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Summary Reasons for performing study: Mesenchymal stromal cells (MSCs) represent an attractive source for regenerative medicine. However, prior to their application, fundamental questions regarding molecular characterisation, growth and differentiation of MSCs must be resolved. Objectives: To compare and better understand the behaviour of equine MSCs obtained from bone marrow (BM) and adipose tissue (AT) in culture. Methods: Five horses were included in this study. Proliferation rate was measured using MTT assay and cell viability; apoptosis, necrosis and late apoptosis and necrosis were evaluated by flow cytometry. The mRNA expression levels of 7 surface marker genes were quantified using RT-qPCR and CD90 was also analysed by flow cytometry. Differentiation was evaluated using specific staining, measurement of alkaline phosphatase activity and analysis of the mRNA expression. Results: High interindividual differences were observed in proliferation in both cell types, particularly during the final days. Statistically significant differences in viability and early apoptosis of cultured AT- and BM-MSCs were found. The highest values of early apoptosis were observed during the first days of culture, while the highest percentage of necrosis and late apoptosis and lowest viability was observed in the last days. Surface marker expression pattern observed is in accordance to other studies in horse and other species. Osteogenic differentiation was evident after 7 days, with an increasing of ALP activity and mRNA expression of osteogenic markers. Adipogenic differentiation was achieved in BM-MSCs from 2 donors with one of the 16 media tested. Chondrogenic differentiation was also observed. Conclusions: Proliferation ability is different in AT-MSCs and BM-MSCs. Differences in viability and early apoptosis were observed between both sources and CD34 was only found in AT-MSCs. Differences in their osteogenic and adipogenic potential were detected by staining and quantification of specific tissue markers. Potential relevance: To provide data to better understand AT-MSCs and BM-MSCs behaviour in vitro. [ABSTRACT FROM AUTHOR]

Summary Teat number is an important trait in sows that should accompany the increase in litter size that has been achieved in the last decades through selection. We have previously identified a genome-wide significant QTL for teat number in porcine chromosome SSC5 by means of an experimental Meishan by Iberian F2 intercross population. In the present report, we have studied the porcine parathyroid hormone-like hormone ( PTHLH) gene, which maps to SSC5, as a candidate gene for this trait, as PTHLH is involved in nipple formation during embryogenesis and nipple development during pregnancy and lactation. We have found that porcine PTHLH gene is transcribed into three mRNA species differing in the 5′UTR region. Two of these variants are reported in pigs here for the first time: one was similar to variant 1 described in humans while the other, which was generated by the retention of two small introns, has not been identified before in any other species. In addition, mRNA expression profile for two of the mRNA variants was assessed in 19 pig tissues. Porcine PTHLH showed a widespread expression as it was present in all tested tissues and relative expression of each variant was tissue dependent. Finally, we have performed an association study between a non-synonymous mutation in the coding region of this gene and sow teat number. The PTHLH polymorphism was segregating in our Meishan by Iberian F2 population at intermediate allelic frequencies. We compared here six different statistical models to choose the one with a better fit and a lower degree of complexity. However, despite the potential negative effect of the PTHLH mutation in the signal peptide of this protein, we did not detect any association between the PTHLH genotype and the sow teat number phenotype, concluding that the causal mutation of the observed QTL is very likely not related to this gene. [ABSTRACT FROM AUTHOR]

Abstract: A total of 255,538 performance records in competitions with Spanish Trotter Horses, collected from 1991 to 2007, were used to include and evaluate competitive information using the Thurstonian model. The model analysis included: sex (2 classes), age (3) and race (3920) as systematic effects; and trainer-driver, permanent environment and genetic effects as random effects. The pedigree file included 10,940 animals. REML methodology was also used to compare the results obtained with the same and similar traits. The heritability obtained was 0.09, which is within the range of the values reported in the reviewed literature for ranking traits in horses, and similar to the value obtained for the same trait with the same model and the same database using a REML methodology (0.05). The trainer-driver effect had a total variability of 17%, similar to the effect of the rider in other equestrian disciplines. Males were 0.15 better than females in standard deviations, and young animals were 0.24 better than middle-aged animals and 0.59 better than the older animals in standard deviations. The differences in the animals'' genetic ranking by their breeding values are also shown using the percentage of coincidence for the top and bottom 20% of the animals in the genetic ranking, and elite horses (top 5%). Higher values were obtained in the comparison with the same trait, the same model and the same database using REML methodology (ranging between 89.39% and 92.81% for the top 5% and bottom 20%, respectively). The practical application of this model has therefore shown adequate results. It allows us to compare between the underlying variable without the effect of race level, and produces more suitable estimations for genetic parameters and breeding values in the population. The inclusion of the race effect in the model is also important, because with a mixed animal model approach, the information for breeding values and permanent environmental effect comes from several races with sufficient genetic connectedness, although competitions are usually structured into categories according to the technical level of difficulty linked to the technical ability of the horses'' performance. [Copyright &y& Elsevier]

