Effect of fibrous diet and vitamin C inclusion on uniformity, carcass traits, skeletal strength, and behavior of broiler breeder pullets.

This experiment studied the effect of broiler breeder nutritional strategies on uniformity, carcass traits, tibia parameters, and behavior during rearing and prebreeder periods (up to 22 wk of age). One-day-old pullets (n = 384) were randomly assigned to 4 treatments arranged as a 2 × 2 factorial, with 2 fiber levels (control vs. fibrous diet, 15% diluted in AMEn and nutrient content) and 2 vitamin C feed inclusions (0 vs. 200 mg/kg). At 6, 15, and 22 wk, blood sampling was carried out (4 birds/replicate) to determine serum alkaline phosphatase (ALP) levels, and behavior was observed by visual scan sampling. At 22 wk, carcass traits, tibia parameters, and intestinal morphology were assessed (2 birds/replicate), and tail- and wing-feather integrity of all birds were scored. Fibrous diet did not modify BW uniformity, mortality, or tibia growth when compared with control diet. Pullets fed the fibrous diet had lower tibia breaking strength, elastic modulus, and ash content values (P < 0.05). They also had lower ALP serum level at 6 and 22 wk (P < 0.05), their breast muscle was less developed (18.5 vs. 19.8%, P < 0.05), and their abdominal fat deposition was higher (1.14 vs. 0.87%, P < 0.05). At 15 and 22 wk, they performed, on average, 97% less grasping feather pecking and 45% less non-food object pecking behaviors, and their wing-feather score was lower (P < 0.05) at 22 wk. Tail- and wing-feather scores of the control treatments were reduced by vitamin C inclusion (tail: 0.30 vs. 1.15, P < 0.05; wing: 0.98 vs. 1.26, P < 0.05) at 22 wk. In conclusion, fibrous diet improves carcass traits (reduces breast muscle and increases abdominal fat deposition), deteriorates bone mineral deposition and thus skeletal strength, and reduces stereotypic behaviors, improving wing-feather integrity. Vitamin C inclusion improves tail- and wing-feather integrity of lower in feed allowance.

Evaluation of the potential use of a meta-population for genomic selection in autochthonous beef cattle populations.

This study investigated the potential application of genomic selection under a multi-breed scheme in the Spanish autochthonous beef cattle populations using a simulation study that replicates the structure of linkage disequilibrium obtained from a sample of 25 triplets of sire/dam/offspring per population and using the BovineHD Beadchip. Purebred and combined reference sets were used for the genomic evaluation and several scenarios of different genetic architecture of the trait were investigated. The single-breed evaluations yielded the highest within-breed accuracies. Across breed accuracies were found low but positive on average confirming the genetic connectedness between the populations. If the same genotyping effort is split in several populations, the accuracies were lower when compared with single-breed evaluation, but showed a small advantage over small-sized purebred reference sets over the accuracies of subsequent generations. Besides, the genetic architecture of the trait did not show any relevant effect on the accuracy with the exception of rare variants, which yielded slightly lower results and higher loss of predictive ability over the generations.

Genomic differentiation between Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta and Rubia Gallega cattle breeds.

The Spanish local beef cattle breeds have most likely common origin followed by a process of differentiation. This particular historical evolution has most probably left detectable signatures in the genome. The objective of this study was to identify genomic regions associated with differentiation processes in seven Spanish autochthonous populations (Asturiana de los Valles (AV), Avileña-Negra Ibérica (ANI), Bruna dels Pirineus (BP), Morucha (Mo), Pirenaica (Pi), Retinta (Re) and Rubia Gallega (RG)). The BovineHD 777K BeadChip was used on 342 individuals (AV, n=50; ANI, n=48; BP, n=50; Mo, n=50; Pi, n=48; Re, n=48; RG, n=48) chosen to be as unrelated as possible. We calculated the fixation index (F ST ) and performed a Bayesian analysis named SelEstim. The output of both procedures was very similar, although the Bayesian analysis provided a richer inference and allowed us to calculate significance thresholds by generating a pseudo-observed data set from the estimated posterior distributions. We identified a very large number of genomic regions, but when a very restrictive significance threshold was applied these regions were reduced to only 10. Among them, four regions can be highlighted because they comprised a large number of single nucleotide polymorphisms and showed extremely high signals (Kullback-Leiber divergence (KLD)>6). They are located in BTA 2 (5 575 950 to 10 152 228 base pairs (bp)), BTA 5 (17 596 734 to 18 850 702 bp), BTA 6 (37 853 912 to 39 441 548 bp) and BTA 18 (13 345 515 to 15 243 838 bp) and harbor, among others, the MSTN (Myostatin), KIT-LG (KIT Ligand), LAP3 (leucine aminopeptidase 3), NAPCG (non-SMC condensing I complex, subunit G), LCORL (ligand dependent nuclear receptor corepressor-like) and MC1R (Melanocortin 1 receptor) genes. Knowledge on these genomic regions allows to identify potential targets of recent selection and helps to define potential candidate genes associated with traits of interest, such as coat color, muscle development, fertility, growth, carcass and immunological response.

