Alteration of gene expression in mammary gland tissue of dairy cows in response to dietary unsaturated fatty acids

The aim of this study was to determine the effects of supplementing unprotected dietary unsaturated fatty acids (UFAs) from different plant oils on gene expression in the mammary gland of grazing dairy cows. A total of 28 Holstein–Friesian dairy cows in mid-lactation were blocked according to parity, days in milk, milk yield and fat percentage. The cows were then randomly assigned to four UFA sources based on rapeseed, soybean, linseed or a mixture of the three oils for 23 days, after which, all 28 cows were switched to a control diet for an additional 28 days. On the last day of both periods, mammary gland biopsies were taken to study genome-wide differences in gene expression on Affymetrix GeneChip® Bovine Genome Arrays (no. 900493) by ServiceXS (Leiden, The Netherlands). Supplementation with UFAs resulted in increased milk yield but decreased milk fat and protein percentages. Furthermore, the proportion of de novo fatty acids (FAs) in the milk was reduced, whereas that of long-chain FAs increased. Applying a statistical cut-off of false discovery rate of q-value

Dietary unsaturated fatty acids affect the mammary gland integrity and health in lactating dairy cows

Background Information about the effects of unsaturated fatty acids (UFA) supplementation on the health and integrity of the mammary gland in lactating dairy cows is lacking. Therefore, the aim of this study was to determine the effects of unprotected dietary UFA on the global expression pattern of genes in the mammary gland tissue of grazing dairy cows, and to translate this information into relevant biological knowledge. Methods Twenty-eight Holstein-Friesian dairy cows were randomly assigned to 4 different concentrated UFA-sources for 23 days after which all cows were switched to a non-UFA-supplemented concentrate for an additional 28 days. On the last day of both periods, mammary gland biopsies were taken to study genome-wide differences in gene expression on Bovine Genome Arrays. Results Supplementation with UFA reduced the concentration of short chain fatty acids (FA), C16 FA and saturated FA in the milk, whereas that of trans-FA increased. One major finding was that canonical pathways associated with remodelling and immune functions of the mammary gland were predominantly down-regulated during UFA supplementation and negatively correlated with the concentration of milk trans-FA. Conclusions Supplementing grazing dairy cows with unprotected dietary UFA can affect the remodelling and immune functions of the mammary gland with potential consequences for its integrity and health, as well as milk quality

Effect of leg conformation of Duroc sow longevity

Ponencia publicada en ITEA, vol.104Caracteres morfológicos como la conformación de los aplomos pueden tener un papel clave en la longevidad de las cerdas. Dentro de este contexto, se evaluó el efecto de los aplomos sobre la longevidad de 587 cerdas Duroc, analizándose tanto la supervivencia global de las cerdas (SG) como la supervivencia bajo tres causas de fallida distintas (competing risk): muerte (BM), baja productividad (BP) y baja fertilidad (BF). La conformación global de los aplomos influyó (p < 0,001) la longevidad de las cerdas en los análisis SG, BP y BF, aumentado el riesgo de fallida a medida que empeoraban los aplomos. El crecimiento anormal de las pezuñas (p < 0,001) y la presencia de golpes o bultos en las patas (p < 0,05) incrementaba el riesgo de fallida en los análisis SG, BP y BF. Las cerdas plantígradas tenían un riesgo mayor de fallida en los análisis SG (p < 0,001) y BP (p < 0,05), las cerdas con hiperextensión de las patas tenían un riesgo mayor en el análisis BF (p < 0,05), mientras que la presencia de pies abiertos aumentaba el riesgo de fallida en el análisis SG (p < 0,05). Las estimaciones de heredabilidad para la longevidad de las cerdas fueron de 0,07 (análisis SG), 0,02 (análisis BP) y 0,08 (análisis BF).Morphologic traits such as leg conformation can play a key role on sow longevity. Within this context, the effect of leg conformation was evaluated on longevity data from 587 Duroc sows, longevity being characterized as overall longevity (OS) or sow failure due to death (DE), low productivity (LP) or low fertility (LF; competing risk analyses). Overall leg conformation score influenced (P < 0.001) sow longevity in OS, LP and LF analyses, impairing sow longevity when leg conformation got worse. Abnormal hoof growth (P < 0.001) and presence of bumps or injuries in legs (P < 0.001) increased the risk of failure in OS, LP and LF analyses. Plantigrade sows showed a higher culling risk in OS (P < 0.001) and LP (P < 0.05) analysis, sows with sickle-hooked leg had a higher culling risk in the LF analysis (P < 0.05), whereas splayed feet increased sow failure in the OS analysis (P < 0.05). Estimates of heritability for sow longevity were 0.07 (GS analysis), 0.02 (LP analysis) and 0.08 (LF analysis)