In livestock, skeletal muscle is a tissue of major economic importance for meat production and muscle mass is largely determined during the prenatal period by the number and the size of muscle fibres. The understanding of gene expression changes during prenatal pig muscle development is still limited. In this study, genes identified as differentially expressed in a previous microarray research and chosen for the function of the coded protein as putative candidate involved in myogenesis were considered to analyse their expression profile during foetal growth of Duroc and Pietrain pigs. The eleven genes were considered by real-time PCR for a time-course evaluation of the transcription level at six stages of prenatal longissimus dorsi development. The results suggest that the most relevant variations in mRNA levels of the analysed genes seem to follow temporal waves of gene expression. Significant changes of transcription were observed at 21-35 and 63-91 days, the two main phases of skeletal muscle development. During the early phases of Pietrain embryos' development, 10 of the 11 genes showed an induction. In Duroc embryos, a second phase of gene up-regulation can be identified in the phase 63-77 days. These results provide new data on developmental changes of expression profile of 11 genes involved in different functional pathways related to prenatal myogenic processes in Duroc and Pietrain pigs. [ABSTRACT FROM AUTHOR]

We developed and implemented change-point recursive models and compared them with a linear recursive model and a standard mixed model (SMM), in the scope of the relationship between litter size (LS) and number of stillborns (NSB) in pigs. The proposed approach allows us to estimate the point of change in multiple-segment modeling of a nonlinear relationship between phenotypes. We applied the procedure to a data set provided by a commercial Large White selection nucleus. The data file consisted of LS and NSB records of 4,462 parities. The results of the analysis clearly identified the location of the change points between different structural regression coefficients. The magnitude of these coefficients increased with LS, indicating an increasing incidence of LS on the NSB ratio. However, posterior distributions of correlations were similar across subpopulations (defined by the change points on LS), except for those between residuals. The heritability estimates of NSB did not present differences between recursive models. Nevertheless, these heritabilities were greater than those obtained for SMM (0.05) with a posterior probability of 85%. These results suggest a nonlinear relationship between LS and NSB, which supports the adequacy of a change-point recursive model for its analysis. Furthermore, the results from model comparisons support the use of recursive models. However, the adequacy of the different recursive models depended on the criteria used: the linear recursive model was preferred on account of its smallest deviance value, whereas nonlinear recursive models provided a better fit and predictive ability based on the cross-validation approach. [ABSTRACT FROM AUTHOR]

The previous results from a genome scan for total number of piglets born and number of piglets born alive in a F2 Iberian by Meishan intercross showed several single and epistatic QTL. One of the most interesting results was obtained for SSC12, where two QTL affecting both traits showed epistatic interaction. In this study, we proposed two genes ( SLC9A3R1 and NOS2) as biological and potentially positional candidates underlying these QTL. Both cDNAs were characterized and 23 polymorphisms were detected. A chromosome scan was conducted with 12 markers, plus one SNP in SLC9A3R1 and one in NOS2, covering 110 cM of SSC12. The epistatic QTL (QTL1 at 15 cM and QTL2 at 97 cM) were confirmed, and SLC9A3R1 and NOS2 were mapped around the QTL1 and QTL2 regions respectively. Several SNPs in both genes were tested with standard animal model and marker assisted association tests. The most significant results were obtained with the NOS2 haplotype defined by one missense SNP c.2192C > T (Val to Ala) and a 15 bp duplication at the 3′UTR. This duplication seems to include AU-rich elements, and could be a target site for miRNA, therefore there are statistical and biological indications to consider this haplotype as the potential causal mutation underlying QTL2. SLC9A3R1 results were not conclusive. Although the interaction between the SNPs was not significant, we cannot reject the possibility of interaction of the NOS2 haplotype with other polymorphisms closely linked to the SL9A3R1 SNPs analysed. [ABSTRACT FROM AUTHOR]