Bayesian analysis of parent-specific transmission ratio distortion in seven Spanish beef cattle breeds.

Transmission ratio distortion (TRD) is the departure from the expected Mendelian ratio in offspring, a poorly investigated biological phenomenon in livestock species. Given the current availability of specific parametric methods for the analysis of segregation data, this study focused on the screening of TRD in 602 402 single nucleotide polymorphisms covering all autosomal chromosomes in seven Spanish beef cattle breeds. On average, 0.13% (n = 786) and 0.01% (n = 29) of genetic markers evidenced sire- or dam-specific TRD respectively. There were no single nucleotide polymorphisms accounting for both sire- and dam-specific TRD at the same time, and only one marker (rs43147474) accounted for (sire-specific) TRD in all seven breeds. It must be noted that rs43147474 is located in the fourth intronic region of the GTP-binding protein 10 gene, and this locus has been previously linked to the maintenance of mitochondria and nucleolar architectures. Alternatively, other candidate genes surround this hot-spot for sire-specific TRD in the cattle genome, and they are related to embryonic and postnatal lethality as well as prostate cancer, among others. This research characterized the distribution of TRD in the bovine genome, highlighting heterogeneous results when comparing across breeds.

Linkage disequilibrium, persistence of phase, and effective population size in Spanish local beef cattle breeds assessed through a high-density single nucleotide polymorphism chip.

Linkage disequilibrium (LD) and persistence of phase are fundamental approaches for exploring the genetic basis of economically important traits in cattle, including the identification of QTL for genomic selection and the estimation of effective population size () to determine the size of the training populations. In this study, we have used the Illumina BovineHD chip in 168 trios of 7 Spanish beef cattle breeds to obtain an overview of the magnitude of LD and the persistence of LD phase through the physical distance between markers. Also, we estimated the time of divergence based on the persistence of the LD phase and calculated past from LD estimates using different alternatives to define the recombination rate. Estimates of average (as a measure of LD) for adjacent markers were close to 0.52 in the 7 breeds and decreased with the distance between markers, although in long distances, some LD still remained (0.07 and 0.05 for markers 200 kb and 1 Mb apart, respectively). A panel with a lower boundary of 38,000 SNP would be necessary to launch a successful within-breed genomic selection program. Persistence of phase, measured as the pairwise correlations between estimates of in 2 breeds at short distances (10 kb), was in the 0.89 to 0.94 range and decreased from 0.33 to 0.52 to a range of 0.01 to 0.08 when marker distance increased from 200 kb to 1 Mb, respectively. The magnitude of the persistence of phase between the Spanish beef breeds was similar to those found in dairy breeds. For across-breed genomic selection, the size of the SNP panels must be in the range of 50,000 to 83,000 SNP. Estimates of past showed values ranging from 26 to 31 for 1 generation ago in all breeds. The divergence among breeds occurred between 129 and 207 generations ago. The results of this study are relevant for the future implementation of within- and across-breed genomic selection programs in the Spanish beef cattle populations. Our results suggest that a reduced subset of the SNP panel would be enough to achieve an adequate precision of the genomic predictions.

Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip.