Consequences of paternally inherited effects on the genetic evaluation of maternal effects

Background: Mixed models are commonly used for the estimation of variance components and genetic evaluation of livestock populations. Some evaluation models include two types of additive genetic effects, direct and maternal. Estimates of variance components obtained with models that account for maternal effects have been the subject of a long-standing controversy about strong negative estimates of the covariance between direct and maternal effects. Genomic imprinting is known to be in some cases statistically confounded with maternal effects. In this study, we analysed the consequences of ignoring paternally inherited effects on the partitioning of genetic variance. Results: We showed that the existence of paternal parent-of-origin effects can bias the estimation of variance components when maternal effects are included in the evaluation model. Specifically, we demonstrated that adding a constraint on the genetic parameters of a maternal model resulted in correlations between relatives that were the same as those obtained with a model that fits only paternally inherited effects for most pairs of individuals, as in livestock pedigrees. The main consequence is an upward bias in the estimates of the direct and maternal additive genetic variances and a downward bias in the direct-maternal genetic covariance. This was confirmed by a simulation study that investigated five scenarios, with the trait affected by (1) only additive genetic effects, (2) only paternally inherited effects, (3) additive genetic and paternally inherited effects, (4) direct and maternal additive genetic effects and (5) direct and maternal additive genetic plus paternally inherited effects. For each scenario, the existence of a paternally inherited effect not accounted for by the estimation model resulted in a partitioning of the genetic variance according to the predicted pattern. In addition, a model comparison test confirmed that direct and maternal additive models and paternally inherited models provided an equivalent fit. Conclusions: Ignoring paternally inherited effects in the maternal models for genetic evaluation can lead to a specific pattern of bias in variance component estimates, which may account for the unexpectedly strong negative direct-maternal genetic correlations that are typically reported in the literature

Effect of inbreeding on the longevity of Landrace sows

Ponencia publicada en ITEA, vol.104La consanguinidad es un fenómeno biológico de especial relevancia en las especies domésticas, pudiéndose caracterizar tanto en términos de coeficiente de consanguinidad como fraccionando la contribución de cada individuo fundador en coeficientes de consanguinidad parcial (CP). A partir de los registros de longevidad de 4.226 cerdas de raza Landrace, este trabajo se ha centrado en la modelización de los CP bajo modelos Weibull de riesgos proporcionales y su posterior comparación mediante el DIC (deviance information criterion). Se asumieron tres distribuciones a priori distintas para los efectos de CP, resultando la normal asimétrica (DIC = 55.064,6) claramente preferible a la normal simétrica (DIC = 55.069,2) y a la distribución uniforme (DIC = 55.077,9). Se descartó, también, el modelo estándar con la consanguinidad global de cada individuo (DIC = 55.078,4). En el caso del modelo con DIC mínimo, la distribución posterior de los efectos de CP fue claramente asimétrica, con el 85,15% de las estimas afectando negativamente a la longevidad de las cerdas y el 14,85% restante con efecto neutro o incluso positivo. Señalar por último, que la heredabilidad para el carácter longevidad fue de 0,159.Inbreeding is a biological phenomenon of special relevance in domestic species, where the overall inbreeding coefficient can be partitioned in founder-specific partial inbreeding (PI) coefficients. Taking longevity data of 4,226 Landrace sows as starting point, this research proposed alternative parameterization for PI effects under Weibull proportional hazard models, and compared their performance through the deviance information criterion (DIC). Three different a priori distributions were assumed for PI effects, asymmetric normal (DIC = 55,064.6), symmetric normal (DIC = 55,069.2) and flat (DIC = 55,077.9). Additionally, the standard model accounting for the overall inbreeding coefficient was clearly discarded (DIC = 55,078.4). For the model with asymmetric Gaussian prior, the posterior distribution of PI effects was clearly skewed. An 85.15% of the estimates showed negative effect on sow longevity whereas the remaining 14.85% ones had null or even positive effect on sow survival. Estimated heritability was 0.159

