Assessment of accuracy of genomic prediction for French Lacaune dairy sheep.

Genomic selection in Lacaune dairy sheep was investigated based on genotypes from the OvineSNP50 BeadChip (Illumina Inc., San Diego, CA). Historical artificial insemination progeny-tested rams formed a population of 2,892 genotyped rams. Additional ungenotyped rams and females were included by single-step genomic BLUP (ssGBLUP). Three prediction strategies were tried: pseudo-BLUP (using all rams and daughter yield deviations), pseudo-ssGBLUP (using all rams and daughter yield deviations), and regular ssGBLUP (using all phenotypes and pedigree in an animal model). The population linkage disequilibrium was determined, with an average squared correlation coefficient of 0.11 for markers closer than 0.1cM (lower than in dairy cattle). The estimated effective population is 370 individuals. Gain in accuracy of genomic selection over parent averages ranged from 0.10 to 0.20. Highest accuracies and lowest bias were found using regular ssGBLUP. Transition to a genomic breeding scheme is possible but costs need to be carefully evaluated.

Within- and across-breed genomic predictions and genomic relationships for Western Pyrenees dairy sheep breeds Latxa, Manech, and Basco-Béarnaise.

Genotypes, phenotypes and pedigrees of 6 breeds of dairy sheep (including subdivisions of Latxa, Manech, and Basco-Béarnaise) from the Spain and France Western Pyrenees were used to estimate genetic relationships across breeds (together with genotypes from the Lacaune dairy sheep) and to verify by forward cross-validation single-breed or multiple-breed genetic evaluations. The number of rams genotyped fluctuated between 100 and 1,300 but generally represented the 10 last cohorts of progeny-tested rams within each breed. Genetic relationships were assessed by principal components analysis of the genomic relationship matrices and also by the conservation of linkage disequilibrium patterns at given physical distances in the genome. Genomic and pedigree-based evaluations used daughter yield performances of all rams, although some of them were not genotyped. A pseudo-single step method was used in this case for genomic predictions. Results showed a clear structure in blond and black breeds for Manech and Latxa, reflecting historical exchanges, and isolation of Basco-Béarnaise and Lacaune. Relatedness between any 2 breeds was, however, lower than expected. Single-breed genomic predictions had accuracies comparable with other breeds of dairy sheep or small breeds of dairy cattle. They were more accurate than pedigree predictions for 5 out of 6 breeds, with absolute increases in accuracy ranging from 0.05 to 0.30 points. They were significantly better, as assessed by bootstrapping of candidates, for 2 of the breeds. Predictions using multiple populations only marginally increased the accuracy for a couple of breeds. Pooling populations does not increase the accuracy of genomic evaluations in dairy sheep; however, single-breed genomic predictions are more accurate, even for small breeds, and make the consideration of genomic schemes in dairy sheep interesting.

Genomic selection in the French Lacaune dairy sheep breed.

Genomic selection aims to increase accuracy and to decrease generation intervals, thus increasing genetic gains in animal breeding. Using real data of the French Lacaune dairy sheep breed, the purpose of this study was to compare the observed accuracies of genomic estimated breeding values using different models (infinitesimal only, markers only, and joint estimation of infinitesimal and marker effects) and methods [BLUP, Bayes Cπ, partial least squares (PLS), and sparse PLS]. The training data set included results of progeny tests of 1,886 rams born from 1998 to 2006, whereas the validation set had results of 681 rams born in 2007 and 2008. The 3 lactation traits studied (milk yield, fat content, and somatic cell scores) had heritabilities varying from 0.14 to 0.41. The inclusion of molecular information, as compared with traditional schemes, increased accuracies of estimated breeding values of young males at birth from 18 up to 25%, according to the trait. Accuracies of genomic methods varied from 0.4 to 0.6, according to the traits, with minor differences among genomic approaches. In Bayes Cπ, the joint estimation of marker and infinitesimal effects had a slightly favorable effect on the accuracies of genomic estimated breeding values, and were especially beneficial for somatic cell counts, the less heritable trait. Inclusion of infinitesimal effects also improved slopes of predictive regression equations. Methods that select markers implicitly (Bayes Cπ and sparse PLS) were advantageous for some models and traits, and are of interest for further quantitative trait loci studies.

The effects of parity, litter size, physiological state, and milking frequency on the metabolic profile of Lacaune dairy ewes.

