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Pedigree, Performance and Progeny Testing
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Many alpaca breeders in the United States use pedigree as a primary selection tool. A pedigree is a record of an animal’s ancestors that contains more than 30 pieces of specific information about an alpaca's heritage. It is an important record for people who breed "pure bred" stock. But, as we will discuss below, the value of pedigree as a selection tool to determine superior stock, is vastly overrated by most alpaca breeders. There is simply too much that a pedigree does not tell you about an alpaca.
There is a lot to be learned from reading an alpaca's ARI pedigree. Beginning at the top, we will walk through Northwest Alpacas, Ltd. Artero's pedigree (Illustration 11.1), and see what it tells us.
- Heading: At the very top, we learn whether the alpaca is a huacaya or a suri. We find the name of the animal, the owner of record, the owner's ranch name, address, and owner code. Preceding the name, you might also find the herd identifier code of the person who owned the dam when she was bred.
- Center of the certificate: Here we find the registered alpaca's ancestors (if known). If the ancestors or the alpaca in question were imported, you will find the country they were imported from, which might be different from where they were born. The center of the certificate also shows what breed the ancestors were, either huacaya (HA) or suri (SA), their registration number, and color. The designation of an ancestor's breed will be important for people who are crossbreeding suris. The information on the color of ancestors will be of interest to breeders concentrating on breeding colored alpacas. If the alpaca was imported, there will be an import number after its name, which was also its ear tag number.
- The left hand column on the pedigree will tell you the following about the animal in question:
A.Sex
B.Date of birth
C.Country of origin
D.Country where born
E.Color
F.DNA or blood type case number
G.Microchip number, if any
H.Ear tattoo, if any
I.Sire owner at conception
J.Dam owner at conception
K.Dam owner when cria born
L.Date certificate issued
M.Date registered
N.Disclaimer
All of the above information is important but even when taken in its entirety; it is not reliable as a predictor of an alpaca's breeding value. The pedigree should only be regarded as a first step in the selection of superior breeding stock.
Before we proceed to a discussion of progeny testing a word about performance records. The primary reason that an animal breeder keeps performance records is to track the breeding value of a given dam or sire.
In the alpaca business, these records are most often used to promote a specific animal's quality. You may have noticed the extensive use of a herdsire's histogram to hype the claim that he is potent and wonderful, simply based on his micron count.
An astute observer might also notice that in successive ads, published over a period of time, the micron count never changes. This is physiologically impossible and, aside from being a misuse of the performance record, it should serve to make the point that one can't always believe the hype of a herdsire's potency offered by an owner.
The idea of a "proven" stud is often misunderstood in the alpaca business. Many people take the term to mean that the stud has simply sired a number of defect-free offspring. When a geneticist or a knowledgeable animal breeder uses the term, they mean that the sire has "proven" that he can consistently pass his positive production traits onto his progeny. In other words, he has a high breeding value.
To make accurate selection decisions about your herd, you must be able to assess the breeding value of a given alpaca - whether or not it will pass its genotype and its phenotypic superiority on to its offspring. To assess a sire's breeding value, you must know how many cria it has and how consistently they express the parent's phenotype. In other words, you must progeny test.
We have seen that pedigree alone is a poor predictor of performance. A geneticist will tell an animal breeder that they must assess the progeny of a given ancestor before deciding if the ancestor is the appropriate sire or dam for a large number of their cria. This is known as a progeny test, a test involving multiple matings of an individual animal and a measured evaluation of its offspring that helps predict that individual's breeding value.
Frederick B. Hutt, Professor Emeritus at Cornell University, and Benjamin A. Rasmusen, of the Department of Animal Science at the University of Illinois proved the value of progeny testing. They measured the breeding value of three white leghorn roosters, each with an identical pedigree, by successfully mating them to the same hens. They then recorded the production of each rooster's progeny. The results of their experiment (Table 11.1) clearly identify the strength of progeny testing and the weakness of pedigree as a selection method.