The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD BeadChip genotyping array was used to describe the genetic variability and divergence among 7 important autochthonous Spanish beef cattle breeds. The within-breed genetic diversity, measured as the marker expected heterozygosity, was around 0.30, similar to other European cattle breeds. The analysis of molecular variance revealed that 94.22% of the total variance was explained by differences within individuals whereas only 4.46% was the result of differences among populations. The degree of genetic differentiation was small to moderate as the pairwise fixation index of genetic differentiation among breeds (F) estimates ranged from 0.026 to 0.068 and the Nei's D genetic distances ranged from 0.009 to 0.016. A neighbor joining (N-J) phylogenetic tree showed 2 main groups of breeds: Pirenaica, Bruna dels Pirineus, and Rubia Gallega on the one hand and Avileña-Negra Ibérica, Morucha, and Retinta on the other. In turn, Asturiana de los Valles occupied an independent and intermediate position. A principal component analysis (PCA) applied to a distance matrix based on marker identity by state, in which the first 2 axes explained up to 17.3% of the variance, showed a grouping of animals that was similar to the one observed in the N-J tree. Finally, a cluster analysis for ancestries allowed assigning all the individuals to the breed they belong to, although it revealed some degree of admixture among breeds. Our results indicate large within-breed diversity and a low degree of divergence among the autochthonous Spanish beef cattle breeds studied. Both N-J and PCA groupings fit quite well to the ancestral trunks from which the Spanish beef cattle breeds were supposed to derive.

Monitoring changes in the demographic and genealogical structure of the main Spanish local beef breeds.

Demographic and pedigree analyses describe the structure and dynamics of livestock populations. We studied information recorded in the herdbooks of Asturiana de los Valles (AV; N = 458,806), Avileña-Negra Ibérica (ANI; N = 204,623), Bruna dels Pirineus (BP; N = 62,138), Morucha (Mo; N = 65,350), Pirenaica (Pi; N = 217,428), Retinta (Re; N = 135,300), and Rubia Gallega (RG; N = 235,511) beef breeds from their creation until 2009. All breeds have increased in the number of registered cows in recent years. In all breeds, herds do not behave as isolated entities and a high rate of exchange of breeding males between herds exists. A percentage of herds (12-52%) make some type of selection and sell bulls to other herds. There were large differences in average number of progeny per bull, ranging from 15.6 (AV) to 373.7 animals (RG, with a high incidence of AI). Generation interval estimates ranged from 4.7 (AV) to 7.6 (RG) yr in the sire pathway and from 5.95 (AV) to 7.8 (Mo) yr in the dam pathway. Density of pedigrees varied among breeds, with Pi, ANI, and Re having the more dense pedigrees, with average completeness indexes of more than 96% in the first generation and 80% when 6 generations were considered. A general increase in average inbreeding was observed in all breeds in the years analyzed. For animals born in 2009, average inbreeding coefficients ranged from 0.6 (BP) to 7.2% (Re) when all animals were considered and from 3.6 (Pi) to 17.6% (BP) when only inbred animals were considered. Due to the lack of completeness of pedigrees in most populations, inbreeding coefficients may be considered as a lower bound of the true parameters. The proportion of inbred animals tended to increase in the periods analyzed in all breeds. Differences between inbreeding and coancestry rates (except in RG) suggest the presence of population structure. Effective population size (Ne) based on the inbreeding rate estimated by regression ranged from 43 to 378 for Re and BP, whereas Ne estimates based on coancestry were greater, with a range of 100 for RG to 9,985 for BP. These facts suggest that an adequate mating policy can help to monitor inbreeding so as not to lose genetic variability. Effective number of ancestors in 2009 for 6 of the breeds ranged from 42 (RG) to 220 (AV), with BP having much a greater value, and was lower than was the effective number of founders in all breeds, suggesting the existence of bottlenecks.

Canalization analysis of birth weight in Bruna dels Pirineus beef cattle.

Although heteroskedasticity has been a main topic of interest in beef cattle during recent decades, the current availability of canalization models provided new insights for animal breeding programs. Within this context, birth BW (BWT) was analyzed in the Bruna dels Pirineus beef cattle breed by implementing canalization models that accounted for heterogeneous residual variances due to systematic, permanent environmental effects and additive genetic effects. Analyses were performed on BWT data from 8,130 calves born in 12 commercial breeding herds contributing to the yield recording scheme of the Bruna dels Pirineus breed. Analytical models accounted for direct additive genetic, permanent environmental, and 4 systematic effects (i.e., age of the dam, sex of the calf, birth type, and herd-year-season), and the same effects were evaluated as potential sources of variation in the residual term. Their relevance was checked by the deviance information criterion (DIC), and only residual additive genetic, permanent environmental, birth type, and herd-year-season remained in the operational model, all of them originating relevant reductions in the DIC parameter. Bruna dels Pirineus calves showed a moderate heritability of 0.30 (95% high posterior density, 0.19 to 0.40) for BWT; additional additive genetic variability was revealed in the residual term, this being positively correlated with the direct additive genetic component (0.44; 95% high posterior density, 0.37 to 0.54). Genetic trends were evaluated on both sources of additive genetic variance, and relevant patterns were identified in several herds. Although this breed did not evidence a homogeneous genetic trend for the whole population, herd-specific positive and negative trends were revealed, suggesting the plausibility of genetic selection for canalization on BWT in beef cattle breeds. These results must be viewed as a contribution to the canalization research field, providing relevant information for the breeding scheme of the Bruna dels Pirineus breed, as well as important insights about the genetic background of BWT for the beef industry worldwide.

