process’ (Sponenberg and Bixby 2007)
The genetic test has really only become available to us in recent years with the extent and accuracy of such tests continuing to increase all the time. Based on analysis of DNA samples these tests have proved a most effective tool with particular application to parent verification and relationship questions. In recent research into Parndon Bullfinch, widely used by A.I. in the U.S.A. and son of Parndon Charley Pudding, alleles (gene versions) were found at three separate points in his DNA analysis which have not been found in samples from any other Dexter either here or in the USA (apart from his descendents or near relatives). Such indisputable genetic evidence has proved the introgression of other breeds’ genetics in the case of Parndon Charley Pudding in the same way that it has in other highly significant bulls such as Shadwell Robert and Grinstead Plover.
Of these three tests, it has always been possible to make decisions on the basis of observable characteristics of animals and their progeny. The second consideration can only be used if there is historic evidence available, although this can often come through a bit of detective work. It is the arrival of these definitive modern genetic tests which has finally allowed us to answer so many of the problematic questions of authenticity and ancestry, which is a truly marvellous tool for us all to have.
Within the context of the rapid increase in the demand for traceability and authenticity, particularly in connection with verifiable branding of meat and animals, the use of DNA testing will continue to escalate. There are significant moves towards this in official circles within DEFRA and Trading Standards, which cattle breeders will need to meet. Ongoing issues relating to GM & cloning will continue to challenge many of us working in farm animal genetics, but it will only be through the advanced DNA technologies of modern times that they will be addressed. There are surely more marvels to come from genetics which will have importance for all of us breeding cattle, or any other sort of livestock.
References
Alderson, L., (1998), ‘Dexter Cattle: Origin and Relationships’, in ‘The World of Dexter Cattle’, Proceedings of the 1st World Congress on Dexter Cattle, Dexter Cattle Society , Dulverton, UK.
Blott, S.C. et al, (1997), ‘Genetic relationships between European Cattle Breeds’, Animal Genetics
Buys, C., and Chiperzak, J., (1992) ‘A comparative study of blood groups in the Kerry and Dexter Cattle breeds’, in Alderson and Bodo (eds.), Genetic Conservation of Domestic Livestock, (Vol 2) CABI, Wallingford, UK
Royle, N.J., (1983), ‘Polymorphisms of Rare Breeds of Cattle, University of Reading
Sponenberg, D.P. & Bixby, D.E. (2007), ‘Managing Breeds for a Secure Future’, The American Livestock Breeds Conservancy, Pittsboro, North Carolina, U.S.A.
Andrew Sheppy
The Marvels of modern Genetics for cattle breeders
Recent advances in genetics make possible many more informed choices by cattle breeders. When I started in the conservation breeding of livestock, genetics was more or less limited to Mendelian character driven selection. After all, the actual structure of the DNA (Deoxyribonucleic acid) which makes up the genes had only been discovered in 1953 and that knowledge had barely started to be used in teaching, let alone practical breeding situations.
It had always been my assumption that this type of genetics would be all that I needed to know to allow me to work effectively in breeding and conserving livestock. By the early 1990s it had become clear to me that genetics was moving on very fast and developing new techniques and tools which would have a profound influence on the world of animal breeding. This prompted me to bite the bullet and take a course in Molecular Genetics at Bristol University, a decision which soon proved its worth in all manner of circumstances in later work. Incidentally, another reason I am glad I did that is that unexpectedly, I actually found it fascinating, totally absorbing in fact.
Among the techniques which we studied was the one which we now routinely use to verify the parentage of animals and their relationships. The Dexter Cattle Society has already made good use of this DNA technology to introduce parent verification on all bulls put forward for registration. Several times anomalies have been detected and usually resolved by a bit of pat detective work. A breed advisor for Holstein-Friesians told a meeting some years ago that there were intentional or unintentional errors in 12-13% of the recorded parentages within their animals. There is no reason to think that the situation in our breed is any different. The new scheme of testing Dexter females at regular intervals may well produce some valuable insights into the relationships within the breed and Council is to be commended for this initiative.
We now have the tools to test for many genetic defects, in our breed, notably Chondrodysplasia, many of which could previously only be detected by test matings and progeny testing. These methods are time consuming and expensive but their biggest drawback is that they cannot be guaranteed to detect the presence of the defective gene concerned. Once such a gene is identified, it can always be detected in a simple and immediate laboratory test. The DCS has made wise use of this technology in testing for chondrodysplasia in bulls before they are used, especially for A.I. bulls.
