Post by midhilldexters on Dec 24, 2014 8:23:14 GMT -5
This is an article by Andrew Sheppy that appears in the latest copy of the DCS Bulletin (England)
Carol K
Introgression in Historic Dexter Bulls
In the April Bulletin some of the recent advances in genetic techniques and their use in the Dexter breed were described. It is now time to look at one of the most significant areas of research where these techniques have been applied to our breed, namely the question of introgression of other breeds’ genetics into the modern Dexter. It is important to know what, if any, other breeds are in the background of animals we choose to use in our breeding programmes. Without this knowledge, it is impossible to make the best informed decisions about potential matings.
This article records the current extent of knowledge in respect of introgression in the Dexter breed and, in particular, the results of the standard tests for purity in three historic bulls in the Herdbook which have had significant influence on the modern breed.
Obviously we already know the situation in respect of animals derived from the Appendix and Experimental Registers, both of which are now closed so that the introgression they contain can easily be calculated in their offspring and will decline in influence as time progresses. In the case of the Experimental Register, there was a deliberate introduction of genes from other breeds in an attempt to eradicate the problem of the bulldog calf defect. Almost all the animals which have come down through the Experimental Register have done so via the AI bull, Atlantic Finbar Exp10/B, where it is clearly reported that 25% of his pedigree derives from Aberdeen Angus and Jersey. It is a simple calculation to determine the likely extent of introgression in animals descended from the Experimental Register.
In animals of Appendix Register descent it is generally equally easy to see how much influence of other breeds remains present in current animals. A good example is the important bull Templeton Michalmas Squeak 2043, which descends from an Appendix cow line where we know that his pedigree shows a Jersey cow in the sixth generation. That gives a purity of 98.44% on pedigree analysis which is high enough for there to be a reasonable chance that Squeak might in fact be pure.
If we apply the standard three (Sponenberg & Bixby 2007) tests of 1: Phenotype (observable and measurable characteristics), 2: History and 3: Genetic analysis we would find that Squeak could indeed be pure, or at least the 98.44% of his pedigree analysis. Both Squeak and his offspring look right, so pass test 1, and the historic records show the only introgression is beyond the five generation standard pedigree.
Applying the three Sponenberg & Bixby tests to animals which have not come from either the Appendix or Experimental Registers can give some very revealing results, none less so than three very important historic Dexter bulls. It is of course the recently available genetic tests which have only now given us the confirming proof of the ancestry of these animals.
The first of the bulls to have repeatedly come into question was Parndon Charley Pudding 1928. In his case, it was the appearance of calves with white marks in various places when Charley Pudding was in the pedigree of both sire and dam, or when he was mated to breeds with the recessive white spotting gene. So, on the first question of the three standard tests, ‘is there visible reason to doubt purity’, the answer is yes. In respect of historic evidence, it was subsequently admitted that Parndon Charley Pudding was in fact out of a Guernsey cow by a Dexter bull. Is there historic evidence of impurity, yes. This was as much as we had been able to determine until very recently when seeking to parent verify a bull in the U.S.A.. Parndon Bullfinch, registered as a son of Parndon Charley Pudding was widely used through A.I. across the U.S.A. and the hope was that he was in fact by Sylvan Ebony, the other bull in use in the Parndon Herd at the time. A DNA profile is availabe for Bullfinch, taken from a straw of semen. Although there is no known sample of Sylvan Ebony, a reasonable profile could be constructed from examination of the profiles of two of his sons, Vycanny Glencally Reiver and Sarum Bullrush. From this it was seen that there were seven separate loci which showed that Ebony could not have been the sire of Bullfinch, so he was indeed by Parndon Charley Pudding as registered. In the course of this process it was noticed that three alleles (TGLA227/89, ETH10/214 & HEL5/163) out of the 22 loci tested were not present in any pure Dexter sample, either here or in the U.S.A.. It is clear that these must have come from Bullfinch’s sire, Charley Pudding, which would be entirely consistent with him being the offspring of another breed, i.e. Guernsey. Is there genetic evidence of impurity, yes, which gives the same outcome to all three standard tests and confirms Parndon Charley Pudding as not being a pure Dexter.