Backfat thickness and longissimus dorsi real-time ultrasound measurements in light lambs.

The aim of this study was to assess the accuracy of ultrasound measurements for predicting carcass traits in 124 Spanish pascual-type lambs (13 to 16 kg carcass weight). Ultrasound images were taken transversal and longitudinal to the vertebral column and at thoracic (TV; between 12th and 13th ribs) and lumbar (LV; between first and second lumbar vertebrae) locations. Skin thickness, subcutaneous backfat thickness (BFT), and depth (DLD), width (WLD), and area (ALD) of longissimus dorsi were obtained with ImageJ 1.42q software. After slaughter, BFT (TV, 2.30 ± 0.06 mm; LV, 2.46 ± 0.06 mm), DLD (TV, 2.47 ± 0.03 cm; LV, 2.48 ± 0.03 cm), WLD (TV, 4.50 ± 0.04 cm; LV, 4.60 ± 0.04 cm), and ALD (TV, 9.96 ± 0.12 cm(2); LV, 10.19 ± 0.13 cm(2)) were directly measured on the lamb carcass. Correlations between ultrasound and direct carcass measurements were greater than 0.61 for DLD, WLD, and ALD (P < 0.05) whereas they fluctuated between 0.32 and 0.60 for BFT (P < 0.05); moreover, correlations were significantly (P < 0.05) greater for transversal than for longitudinal views. In a similar way, linear regression analyses suggested a moderate underestimation for BFT and lumbar DLD when using real-time ultrasound technologies whereas WLD, ALD, and thoracic DLD suffered from under- and overestimation for small and large values of carcass traits, respectively. After decomposing the mean square prediction error (MSPE) for the different ultrasound measurements, we found that the error due to disturbance contributed most to the MSPE followed by the error of central tendency and the error due to regression. The SE of prediction (SEP) was also calculated as an additional precision indicator, obtaining estimates less than that in previous studies with larger lambs. In conclusion, transversal ultrasound measurements at the thoracic and lumbar levels could be a useful tool for predicting DLD, WLD, and ALD in light lambs, perhaps suffering from worse prediction properties when focusing on BFT. This information could be of special relevance for light lamb producers worldwide, with a special emphasis in the Mediterranean basin where this kind of production system accounts for a large percentage of the sheep industry.

Sources of sire-specific genetic variance for birth and weaning weight in Bruna dels Pirineus beef calves.

This research investigated two sources of sire-specific genetic effects on the birth weight (BWT) and weaning weight (WWT) of Bruna dels Pirineus beef calves. More specifically, we focused on the influence of genes located in the non-autosomal region of the Y chromosome and the contribution of paternal imprinting. Our analyses were performed on 8130 BWT and 1245 WWT records from 12 and 2 purebred herds, respectively, they being collected between years 1986 and 2010. All animals included in the study were registered in the Yield Recording Scheme of the Bruna dels Pirineus breed. Both BWT and WWT were analyzed using a univariate linear animal model, and the relevance of paternal imprinting and Y chromosome-linked effects were checked by the deviance information criterion (DIC). In addition to sire-specific and direct genetic effects, our model accounted for random permanent effects (dam and herd-year-season) and three systematic sources of variation, that is, sex of the calf (male or female), age of the dam at calving (six levels) and birth type (single or twin). Both weight traits evidenced remarkable effects from the Y chromosome, whereas paternal imprinting was only revealed in WWT. Note that differences in DIC between the preferred model and the remaining ones exceed 39 000 and 2 800 000 DIC units for BWT and WWT, respectively. It is important to highlight that Y chromosome accounted for ∼2% and ∼6% of the total phenotypic variance for BWT and WWT, respectively, and paternal imprinting accounted for ∼13% of the phenotypic variance for WWT. These results revealed two relevant sources of sire-specific genetic variability with potential contributions to the current breeding scheme of the Bruna dels Pirineus beef cattle breed; moreover, these sire-specific effects could be included in other beef cattle breeding programs or, at least, they must be considered and appropriately analyzed.

