B. Villanueva

Analyses of lamb survival of Scottish Blackface sheep

Scottish Blackface lamb viability records at birth, and postnatal survival from 1 day to 14 days, from 15 days to 120 days and from 121 days to 180 days were used to determine influential factors and to estimate variance components of lamb survival traits. The binary trait viability at birth was analysed using a linear model whereas the postnatal survival traits were analysed as continuous traits using a Weibull model. The data consisted of about 15xa0000 survival records of lambs born from 1996 to 2005 on two farms in Scotland. The models included fixed factors that had significant effects and random direct and maternal additive genetic effects and maternal litter effects for viability at birth, and sire and maternal litter effects for the postnatal survival traits. The possible effect of maternal behaviour measured around lambing on lamb survival was investigated in separate analyses. Male lambs were found to be at a higher risk of mortality than females during all periods considered. The effect of type of birth and age of dam was more important during the preweaning period than at later ages. The postnatal hazard rate was not significantly affected by the behaviour score of the dams. The genetic merit of dams had more influence on viability at birth than the genetic merit of lambs themselves. Estimates of heritability for postnatal survival traits were in the range of 0.18 to 0.33 and were significantly greater than zero. These results indicate that lamb survival can be improved through farm management practices and genetic selection. Both animal and maternal genetic effects should be considered in breeding programmes for improving viability at birth.

Dynamic selection for maximizing response with constrained inbreeding in schemes with overlapping generations.

A dynamic selection algorithm for maximizing annual genetic response while constraining the rate of inbreeding per generation in populations with overlapping generations is presented. The procedure gives the optimum number of individuals to be selected and the progeny they each produce. The solution to the problem was obtained by using BLUP estimated breeding values, the augmented numerator relationship matrix and lifetime breeding profiles. The procedure was able to constrain the rate of inbreeding per generation to a predefined level across generations of selection by considering all gene flow pathways. The optimization procedure represents an improvement on standard truncation BLUP selection, as it yielded substantially more genetic response (up to 35%) at the same rate of inbreeding.

Accuracy of genome-wide evaluation for disease resistance in aquaculture breeding programs1

Current aquaculture breeding programs aimed at improving resistance to diseases are based on challenge tests, where performance is recorded on sibs of candidates to selection, and on selection between families. Genome-wide evaluation (GWE) of breeding values offers new opportunities for using variation within families when dealing with such traits. However, up-to-date studies on GWE in aquaculture programs have only considered continuous traits. The objectives of this study were to extend GWE methodology, in particular the Bayes B method, to analyze dichotomous traits such as resistance to disease, and to quantify, through computer simulation, the accuracy of GWE for disease resistance in aquaculture sib-based programs, using the methodology developed. Two heritabilities (0.1 and 0.3) and 2 disease prevalences (0.1 and 0.5) were assumed in the simulations. We followed the threshold liability model, which assumes that there is an underlying variable (liability) with a continuous distribution and assumed a BayesB model for the liabilities. It was shown that the threshold liability model used fits very well with the BayesB model of GWE. The advantage of using the threshold model was clear when dealing with disease resistance dichotomous phenotypes, particularly under the conditions where linear models are less appropriate (low heritability and disease prevalence). In the testing set (where individuals are genotyped but not measured), the increase in accuracy for the simulated schemes when using the threshold model ranged from 4 (for heritability equal to 0.3 and prevalence equal to 0.5) to 16% (for heritability and prevalence equal to 0.1) when compared with the linear model.

Mendelian sampling terms as a selective advantage in optimum breeding schemes with restrictions on the rate of inbreeding

Quadratic indices are a general approach for the joint management of genetic gain and inbreeding in artificial selection programmes. They provide the optimal contributions that selection candidates should have to obtain the maximum gain when the rate of inbreeding is constrained to a predefined value. This study shows that, when using quadratic indices, the selective advantage is a function of the Mendelian sampling terms. That is, at all times, contributions of selected candidates are allocated according to the best available information about their Mendelian sampling terms (i.e. about their superiority over their parental average) and not on their breeding values. By contrast, under standard truncation selection, both estimated breeding values and Mendelian sampling terms play a major role in determining contributions. A measure of the effectiveness of using genetic variation to achieve genetic gain is presented and benchmark values of 0.92 for quadratic optimisation and 0.5 for truncation selection are found for a rate of inbreeding of 0.01 and a heritability of 0.25.