Remember, in this experiment the roosters were identical by pedigree, and they were each mated with exactly the same hens. U2's daughters were obviously superior egg producers and therefore U2 was obviously the superior cock (male chicken). The other two roosters' offspring were sub-par egg producers by a significant margin.
Alpaca breeders need to realize that even full brothers of identical pedigree will have varying breeding values. This is why we spend so much time and effort at www.IdealAlpaca.com on making information on a parent's progeny available.
Progeny testing for alpacas involves using a phenotypic evaluation form to evaluate the phenotype of a stud's offspring for such important traits as, fleece weight and fineness. Other heritable traits such as size and bite can also be scored. (For a full discussion of selection, see Alpacas: Synthesis of a Miracle, Chapter 4.) The records that are gathered on phenotype evaluation forms or from the breeder's production, records become the basis for establishing Estimated Progeny Differences (EPDs). Evaluating only the outstanding cria is not sufficient. EPDs allow the comparison of breeding values between multiple herdsires. (For a complete discussion of EPDs, see Ideal Alpacas: From Myth to Reality, Chapter 12.)
In addition, to be accurate, progeny testing must be done in an environmentally neutral manner. This means that all the sires whose cria are examined must have been raised in similar circumstances with similar feed and care, or there must be multiple records from animals raised in diverse environments for each of the sires being compared.
Many livestock industries have successfully adopted progeny tests. Prospective bulls breed dairy cows, their daughters are milked to determine volume, and fat content before the bull is put into general service. Boar pigs are bred to a limited number of sows to determine their influence on litter size, survivability, and weaning weight before they are widely used. The same system is employed in poultry breeding operations.
Progeny testing is not just a strategy for large breeders. Small breeders can use the concept to choose service sires for outside breeding. Purchasers can use it to select foundation-breeding stock. If employed industry wide or across multiple herds, the rate of genetic gain would accelerate dramatically.
PROGENY TESTING AND HERD IMPROVEMENT
Once breeders have established their herds, how can they use progeny testing to improve their cria?
The most important decision any breeder makes is when they select the male that will breed their females. The next most important decision is when they select a replacement male.
To make these selections successfully you must breed a prospective male alpaca to between 10 to 20 females. Then you must assess the progeny of the prospective herdsire before using the male across a large number of females. If you decide to use a male owned by someone else, you should inspect its progeny. To succeed, progeny testing must be rigorously applied. It is of little value if a breeder measures only the best cria or only cria from his best dams.
Once this testing method is used to evaluate several males, breeders can select superior animals as studs and avoid using the males with low breeding values across their herd. The males they finally choose, and which they most frequently use, will have higher breeding values as will their offspring over time. In this manner, the herd's quality will rapidly compound.
We have discussed the relative value of pedigree as a selection tool, adding performance or production records to an individual's pedigree information, and finally the importance of analyzing the performance records of an individual's progeny before selecting breeding stock. Making good decisions about improving their livestock is what everyone wants. We must avoid the poor producers as sires.
To make the point with the utmost of clarity, we rely on the following excerpt from Understanding Animal Breeding by Richard M. Bourdon, Prentice Hall, 1997 (pgs. 228-230). Study this material carefully. It is the key to selecting and breeding the ideal Alpaca.
"As you might guess, the weighting factors needed for a selection index involving multiple sources of information, vary depending on the amount and relevance of data from each source. For example, if an animal has extensive pedigree data and a performance record of its own, but little progeny data, we expect that in calculating that animal's EBV [estimated breeding value], most of the emphasis will be placed on the pedigree and the animal's own performance information. On the other hand, if the same animal acquires vast amounts of progeny data; we expect the emphasis to shift to that source of information. Progeny data, after all, provide the ultimate test of an individual's breeding value. When simultaneous equations are used to solve for selection index weights, each weight automatically reflects the appropriate amount of emphasis that should be placed on its corresponding source of information. You can think of this as the "magic" of simultaneous solution of equations. Table 11.3 has been constructed to illustrate some aspects of this mathematical magic.