Parametric bootstrap for testing model fitting of threshold and grouped data models: an application to the analysis of calving ease of Bruna dels Pirineus beef cattle.

The aim of this study was to compare the goodness of fit of the threshold models with homoscedasticity or heteroscedasticity and the grouped data model for the analysis of calving ease in beef cattle by using a parametric bootstrap procedure. Field data included 8,205 records of the Bruna dels Pirineus beef cattle breed in the Pyrenean mountain areas of Catalonia (Spain). The actual distribution was 81.81% of calvings without assistance, 11.02% slightly assisted by the farmer, 5.12% strongly assisted by the farmer, 0.89% assisted by the veterinarian, and 1.16% cesarean, but these percentages were very different in the different herds. This can be explained partially by the different subjective way of scoring of each farmer. Primiparous cows had a greater (P < 0.001) difficulty calving than cows with 5 or more parities (11.74 vs. 4.49% of calvings strongly assisted by the farmer or the veterinarian and 2.8 vs. 0.65% cesarean). Male calves caused greater (P < 0.001) calving difficulty than females (7.71% of male calvings strongly assisted by the farmer or the veterinarian vs. 4.25% of females and 1.83% cesarean in males vs. 0.47% in females). The month and year of calving also had a strong influence on calving ease. These data were analyzed using 3 different models: the threshold models with homoscedasticity or heteroscedasticity and the grouped data model. The bootstrap comparison among models suggested that the threshold models, even allowing for heteroscedasticity, did not fit the herd effects well. In contrast, fitting deficiencies were not observed for the grouped data model in any factor. The variance of direct effect of the calf was estimated using the 3 models, and the heritability estimate ranged from 0.165 for the grouped data model to 0.185 for the hereroscedastic threshold model. This heritability was moderate, but it would justify the inclusion of direct effects of the calf on calving ease in the breeding objective. Overall, results highlighted the flexibility of the grouped data model for the analysis of discrete traits, like calving ease of beef calves.

Accounting for additive genetic mutations on litter size in Ripollesa sheep.

Little is known about mutational variability in livestock, among which only a few mutations with relatively large effects have been reported. In this manuscript, mutational variability was analyzed in 1,765 litter size records from 404 Ripollesa ewes to characterize the magnitude of this genetic source of variation and check the suitability of including mutational effects in genetic evaluations of this breed. Threshold animal models accounting for additive genetic mutations were preferred to models without mutational contributions, with an average difference in the deviance information criterion of more than 5 units. Moreover, the statistical relevance of the additive genetic mutation term was checked through a Bayes factor approach, which showed that the models with mutational variability were 8.5 to 22.7 times more probable than the others. The mutational heritability (percentage of the phenotypic variance accounted for by mutational variance) was 0.6 or 0.9%, depending on whether genetic dominance effects were accounted for by the analytical model. The inclusion of mutational effects in the genetic model for evaluating litter size in Ripollesa ewes called for some minor modifications in the genetic merit order of the individuals evaluated, which suggested that the continuous uploading of new additive mutations could be taken into account to optimize the selection scheme. This study is the first attempt to estimate mutational variances in a livestock species and thereby contribute to better characterization of the genetic background of productive traits of interest.

Analysis of founder-specific inbreeding depression on birth weight in Ripollesa lambs.

