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.

Novel retinoid-related molecules as apoptosis inducers and effective inhibitors of human lung cancer cells in vivo.

Lung cancer causes more than 140,000 deaths annually in the United States alone, and the prognosis for non-small cell lung cancer (NSCLC) is particularly poor. Therapies using small molecules that preferentially kill lung tumor cells by inducing cellular suicide (apoptosis) would therefore be highly desirable. Retinoids have shown promise as cancer preventive and cancer therapeutic agents. Retinoid signals are mediated by two classes of nuclear receptors: the retinoic acid receptors (RAR alpha, beta, and gamma) and the retinoid X receptors (RXR alpha, beta and gamma). These receptors usually bind as heterodimers to specific DNA sequences and/or interact with other transcriptional regulators, such as AP-1 (ref. 10) to regulate gene transcription. Synthetic retinoids can be made that activate only specific portions of the complex retinoid response network and activate selective biological programs. To identify retinoids with novel biological activities, we used a high-throughput "biological activity fingerprint" screen on a large library of retinoids and retinoid-related molecules (RRMs). We identified new structures that are highly effective against lung cancer cells in vitro, inducing apoptosis. We show here for one of these compounds that it is very effective against a human NSCLC in vivo in an animal model. These new molecules show a distinct pattern of receptor signaling.

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.

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).

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.

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.

Effect of medium- and long-chain triglyceride supplementation on small newborn-pig survival.

The pre-weaning survival of 508 piglets was studied with a categorical survival analysis, evaluating the effect of medium-long-chain triglyceride (MCT-LCT) supplementation on small newborn pigs, and determining additional risk factors. Half of the 98 piglets born with birth weight (BW)<1250 g received 1.95 g of MCT-LCT each 24 h during the first 3 days of life, and their death hazard was reduced 1.9-fold in relation with small unsupplemented siblings. The death hazard ratio (HR) of supplemented animals compared to 410 heavier littermates was not different. However, the HR for newborn pigs that were small in relation with their siblings was 2.8, and the HR for litters with >12 piglets born alive was 4.5. There was variation across months, and also piglets from primiparous sows had increased hazard of death (HR=4.0).

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.

Resistance to hyperosmotic stress in boar spermatozoa: the role of the ionic pumps and the relationship with cryosurvival.

The resistance to changes in the osmolarity of boar sperm was used to measure the resistance of boar sperm cells against freezing/thawing. Semen was incubated for 5 min in different solutions ranging from about 600 mOsm to about mOsm, and at 4 degrees C, 16 degrees C or 37 degrees C (undisturbed media). This undisturbed media was constituted by NaCl, glycerol or glucose. This semen was then placed in an isoosmotic solution (disrupted solutions). Incubation in undisturbed media did not alter the percentages of viability or altered acrosomes, except when the initial incubation has been at 37 degrees C and with osmolarities above 1000 mOsm. Viability and altered acrosome statistics were strongly modified in disrupted media. These effects are dependent upon the initial osmolarity of the media, but not upon the temperature. Pre-incubation with ouabain or amiloride did not affect spermatozoa incubated at 16 degrees C in a 2211 mOsm, NaCl medium. However, in sperm incubated in this 2211 mOsm medium and then rapidly placed in an isoosmotic solution, ouabain induced a decrease in viability and an increase in altered acrosomes. Amiloride did not affect the response of cells to the disrupted medium. Some significant correlations were observed among the percentages of altered acrosomes after hyperosmotic stress and some quality parameters of the fresh boar semen, especially the motion parameters. Although the resistance to hyperosmotic stress could be a valuable parameter in assessing fresh quality analysis, its usefulness in frozen-thawed semen is compromised, since other factors beside osmotic changes are involved in the resistance of boar semen to freezing-thawing. The NA+/K+, ouabain-dependent ATP-ase activity seems to be related to the mechanisms of resistance to hyperosmotic stress in boar sperm.