Acetyl-coenzyme A carboxylase α (ACACA) catalyses the first committed step in the biosynthesis of long-chain fatty acids (FA) by converting acetyl-CoA into malonyl-CoA. In pigs, the ACACA gene maps to a chromosome 12 QTL with important effects on FA composition. In the present study, we have sequenced the coding region of the pig ACACA gene in 15 pigs, identifying 21 polymorphic sites that were either synonymous or non-coding. Ten of these SNPs segregated in a Duroc commercial population ( n = 350) for which lipid metabolism and meat and carcass quality trait records were available. Significant associations were found between two linked single nucleotide polymorphisms (c.4899G>A and c.5196T>C) and percentages of carcass lean, intramuscular fat, monounsaturated, saturated (myristic, palmitic and stearic) and polyunsaturated (linoleic) FAs in the longissimus thoracis et lumborum muscle, along with serum HDL-cholesterol concentration. The most important allele substitution effects were observed for the polyunsaturated/saturated FA ratio (13–21% of the phenotypic mean) as well as for the percentages of ω-6 and polyunsaturated FAs, especially linoleic acid (7–16% of the phenotypic mean). These results suggest the existence of a causal mutation, mapping to the chromosomal region containing the pig ACACA gene, with marked effects on FA composition of meat. [ABSTRACT FROM AUTHOR]

Current selection schemes for livestock improvement use a wide variety of phenotypic traits. Some of them, such as sensory, type, or carcass traits, obtain their records from subjective grading performed by trained technicians. Data from this subjective evaluation usually involve classification under a categorical and arbitrary predefined scale, whose output may lead to strong departures from the Gaussian distribution. In addition, the scale of grading may be different according to different technicians. To study this phenomenon, we have analyzed subjective conformation (CON) and fat cover (FAT) scores in the Pirenaica beef cattle breed from data provided by 12 different slaughterhouses. Three statistical models were used: 1) a Gaussian linear model; 2) an ordered category threshold model; and 3) a specific slaughterhouse ordered category threshold model. These models were analyzed through a Bayesian analysis via a Gibbs sampler with a data augmentation step. Posterior mean estimates of heritability ranged from 0.23 to 0.26 for CON, and from 0.13 to 0.16 for FAT. Statistical models were compared by the deviance information criteria, and the slaughterhouse-specific ordered category threshold model was selected as the most plausible. This result was confirmed by the fact that the threshold estimates differed noticeably between slaughterhouses. Finally, the proposed model for genetic evaluation increased the expected selection response by up to 7.6% for CON and 11.2% for FAT. [ABSTRACT FROM AUTHOR]

This work aims to compare different nonlinear functions for describing the growth curves of Nelore females. The growth curve parameters, their (co)variance components, and environmental and genetic effects were estimated jointly through a Bayesian hierarchical model. In the first stage of the hierarchy, 4 nonlinear functions were compared: Brody, Von Bertalanffy, Gompertz, and logistic. The analyses were carried out using 3 different data sets to check goodness of fit while having animals with few records. Three different assumptions about SD of fitting errors were considered: constancy throughout the trajectory, linear increasing until 3 yr of age and constancy thereafter, and variation following the nonlinear function applied in the first stage of the hierarchy. Comparisons of the overall goodness of fit were based on Akaike information criterion, the Bayesian information criterion, and the deviance information criterion. Goodness of fit at different points of the growth curve was compared applying the Gelfand's check function. The posterior means of adult BW ranged from 531.78 to 586.89 kg. Greater estimates of adult BW were observed when the fitting error variance was considered constant along the trajectory. The models were not suitable to describe the SD of fitting errors at the beginning of the growth curve. All functions provided less accurate predictions at the beginning of growth, and predictions were more accurate after 48 mo of age. The prediction of adult BW using nonlinear functions can be accurate when growth curve parameters and their (co)variance components are estimated jointly. The hierarchical model used in the present study can be applied to the prediction of mature BW in herds in which a portion of the animals are culled before adult age. Gompertz, Von Bertalanffy, and Brody functions were adequate to establish mean growth patterns and to predict the adult BW of Nelore females. The Brody model was more accurate in predicting the birth weight of these animals and presented the best overall goodness of fit. [ABSTRACT FROM AUTHOR]

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 × 1035), 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 × 1019). 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. [ABSTRACT FROM AUTHOR]