These techniques are based on the differences which can be detected in fragments of DNA, quite large chunks in molecular terms. In general, we look at 20-30 of these fragments which is usually quite enough to do what we need. In recent years a new technology has been developed, commonly pronounced ‘snip’, this is SNP (Single Nucleotide Polymorphism) which looks at differences at the level of the individual units which make up the DNA.
The speed of development of some of these techniques is breathtaking. Two or three years ago, Prof. John Woolliams was talking in a Farm Animal Genetic Resources Committee about a computer chip which could read 50,000 SNP. Recently we were talking about this and he told me that they no longer use it, as they now had a 700,000 ‘snip chip’.
It has long been known that the modern Dexter has a complicated mixture of breeds in its ancestry. Alderson concluded this in his paper to the 1st World Congress on Dexter Cattle (Alderson 1998). Studies of the blood and genetic polymorphisms have shown that the modern Dexter breed is a multiple composite of influences from many other breeds (Royle 1983; Buys & Chiperzak 1992; Blott 1997). These studies were on the generality of the breed of the day, no attempt was made to separate animals with known recent introgression from any which might be free of such influences.
Alderson also commented that, ‘The appearance in a breed, which has been selected for whole colour for many generations, of calves with significant white markings suggests that illicit introgression may have occurred’ (Alderson 1998). The standard text on pedigree breed management (Sponenberg & Bixby 2007) gives three specific tests for the authenticity of animals within a specific breed. ‘The three most useful investigations into animals presented as members of a breed include phenotype, history and finally genetic analysis, Any of the three, if used alone, can lead to a wrong conclusion. In contrast, when all three are used in concert, it is rare to misclassify animals.’ (Sponenberg & Bixby 2007).
The phenotype test is an assessment of visible and measurable characteristics of the animal itself, but often more significantly, their descendents. This has to be on the basis of ‘if it looks right, it could be right, but if it looks wrong it is wrong’
The history test takes into account any information on an animal from sources such as written records and interviews with breeders. In the case of an animal which is questionable because of the phenotypes, is their any evidence to suggest a possible reason for the atypical appearance of the animal or its offspring. However, ‘Historical investigation can be quite difficult because many of the people involved have a vested interest in the process’ (Sponenberg and Bixby 2007)
The genetic test has really only become available to us in recent years with the extent and accuracy of such tests continuing to increase all the time. Based on analysis of DNA samples these tests have proved a most effective tool with particular application to parent verification and relationship questions. In recent research into Parndon Bullfinch, widely used by A.I. in the U.S.A. and son of Parndon Charley Pudding, alleles (gene versions) were found at three separate points in his DNA analysis which have not been found in samples from any other Dexter either here or in the USA (apart from his descendents or near relatives). Such indisputable genetic evidence has proved the introgression of other breeds’ genetics in the case of Parndon Charley Pudding in the same way that it has in other highly significant bulls such as Shadwell Robert and Grinstead Plover.
Of these three tests, it has always been possible to make decisions on the basis of observable characteristics of animals and their progeny. The second consideration can only be used if there is historic evidence available, although this can often come through a bit of detective work. It is the arrival of these definitive modern genetic tests which has finally allowed us to answer so many of the problematic questions of authenticity and ancestry, which is a truly marvellous tool for us all to have.
Within the context of the rapid increase in the demand for traceability and authenticity, particularly in connection with verifiable branding of meat and animals, the use of DNA testing will continue to escalate. There are significant moves towards this in official circles within DEFRA and Trading Standards, which cattle breeders will need to meet. Ongoing issues relating to GM & cloning will continue to challenge many of us working in farm animal genetics, but it will only be through the advanced DNA technologies of modern times that they will be addressed. There are surely more marvels to come from genetics which will have importance for all of us breeding cattle, or any other sort of livestock.
References
Alderson, L., (1998), ‘Dexter Cattle: Origin and Relationships’, in ‘The World of Dexter Cattle’, Proceedings of the 1st World Congress on Dexter Cattle, Dexter Cattle Society , Dulverton, UK.
Blott, S.C. et al, (1997), ‘Genetic relationships between European Cattle Breeds’, Animal Genetics
Buys, C., and Chiperzak, J., (1992) ‘A comparative study of blood groups in the Kerry and Dexter Cattle breeds’, in Alderson and Bodo (eds.), Genetic Conservation of Domestic Livestock, (Vol 2) CABI, Wallingford, UK
Royle, N.J., (1983), ‘Polymorphisms of Rare Breeds of Cattle, University of Reading
Sponenberg, D.P. & Bixby, D.E. (2007), ‘Managing Breeds for a Secure Future’, The American Livestock Breeds Conservancy, Pittsboro, North Carolina, U.S.A.
Andrew Sheppy
