Genetic diversity loss due to selection for scrapie resistance in the rare Spanish Xalda sheep breed

The effect of selection for scrapie resistance on genetic variability in the rare Xalda sheep breed was studied. Pedigree information comprised 1851 animals (1444 alive) at the moment of sampling. A total of 304 reproductive (or selected for reproduction) Xalda individuals were sampled and genotyped for 14 microsatellites. Genetic variability was assessed using: gene diversity (1 − average kinship, GD), mean average relatedness (AR) and self-coancestry (c_i) at the genealogical level; and expected heterozygosity (H_e), molecular mean kinship (Mk), molecular self-coancestry (s_i) and rarefacted average number of alleles per locus (A) at the molecular level. Two breeding strategies were evaluated: a) use of only young rams with genotype ARR/ARR and young ewes with low to moderate risk (risk groups R1 to R3); b) breeding without selection for PrP genotypes. The major cause of losses of genetic variability in the Xalda breed is the drift that occurs when a new group of reproductive individuals is selected. The loss of genetic variability is small in females compared to the males, where it is considerable. However, losses at the molecular level for young females with respect to adult females were above 5%. Young male individuals also retained most of the genetic variability assessed in adult rams. Selection against susceptibility to scrapie produced additional losses of more than 2% for H_e and A when rYF individuals are considered. As regards males, the situation becomes critical because of the scant number of available ARR/ARR young rams. The consequences for the management of the Xalda breed are discussed.     

Genetic variability in the endangered Asturcón pony assessed using genealogical and molecular information

The aim of this analysis is to assess the genetic diversity in the black-coated Asturcón pony population using genealogical and molecular methods in order to ascertain the possible impact of the inclusion of the bay Asturcón individuals on the breed's recovery programme. Pedigree information registered in the studbook of the black-coated Asturcón (including a total of 1080 individuals) was analysed. Additionally, 261 blood samples from the black-coated Asturcón individuals were obtained and genotyped for 15 microsatellites. Furthermore, 58 blood samples were obtained and genotyped from bay Asturcón individuals in order to place the results within the context of an unselected population with no known genealogies. The results indicated high losses of genetic representation of founders in the present population of black-coated Asturcón ponies. Roughly 60% and 30% of the founder stallion and dam lines, respectively, are lost in the present population. Average inbreeding was 4.7%. The equivalent number of founders and equivalent number of ancestors were 18.1 and 13. The most relevant founders and ancestors identified belonged to the three major studs involved in the recovery of the breed. However, the results highlight the dependence of the breed on the management of the government-run Cayón stud, which has increased its genetic contribution to the breed over time from 35.6% to 50.1%. At a molecular level, genetic variability assessed in the black-coated Asturcón was lower than that observed in the bay Asturcón. Expected heterozygosity, F_IS(m) and rarefacted average number of alleles per locus were 0.755 and 0.828, 4.1% and 1.3%, and 9.5 and 9.2, respectively, for the black-coated and bay Asturcón. The expected molecular coancestry in the black-coated Asturcón base population (Ef₀) took a value of 0.229, which was near to the molecular coancestry computed in the bay Asturcón (0.231). Implications of the reported results in the recovery programme of the Asturcón pony breed are discussed.     

Effect of selection for scrapie resistance on genetic diversity in a rare and locally adapted sheep breed: The case of Sambucana

In Italy, since 2005 a breeding plan to increase scrapie resistance has been adopted. The impact of this selection on genetic diversity was assessed on Sambucana, an autochtonous sheep breed reared in southern Piedmont, by analysing the evolution of allele frequencies at different levels: PRNP (prion protein) gene, microsatellite loci on OAR13 (where PRNR maps), and microsatellite loci on other chromosomes, not subjected to selection for scrapie resistance. A total of 147 young rams, 80 born in 2004 and 67 in 2008–2009 were analysed. Evidence of diversity loss was observed for PRNP gene as a consequence of the directional selection. Diversity was affected in the immediate vicinity of PRNP but the effect on more distant loci on the same chromosome was trivial. With regard to neutral markers, lack of heterozygosis with no changeover of allele frequencies was observed suggesting an increase of inbreeding. Mating policies would be sufficient to solve these problems. A selection scheme based on genotyping rams and eliminating carriers of both susceptible and high susceptible alleles is the best way to improve natural resistance to scrapie with low costs and minimal problems in the current conservation programmes targeting rare breeds.     

Case study: The effect of inbreeding on the production and reproduction traits in the Elsenburg Dormer sheep stud

Data of the Elsenburg Dormer sheep stud, which was kept closed since inception, were collected over a period of 62 years (1941–2002). The breed is a composite, resulting from a cross of Dorset Horn rams with South African Mutton Merino ewes. These data were analysed to quantify the increase in actual level of inbreeding and to investigate the effect of inbreeding on phenotypic values, genetic parameters and estimated breeding values. After editing 11954 pedigree, 11721 birth weight (BW) and survival, 9205 weaning weight (WW) and 7504 reproduction records were available for analysis. The mean level of inbreeding (F) of all animals over all years was 16%; 14% for dams and 16% for sires. Mean, minimum and maximum F for the lambs in 1997 (when 3 rams from outside were introduced) were 22%, 21% and 24% respectively. Estimates of inbreeding depression for individual inbreeding of 1% were − 0.006 kg for birth and − 0.093 kg for weaning weight respectively. These were the only estimates that were significantly (P < 0.01) different from zero. No significant effects of inbreeding on the other traits were found. There were virtually no differences in the genetic parameters estimated when fitting the two models (inclusion or exclusion of inbreeding coefficients as covariates). Estimates of the phenotypic variance differed slightly for WW between the two models. Ranking of animals were studied for weaning weight when the two models were considered. The high correlation coefficients (0.990) indicate that the use of inbreeding coefficients did not cause important changes in ranking of animals and sires for WW. It was concluded that slow inbreeding (rate of inbreeding of approximately 1.53% per generation over 19 generations) allows natural selection to operate and to remove the less fit animals. At any given mean level of F, less inbreeding depression would then be expected among the individuals who accumulated the inbreeding over a larger number of generations. Nevertheless, inbreeding coefficients should be considered when mating decisions are made, to limit the possible deleterious effects of inbreeding on productive and reproductive traits and to detect animals “resilient to” higher levels of inbreeding.     

Relationship between residual energy intake and the behaviour of growing pigs from three genetic lines

Residual metabolizable energy intake (RMEI) is the difference between metabolizable energy intake (MEI) and predicted production and maintenance requirements. In growing pigs from three genetic lines, namely Genex Meishan-derived dam line (GM), Synthetic Genex 3000 (SG) and purebred Large White (LW), RMEI was determined and related to behaviour by factorial Partial Least Squares analysis. Behaviour was measured by observations of daily behaviour in the pen, postures, feeding behaviour, aggressive behaviour after mixing and ease of handling at weighing. The RMEI obtained for the GM pigs was lower (P = 0.003) than that of the two other lines studied (LW and SG). This difference may result from inaccuracy in the estimation of requirements. A small proportion of these differences were explained by differences in behaviour. Indeed, standing posture, time spent in the feeder, toy manipulation, aggressive and locomotor behaviour explained part of the variation in RMEI, presumably because an increase in these physical activities induces higher energy expenditure. Vocalisations during manipulations at weighing were the only behaviour related to stress that influenced RMEI.