Breeding Issues (Conservation Genetics, Scrapie, et)

Howling Oak Ranch

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Scrapie: Selection for Resistance and Consequences for Genetic Diversity

by K. Gerhart of Howling Oak Ranch

What is Scrapie?

The Genetics of Scrapie

The Importance of Genetic Diversity in Breed Conservation

Widespread Selection for R genes will reduce Genetic Diversity

What is Scrapie?

Scrapie, like mad-cow disease (BSE), is thought to be caused by a change in the shape of a brain protein called PrP (prion protein). However, unlike BSE, there is no evidence that scrapie can be transferred to people by eating meat from an infected animal. Also, in sheep it is possible to reduce vulnerability to some forms of scrapie through genetic testing and selective breeding; this is not yet an option in cattle.

BSE and scrapie are typified by holes that develop in the brain, leading to unusual behaviors; in sheep, these include excessive scratching and rubbing. Eventually, the infected individuals die. The widely accepted cause for this disease (first proposed by Pruisner, for which he received a Nobel Prize in 200x) is that normal PrP proteins change shape due to interactions with a misfolded PrP protein. Thus one misfolded protein is "contagious" and spreads its shape to other PrP proteins in an animal's brain. Prion proteins provide the only known example of an infectious agent that does not contain nucleic acids (DNA or RNA). Pruisner theorizes that proteins can misfold spontaneously within an individual, and misfolded prion proteins can be spread between individuals.

The Genetics of Scrapie

Different amino acid sequences within the PrP protein are associated with different vulnerabilities to scrapie infection. The amino acid sequence of the PrP protein varies between individual sheep due to differences (polymorphisms) in the DNA. A codon is a group of 3 bases within the DNA (or RNA) that specify a particular amino acid within a protein.

Within one particular section of DNA coding for the PrP protein (exon 3) there are three locations where the DNA sequence is variable and affects vulnerability to scrapie: at codon 136, the DNA codes for either Alanine or Valine (A or V), at codon 154, it codes for Histidine or Arginine (H or R), and at Codon 171 it codes for Glutamine, Arginine, or Histidine (Q, R, or H). Variation at these 3 loci leads to 5 common genotypes in sheep: A136R154R171 (or ARR for short), ARQ, VRQ, AHQ, and ARH. VRQ and ARQ are highly vulnerable to typical forms of scrapie, while ARR is highly resistant. ARH is neutral, and AHQ seems to be associated with resistance in some breeds. Seven additional polymorphisms have been discovered, but appear to have no affect on vulnerability to scrapie.

Sheep have two copies of the PrP gene in their cells, and so can have various combinations of the alleles listed above. ARR/ARR is known to confer global resistance to scrapie and experimental BSE. ARQ/ARQ generally has increased vulnerability. In the U.S., scrapie has only been confirmed in sheep with Q/Q at codon 171, regardless of breed. Thus, codon 171 is the only codon commonly examined in the U.S. to determine vulnerability to scrapie, with R/R or Q/R sheep considered resistant and Q/Q sheep considered vulnerable. The genotype of sheep can be determined from tissues retained in a special ear tag; RR rams are particularly sought after currently, as all of their offspring will have at least one copy of the R allele (will be Q/R or R/R). (but see Does Q stand for quality?)

Research involving St Croix sheep (Seabury and Derr, 2003) led to the discovery of a new polymorphism at codon 116 of the PrP protein. One copy of this novel allele was identified in 1 of 6 St Croix sheep examined; the mutant codon occurs in a portion of the protein that does not usually contain polymorphisms. The new allele "P" was found in combination with ARQ to give the variant PARQ. The vulnerability of PARQ animals to scrapie is currently unknown, although the authors provided reasons why they expect PARQ sheep to be more resistant to scrapie than are normal ARQ sheep. Prevalence of the PARQ gene in the St Croix sheep is also unknown. Within the small group of St Croix sheep included in Seabury and Derr’s study, all 6 individuals had at least one copy of the R allele at codon 171 (that is, they were all Q/R or R/R). From this study, there is no reason to believe that an ARQ/ARQ St Croix sheep would be less vulnerable to scrapie that a Q/Q individual from some other breed. If its Prp protein were described more fully, a Q/Q St Croix sheep might turn out to be PARQ/PARQ, or ARQ/PARQ; in this case, the sheep might show more resistance to scrapie than other Q/Q sheep. However, the possibility of increased resistance for PARQ St Croix remains conjectural at this time.

The Importance of Genetic Diversity in Breed Conservation

Conservation breeding programs focus on maintaining genetic diversity within a breed, species, or population. Genetic diversity allows for high productivity and effective immune system function and is thus essential to breed survival. Decreases in genetic variability can lead to inbreeding depression, characterized by reductions in viability (survival of lambs), birth weight, fecundity (number of young produced), and fertility (conception rate). Many of these problems are caused by an increase in the frequency of previously rare, deleterious alleles. Such genes may be harmful when paired with identical alleles (forming a homozygote), but may be neutral or even provide an advantage when paired with a dissimilar allele (forming a heterozygote). Additionally, it appears there are advantages in immune system function to having copies of two different alleles. For instance, the genes of the major histocompatability complex (MHC) help distinguish “self” from “nonself”, and an individual with non-identical alleles can distinguish more foreign agents than can a homozygous individual. A variety of MHC alleles is even more important within a population, as high genetic diversity within a population makes it more resistant to different types of pathogens. Parents that carry different MHC alleles also appear to have fewer fertility problems. Even strong selection for increased production in sheep is quickly offset by increases in inbreeding and the corresponding losses in productivity, according to published research.