Bayes factor between Student t and Gaussian mixed models within an animal breeding context

[EN] The implementation of Student t mixed models in animal breeding has been suggested as a useful statistical tool to effectively mute the impact of preferential treatment or other sources of outliers in field data. Nevertheless, these additional sources of variation are undeclared and we do not know whether a Student t mixed model is required or if a standard, and less parameterized, Gaussian mixed model would be sufficient to serve the intended purpose. Within this context, our aim was to develop the Bayes factor between two nested models that only differed in a bounded variable in order to easily compare a Student t and a Gaussian mixed model. It is important to highlight that the Student t density converges to a Gaussian process when degrees of freedom tend to infinity. The two models can then be viewed as nested models that differ in terms of degrees of freedom. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling of the complex model (Student t mixed model). The performance of this Bayes factor was tested under simulation and on a real dataset, using the deviation information criterion (DIC) as the standard reference criterion. The two statistical tools showed similar trends along the parameter space, although the Bayes factor appeared to be the more conservative. There was considerable evidence favoring the Student t mixed model for data sets simulated under Student t processes with limited degrees of freedom, and moderate advantages associated with using the Gaussian mixed model when working with datasets simulated with 50 or more degrees of freedom. For the analysis of real data (weight of Pietrain pigs at six months), both the Bayes factor and DIC slightly favored the Student t mixed model, with there being a reduced incidence of outlier individuals in this population.The authors are indebted to Dr. J.L. Noguera and COPAGA for field data on pig weight at six months, and to Dr. J. Piedrafita and Dr. G. Caja for providingadditional field data sets during preliminary tests of the Bayes factor. The research contract of J. Casellas was partially financed by Spain s Ministerio de Educación y Ciencia (Programa Juan de la Cierva).Casellas, J.; Ibáñez-Escriche, N.; Garcia-Cortes, L.; Varona, L. (2008). Bayes factor between Student t and Gaussian mixed models within an animal breeding context. Genetics Selection Evolution. 40(4):395-413. https://doi.org/10.1051/gse:2008007S39541340