Restricting coancestry and inbreeding at a specific position on the genome by using optimized selection

Over recent years, selection methodologies have been developed to allow the maximization of genetic gain whilst constraining the rate of inbreeding. The desired rate of inbreeding is achieved by constraining the group coancestry using the numerator relationship matrix computed from pedigree. It is shown that when the method is applied to mixed inheritance models, where a QTL is segregating together with polygenes, the rate of inbreeding achieved in the region around a QTL is greater than the desired level. The constraint on group coancestry at specific positions around the QTL is achieved by using a relationship matrix computed from pedigree and genetic markers. However, the rate of inbreeding realized at the position of constraint is lower than that expected given the assumed relationship between group coancestry and the subsequent rate of inbreeding. The use of markers in the calculation of the relationship matrix allows the selection of candidates with very low or zero relationships because they are homozygous for alternative alleles, which results in a heterozygosity amongst their offspring higher than would be expected given their allele frequencies. A generation of random selection restored the expected relationship between group coancestry and inbreeding.

Predicting the consequences of selecting on PrP genotypes on PrP frequencies, performance and inbreeding in commercial meat sheep populations

Selection programmes based on prion protein (PrP) genotypes are being implemented for increasing resistance to scrapie. Commercial meat sheep populations participating in sire-referencing schemes were simulated to investigate the effect of selection on PrP genotypes on ARR and VRQ allele frequencies, inbreeding and genetic gain in a performance trait under selection. PrP selection strategies modelled included selection against the VRQ allele and in favour of the ARR allele. Assuming realistic initial PrP frequencies, selection against the VRQ allele had a minimal impact on performance and inbreeding. However, when selection was also in favour of the ARR allele and the frequency of this allele was relatively low, there was a loss of up to three to four years of genetic gain over the 15 years of selection. Most loss in gain occurred during the first five years. In general, the rate of inbreeding was reduced when applying PrP selection. Since animals were first selected on their PrP genotype before being selected on the performance trait, the intensity of selection on performance was weaker under PrP selection (compared with no PrP selection). Eradication of the VRQ allele or fixation of the ARR allele within 15 years of selection was possible only with PrP selection targeting all breeding animals.

Prediction of prion protein genotype and association of this genotype with lamb performance traits of Suffolk sheep

The association of the prion protein (PrP) gene with susceptibility to scrapie has formed the basis of selection programs aimed at eradicating the disease from sheep populations. Animals are genotyped for the PrP gene and those with the less susceptible genotypes are selected. The objectives of this study were to determine the effectiveness of predicting PrP genotypes by using information from relatives and to investigate the association of the PrP genotype with lamb performance traits in Suffolk sheep. Data were obtained from a scrapie-affected flock maintained in Scotland. A total of 643 were animals genotyped at codon 171 of the PrP gene with 2 alleles, R and Q. The genotypes of these animals were used to predict the genotypes of 5,173 nongenotyped animals in the same flock using segregation analysis. The genotype of nongenotyped animals was predicted from the probabilities for each possible genotype; further, an overall index for each animal was calculated to reflect the accuracy of prediction. Association analyses of the PrP gene (using animals with both known and inferred genotypes) with BW at birth, at weaning (56 d), and at 150 d, and for backfat and muscle depths at 150 d of age were carried out. A linear mixed model with random direct and maternal additive genetic effects, maternal permanent and temporary environmental effects, and year of birth was tested, and the most appropriate model was used for each trait. The expected number of Q alleles carried (from 0 to 2) by each animal was calculated and used in the model as a linear and quadratic covariate to test for associations with possible additive and dominance PrP gene effects, respectively. Results showed that the genotypes of relatively few animals (235) were inferred with certainty (compared with the 5,173 nongenotyped animals). Approximately 25% of the 5,173 predicted genotypes were inferred with a genotype probability index of 50% and greater. There was no significant association of the PrP gene with any of the performance traits studied (there were no significant additive or dominance effects). Such was the case whether data on animals with known or with both known and predicted genotypes were considered. It can be concluded that selection for PrP-resistant alleles in Suffolk sheep is unlikely to affect performance directly.