Although inbreeding (F) is a topic of major concern in animal breeding, estimates of inbreeding depression are usually obtained by modeling the overall F coefficient of each individual, without considering that the recessive (deleterious) genetic load of a given population may be unevenly distributed among the founder genomes. The founder-specific partial F coefficient is calculated as the identity-by-descent probability at any given autosomal locus related to a particular founder and allows a more detailed analysis of inbreeding depression on productive traits. Within this context, birth BW data from 2,459 Ripollesa lambs were analyzed under a hierarchical animal model without F-related covariates (model 0), with inbreeding depression modeled by the overall F coefficient (model F1), or by the partial F coefficient of 9 founders that made a relevant contribution to the population inbreeding (model F2). A straightforward empirical Bayes factor (BF) was developed for testing statistical relevance of each F-related covariate, in which greater-than-1 values favored the model including the covariate. The deviance information criterion (DIC) clearly supported model F1 (5,767.8) rather than model 0 (5,771.2), suggesting that inbreeding depression had a relevant influence on birth BW data. The linear effect of inbreeding depression was statistically relevant in model F1 (BF = 2.52 x 10(35)), with lamb birth BW declining by -13.6 g with each 1% F increase. The quadratic effect of inbreeding depression was almost null in model F1 (BF = 0.02), as suggested by the reduction in DIC (5,766.9) when this effect was removed from model F1. On the other hand, model F2 provided a similar DIC (5,767.9) value, with this parameter decreasing to 5,764.7 when nonrelevant founder-specific inbreeding depression effects were removed. Substantial heterogeneity in founder-specific inbreeding depression was reported by model F2, in which estimates for 4 of the 9 founders did not differ from zero (BF between 0.05 and 0.42), whereas 5 founders originated moderate (-8.2 g for each 1% F increase; BF = 1.42) to large inbreeding depression (-96.2 g for each 1% F increase; BF = 8.80 x 10(19)). The substantial variability between founder estimates suggested that inbreeding depression effects may mainly be due to a few alleles with major deleterious effects. These results contribute valuable information that should help to achieve more accurate management of inbreeding in the Ripollesa breed.

Using haplotype probabilities in categorical survival analysis: a case study with three candidate genes in an Iberian x Meishan F2 population of newborn piglets.

Haplotype probabilities have been implemented in association analyses performed between three candidate genes and the preweaning survival of F2 Iberian x Meishan piglets, under a categorical proportional hazard model. The additive effect of substitution of each haplotype was estimated using information of parental genotypes for non-genotyped piglets. Analysed loci were the bone morphogenetic protein type 1B receptor (BMPR1B) gene at 8q25 (three SNPs; haplotypes BMPR1B A, BMPR1B B, BMPR1B C and BMPR1B D), the dopamine beta-hydroxylase (DBH) gene at 1q2.13 (two SNPs; haplotypes DBH X, DBH Y and DBH Z), and the prolactin receptor (PRLR) gene at 16q1.4-q2.3 (six SNPs; haplotypes PRLR A, PRLR B, PRLR C, PRLR D and PRLR E). The number of analysed records were 899 (BMPR1B), 850 (DBH) and 822 (PRLR) with a censoring percentage ranged between 87 and 89%. Associations with preweaning survival were suggested for BMPR1B (p < 0.10) and associations were clearly significant for DBH haplotypes (p < 0.05), whereas the PRLR locus did not reach statistical significance (p > 0.10). The BMPR1B A haplotype could increase piglet survivability in relation to the BMPR1B B haplotype with a hazard ratio of 0.751 and a confidence interval (CI) between 0.550 and 1.025 (p < 0.10). The two remaining haplotypes did not differ significantly from the BMPR1B B haplotype, with a hazard ratio higher than 0.90 (p > 0.10). For the DBH locus, the DBH X and the DBH Z haplotypes were associated with an improved preweaning survival in relation to the DBH Y haplotype. The advantage for DBH X in terms of hazard ratio was 0.789 (CI = 0.625 to 0.994; p < 0.05) and differences between DBH Y and DBH Z reached a hazard ratio of 0.770 (CI = 0.606 to 0.977; p < 0.05). Although further researches are required, BMPR1B and DBH genes could be a useful tool to improve piglet survival under a marker assisted selection strategy.

Eating quality of young bulls from three Spanish beef breed-production systems and its relationships with chemical and instrumental meat quality.

Sensory characteristics of longissimus thoracis muscle from three local Spanish beef breed-production systems and their relationships with chemical and instrumental meat quality traits were studied. Young bulls of Bruna dels Pirineus (BP; n=69), Avileña-Negra Ibérica (A-NI; n=70) and Morucha (MO; n=70) breeds were reared in their own production systems. MO breed showed the highest water holding capacity and also the highest thawing loss and haem pigment content (P<0.001). No differences in moisture and protein contents were found among breeds. A-NI showed the highest intramuscular fat (IMF, P<0.05) and total collagen (P<0.001) contents, whereas BP showed the lowest IMF content (P<0.05) and the highest collagen solubility (P<0.001). Beef flavour, tenderness and juiciness accounted for the eating quality differences among the three breed-production systems. Meat from A-NI was rated significantly higher (P<0.01) for beef flavour and tenderness than that from BP and MO animals. Furthermore, MO showed the lowest juiciness (P<0.001) which could be due to its higher thawing loss. Within the three breeds, thawing loss was negatively correlated with juiciness and, likewise cooking loss with juiciness and tenderness (P<0.05). The canonical discriminant analysis showed that the three breeds were significantly different (P<0.05) from each other according to sensory attributes, which justifies their involvement in different protected geographical indications (PGI).