Effect of column filtration upon the quality parameters of fresh dog semen.

We filtered dog semen through various resin columns to obtain a quick, simple system for improving semen quality. Fresh ejaculates were filtered through columns with either glasswool or a chemically-inert polypropylene network disc. The columns were filled with Sephadex G-15 (nonionic resin), Sephadex A-50 (anionic-exchange resin), Sephadex C-50 (cationic-exchange resin) or a combination of Sephadex A-50 and C-50. Filtration through glasswool improved semen quality, with a significant (P < 0.001) increase in the percentage of viability and decrease in the percentage of altered acrosomes (P < 0.001) and total abnormalities (P < 0.001). Total motility was not modified, but curvilinear velocity or linearity of the movement were improved using the glasswool bed. The effect of the glasswool was so intense that it masked the effects of the filtration resins. Substitution of glasswool by polypropylene discs resulted in an unmasking of the effects of the resins, although the polypropylene exerted slight effects on semen. Elution of the spermatozoa through Sephadex G-15 or Sephadex C-50 resulted in a decrease of altered acrosomes. However, filtration through Sephadex A-50 increased viability and decreased the percentage of altered acrosomes and total abnormalities. Combined filtration through Sephadex A-50 and C-50 yielded the combined results observed with the resins individually. Ultrastructural imaging of the interaction between spermatozoa and the beds and resins showed that the cells were loosely deposited upon the glasswool fibers and the Sephadex G-15 particles, whereas close interaction was observed between spermatozoa and Sephadex A-50 and C-50 particles. The whole of the sperm cell bound to C-50 particles, whereas spermatozoa were specifically bonded to A-50 particles in the apical region of the head and in segments of the tail, which were periodically distributed. The data suggest that filtration through glasswool or an anionic resin-exchange can significantly improve dog semen quality.

Maternal animal model with correlation between maternal environmental effects of related dams.

A procedure to take into account the nongenetic relationship between maternal effects in adjacent generations is presented. It considers a correlation between maternal environments provided by a dam and its daughters (lambda). The dispersion structure of the maternal animal model was modified to include a correlation matrix (E) that relates the maternal permanent environmental effects. The structures of the E matrix and its inverse (E(-1)) are described. Both matrices are completely defined by the correlation coefficient lambda. An algorithm to compute these matrices from pedigree information was also developed. Furthermore, a Bayesian analysis of this model including the lambda parameter was developed using Gibbs sampling, with Metropolis steps for the nonstandard conditional distributions. With simulated data, the proposed model reduced the bias in all estimates of dispersion parameters when an antagonism between the maternal effects received by a daughter and its future maternal environment existed. This model also provides an estimate of the environmental relationship between the maternal effects of dams and daughters by the lambda parameter. The same Bayesian analysis was also carried out with weaning weight data of the Bruna dels Pirineus breed. The posterior means (standard deviation) of (co)variance ratios were .214 (.081) for direct heritability (h2d), .107 (.033) for maternal heritability (h2m), .047 (.020) for the proportion of variance due to maternal environmental effects (c2m), and -.034 (.043) for the genetic correlation between direct and maternal effects (r(dm)). The posterior mean of lambda parameter was -.190, and 76% of its marginal posterior distribution took negative values. As occurred with simulated data, considering the maternal environmental correlation in the analysis implied higher h2m estimates, lower c2m and h2d estimates, and less negative values for the marginal posterior distribution of r(dm). These results were considered as evidence of the environmental antagonism between maternal effects provided by a dam and its daughters to weaning weight of their progeny in the Bruna dels Pirineus breed.

Viability of Iberian x Meishan F2 newborn pigs. I. Analysis of physiological and vitality variables.