The objective of this work was to evaluate the Nelore beef cattle, growth curve parameters using the Von Bertalanffy function in a nested Bayesian procedure that allowed estimation of the joint posterior distribution of growth curve parameters, their (co)variance components, and the environmental and additive genetic components affecting them. A hierarchical model was applied; each individual had a growth trajectory described by the nonlinear function, and each parameter of this function was considered to be affected by genetic and environmental effects that were described by an animal model. Random samples of the posterior distributions were drawn using Gibbs sampling and Metropolis-Hastings algorithms. The data set consisted of a total of 145,961 BW recorded from 15,386 animals. Even though the curve parameters were estimated for animals with few records, given that the information from related animals and the structure of systematic effects were considered in the curve fitting, all mature BW predicted were suitable. A large additive genetic variance for mature BW was observed. The parameter a of growth curves, which represents asymptotic adult BW, could be used as a selection criterion to control increases in adult BW when selecting for growth rate. The effect of maternal environment on growth was carried through to maturity and should be considered when evaluating adult BW. Other growth curve parameters showed small additive genetic and maternal effects. Mature BW and parameter k, related to the slope of the curve, presented a large, positive genetic correlation. The results indicated that selection for growth rate would increase adult BW without substantially changing the shape of the growth curve. Selection to change the slope of the growth curve without modifying adult BW would be inefficient because their genetic correlation is large. However, adult BW could be considered in a selection index with its corresponding economic weight to improve the overall efficiency of beef cattle production. [ABSTRACT FROM AUTHOR]

A Bayesian procedure, which allows consideration of the individual variation in the feed resource allocation pattern, is described and implemented in 2 sire lines of rabbit (Caldes and R). The procedure is based on a hierarchical Bayesian scheme, where the first stage of the model consists of a multiple regression model of feed intake on metabolic BW and BW gain. In a second stage, an animal model was assumed including batch, parity order, litter size, and common environmental litter effects. Animals were reared during the fattening period (from weaning at 32 d of age to 60 d of age) in individual cages on an experimental farm, and were fed ad libitum with a commercial diet. Body weight (g) and cumulative feed in- take (g) were recorded weekly. Individual BW gain (g) and average BW (ABW, g) were calculated from these data for each 7-d period. Metabolic BW (g075) was estimated as ABW075. The number of animals actually measured was 444 and 445 in the Caldes and R lines, respectively. Marginal posterior distributions of the genetic parameters were obtained by Gibbs sampling. Posterior means (posterior SD) for heritabilities for partial coefficients of regression of feed intake on metabolic BW and feed intake on BW gain were estimated to be 0.35 (0.17) and 0.40 (0.17), respectively, in the Caldes line and 0.26 (0.19) and 0.27 (0.14), respectively, in line R. The estimated posterior means (posterior SD) for the proportion of the phenotypic variance due to common litter environmental effects of the same coefficients of regression were respectively, 0.39 (0.14) and 0.28 (0.13) in the Caldes line and 0.44 (0.22) and 0.49 (0.14) in line R. These results suggest that efficiency of use of feed resources could be improved by including these coefficients in an index of selection. [ABSTRACT FROM AUTHOR]

We identified 22 polymorphisms in the adipocyte fatty-acid binding protein (FABP4) gene, a strong positional candidate gene for the FAT1 locus in porcine chromosome 4. The most informative polymorphism, an insertion/deletion in intron 1, together with a single nucleotide polymorphism in intron 3, was genotyped in a cross between Iberian and Landrace pigs. After performing QTL, single marker, and haplotype analyses, we showed that there were at least 2 quantitative trait genes in the FAT1 region and that the FABP4 polymorphism was tightly associated to fatness. A comparison of allelic frequencies in a panel of pig breeds suggested that the Del2634C polymorphism was under indirect selection. We also showed that FABP4 is tightly associated to fatness but not growth. Furthermore, a haplotype analysis suggests that there is genetic heterogeneity at the FAT1 locus within the Landrace breed. [ABSTRACT FROM AUTHOR]

The effect of a previously reported PvuII polymorphism in oestrogen receptor 1 ( ESR1) was analysed in an F2 population of Iberian × Meishan pigs. We tested three hypotheses: (1) that a causal mutation was fixed in the parental populations, (2) that a causal mutation existed that was in complete linkage disequilibrium with the alleles of the PvuII polymorphism and (3) that a causal mutation existed in linkage disequilibrium within each parental population. The third model was the most plausible based on the available data. ESR1 alleles displayed different patterns of linkage disequilibrium with the causal mutation in each of the parental populations and the PvuII polymorphism was clearly not the causal mutation. As a consequence, the use of the ESR1 mutation for selection must be evaluated for a particular pig population before it is applied. [ABSTRACT FROM AUTHOR]