Listed, in Table 11.3, are decimal proportions representing the relative emphasis being placed on particular sources of information for breeding value prediction. Each row represents a different scenario, with each scenario involving different amounts of data on individual performance (IND), average performance of paternal half sibs (PHS), average performance of maternal half sibs (MHS), and average performance of progeny (PROG). The measured trait is assumed to be non-repeated (animals may have only one record apiece) with a heritability of .3.
The rows (scenarios) in Table 11.3 are grouped in three sections. The first three rows represent situations in which only pedigree information is available on an individual. Perhaps the individual is not yet born, or is too young, to have a performance record of its own. The next two rows reflect combinations of pedigree and own performance information. The last four rows combine pedigree, own performance, and progeny informationdata that would be available only on an older animal. Note that accuracy of breeding value prediction (right-hand column) increases with additional information.
The scenario depicted in the very first row represents a modest amount of pedigree information. The dam of the individual of interest - the individual whose breeding value we are predictinghas two previous offspring, and the sire is probably young, having only 10 other progeny. More emphasis is placed on paternal than maternal sib records because there are more paternal sib records, but altogether there is little information to go on, and accuracy is low (.38). In the second row, the sire of the individual of interest, having 200 progeny records, is well evaluated. The emphasis on paternal sib information increases accordingly, and accuracy is higher.
In row three of the table, numbers of records have been doubled. The number of paternal sib records increases from 200 to 400, and the number of maternal sib records increases from two to four. Despite the much larger increase in the number of paternal sibs, the relative emphasis on paternal sib decreases. This is because the paternal side of the pedigree is already well established. With 200 progeny, the breeding value of the sire of the individual of interest is predicted with high accuracy, and adding 200 more progeny will not help a great deal. The dam's side of the pedigree, on the other hand, is the "mystery" side. With only two offspring, we know little about her breeding value. Adding two more offspring may not seem like much of an improvement, but those two records provide information on a part of the pedigree where there was little before. Scarce information carries more weight per record than abundant information.
Accuracy of breeding value prediction based solely on pedigree information is not very high. In the examples in Table 11.3, accuracy peaks at .55 in row three. As explained in the discussion of single-source predictions, pedigree data cannot account for Mendelian sampling. A pedigree estimate [a genetic prediction based solely on pedigree data] is useful as a best first guess, but we cannot expect it to be reliable.
"Rows four and five of the table combine pedigree information with the individual's own performance record. Because the trait is moderately heritable (h2 = .3), the individual's own record carries considerable weight - 71% when there is little pedigree data and 54% when there is an abundance of paternal sib data. The individual's record is just one record, but it is a record on the individual's closest relative (itself), and it reflects the Mendelian sampling of genes; it tells us something about the value of the genes that the individual actually received from its parents.
"The last four rows of Table 11.3 incorporate all three kinds of information: pedigree, own performance, and progeny data. Note the relative importance of progeny data, even when progeny numbers are small. With large numbers of progeny (last two rows), other sources of information become practically inconsequential, even when they are represented by many records. And with enough progeny data, accuracy of prediction is very high --.97+ in this example."
If you will study the material above from Bourdon's book, you cannot escape the following conclusions:
- Pedigree alone is the least reliable way to select for breeding stock with high breeding value.
- Incorporating an animal's own phenotypic performance records with the animal's pedigree information adds accuracy to decisions about which animals should be parents.
- Adding the phenotypic performance records of an ancestor's progeny to the available information is crucial to making highly accurate selection decisions.
Breeders who incorporate the information gleaned from progeny testing into their mating decisions will experience a steep improvement curve within their herd. The myth that 'pedigree equals breeding value' or that, 'the best way to select breeding stock is by analyzing their phenotype' will no longer be a roadblock to breed improvement. The increased quality herd wide will quickly compound and be reflected in fleece weights, fiber fineness and other quantifiable economic and conformation traits. The gains made over three to four generations will be dramatic.
There are several factors which inhibit the ability of breeder's successful deployment of the factors which are described above. They include average herd size, a poor central record-keeping facility, lack of shared records, and lack of access to progeny tested males.
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