The second bull where concerns were raised about his purity is Shadwell Robert 1978. Here again the first questions were raised by his inbred offspring, in this case the huge variance in his red descendents which are of two totally different types. This situation could not happen if the red variant came from a pure Dexter, where only one is known to exist. When first raised in a paper at the 1st World Congress on Dexter Cattle in 1998 [Sheppy 1998], there was no historic or genetic evidence to help us explain this. Subsequently it came to light that Shadwell Robert’s grand dam was not a Dexter but a small red cow of unknown breeding. This information was provided by the late Valerie Roberts, who was the niece of the breeder of the cow who was Shadwell Robert’s dam. So question one, physical evidence of impurity, yes and question two, historic evidence of sources of introgression, yes.
Here, once again, is where modern genetic techniques give the final proof. A comparison of the DNA profile of Shadwell Robert with all the purebred Dexter samples from the UK and a selection from the U.S.A. showed that he had four separate alleles (HEL9/169, INRA037/144. HEL5/163 & BM1818/267) which were not found in any of those samples. Such a result entirely supports the historic evidence that Shadwell Robert is only three quarters Dexter, so is there genetic evidence, yes.
The third case is slightly different in that the evidence of introgression was from phenotypic and genetic evidence before there was any known historical knowledge of a possible route by which such introgression happened. In the case of Grinstead Plover 1696, his closely inbred descendents in the Woodmagic Herd showed a very atypical conformation until the expert breeding of the late Beryl Rutherford selectively bred a more mainstream type from them. In addition, in that herd the novel dun gene made its appearance, giving rise to animals identical in appearance with the extinct Suffolk Dun, a very curious coincidence indeed. In the genetic research into the breed at Cardiff University, Tim Bray demonstrated that the closely bred Woodmagic animals formed a clearly different genetic group when considered with the other Dexter samples (Bray et al, 2009).
It was not until an unconnected research caused reference to be made to the 1957 Dexter Herdbook (DCS 1957) that the evidence of the possibility of introgression in Grinstead Plover’s pedigree came to light. In that year, several of the Grinstead Dexter cows were shown as having calved to a Red Poll bull, including Plover’s mother Grinstead Peachblossom VIII 5830. It was common practice at Grinstead to use a crossing bull on high yielding shortleg Dexter cows to avoid any chance of a bulldog calf disrupting the cow’s milk records and Peachblossom VIII came into that category. As the Red Poll was derived from a cross of the Norfolk Red with the Suffolk Dun, a route for the possible introgression and the ancestry of the dun colour immediately presents itself.
Thus all three questions (1: Is there phenotypic evidence of introgression?, 2: Is there historic evidence to explain introgression? and 3 : Is there genetic evidence of the presence of introgression?) are answered ‘yes’ in respect of all three of the bulls considered (Parndon Charley Pudding, Shadwell Robert and Grinstead Plover). As a result, when calculating purity by pedigree, Shadwell Robert is treated as being 75% Dexter with both Parndon Charley Pudding and Grinstead Plover treated as only 50% Dexter.
As if to demonstrate the speed of advance in genetic techniques, the article in the April Bulletin is already out of date, with a revolutionary new process about to be published in livestock science journals. This is likely to offer a technique specifically to address issues of introgression in populations and to remove it. We live in exciting times in respect of genetic techniques.
Andrew Sheppy
References
Bray, T.C. et al, 2009; ‘The population genetic effects of ancestry and admixture in a subdivided cattle breed’, Animal Genetics, International Society of Animal Genetics.
Dexter Cattle Society, 1957; The Dexter Herd Book, Vol LVII, The Dexter Cattle Society, Tadworth, Surrey.
Sponenberg, D.P. & Bixby, D.E., 2007; ‘Managing Breeds for a Secure Future’, American Livestock Breeds Conservancy, Pittsboro, North Carolina, U.S.A.