Long-chain acyl-CoA synthetase (ACSL) catalyses the formation of long-chain acyl-CoA from fatty acid, ATP and CoA, activating fatty acids for subsequent reactions. Long-chain acyl-CoA synthetase thus plays an essential role in both lipid biosynthesis and fatty acid degradation. The ACSL4 gene was evaluated as a positional candidate gene for the quantitative trait loci (QTL) located between SW2456 and SW1943 on chromosome X. We have sequenced 4906 bp of the pig ACSL4 mRNA. Sequence analysis allowed us to identify 10 polymorphisms located in the 3′-UTR region and to elucidate two ACSL4 haplotypes. Furthermore, a QTL and an association study between polymorphisms of the ACSL4 gene and traits of interest were carried out in an Iberian × Landrace cross. We report QTL that have not been previously identified, and we describe an association of the ACSL4 polymorphisms with growth and percentage of oleic fatty acid. Finally, we have determined allelic frequencies in 140 pigs belonging to the Iberian, Landrace, Large White, Meishan, Pietrain, Duroc, Vietnamese, Peccary and Babirusa populations. [ABSTRACT FROM AUTHOR]

Malic enzyme 1 (ME1) is a part of the tricarboxylate shuttle that provides NADPH and acetyl-CoA required in fatty acid biosynthesis. The pig ME1 locus maps on the proximal end of chromosome 1, where a quantitative trait loci (QTL) affecting fat deposition has been previously described. We amplified fragments of 1457 and 1459 bp that corresponded to the complete coding region and the 3′-untranslated region (UTR), respectively, of the pig ME1 gene. The sequences of these two fragments in pigs from three breeds (Landrace, Large White and Piétrain) contained five single nucleotide polymorphisms (SNP) in the 3′-UTR: C1706T, G1762T, A1807C, C1857A and T1880A. Three haplotypes were found in two generations of a selected Landrace population: H1 (C1706 G1762 A1807 C1857 A1880), H2 (C1706 G1762 A1807 C1857 T1880) and H3 (T1706 T1762 C1807 A1857 T1880). Using Bayesian association analyses, significant associations (highest posterior density at 95%) between ME1 genotype and backfat (BF) thickness at 171 days and muscular pH were found in a Landrace population. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate chromosomal regions affecting the number of teats in pigs and possible epistatic interactions between the identified quantitative trait loci (QTL). An experimental F2 cross between Iberian and Chinese Meishan lines was used for this purpose. A genomic scan was conducted with 117 markers covering the 18 porcine autosomes. Linkage analyses were performed by interval mapping using an animal model to estimate QTL and additive polygenic effects. Complementary analyses with models fitting two QTL were also carried out. The results showed three genomewide significant QTL mapping on chromosomes 5, 10 and 12, whose joint action control up to 30% of the phenotypic variance of the trait. Meishan alleles had a positive additive effect on teat number, and a positive-additive × additive-epistatic interaction was detected between QTL on chromosomes 10 and 12. [ABSTRACT FROM AUTHOR]

A QTL analysis of multibreed experiments (i.e., crossed populations involving more than two founder breeds) offers clear advantages over classical two-breed crosses, among them increased power and a more comprehensive coverage of the total genetic variability in the species. An alternative to designed multibreed crosses is to reanalyze jointly several experiments involving different breeds. We report a multibreed, multitrait QTL analysis of SSCX that involves five different crosses, six breeds, and almost 3,000 genotyped individuals using a truly multibreed strategy to allow for any number of founder breed origins. Traits analyzed were growth, fat thickness, carcass length, and shoulder and ham weights. Generally, the joint analysis resulted in more significant QTL than the single-experiment analyses. We show that the QTL for fatness, which is highly significant (nominal P < 10-43), is of Asiatic origin (Meishan). The next most significant QTL (nominal P < -10) affected ham weight and seems to be segregating only between Large White and the rest of the breeds. A multitrait, multi-QTL analysis suggests that these are two distinct loci. Additionally, a locus segregating only between Iberian and Landrace affects live weight. The advantages of joint, multibreed analyses clearly outweigh their potential risks. [ABSTRACT FROM AUTHOR]