Effects of parity (primiparous, PRIM vs multiparous, MULT) and litter size (singletons, SING vs twins, TWIN) on metabolic profiles from 1 wk before lambing to the end of lactation were studied in 48 Lacaune dairy ewes reared in confinement during most of the year and grazed on improved pastures at the end of lactation (summer). Another group of 48 ewes was incorporated during the milking period (ie, from 1 wk after weaning), to measure the effects of milking frequency (1 vs 2 milkings per day) on intake, milk production and composition, and body energy usage. Thus, in a 2 × 2 × 2 factorial design, ewes (n = 96) were allocated to homogeneous groups according to body weight (BW) and body condition score (BCS) and were monitored from late pregnancy to late lactation as a function of parity (PRIM, n = 48; MULT, n = 48), litter size (LSi) (SING, n = 40; TWIN, n = 56) and daily milking frequency (FREQ; milked once, ONE; n = 48; or twice, TWO; n = 48). Individual BW, BCS, plasma metabolites, and metabolic hormones were measured regularly (ie, 9 consecutive sampling dates). The BW was higher in MULT but no differences because of LSi or FREQ were detected at the intra-parity group level. The BCS was higher in MULT and in ewes with SING throughout the experiment. The latter was related to the demands for body reserves mobilization, as expressed by higher nonesterified fatty acids and ß-hydroxybutyrate concentrations in ewes with TWIN from late pregnancy to weaning (35 d postpartum) in both PRIM and MULT ewes. This was consistent with higher insulin in MULT and higher triiodothyronine, leptin and insulin-like growth factor 1 in ewes with SING during this period. Differences in energy balance because of FREQ were evident after interpretation of plasma nonesterified fatty acids, glucose, insulin, and leptin concentration during the milking period. At similar feed intakes, ewes in ONE were in positive balance with regard to TWO. Overall, clear effects of parity, LSi, physiological states, and FREQ on metabolic profiles were found because of differences in nutrient partitioning when combining these experimental factors. Without considering FREQ, changes in metabolic measures in milking period were marginal compared with the periparturient adjustments performed until weaning to compensate energy deficiencies.

Comparison of French natural scrapie isolates with bovine spongiform encephalopathy and experimental scrapie infected sheep.

We compared the glycoform pattern of the abnormal prion protein (PrP(Sc)) detected by immunoblotting in 21 sheep with natural scrapie, from 21 different outbreaks identified in France since 1996, with a bovine spongiform encephalopathy (BSE)-infected sheep. All the natural scrapie isolates had a higher molecular mass of the unglycosylated PrP(Sc) than in BSE-infected sheep. In the latter case, this molecular mass appeared identical to that found in the CH 1641 experimental scrapie strain (type C pattern), whereas in natural scrapie cases it was similar to that found in the SSBP/1 experimental scrapie strains. These results suggest that all French natural scrapie isolates studied so far would belong, as SSBP/1, to the group of scrapie cases with type A electrophoretic pattern.

Identification of seven haplotypes of the caprine PrP gene at codons 127, 142, 154, 211, 222 and 240 in French Alpine and Saanen breeds and their association with classical scrapie.

In sheep, susceptibility to scrapie is mainly influenced by polymorphisms of the PrP gene. In goats, there are to date few data related to scrapie susceptibility association with PrP gene polymorphisms. In this study, we first investigated PrP gene polymorphisms of the French Alpine and Saanen breeds. Based on PrP gene open reading frame sequencing of artificial insemination bucks (n=404), six encoding mutations were identified at codons 127, 142, 154, 211, 222 and 240. However, only seven haplotypes could be detected: four (GIH(154)RQS, GIRQ(211)QS, GIRRK(222)S and GIRRQP(240)) derived from the wild-type allele (G(127)I(142)R(154)R(211)Q(222)S(240)) by a single-codon mutation, and two (S(127)IRRQP(240) and GM(142)RRQP(240)) by a double-codon mutation. A case-control study was then implemented in a highly affected Alpine and Saanen breed herd (90 cases/164 controls). Mutations at codon 142 (I/M), 154 (R/H), 211 (R/Q) and 222 (Q/K) were found to induce a significant degree of protection towards natural scrapie infection. Compared with the baseline homozygote wild-type genotype I(142)R(154)R(211)Q(222)/IRRQ goats, the odds of scrapie cases in IRQ(211)Q/IRRQ and IRRK(222)/IRRQ heterozygous animals were significantly lower [odds ratio (OR)=0.133, P<0.0001; and OR=0.048, P<0.0001, respectively]. The heterozygote M(142)RRQ/IRRQ genotype was only protective (OR=0.243, P=0.0186) in goats also PP(240) homozygous at codon 240. However, mutated allele frequencies in French Alpine and Saanen breeds were low (0.5-18.5 %), which prevent us from assessing the influence of all the possible genotypes in natural exposure conditions.

No associations between PrP genotypes and reproduction traits in INRA 401 sheep.

In this study, the potential association of PrP genotypes with ewe reproductive traits and lamb growth traits was investigated. Data were included on ewes and lambs of the INRA 401 breed from the Bourges-La Sapinière INRA experimental farm. This breed was chosen because of good breeding (prolificacy and maternal abilities) and carcass qualities, and the large number of available animals with performance records and PrP genotypes. Ewes were categorized into 3 PrP genotype classes: ARR homozygous, ARR heterozygous, and animals without any ARR haplotype. Two analyses differing in the traits considered were carried out. Firstly, the potential association of the PrP genotype of ewes with their reproduction traits (fertility, litter size, and ovulation rate) was studied. The data included 801, 779, and 587 genotyped ewes for fertility, litter size, and ovulation rate, respectively. Secondly, the association of the PrP genotype of the ewes with growth traits of their lambs (birth weight, ADG between 10 and 30 d of age) was investigated. The data included 3,749 and 3,512 lambs for birth weight and ADG, respectively. The different traits were analyzed using an animal model, where the PrP genotype effect was included as a fixed effect. The reproductive traits were modeled under a probit or a threshold approach. The results of this study indicate no evidence of an association between PrP genotypes and reproductive and growth traits. It is unlikely that selection for scrapie resistance will have an effect on the reproductive or performance traits studied in the INRA 401 breed.