Elimination de l'azote et du phosphore dans un lagunage à haut rendement

L'objectif de cette étude est de comprendre le fonctionnement épuratoire de l'écosystème particulier que constitue le lagunage à haut rendement (LHR) afin de déterminer les principaux facteurs responsables de l'élimination de l'azote et du phosphore.Sur un bassin de 48 m2, alimenté eu eaux usées domestiques préalablement traitées pendant une semaine dans un bassin primaire ont été suivies selon un rythme hebdomadaire les formes carbonées, azotées et phosphorées dis-soutes et particulaires, les variables caractéristiques de l'activité photosynthétiques (chlorophylle a, pH et 02) et les données climatiques (rayonnement solaire et température). Une analyse en composantes principales réalisée sur l'ensemble des résultats a montré, d'une part l'opposition des variables climatiques et photosynthétiques aux formes minérales de l'azote et du phosphore (N-NH4 et P-PO4) et d'autre part l'influence de la charge organique sur le fonctionnement du système.L'évolution des formes azotées et phosphorées présente un effet saisonnier marqué. En hiver ou lors de surcharge organique importante, une augmentation du temps de séjour peut améliorer les rendements épuratoires. L'évolution de la matière organique dissoute est indépendante du cycle saisonnier. Au cours des deux années du suivi on observe une adaptation progressive de l'écosystème à la dégradation de la matière organique.Dans le lagunage à haut rendement l'élimination de l'azote et du phosphore est liée principalement à l'activité algale, qui entraîne une assimilation biologique et une élévation du pH, responsables des phénomènes chimiques de volatilisation de l'azote ammoniacal et de précipitation de phosphate de calcium.High rait algal ponds (HRAP) for wastewater treatment have been the locus of a lot of attention since their creation by Professor W.J. OSWALD in the early 1960' s. These aquatic ecosystems are hypereutrophic because of massive nutrient introduction with the wastewater influent. This kind of pond is very different from oxidation ponds because al short residence times (2 to 12 days), shallow depths (0.30 to 0.60 m) and constant mechanical mixing which improves algal growth.This study has been carried out in a small town in the department of Herault (France). The objective is to establish the efficiencies and mechanisms for nitrogen and phosphorus remval from secondary domestic wastewater by treatment by HRAP. A high rate algal pond of 48 m2 surface area and 35 cm depth, constantly mixed with paddle wheels was studied (fig. 1). Residence limes changed from 2 te 12 days with solar radiations and influent loading. The samples were collected once a week from the in- and outflow at 3 p.m. - Dissolved and particulate COD, varions nitrogen and phosphorus compounds, suspended solide, chlorophyll-a, pH, dissolved oxygen, temperature and irradiation were determined.The results of principal component analysis show a negative correlation between (1) the climatic and photosynthetic parameters and (2) inorganic nitrogen and phosphorus compounds, as well as the influence of organic loading on the HRAP efficiency.The chronological clustering analysis was performed on the data taking into account the discontinuities of effluent autrient contents (fig. 4). During the first year, from February to September 1988, good climatic conditions were shown to favour photosynthetic activity and consequently a good ammonia and orthophosphate removal. Front September 1988 to February 1989, the effluent was characterized by high ammonia and orthophosphate levels because of unfavourable climatic conditions and low photosynthetic activity. During the second year, the objective was to improve removal efficiencies ; the residence time was changed with solar radiations and influent loading. The results of the chronological clustering analysis of ammonia and orthophosphate levels showed only one sequence (February 1989-January1990) because the seasonal variations of nutrient removal were attenuated. The optimal residence time was found to be 4 days in summer and 12 days in winter.The evolution of dissolved chemical oxygen demand is independent of seasonal conditions but decreases with the maturity of the system (< 50 mg . l-1).The mass balance of nitrogen and phosphorus compounds has been established (fig. 5). In high rate algal pond influent, the main nitrogen form is ammonia. In the effluent the main nitrogen form is suspended organic nitrogen. The oxidized forms (NO2- et NO3) present very low levels ; nitrification is a minor process in the system. Ammonia is reduced by both assimilation and stripping ; suspended organic nitrogen in the effluent is an indicator of assimilation by algal biomass and loss of nitrogen is an indicator of ammonia stripping. With regard to directive 91/271 EEC concerning domestic wastewater treatment, partial algal separation is necessary in order to achieve 15 mg • l-1 total nitrogen, which is the limit for zones sensitive to eutrophication.The residual phosphate levels are controlled by pH, which is responsible for instantaneous calcium phosphate precipitation. As the dissolved calcium concentrations are high in the calcareous region near the site (Ca = 125 mg • l-1), the pH of the water will be the main contraint on phosphate elimination in the HRAP. Theoretical calculations indicate that the precipitate is probably an amorphous tricalcium phosphate in pseudoequilibrium (fig.6). Phosphate concentrations are much higher titan the values expected for calcium hydroxyapatite in equilibrium (MOUTIN et al., 1992). The limit of 2 mg • l-1 for phosphores can only be attained when pH reaches or exceeds 9.Nitrogen and phosphorus removal is correlated mainly with phytoplanktonic activity, which controls biological nutrients assimilation and pH levels. High pH values are responsable for ammonia stripping and calcium phosphate precipitation

Genetic parameters and direct, maternal and heterosis effects on litter size in a diallel cross among three commercial varieties of Iberian pig