Optimization of the sampling strategy for establishing a gene bank: storing PrP alleles following a scrapie eradication plan as a case study

Gene banks are usually used for storing general genetic variability of endangered living populations but can be also used for storing alleles of a particular locus that are being eradicated through artificial selection programmes. In such scenarios gene banks would allow future re-introduction of one or more of the alleles being eradicated (and the associated diversity) into living populations. Frequencies within the bank for the locus of interest should have pre-determined target values. In this study, an algorithm is derived to obtain the optimal contributions of all candidate donors to achieve the target frequencies of the removed alleles in the bank while maintaining at the same time genetic variability in other loci unlinked to those targeted in the eradication programme. The efficiency of the algorithm is tested using the case of gene banks storing prion protein alleles currently disfavoured in scrapie eradication programmes (i.e., the AHQ, ARH, ARQ and VRQ alleles). Results showed that the algorithm was able to find the combinations of candidate contributions fulfilling different objectives regarding target frequencies and restrictions on coancestry. The most important factors influencing the optimal contributions were the allelic frequencies and the levels of diversity (coancestry) of the living population. Heterozygotes were favoured over homozygous individuals as, for a given number of animals contributing to the bank, the use of heterozygotes leads to lower levels of coancestry. Notwithstanding, almost all donors were sampled when restrictions on the global genetic diversity to be stored were severe.

Association of the prion protein gene with individual tissue weights in Scottish Blackface sheep.

This study investigated associations of prion protein (PrP) genotype with body composition and weight traits of Scottish Blackface ewes. Body composition was predicted using computer tomography (CT) scans to estimate muscle, carcass fat, internal fat, and bone weights. The traits were measured at 4 key seasonal production points (pre-mating, pregnancy, midlactation, and weaning) over 4 production cycles (2 to 5 yr old). There were 2,413 records for each of the CT traits measured on 335 ewes, and 26,649 records for each of the body condition score and BW traits for 2,356 ewes. From 1999 to 2004, animals were genotyped to determine polymorphisms at codons 136, 154, and 171, which are associated with scrapie susceptibility. Four alleles were found in the population (ARR, AHQ, ARQ, and VRQ). The data were analyzed using a linear mixed random regression model assuming that the direct additive genetic effect was a 2nd order Legendre polynomial function of time. The PrP genotype was included in the model as a fixed effect along with other fixed factors with significant effects (P < 0.05). Five separate analyses were carried out for each trait, depending on the method of classifying the PrP genotype. In the first analysis, animals were categorized according to the genotype. Only the 5 most common genotypes (ARR/ARR, ARR/AHQ, ARR/ARQ, AHQ/ARQ, and ARQ/ARQ) were included. In the last 4 analyses, animals were categorized according to the number of each PrP allele carried. For CT traits and body condition score, results showed that the PrP genotype has no association with the overall mean of the traits (averaged over age). For BW, ewes without the ARQ allele were at least 0.5 kg heavier than ARQ homozygous and heterozygous ewes. On the other hand, there was a significant interaction between PrP genotype and age of the ewe (i.e., the effect of PrP genotype was not the same at different ages for 5 out of the 6 traits studied). In general, ARQ carrying ewes mobilized more fat reserves at times of nutrient deficiency, such as during lactation, and gained it back more quickly by the mating season (when nutrients became abundant) than non-ARQ carriers. Therefore, selecting against this allele would have consequences on BW and seasonal mobilization of body reserves. The number of VRQ alleles (the most scrapie susceptible allele) carried was not significantly associated with any of the traits.

Accuracy of genomic within-family selection in aquaculture breeding programmes

In aquaculture breeding programmes, selection within families cannot be applied for traits that cannot be recorded on the candidates (e.g., disease resistance or fillet quality). However, this problem can be overcome if genomic evaluation is used. Within-family genomic evaluation has been proposed for these programmes as large family sizes are available and substantial levels of linkage disequilibrium (LD) within families can be attained with a limited number of markers even in populations in global linkage equilibrium. Here, we compare by computer simulation: (i) within-family and population-wide LD; and (ii) the accuracy of within-family genomic selection when genomic evaluations are carried out either at the population level or within families. The population simulated was composed by a varying number of families of full-sibs (half for training and half for testing). The results indicate that, to practice within-family selection, performing the genomic evaluation separately for each family using only molecular information from the family could be recommended for populations either in linkage equilibrium or with a low level of disequilibrium.