Genetic parameters for milk somatic cell scores and relationships with production traits in French Lacaune dairy sheep.

Records from 94,445 and 45,499 French Lacaune dairy ewes in first and second lactations, respectively, were used to estimate genetic parameters for somatic cell scores. Somatic cell count data came from an extensive recording scheme and sample testing that began in 1999 using the flocks enrolled in the official milk recording system. Somatic cell count data were from 2 to 4 test days per lactation. Lactation average and single test-day somatic cell scores were considered in multitrait sire models. The heritability estimate of lactation somatic cell score was close to 0.13 and similar for first and second parity. Heritabilities of somatic cell scores increased from first to fourth test day (from 0.07 to 0.11 in first lactation and from 0.05 to 0.13 in second lactation). Genetic correlations between somatic cell scores were high, usually more than 0.91, but lower between first test day and later test days in first lactation (0.64 to 0.88). The genetic correlations between lactation somatic cell score and milk yield, between lactation somatic cell score and fat content, and between lactation somatic cell score and protein content were 0.18, 0.04, and 0.03 in first lactation, respectively. The genetic antagonism between test day somatic cell score and milk yield measured in first lactation increased from beginning to the end of the lactation (0.05 to 0.23). This antagonism was slightly lower for somatic cell score in second lactation (from 0.09 to 0.14, and 0.08 for lactation mean). Environmental correlations in first lactation between lactation somatic cell score and milk yield, between lactation somatic cell score and fat content, and between lactation somatic cell score and protein content were -0.18, 0.13, and 0.30, respectively.

Genetic analysis for mastitis resistance and milk somatic cell score in French Lacaune dairy sheep.

Genetic analysis for mastitis resistance was studied from two data sets. Firstly, risk factors for different mastitis traits, i.e. culling due to clinical or chronic mastitis and subclinical mastitis predicted from somatic cell count (SCC), were explored using data from 957 first lactation Lacaune ewes of an experimental INRA flock composed of two divergent lines for milk yield. Secondly, genetic parameters for SCC were estimated from 5 272 first lactation Lacaune ewes recorded among 38 flocks, using an animal model. In the experimental flock, the frequency of culling due to clinical mastitis (5% ) was lower than that of subclinical mastitis (10% ) predicted from SCC. Predicted subclinical mastitis was unfavourably associated with the milk yield level. Such an antagonism was not detected for clinical mastitis, which could result, to some extent, from its low frequency or from the limited amount of data. In practice, however, selection for mastitis resistance could be limited in a first approach to selection against subclinical mastitis using SCC. The heritability estimate of SCC was 0.15 for the lactation mean trait and varied from 0.04 to 0.12 from the first to the fifth test-day. The genetic correlation between lactation SCC and milk yield was slightly positive (0.15) but showed a strong evolution during lactation, i.e. from favourable (-0.48) to antagonistic (0.27). On a lactation basis, our results suggest that selection for mastitis resistance based on SCC is feasible. Patterns for genetic parameters within first lactation, however, require further confirmation and investigation.

Management of myiasis: current status and future prospects.

The management of myiasis in livestock has been an example of the success of modern chemical approaches for parasite control, yet in some cases remains extremely intractable, requiring the development of novel strategies. In addition, the growing and urgent need to develop integrated strategies that enhance the sustainability of livestock production systems drives the search for new techniques [see Int. J. Parasitol. 29 (1999) 7].The following summary represents a synthesis of a symposium presented at the 19th International Conference of the World Association for the Advancement of Veterinary Parasitology, New Orleans,USA, 10­14 August 2003. The coverage began with a review of the need for more subtle economic analysis of the impact of myiasis based on the use of the sterile insect technique (SIT) for control of bovine hypodermosis in North America. This was followed by a review of the status of chemical control with particular emphasis on the macrocyclic lactones. The outcome of the use of these compounds in a regulated control program for eradication of bovine hypodermosis in EU was surveyed. Similarly, the success of the screwworm eradication program, using the sterile insect technique has shown how effective this approach can be given the appropriate target. Several aspects of the development of newer approaches were surveyed in discussion of newer chemical control products, development of vaccines, use of host genetics, use of predictive simulation modelling and trapping for monitoring and control and the development of new diagnostic approaches for occult infestations. Finally, use of the latest molecular tools for identification of larvae causing myiasis and their use for the identification of species coming from different and distant geographical areas to colonize regions where they have been eradicated was reviewed.