[EN] The Iberian pig is one of the pig breeds that has the highest meat quality. Traditionally, producers have bred one of the available varieties, exclusively, and have not used crosses between them, which has contrasted sharply with other populations of commercial pigs for which crossbreeding has been a standard procedure. The objective of this study was to perform an experiment under full diallel design among three contemporary commercial varieties of Iberian pig and estimate the additive genetic variation and the crossbreeding effects (direct, maternal and heterosis) for prolificacy. The data set comprised 18 193 records for total number born and number born alive from 3800 sows of three varieties of the Iberian breed (Retinto, Torbiscal and Entrepelado) and their reciprocal crosses (Retinto × Torbiscal, Torbiscal × Retinto, Retinto × Entrepelado, Entrepelado × Retinto, Torbiscal × Entrepelado and Entrepelado × Torbiscal), and a pedigree of 4609 individuals. The analysis was based on a multiple population repeatability model, and we developed a model comparison test that indicated the presence of direct line, maternal and heterosis effects. The results indicated the superiorities of the direct line effect of the Retinto and the maternal effect of the Entrepelado populations. All of the potential crosses produced significant heterosis, and additive genetic variation was higher in the Entrepelado than it was in the other two populations. The recommended cross for the highest yield in prolificacy is a Retinto father and an Entrepelado mother to generate a hybrid commercial sow.The work was partially funded by the Center for Industrial Technological Development (CDTI) via grant IDI-20170304 and by grant CGL-2016-80155 from the Ministry of Economy, Industry and Competitiveness (MINECO), Spain.Noguera, J.; Ibáñez-Escriche, N.; Casellas, J.; Rosas, J.; Varona, L. (2019). Genetic parameters and direct, maternal and heterosis effects on litter size in a diallel cross among three commercial varieties of Iberian pig. Animal. 13(12):2765-2772. https://doi.org/10.1017/S1751731119001125S276527721312Tsai, T.-S., Rajasekar, S., & St. John, J. C. (2016). The relationship between mitochondrial DNA haplotype and the reproductive capacity of domestic pigs (Sus scrofa domesticus). BMC Genetics, 17(1). doi:10.1186/s12863-016-0375-4Wolf, J. B., & Wade, M. J. (2009). What are maternal effects (and what are they not)? Philosophical Transactions of the Royal Society B: Biological Sciences, 364(1520), 1107-1115. doi:10.1098/rstb.2008.0238Srirattana, K., McCosker, K., Schatz, T., & St. John, J. C. (2017). Cattle phenotypes can disguise their maternal ancestry. BMC Genetics, 18(1). doi:10.1186/s12863-017-0523-5Fernández, A., Rodrigáñez, J., Zuzúarregui, J., Rodríguez, M. C., & Silió, L. (2008). Genetic parameters for litter size and weight at different parities in Iberian pigs. Spanish Journal of Agricultural Research, 6(S1), 98. doi:10.5424/sjar/200806s1-378García-Casco, J. M., Fernández, A., Rodríguez, M. C., & Silió, L. (2012). Heterosis for litter size and growth in crosses of four strains of Iberian pig. Livestock Science, 147(1-3), 1-8. doi:10.1016/j.livsci.2012.03.005Cameron, N. M. (2011). Maternal Programming of Reproductive Function and Behavior in the Female Rat. Frontiers in Evolutionary Neuroscience, 3. doi:10.3389/fnevo.2011.00010Noguera, J. L., Rodríguez, C., Varona, L., Tomàs, A., Muñoz, G., Ramírez, O., … Sánchez, A. (2009). A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL. BMC Genomics, 10(1), 636. doi:10.1186/1471-2164-10-636Southwood, O. I., & Kennedy, B. W. (1990). Estimation of direct and maternal genetic variance for litter size in Canadian Yorkshire and Landrace swine using an animal model. Journal of Animal Science, 68(7), 1841. doi:10.2527/1990.6871841xMartınez, A. M., Delgado, J. V., Rodero, A., & Vega-Pla, J. L. (2000). Genetic structure of the Iberian pig breed using microsatellites. Animal Genetics, 31(5), 295-301. doi:10.1046/j.1365-2052.2000.00645.xDekkers, J. C. M., Mathur, P. K., & Knol, E. F. (s. f.). Genetic improvement of the pig. The genetics of the pig, 390-425. doi:10.1079/9781845937560.0390Haley, C. S., Lee, G. J., & Ritchie, M. (1995). Comparative reproductive performance in Meishan and Large White pigs and their crosses. Animal Science, 60(2), 259-267. doi:10.1017/s1357729800008420Hwang, J. H., An, S. M., Kwon, S., Park, D. H., Kim, T. W., Kang, D. G., … Kim, C. W. (2017). DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta. PLOS ONE, 12(9), e0184539. doi:10.1371/journal.pone.0184539Fabuel, E., Barragán, C., Silió, L., Rodríguez, M. C., & Toro, M. A. (2004). Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Heredity, 93(1), 104-113. doi:10.1038/sj.hdy.6800488Serra, X., Gil, F., Pérez-Enciso, M., Oliver, M. ., Vázquez, J. ., Gispert, M., … Noguera, J. . (1998). A comparison of carcass, meat quality and histochemical characteristics of Iberian (Guadyerbas line) and Landrace pigs. Livestock Production Science, 56(3), 215-223. doi:10.1016/s0301-6226(98)00151-1Gelfand, A. E., & Smith, A. F. M. (1990). Sampling-Based Approaches to Calculating Marginal Densities. Journal of the American Statistical Association, 85(410), 398-409. doi:10.1080/01621459.1990.10476213Irgang, R., Fávero, J. A., & Kennedy, B. W. (1994). Genetic parameters for litter size of different parities in Duroc, Landrace, and large white sows. Journal of Animal Science, 72(9), 2237-2246. doi:10.2527/1994.7292237xOgawa, S., Konta, A., Kimata, M., Ishii, K., Uemoto, Y., & Satoh, M. (2018). Estimation of genetic parameters for farrowing traits in purebred Landrace and Large White pigs. Animal Science Journal, 90(1), 23-28. doi:10.1111/asj.13120Ibáñez-Escriche, N., Magallón, E., Gonzalez, E., Tejeda, J. F., & Noguera, J. L. (2016). Genetic parameters and crossbreeding effects of fat deposition and fatty acid profiles in Iberian pig lines1. Journal of Animal Science, 94(1), 28-37. doi:10.2527/jas.2015-9433Peripato, A. C., De Brito, R. A., Matioli, S. R., Pletscher, L. S., Vaughn, T. T., & Cheverud, J. M. (2004). Epistasis affecting litter size in mice. Journal of Evolutionary Biology, 17(3), 593-602. doi:10.1111/j.1420-9101.2004.00702.xSerrano, M. P., Valencia, D. G., Nieto, M., Lázaro, R., & Mateos, G. G. (2008). Influence of sex and terminal sire line on performance and carcass and meat quality of Iberian pigs reared under intensive production systems. Meat Science, 78(4), 420-428. doi:10.1016/j.meatsci.2007.07.006Quaas, R. L. (1976). Computing the Diagonal Elements and Inverse of a Large Numerator Relationship Matrix. Biometrics, 32(4), 949. doi:10.2307/2529279Quinton, V. M., Wilton, J. W., Robinson, J. A., & Mathur, P. K. (2006). Economic weights for sow productivity traits in nucleus pig populations. Livestock Science, 99(1), 69-77. doi:10.1016/j.livprodsci.2005.06.002Barea, R., Nieto, R., Vitari, F., Domeneghini, C., & Aguilera, J. F. (2010). Effects of pig genotype (Iberian v. Landrace × Large White) on nutrient digestibility, relative organ weight and small intestine structure at two stages of growth. animal, 5(4), 547-557. doi:10.1017/s1751731110002181Bidanel, J. P. (s. f.). Biology and genetics of reproduction. The genetics of the pig, 218-241. doi:10.1079/9781845937560.0218Boletín Oficial del Estado 2014. Real Decreto 4/2014, de 10 de enero, por el que se aprueba la norma de calidad para la carne, el jamón, la paleta y la caña de lomo ibérico. BOE-A-2014-318.Putz, A. M., Tiezzi, F., Maltecca, C., Gray, K. A., & Knauer, M. T. (2015). Variance component estimates for alternative litter size traits in swine. Journal of Animal Science, 93(11), 5153-5163. doi:10.2527/jas.2015-9416Cassady, J. P., Young, L. D., & Leymaster, K. A. (2002). Heterosis and recombination effects on pig reproductive traits. Journal of Animal Science, 80(9), 2303. doi:10.2527/2002.8092303xGilles, G. (2009). Dry cured ham quality as related to lipid quality of raw material and lipid changes during processing: a review. Grasas y Aceites, 60(3), 297-307. doi:10.3989/gya.130908Perez-Enciso, M., & Gianola, D. (1992). Estimates of genetic parameters for litter size in six strains of Iberian pigs. Livestock Production Science, 32(3), 283-293. doi:10.1016/s0301-6226(12)80007-8Rodriguez, C., Rodrigañez, J., & Silio, L. (1994). Genetic analysis of maternal ability in Iberian pigs. Journal of Animal Breeding and Genetics, 111(1-6), 220-227. doi:10.1111/j.1439-0388.1994.tb00461.xSpiegelhalter, D. J., Best, N. G., Carlin, B. P., & van der Linde, A. (2002). Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 64(4), 583-639. doi:10.1111/1467-9868.00353Coster, A., Madsen, O., Heuven, H. C. M., Dibbits, B., Groenen, M. A. M., van Arendonk, J. A. M., & Bovenhuis, H. (2012). The Imprinted Gene DIO3 Is a Candidate Gene for Litter Size in Pigs. PLoS ONE, 7(2), e31825. doi:10.1371/journal.pone.0031825Willham, R. L. (1972). The Role of Maternal Effects in Animal Breeding: III. Biometrical Aspects of Maternal Effects in Animals. Journal of Animal Science, 35(6), 1288-1293. doi:10.2527/jas1972.3561288xFerraz, J. B. S., & Johnson, R. K. (1993). Animal model estimation of genetic parameters and response to selection for litter size and weight, growth, and backfat in closed seedstock populations of large white and Landrace swine2. Journal of Animal Science, 71(4), 850-858. doi:10.2527/1993.714850

Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties

[EN] Individual-specific hidden inbreeding depression load (IDL) can be accounted for in livestock populations by appropriate best linear unbiased prediction approaches. This genetic effect has a recessive pattern and reveals when inherited in terms of identity-by-descent. Nevertheless, IDL inherits as a pure additive genetic background and can be selected using standard breeding values. The main target of this research was to evaluate IDL for litter size in 2 Iberian pig varieties (Entrepelado and Retinto) from a commercial breeding-stock. Analyses were performed on the total number of piglets born (both alive and dead) and used data from 3,200 (8.02 ± 0.04 piglets/litter) Entrepelado and 4,744 Retinto litters (8.40 ± 0.03 piglets/litter). Almost 50% of Entrepelado sows were inbred (1.7% to 25.0%), whereas this percentage reduced to 37.4% in the Retinto variety (0.2% to 25.0%). The analytical model was solved by Bayesian inference and accounted for 2 systematic effects (sow age and breed/variety of the artificial insemination boar), 2 permanent environmental effects (herd-year-season and sow), and 2 genetic effects (IDL and infinitesimal additive). In terms of posterior means (PM), additive genetic and IDL variances were similar in the Entrepelado variety (PM, 0.68 vs. 0.76 piglets2, respectively) and their 95% credibility intervals (95CI) overlapped, although without including zero (0.38 to 0.94 vs. 0.15 to 1.31 piglets2, respectively). The same pattern revealed in the Retinto variety, with IDL variance (PM, 0.41 piglets2; 95CI, 0.07 to 0.88 piglets2) slightly larger than the additive genetic variance (PM, 0.37 piglets2; 95CI, 0.16 to 0.59 piglets2). The relevance of IDL was also checked by a Bayes factor and the deviance information criterion, the model including this effect being clearly favored in both cases. Although the analysis assumed null genetic covariance between IDL and infinitesimal additive effects, a moderate negative correlation (¿0.31) was suggested when plotting the PM of breeding values in the Entrepelado variety; a negative genetic trend for IDL was also revealed in this Iberian pig variety (¿0.25 piglets for 100% inbred offspring of individuals born in 2014), whereas no trend was detected in Retinto breeding-stock. Those were the first estimates of IDL in a commercial livestock population, they giving evidence of a relevant genetic background with potential consequences on the reproductive performance of Iberian sows.The authors gratefully acknowledge the company INGA FOOD SA (Almendralejo, Spain) and its technicians (E. Magallon, M. J. Garcia-Santana, L. Munoz, P. Diaz, D. Iniesta, and M. Ramos), as well as S. Negro (IRTA), for their cooperation and technical support. 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