We characterized the nearly complete coding sequence of the pig 2,4-dienoyl CoA reductase 1 (DECR1) gene, which encodes an enzyme involved in the β-oxidation of polyunsaturated fatty enoyl-CoA esters and maps on a linoleic QTL located on Chromosome 4. Sequencing of a 937-bp fragment encompassing exons 2 and 10 revealed the existence of two missense SNP at exon 2 (C181 → G181) and exon 5 (C458 → G458). These two SNP are associated with Val (C) → Leu (G) and Ser (C) → Thr (G) conservative AA replacements at positions 61 and 153 of the DECR1 protein, respectively. Moreover, DECR1 genotyping in a representative sample of 184 pigs from the Large White, Piétrain, Iberian, Duroc, and Landrace breeds demonstrated the existence of disequilibrium linkage between these two SNP (Haplotype 1:C181C458; Haplotype 2: G181G458). An association analysis between DECR1 genotype and growth, carcass, and meat quality traits in a highly selected Landrace population (n = 470) revealed differences among genotypes for isocitrate dehydrogenase activity (highest posterior density [HPD] of 90%), longissimus thoracis pH (HPD of 95%), lightness (HPD of 90 to 95%), and redness (HPD of 95%). Because these associations were not consistently found in the three available genotype comparisons, we believe that exon 2 and 5 polymorphisms at the DECR1 gene might be in linkage disequilibrium with the true causal mutation influencing isocitrate dehydrogenase activity and muscle color and pH. [ABSTRACT FROM AUTHOR]

The genetic basis of the main components of boar taint was investigated in intact male pigs in a commercial population. We analyzed fat androstenone and skatole concentrations from 217 males of an outbred Landrace population. Records were normalized using a logarithm transformation and tested for normality using a Wilk-Shapiro test. Bayesian analysis was then used to map QTL in 10 candidate regions previously selected on chromosomes 1, 2, 3, 4, 6, 7, 8, 9, 10, and 13. The criterion for QTL detection was the Bayes factor (BF) between polygenic models with and without QTL effects. Both traits had considerable genetic determination, with posterior means of total heritabilities ranging from 0.59 to 0.73 for androstenone and from 0.74 to 0.89 for skatole. Positive evidence for a fat skatole QTL was detected on SSC6 (BF = 5.16); however, no QTL for androstenone were found in any of the 10 chromosomal regions analyzed. With the detection of a QTL for the fat skatole concentration segregating in this population, marker-assisted selection or even gene-assisted selection could be used once the causal mutation of the QTL was identified. [ABSTRACT FROM AUTHOR]

The Bayes factor (BF) procedure was applied to examine the additive genetic component of several physiological and vitality variables for newborn pigs. Nine variables were studied: heart rate, arterial oxygen saturation, rectal temperature (all at birth and 60 mm later), birth weight, interval between birth and first teats contact, and interval between birth and first colostrum intake. The available numbers of data ranged from 288 (heart rate at 60 mm) to 839 records (birth weight) from F2 Iberian × Meishan newborn pigs. We compared a model with zero heritability (nonheritable) with the one where the additive genetic background was included. The BF was used to discriminate between both candidate models. Very strong evidence of genetic background was detected for heart rate 60 mm after birth (BF = 48.90), and strong evidence was detected for rectal temperature at birth (BF = 13.82). Posterior modes (means) of heritabilities were 0.29 (0.32) and 0.40 (0.39), respectively. In addition, substantial evidence of absence of genetic background was detected for arterial oxygen saturation at birth. [ABSTRACT FROM AUTHOR]

A simulation study has been performed to evaluate the power and the rate of false positives for the detection of causal mutations under two different models of analysis. We used an F2 design generated from an F0 population of five sires of line 1 and 40 dams of line 2 to produce an F1 population of 10 sires and 80 dams. Two different locations of the causal mutation and several frequencies of the mutations in the parental populations were considered. The first model included only the genetic configuration of the mutation, while the second model also included the probability of line origin given the neutral markers. Both models performed well when the mutation at the candidate gene was the causal mutation, although a greater power was obtained using the first model, because of its relative simplicity compared to the second one. However, when the candidate gene mutation was a neutral mutation, the second model presented a lower rate of false positives than the first. Moreover, in some cases the second model allowed distinction between the neutral and the causal mutation. The F2 design has a great power to detect quantitative trait loci provided by linkage disequilibrium, but also makes it difficult to discriminate between causal and neutral mutations. Therefore a high percentage of false positives can be expected. The limitations of F2 designs for discriminating between neutral and causal mutations are discussed. [ABSTRACT FROM AUTHOR]