Survival analysis from birth to slaughter of Ripollesa lambs under semi-intensive management.

The survivability from birth to slaughter of 1,487 Ripollesa lambs with a preslaughter overall mortality of 9.6% was studied under the proportional hazards framework, assuming a Weibull distribution for the baseline hazards function. A sire frailty model was fitted, with the common environment received by the lamb as an additional random source of variation. Common environment was considered time-dependent and was characterized by the dam and the contemporary lamb group during the preweaning and fattening periods, respectively. Only 3 fixed effects were statistically significant: the linear and quadratic effects of birth weight (P < 0.001), the relative position of the delivery within the lambing season (P < 0.001), and the presence of stillbirths or mummified fetuses within the litter (P < 0.05). Birth type and parity of the ewe were significant only when birth weight was removed from the model (P < 0.001 and P < 0.05, respectively). Nevertheless, the model including birth weight became preferable according to the Akaike's information criterion. Survivability dramatically decreased with extreme birth weights, although it reached a survival probability greater than 93.5% within the 3.3 to 5.4 kg range, indicating an optimum birth weight range of Ripollesa lambs for survival purposes. The hazard ratio (HR) increased for births occurring within the last third of the lambing period (HR = 1.70; P < 0.05), as well as for primiparous ewes that lambed in December and January (HR = 5.36; P < 0.001). Survival probability decreased for lambs born from litters with 1 or more stillbirths or mummified fetuses (HR = 1.61; P < 0.05). The variance component estimated for sire variance (0.07) was clearly lower than that of the common environment (1.87), with a heritability estimate of 0.027.

Analysis of litter size and days to lambing in the Ripollesa ewe. I. Comparison of models with linear and threshold approaches.

The analysis focused on model fitting of 2 ewe reproductive traits, litter size, and days to lambing (interval between the introduction of the ram into the flock and the subsequent parturition of the ewes). The experimental data set of the Universitat Autònoma of Barcelona flock was used, including 1,598 records of litter size and 1,699 records of days to lambing from 376 Ripollesa ewes between 1986 and 2005. Univariate and bivariate models were considered as beginning points with linear or threshold approximation for litter size. Model fitting was evaluated in terms of goodness-of-fit and predictive ability, using the mean square error and the correlation between phenotypic and predicted records (rho(y,y)) as reference parameters. The bivariate model was preferable for both variables, minimizing mean square error and maximizing rho(y,y). A threshold approximation for litter size was preferable over a linear approximation. Models were also compared with a simulation study, comparing the correlation coefficient between simulated and predicted breeding values (rho(a,â)). The bivariate threshold model was favored, with a rho(y,y) of 0.677 and 0.834 for litter size and days to lambing, respectively. Correlation coefficients between simulated and predicted breeding values in the bivariate linear model were reduced slightly to 0.651 and 0.831, respectively, and they were lowest with linear univariate models (0.642 and 0.802). Although the bivariate models for ewe litter size and days to lambing were more accurate than the univariate models, the threshold approaches showed a greater advantage under the bivariate model. For the purpose of genetic evaluation of litter size in sheep, use of the threshold-linear model seems justified. In the Ripollesa breed, the evaluation of litter size can benefit from recording birth weight.

Genetic determinism for within-litter birth weight variation and its relationship with litter weight and litter size in the Ripollesa ewe breed.