Sheppy, A.J., 1998; ‘Bloodlines, Breed Structure and the Influence of Artificial Insemination in Dexter Cattle’
Carol K
Introgression in Historic Dexter Bulls
In the April Bulletin some of the recent advances in genetic techniques and their use in the Dexter breed were described. It is now time to look at one of the most significant areas of research where these techniques have been applied to our breed, namely the question of introgression of other breeds’ genetics into the modern Dexter. It is important to know what, if any, other breeds are in the background of animals we choose to use in our breeding programmes. Without this knowledge, it is impossible to make the best informed decisions about potential matings.
This article records the current extent of knowledge in respect of introgression in the Dexter breed and, in particular, the results of the standard tests for purity in three historic bulls in the Herdbook which have had significant influence on the modern breed.
Obviously we already know the situation in respect of animals derived from the Appendix and Experimental Registers, both of which are now closed so that the introgression they contain can easily be calculated in their offspring and will decline in influence as time progresses. In the case of the Experimental Register, there was a deliberate introduction of genes from other breeds in an attempt to eradicate the problem of the bulldog calf defect. Almost all the animals which have come down through the Experimental Register have done so via the AI bull, Atlantic Finbar Exp10/B, where it is clearly reported that 25% of his pedigree derives from Aberdeen Angus and Jersey. It is a simple calculation to determine the likely extent of introgression in animals descended from the Experimental Register.
In animals of Appendix Register descent it is generally equally easy to see how much influence of other breeds remains present in current animals. A good example is the important bull Templeton Michalmas Squeak 2043, which descends from an Appendix cow line where we know that his pedigree shows a Jersey cow in the sixth generation. That gives a purity of 98.44% on pedigree analysis which is high enough for there to be a reasonable chance that Squeak might in fact be pure.
If we apply the standard three (Sponenberg & Bixby 2007) tests of 1: Phenotype (observable and measurable characteristics), 2: History and 3: Genetic analysis we would find that Squeak could indeed be pure, or at least the 98.44% of his pedigree analysis. Both Squeak and his offspring look right, so pass test 1, and the historic records show the only introgression is beyond the five generation standard pedigree.
Applying the three Sponenberg & Bixby tests to animals which have not come from either the Appendix or Experimental Registers can give some very revealing results, none less so than three very important historic Dexter bulls. It is of course the recently available genetic tests which have only now given us the confirming proof of the ancestry of these animals.
The first of the bulls to have repeatedly come into question was Parndon Charley Pudding 1928. In his case, it was the appearance of calves with white marks in various places when Charley Pudding was in the pedigree of both sire and dam, or when he was mated to breeds with the recessive white spotting gene. So, on the first question of the three standard tests, ‘is there visible reason to doubt purity’, the answer is yes. In respect of historic evidence, it was subsequently admitted that Parndon Charley Pudding was in fact out of a Guernsey cow by a Dexter bull. Is there historic evidence of impurity, yes. This was as much as we had been able to determine until very recently when seeking to parent verify a bull in the U.S.A.. Parndon Bullfinch, registered as a son of Parndon Charley Pudding was widely used through A.I. across the U.S.A. and the hope was that he was in fact by Sylvan Ebony, the other bull in use in the Parndon Herd at the time. A DNA profile is availabe for Bullfinch, taken from a straw of semen. Although there is no known sample of Sylvan Ebony, a reasonable profile could be constructed from examination of the profiles of two of his sons, Vycanny Glencally Reiver and Sarum Bullrush. From this it was seen that there were seven separate loci which showed that Ebony could not have been the sire of Bullfinch, so he was indeed by Parndon Charley Pudding as registered. In the course of this process it was noticed that three alleles (TGLA227/89, ETH10/214 & HEL5/163) out of the 22 loci tested were not present in any pure Dexter sample, either here or in the U.S.A.. It is clear that these must have come from Bullfinch’s sire, Charley Pudding, which would be entirely consistent with him being the offspring of another breed, i.e. Guernsey. Is there genetic evidence of impurity, yes, which gives the same outcome to all three standard tests and confirms Parndon Charley Pudding as not being a pure Dexter.