A Bayesian analysis with a threshold model was performed for fertility defined as a binary trait (1 = successful mating, 0 = unsuccessful mating) in two populations of rabbits of different reproductive potential and different genetic origin: Line P selected for litter size and Line C selected for growth rate. There were 20,793 records of natural mating (86.2% successful) in Line C between 1983 and 2003, and 17,548 records (80.5% successful) in Line P, between 1992 and 2003. Data related to 5,388 and 3,848 females and 1,021 and 685 males in Lines C and P, respectively. The pedigree included 6,409 and 4,533 individuals in Lines C and P, respectively. The binary response was modeled under a probit approach. The model for the latent vari- able included male and female additive genetic effects, male and female permanent environmental effects, and the year-season and physiological status of the female (nulliparous, multiparous lactating, or multiparous nonlactating) as systematic effects. Means (standard deviation in parentheses) of the estimated marginal posterior distribution (EMPD) of male heritability were 0.013(0.006) and 0.010(0.008) in Lines C and P, respectively, and those of EMPD of female heritability were 0.056(0.013) and 0.062(0.018) in Lines C and P, respectively. Means of the EMPD of the proportion of the phenotypic variance due to environmental male and female effects were, respectively, 0.03 1 (0.007) and 0.128 (0.018) in Line C and 0.053 (0.010) and 0.231 (0.024) in Line P. Means (standard deviations in parentheses) of the EMPD of genetic correlation between male and female fertility were 0.733 (0.197) in Line C and 0.434 (0.381) in Line P. The posterior distribution of genetic correlations presents a huge dispersion, and the estimates should be taken with caution because of the almost negligible estimate of the male genetic component. Results indicate that little genetic variation exists for female fertility, and practically none for male fertility. It would, therefore, be possible to improve re- productive performance by including female fertility in a breeding program, but response to selection would be very small. [ABSTRACT FROM AUTHOR]

The identification of QTL related to production traits that are relevant for the pig industry has been mostly performed by using divergent crosses. The main objective of the current study was to investigate whether these growth, fatness, and meat quality QTL, previously described in diverse experimental populations, were segregating in a Landrace commercial population selected for litter size, backfat thickness, and growth performance. We have found QTL for carcass weight (posterior P > 0.75), cutlet weight (posterior P > 0.99), weight of ham (posterior P > 0.75), shoulders weight (posterior probability > 0.99), and shear firmness (posterior F> 0.99) on pig Chromosome 2. Moreover, QTL with posterior P > 0.75 for fat thickness between the 3rd and 4th ribs (Chromosome 7), rib weights (Chromosome 8), backfat thickness (Chromosomes 8, 9, and 10), and b Minolta color component (Chromosome 7) were identified. These results indicate that commercial purebred populations retain a significant amount of genetic variation, even for traits that have been selected for many generations. [ABSTRACT FROM AUTHOR]

Iberian × 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°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. [ABSTRACT FROM AUTHOR]

A simple procedure to calculate the Bayes factor between linked and pleiotropic QTL models is presented. The Bayes factor is calculated from the marginal prior and posterior densities of the locations of the QTL under a linkage and a pleiotropy model. The procedure is computed with a Gibbs sampler, and it can be easily applied to any model including the location of the QTL as a variable. The procedure was compared with a multivariate least-squares method. The proposed procedure showed better results in terms of power of detection of linkage when low information is available. As information increases, the performance of both procedures becomes similar. An example using data provided by an Iberian by Landrace pig intercross is presented. The results showed that three different QTL segregate in SSC6: a pleiotropic QTL affects myristic, palmitic, and eicosadienoic fatty acids; another pleiotropic QTL affects palmitoleic, stearic, and vaccenic fatty acids; and a third QTL affects the percentage of linoleic acid. In the example, the Bayes factor approach was more powerful than the multivariate least-squares approach. [ABSTRACT FROM AUTHOR]

A hierarchical model for inferring the parameters of the joint distribution of a trait measured longitudinally and another assessed cross-sectionally, when selection has been applied to the cross-sectional trait, is presented. Distributions and methods for a Bayesian implementation via Markov Chain Monte Carlo procedures are discussed for the case where information about the selection criterion is available for all the individuals, but longitudinal records are available only in the later generations. Alternative specifications of the residual covariance structure are suggested. The procedure is illustrated with an analysis of correlated responses in growth curve parameters in a population of rabbits selected for increased growth rate. Results agree with those obtained in a previous study using both selected and control populations. The high correlation between samples indicates slow mixing, resulting in small effective sample sizes and high Monte Carlo standard errors. [ABSTRACT FROM AUTHOR]