It can therefore be argued that all purebred animals will eventually succumb to inbreeding depression unless occasional crossings from outside the breed occur. Breeds with small populations are particularly vulnerable as there are fewer individuals of different genotypes within the population. Breeders can delay inbreeding problems through practices that maintain genetic diversity while maintaining type, such as conservation breeding, in which a population is alternatively line-bred and line-crossed to maintain both the diversity and the genetic distinctiveness of certain lines.

The St Croix breed currently has a narrow genetic base, as the breed was founded using 22 females (some of which were pregnant) and 3 rams. It is likely that some of these foundation sheep have no living descendents, and therefore have not contributed to the genetic diversity found in the breed today. Fortunately there have been some additional imports of sheep and semen since the foundation stock was brought to the US from the Virgin Island of St Croix. Nonetheless, the genetic diversity of the breed remains relatively low and it is unlikely that further imports will be possible due to both import restrictions imposed for new disease concerns, and widespread crossbreeding with Dorpers on the islands (Charlie Bedinger, pers. comm.).

Widespread Selection for R genes will reduce Genetic Diversity

There are at least three problems with selecting for R genes in any sheep breed, and in the St Croix breed these problems are exacerbated by the small gene pool of the foundation stock. The core of the issue is loss of genetic diversity.

First, strong selection for one trait (the R gene) inevitably means a reduction of selection pressure for other traits. While focusing on selecting RR stock, breeders will inevitably put less emphasis on other important traits such as out of season breeding, prolificacy and other maternal traits, growth, and conformation. While the proportion of RR and QR sheep will increase, the utility of these sheep will be lower than it would have been if selection had been based on a more holistic trait, like pounds of lamb weaned per ewe. Because our breed is small, it is possible that valuable traits could be lost entirely if they are by chance more common in QQ sheep.

If a breeder decides to make slower progress toward an RR and QR flock, and selects carefully for the whole animal by using only above average animals of the RR and QR genotypes as well as good QQ animals, the process of increasing the proportion of R genes in the flock will occur more slowly and with less loss of production traits -- but the effort will nonetheless reduce diversity. The PrP protein is carried on one of the 27 pairs of chromosomes that make up the genome of the sheep. A breeder selecting for the R genotype is also inadvertently selecting for all other alleles that are carried on the same chromosome – that is, traits that are linked to the R genotype because of their proximity, and that will not assort independently. The breeder is also selecting against every other allele located on the chromosome with the Q gene. While genes that travel on the same chromosome can become unlinked over time (through crossing over during meiosis, during which chromosome pairs exchange genetic information) such events are relatively uncommon and unpredictable. Over the course of a few generations, it is extremely unlikely that the R gene would become unlinked to all the other alleles travelling on the same chromosome. Thus the diversity in other genes is also being reduced when selecting for the RR genotype.

For these two reasons, in the quest for QR and RR stock it is almost certain that other important alleles in the St Croix breed will be reduced or lost. Further genetic restriction due to the culling of quality QQ sheep is particularly shortsighted and problematic in a rare breed such as ours. Widespread selection for the R genotype will likely reduce the genetic diversity within our breed. This is especially problematic as the St Croix sheep breed is based on far fewer than the 200 or so distinct individuals that are considered necessary to provide adequate genetic diversity for long term survival. Selection for the RR genotype could have similar affects as the use of a popular sire in dogs or horses, restricting genetic diversity and leading to problems with inbreeding depression and loss of quality in the future (see also “Does Q stand for quality?”).

The third argument against selection for the RR genotype in St Croix sheep is that the typical form of scrapie in the US is not the only form of scrapie that exists, and there is evidence that RR sheep are MORE vulnerable to some of these atypical scrapie strains. Thus selection for RR in the short term may result in INCREASED susceptibility to scrapie in the long term! (see also “Breeding Lambs for Longterm Scrapie Resistance").

The concerns (expressed by John Bare in "Does Q stand for Quality?") that people are discarding good sheep and genetic variability in quest of an RR genotype are particularly troubling when they occur in a rare breed, such as the St Croix, as the choices of any one breeder will have a larger affect in a rare breed than they do in a common one. If scrapie is indeed eradicated in the US in the next decade, we may find that we have lost irretrievable genes in a quest for short-term profits and protection. If other forms of scrapie reach US shores, we may find that we have deliberately selected against the genotypes needed to protect our sheep from these variant forms of scrapie. Because of these concerns, I urge breeders to think hard before jumping onto the bandwagon and selecting for R genes in their flocks.