Birth weight plays a central role in lamb survival and growth, and the knowledge of its genetic determinism has become essential in worldwide selection programmes. Within this context, within-litter birth weight variation (BWV) has been suggested as an attractive trait to homogenise litters in prolific species, although it has not been analysed in sheep. The objective of this study was to ascertain whether maternal additive genetic variance exists for BWV in Ripollesa ewes, and to study its genetic, permanent environmental and residual relationships with litter weight (LW) and litter size (LS) at birth. Data were recorded in the Ripollesa experimental flock of the Universitat Autònoma of Barcelona, between 1986 and 2005, and included 1 662 litters from 380 ewes, with 712 records of BWV and 1 530 records of LW. Traits were analysed with a multivariate animal model solved through Bayesian methodologies, and with a threshold characterisation of LS. Additionally, the effect of BWV on lamb survival was studied. Additive genetic variance was observed for BWV (h2 = 0.061), as well as for LW (h2 = 0.200) and LS (h2 = 0.141). Nevertheless, genetic correlations among those traits were not substantial (BWV and LW = 0.151; BWV and LS = - 0.219; LW and LS = - 0.320) and suffered from a high degree of uncertainly, with the null correlation included within the highest posterior interval at 95%. Within-litter birth weight variation and LS showed a negative and large permanent environmental correlation ( - 0.872), and LW and LS were negatively correlated due to residual ( - 0.762) and permanent environmental ( - 0.449) random sources of variation. Within-litter birth weight variation influenced lamb mortality during the first 7 days of life (P < 0.05), increasing and decreasing survivability in heavier and lighter littermates, respectively. Nevertheless, stillbirths and lambs died after the 1st week of life were not affected by BWV (P>0.05). The low heritability found indicates that slow genetic progress may be expected from selecting for BWV. Close to zero genetic correlations suggest that this selection will probably not affect LS and LW, although some significant permanent and residual correlations must be taken into account. Further studies are needed to understand better the genetic architecture among these three reproductive traits.

Analysis of litter size and days to lambing in the Ripollesa ewe. II. Estimation of variance components and response to phenotypic selection on litter size.

A performance data set from 376 Ripollesa purebred ewes of the experimental flock of the Universitat Autònoma of Barcelona was analyzed using a bivariate Bayesian threshold-linear model. The data set contained 1,598 litter size records and 1,699 days-to-lambing records. The model included the additive genetic effect of each animal and 3 nongenetic sources of variation: ewe age, year of lambing, and the permanent environmental effect characterized by the ewe. The flock was phenotypically selected for litter size since 1986, and replacement ewes and rams were selected from the progeny of the more prolific ewes, which had at least 3 deliveries recorded. The phenotypic trend for litter size was positive, whereas days to lambing followed an unclear pattern. Both traits had low heritabilities; 0.13 for litter size and 0.11 for days to lambing. Response to selection was evaluated through (a) the average breeding value of the ewe lambs chosen annually, and (b) the average breeding value of the overall flock. The first measurement suggested a positive trend for litter size, although it showed important oscillations. On the other hand, the average breeding value for the overall flock showed a stable positive tendency after yr 4 of selection, with estimates clearly different from zero after yr 11 of selection. A significant increase in the incidence of multiple births was observed, with a mode of approximately 10%. The correlated response in days to lambing did not show a significant trend. The effect of year of lambing also positively influenced both litter size and days to lambing, although important oscillations were observed between years. Results indicated that litter size in sheep can be effectively improved through phenotypic selection, even in small flocks; moreover, days to lambing could also be genetically improved, given the estimate obtained for its heritability.

Association analyses between the prion protein locus and reproductive and lamb weight traits in Ripollesa sheep.

The objective of this study was to analyze the association between the haplotypes of the prion protein (PrP) locus and several reproductive and lamb weight traits in Ripollesa sheep. Prion protein genotypes were available for a total of 310 sheep (7 rams, 114 ewes, and 189 lambs), all of them belonging to the purebred Ripollesa flock of the Universitat Autònoma of Barcelona, for which all sheep had a known pedigree. In addition, the genotype of 24 historical descendants of the previously genotyped adult individuals was reconstructed, provided that both parents were homozygous for PrP haplotypes. Only 3 haplotypes (ARR, ARQ, and ARH) were observed in the PrP locus of the sheep sampled. Reproductive traits included conception rate and litter size, whereas birth BW and 90-d BW were the lamb weight traits studied. The additive effect of PrP haplotypes was analyzed through Bayesian animal threshold and linear models, for reproduction and weight traits, respectively. Ewe reproductive data belonged to 89 ewes that gave 492 conception rate records and 440 litter size records. Analyses of BW at birth and at 90 d of age were made on 323 and 164 lamb records, respectively. No associations between PrP haplotypes and conception rate and BW traits were observed. For litter size, the effect of the ARH haplotype was greater than that of the ARQ haplotype. Differences between ARH and ARR haplotypes also suggested an advantage for the ARH. As a whole, our results indicated that the selection favorable to increase litter size in Ripollesa ewes may also increase the ARH haplotype frequency, which contradicts the recommendations of the current European Union legislation aiming to increase the genetic resistance to scrapie. As a consequence, scrapie genotyping needs to be included as a new selection criterion in the breed.