In commercial livestock populations, QTL detection methods often use existing half-sib family structures and ignore additional relationships within and between families. We reanalyzed the data from a large QTL confirmation experiment with 10 pig lines and 10 chromosome regions using identity-by-descent (IBD) scores and variance component analyses. The IBD scores were obtained using a Monte Carlo Markov Chain method, as implemented in the LOKI software, and were used to model a putative QTL in a mixed animal model. The analyses revealed 61 QTL at a nominal 5% level (out of 650 tests). Twenty-seven QTL mapped to areas where QTL have been reported, and eight of these exceeded the threshold to claim confirmed linkage (P < 0.01). Forty-two of the putative QTL were detected previously using half-sib analyses, whereas 46 QTL previously identified by half-sib analyses could not be confirmed using the variance component approach. Some of the differences could be traced back to the underlying assumptions between the two methods. Using a deterministic approach to estimate IBD scores on a subset of the data gave very similar results to LOKI. We have demonstrated the feasibility of applying variance component QTL analysis to a large amount of data, equivalent to a genome scan. In many situations, the deterministic IBD approach offers a fast alternative to LOKI. [ABSTRACT FROM AUTHOR]

Polymorphism at the estrogen receptor locus (ESR) and its association with reproductive performance in Landrace pig is reported. A total of 124 sows from a control line, and 163 sows from a line selected for litter size were genotyped. The traits studied were number born alive (NBA) and total number born (TNB). Prolificacy in first, second and third or later parities were considered as three different traits. A mixed model considering the ESR genotype as a fixed effect and polygenic background as a random effect, was carried out using Bayesian inference, implemented via the Gibbs sampling procedure. Two alternative statistical models, with and without ESR genotype by line interaction, were considered. Association of an additive ESR effect with NBA and TNB was not detected. Moreover, in third and further parities, a line by ESR genotype interaction was observed for both NBA and TNB. For third and further parities, allele B was associated with increasing litter size in selected animals, whereas the opposite was observed in control animals. These results suggest that a background genotype by ESR interaction exists, although a spurious association due to sampling or the possibility of different linkage phases between the ESR polymorphism and a putative QTL close by cannot be ruled out. [Copyright &y& Elsevier]

The present study investigated differences in the allocation patterns of body stores in lactating female mice from a line selected for high litter size at birth (S-line, average litter size of 20) and dams from a nonselected control line (C-line, average litter size of 10). Body weight, litter size, litter weight, and absolute and relative lipid and protein mass were measured at peak lactation (2 wk in lactation) and at weaning (3 wk in lactation). Body size in S-line females has been increased as a correlated effect of selection for high litter size at birth, allowing for larger litters and higher absolute milk production. However, these dams produce larger litters relative to their own body weight. At peak lactation, lipid and protein percentage did not differ between lines. At weaning, S-line females had a higher protein percentage (P < 0.001) and lower lipid percentage (P < 0.05) than C-line females. Apparently, S-line females produce more offspring but at a greater cost to their own metabolism. This process was insufficient to supply the offspring with adequate resources, resulting in reduced (P < 0.0001) pup development and increased (P < 0.0001) preweaning mortality rates. [ABSTRACT FROM AUTHOR]

An experimental F[sub 2] cross between Iberian and Landrace pig strains was performed to map quantitative trait loci (QTL) for diverse productive traits. Here we report results for meat quality traits from 369 F[sub 2] animals with records for pH 24 h postmortem (pH 24 h), muscle color Minolta measurements L[sup *] (lightness), a[sup *] (redness), and b[sup *] (yellowness), H[sup *] (hue angle), C[sup *] (chroma), intramuscular fat (IMF) and haematin pigment content measured in the longissimus thoracis. Pigs were genotyped for 92 markers covering the 18 porcine autosomes (SSC). Results of the genome scan show evidence for QTL for IMF (SSC6; F = 27.16), pH 24 h (SSC3; F = 7.73), haematin pigments (SSC4 and SSC7; F = 8.68 and 9.47 respectively) and Minolta color measurements L[sup *] (SSC4 and SSC7; F =16.42 and 7.17 respectively), and a[sup *] (SSC4 and SSC8; F = 8.05 and 7.36 respectively). No QTL were observed for the color measurements b[sup *], H[sup *], and C[sup *]. Alternative models fitting epistasis between QTL were also tested, but detected epistatic interactions were not significant at a genome-wise level. In this work we identify genomic regions related with meat quality traits. Improvement by traditional selection methods is complicated, and finer mapping would be required for their application in introgression programs. [ABSTRACT FROM AUTHOR]

Part I. Examines the litter size for multiple parities with the production traits in pigs. Estimation on the genetic parameters through Bayesian variance; Sensitivity of Gibbs sampler; Use of operational model for genetic evaluation; Correlation of genetics and production traits.

Part II. Examines the litter size for multiple parities with production traits in pigs. Use of BLUP repeatability animal model to select the number of piglets born alive; Bayesian analysis of genetic response using multivariate model by Gibbs sampler; Analysis of genetic response through genealogical and phenotypic information.