The second bull where concerns were raised about his purity is Shadwell Robert 1978. Here again the first questions were raised by his inbred offspring, in this case the huge variance in his red descendents which are of two totally different types. This situation could not happen if the red variant came from a pure Dexter, where only one is known to exist. When first raised in a paper at the 1st World Congress on Dexter Cattle in 1998 [Sheppy 1998], there was no historic or genetic evidence to help us explain this. Subsequently it came to light that Shadwell Robert’s grand dam was not a Dexter but a small red cow of unknown breeding. This information was provided by the late Valerie Roberts, who was the niece of the breeder of the cow who was Shadwell Robert’s dam. So question one, physical evidence of impurity, yes and question two, historic evidence of sources of introgression, yes.
Here, once again, is where modern genetic techniques give the final proof. A comparison of the DNA profile of Shadwell Robert with all the purebred Dexter samples from the UK and a selection from the U.S.A. showed that he had four separate alleles (HEL9/169, INRA037/144. HEL5/163 & BM1818/267) which were not found in any of those samples. Such a result entirely supports the historic evidence that Shadwell Robert is only three quarters Dexter, so is there genetic evidence, yes.
The third case is slightly different in that the evidence of introgression was from phenotypic and genetic evidence before there was any known historical knowledge of a possible route by which such introgression happened. In the case of Grinstead Plover 1696, his closely inbred descendents in the Woodmagic Herd showed a very atypical conformation until the expert breeding of the late Beryl Rutherford selectively bred a more mainstream type from them. In addition, in that herd the novel dun gene made its appearance, giving rise to animals identical in appearance with the extinct Suffolk Dun, a very curious coincidence indeed. In the genetic research into the breed at Cardiff University, Tim Bray demonstrated that the closely bred Woodmagic animals formed a clearly different genetic group when considered with the other Dexter samples (Bray et al, 2009).
It was not until an unconnected research caused reference to be made to the 1957 Dexter Herdbook (DCS 1957) that the evidence of the possibility of introgression in Grinstead Plover’s pedigree came to light. In that year, several of the Grinstead Dexter cows were shown as having calved to a Red Poll bull, including Plover’s mother Grinstead Peachblossom VIII 5830. It was common practice at Grinstead to use a crossing bull on high yielding shortleg Dexter cows to avoid any chance of a bulldog calf disrupting the cow’s milk records and Peachblossom VIII came into that category. As the Red Poll was derived from a cross of the Norfolk Red with the Suffolk Dun, a route for the possible introgression and the ancestry of the dun colour immediately presents itself.
Thus all three questions (1: Is there phenotypic evidence of introgression?, 2: Is there historic evidence to explain introgression? and 3 : Is there genetic evidence of the presence of introgression?) are answered ‘yes’ in respect of all three of the bulls considered (Parndon Charley Pudding, Shadwell Robert and Grinstead Plover). As a result, when calculating purity by pedigree, Shadwell Robert is treated as being 75% Dexter with both Parndon Charley Pudding and Grinstead Plover treated as only 50% Dexter.
As if to demonstrate the speed of advance in genetic techniques, the article in the April Bulletin is already out of date, with a revolutionary new process about to be published in livestock science journals. This is likely to offer a technique specifically to address issues of introgression in populations and to remove it. We live in exciting times in respect of genetic techniques.
Andrew Sheppy
References
Bray, T.C. et al, 2009; ‘The population genetic effects of ancestry and admixture in a subdivided cattle breed’, Animal Genetics, International Society of Animal Genetics.
Dexter Cattle Society, 1957; The Dexter Herd Book, Vol LVII, The Dexter Cattle Society, Tadworth, Surrey.
Sponenberg, D.P. & Bixby, D.E., 2007; ‘Managing Breeds for a Secure Future’, American Livestock Breeds Conservancy, Pittsboro, North Carolina, U.S.A.
Sheppy, A.J., 1998; ‘Bloodlines, Breed Structure and the Influence of Artificial Insemination in Dexter Cattle’