Eight physiological and vitality variables related to the first minutes of the life of Iberian x Meishan F2 piglets were analyzed. Variables included rectal temperature, arterial oxygen saturation, heart rate (all were monitored at birth and 60 min later), time to reach the udder, and time to the first colostrum intake. Litter effect within boar, a random source of variation, influenced all variables, whereas the random boar effect was not significant for heart rate and arterial oxygen saturation at birth and the time to reach the udder. Birth weight influenced rectal temperature at birth (P < 0.01) and 60 min later (P < 0.001), arterial oxygen saturation 1 h after birth (P < 0.05), heart rate 1 h after birth (P < 0.001), time to reach the udder (P < 0.05), and time to the first suckle (P < 0.01), whereas viability score influenced rectal temperatures (at birth and 60 min later; P < 0.001), and time to reach the udder (P < 0.001) and to suckle (P < 0.001). Finally, the order of birth showed significant effects for rectal temperature 1 h after birth (P < 0.001) and time to first colostrum intake (P < 0.001). Correlation coefficients between physiological variables were generally low, with the exception of the ones for rectal temperature 1 h after birth and arterial oxygen saturation 1 h after birth (0.38; P < 0.001), and for rectal temperature at birth and rectal temperature 1 h after birth (0.34; P < 0.001). Times to reach the udder and to suckle were highly correlated (0.67; P < 0.001) and also were moderately and negatively correlated with rectal temperature 1 h after birth (-0.36 and -0.38 respectively; P < 0.001). Heart rates at birth and 1 h later, as well as arterial oxygen saturation at birth and 1 h later, were not correlated, showing that the values at birth do not necessarily provide information about the physiological status of the pig 1 h after birth. The recording of physiological variables, birth weight, and viability score may be useful to identify weak piglets quickly and to establish palliative measures.

Viability of Iberian x Meishan F2 newborn pigs. II. Survival analysis up to weaning.

Iberian x Meishan F2 piglet's preweaning survivability was analyzed using categorical data regression procedures within the proportional hazards assumption. A frailty sire model was assumed with the litter effect treated as an additional random source of variation. Moreover, the relative birth weight within litter and the litter effect were considered time-dependent covariates that changed their values in the second day of life due to cross fostering carried out to standardize litters. Six variables had a significant effect on survivability: birth weight (P < 0.01), relative birth weight within litter (P < 0.001), rectal temperature 60 min after birth (P < 0.01), type of presentation at birth (P < 0.05), presence of stillbirths (P < 0.001), and presence of mummified fetuses (P < 0.001). Small piglets (<0.98 kg) suffered a high hazard ratio (6.57; P < 0.001), with this variable being clearly lower for the rest of birth weight categories. Piglets that were small in relation to their siblings (relative birth weight within litter) also suffered an increased death risk, with a hazard ratio of 1.81 (P < 0.05), which was similar to animals with posterior presentations at birth (hazard ratio = 1.80; P < 0.05). Piglets with a rectal temperature lower than 35.4 degrees C 60 min after birth showed the highest hazard ratio (7.18; P < 0.01). Furthermore, the presence of mummified fetuses decreased the survivability of the remaining siblings, with a hazard ratio of 2.03 (P < 0.01), as did the presence of stillbirths (hazard ratio = 3.55; P < 0.001). The inclusion of the two random effects allowed us to estimate the mode of the joint posterior density of the sire variance (0.08) and the litter variance (1.98). The estimated heritability of preweaning survival reached a value of 0.03. We conclude that piglet survival involves several systematic influences related to birth weight, thermoregulatory ability, and injuries suffered during gestation and farrowing. The genetic variance was small compared with those generated by the common environment, for which the genetic improvement of piglet survival seems difficult.

Fatty acid profiles in three stress genotypes of swine and relationships with performance, carcass and meat quality traits.

