Breeding values – principles and practice

Recent US Alpaca Owners Association (AOA) president, and former chief scientist of the US Alpaca Registry, Shauna R Brummet, outlines the key concepts behind breeding values – or EPDs as they are known in the US. Shauna is from Hobby Horse Farm Alpacas, Wooster, Ohio.

Estimated or expected progeny differences (EPDs) are calculated based on mathematical models that allow us to elucidate the contribution of genetics and that of environment to the expression of specific, measurable performance traits. The Alpaca Owners Association (originally ARI) EPD programme started in 2008 with its first calculation in 2009 and is proven in practice.

EPDs are generated from data collected on individual animals and their relatives (progeny, parents, siblings). EPDs estimate the true genetic value of an animal for specific traits compared to others of the same breed. The “expected difference” is between the average trait value of a specific animal’s progeny and the average trait value in the rest of the population. The performance of two animals can be compared by subtracting one animal’s EPD from the other – this will give the average expected difference between the two animal’s progeny for each trait. It is important to understand that EPDs do not give an absolute or individual performance prediction. They give average performance differences of progeny as compared to average performance of others in the population. I will not go into the mathematics, which are complex matrix algebra equations used to estimate the portion of trait performance that can be attributed to the genetic contribution of one or the other parent, rather I will discuss the concepts needed to understand EPDs and to collect good data.

Connectedness

Connectedness simply means we must measure traits on alpacas that are genetically related and are living in different environmental conditions. This allows the mathematical model to “remove” the impact of environment on each trait and determine the genetic impact on the expression of the trait. Alpacas in many countries are well set in this respect. Original import animals have been spread across countries and the use of many herd sires and widespread sale of alpacas has placed similar genetics in various environments. In other words, we have very good genetic connections between registered herds so that the mathematical models can effectively separate the impact of genetics from environment.

Contemporary Groups

Contemporary groups are defined as uniformly managed groups of animals of the same breed, age and gender. Because the models will use genetic relationships among animals to tease out the separate influence of genetics and environment the data provided must be uniformly impacted by the environment under which the trait was expressed. For meaningful data to be collected all of the alpacas measured must have developed the trait under the same environmental conditions. This is a little more difficult to manage and something that all breeders need to think about as they collect and report data. To be a good contemporary group the alpacas need to have been exposed to the same weather conditions, fed the same feed (hay and grain, supplements and pasture), subjected to similar levels of stress and measured (sheared) at the same point in time. Contemporary groups of 20 or more alpacas having at least two herdsires represented as a parent in the group are preferred. It should not discourage smaller farms from participating if their contemporary groups are less than 20 though. A smaller number of animals in a contemporary group may impact the accuracy/prediction error somewhat (see below) but are not much of an issue. Fibre samples for analysis should be taken from all alpacas within a contemporary group within a couple of days of one another so that the fleece snippets tested are all affected by the same growing conditions. This is one reason that the mid-side sample location and 2mm snippet ‘base of staple’ sampling generates the optimal data for assessing the fibre traits. Some farms may need to report separate contemporary groups for the fibre analysis. If males, pregnant females, weanling males and females, fibre animals or other groups are treated differently they should be labelled as such when the samples are submitted for analysis. An animal that has been off farm for more than a week and comes back on the day of shearing should not be included in that year’s contemporary group. It could be included in the contemporary group of the farm where it resided before returning home.

Prediction error/accuracy

EPDs are accompanied by an accuracy or prediction error figure. This number (a decimal between 0 and 1) shows the current reliability of the EPD. It is the level of confidence that the predicted value is near the true genetic value of the animal for the specific trait. Accuracy/Prediction Error is dependent on the heritability of the trait and the number of records from the individual, relatives and progeny used in the evaluation. The greater the heritability the higher the EPD accuracy will be. Accuracy is dependent on an animal having relatives in different herds, on the cohesiveness of the contemporary group, its size and on the number of sires represented in the contemporary group. It is important to note that alpacas with high accuracy EPDs will produce as much variation in offspring as animals with low accuracy EPDs, but the high accuracy EPD is closer to the true breeding value of the animal for the trait.

Data collection

Accurate performance records are critical to the success of genetic evaluation and selection programs. Consistent and accurate collection of data is important for generating EPDs with as high accuracy as possible. EPDs are calculated up and down and across the pedigrees in the database. This is a strength of the methodology. The data submitted from a single alpaca is incorporated into EPD calculations for that alpaca’s parents, progeny, siblings, aunts/uncles, grandparents, and nieces/nephews out three generations. The value of the data for each generation is lessened, which means that the data has less impact on the accuracy of more distant relative’s EPDs. The data of greatest impact on the EPD and its accuracy is data from the alpaca itself and its first-degree relatives. Your herdsire may have progeny in several different herds and you have progeny of other producer’s alpacas in your herd. Owners may submit fleece samples for the progeny they own. These data will contribute to the calculation of EPDs for your herdsire. These data are as valid and valuable to the calculation as data you submit. In fact, it is quite valuable when other progeny are in herds that experience a different environment than your herd. Those progeny allow your alpaca’s genetics to be assessed as they perform in a different environment. Submitting all data is important. Because different environments will impact the traits differently alpacas might well have better genetic value than appears under some conditions. In order for the industry to quickly produce useable data it is important for you to submit data on all animals that you maintain whether they are herdsires, prize females, young unproven stock or fibre animals. So, collect samples from all your animals and let the calculations sort out the differences. Submitting only “good data” is actually detrimental.

Making use of objective tools

I would like to conclude this discussion with some thoughts on using objective tools, specifically EPDs, to answer the question “are you achieving your breeding plan or fibre production goals?” Whatever your goals are for breeding stock or production animals the EPD programme can help you to realize them. Let’s say you want to produce grade 2 fibre (20-23 microns) with exceptional uniformity (low standard deviation( SD) of average fibre diameter (AFD). You can make use of EPDs to select mates or purchase alpacas that have the genetic propensity to do exactly that. You can use alpacas with rather neutral EPDs for average fibre diameter (AFD) but negative EPDs for SD and percent of fibres over 30 microns to achieve your goals. Perhaps you have a fine fleeced herd, but need a herdsire that can help stem the production of ever shorter staple lengths. You can use EPDs to identify such a herdsire by looking at the EPDs for staple length in conjunction with mean curvature. In combination with histograms of your own herd ( remember, there is little use in comparing histograms when selecting matings or purchases because they reflect the significant impact of the alpaca’s environment) conformational assessment, maternal instincts evaluations and other tools along with the powerful EPDs we can produce alpaca fibre that is economically valuable and gives each farm the highest return on their business model.

Hobby Horse Dancing on the Ceiling fleece

Hobby Horse Kitty Kat fleece