The objective of this study was to investigate differences in adipose tissue fatty acid composition among stress genotypes as well as to determine relationships of those fatty acids with performance, carcass and meat quality traits. Haplotypic analysis of parents and offspring was employed to assign 48 pigs to three stress genotypes of swine. Individual fatty acid profiles were determined on subcutaneous backfat. Stress genotype had a significant effect on the proportions of C14:0 (P<0.05), C16:0 (P<0.10), C16:1 (P<0.05) and C18:0 (P<0.05) fatty acids. After adjusting for stress and gender, there was a negative correlation between backfat thickness and essential fatty acids (linoleic and linolenic) (P<0.001). In contrast, the correlation of loin muscle area with C18:2 (P<0.01) and C18:3 (P<0.001) was positive. The degree of fat firmness was negatively correlated to the proportion of total unsaturated fatty acids (P<0.01). No significant correlations were observed between fatty acid contents and lean meat quality traits.

Characterisation of young bulls of the Bruna dels Pirineus cattle breed (selected from old Brown Swiss) in relation to carcass, meat quality and biochemical traits.

Seventy-four young bulls of the Bruna dels Pirineus beef cattle breed were reared in a typical production system and slaughtered at an average age of 381 days and live weight of 541 kg. The animals were evaluated for productive traits, carcass quality, meat quality, eating quality and biochemical characteristics of m. longissimus thoracis (LT). Biochemical measurements included intramuscular fat (IMF) and collagen proportion, haem pigment concentration, lactate dehydrogenase and isocitrate dehydrogenase activities and type I (MHC I) fibre percentage determined by ELISA. Bruna dels Pirineus bulls achieved high growth rates during the fattening period (1.63 kg/day) and showed good carcass quality, with a high dressing-out proportion (607 g/kg, hot carcass), a good conformation score (U; EUROP) and a moderate fatness score (3;1-5). Carcass composition was estimated from the sixth rib joint dissection (682 g/kg lean proportion, 127 g/kg total dissectable fat and 163 g/kg bone). IMF (24.3 g/kg) and MHC I (27.9%) showed high variabilities (CV>30%). Sensory analysis of LT included beef and livery odour and flavour intensity, and overall tenderness and juiciness assessment of loin samples (14-day ageing). Beef odour and flavour were slightly positively correlated with IMF and carcass fatness score (P<0.05). Fatness, MHC I, insoluble collagen and cooking losses tended to affect the livery flavour intensity positively. This variable was significantly higher in meat from bulls of lower carcass quality (i.e. lower conformation score, lower lean proportion; P<0.05) and higher type I fibre percentage. Loin overall tenderness and juiciness were not affected by the biochemical traits studied, however, they were negatively affected by cooking loss (P<0.05).

The effect of breed-production systems on the myosin heavy chain 1, the biochemical characteristics and the colour variables of Longissimus thoracis from seven Spanish beef cattle breeds.

The effect of breed-production system on the myosin heavy chain 1 (MHC-I), the biochemical characteristics and the colour variables of longissimus thoracis (LT) from seven beef breeds was studied: Asturiana de la Montaña (AM), Asturiana de los Valles (AV), Avileña-Negra Ibérica (A-NI), Bruna dels Pirineus (BP), Morucha (MO), Pirenaica (PI) and Retinta (RE) (Age at slaughter between 368 and 541 days; carcass weight between 249 and 334 kg). Significant differences between breed-production systems were found for all traits evaluated. LT from the MO, a rustic type breed, was the most oxidative (MHC-I, 39.3%; isocitrate dehydrogenase activity, 52 nmol min(-1) mg(-1); pigment content, 188.4 µg acid haematin g(-1)) and showed a low L* value (32.6) and high a* and C* values (24 and 27.2, respectively). In terms of meat colour (L* and a*) the canonical discriminant analysis separated the breeds into two groups, the AV, the PI and the A-NI (the lightest ones) from the AM and the MO breeds (the reddest and darkest) whereas the BP showed an intermediate position. The RE and the A-NI were distinguished from the others by their high intramuscular fat content. Meat colour was affected by the muscle biochemical traits in the breed-production systems studied.

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.

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.