Skew distribution of founder-specific inbreeding depression effects on the longevity of Landrace sows

Genetics Research

Volumn 90, Issue 6, 2008, Pages 499-508

  Casellas, Joaquim ^a   Varona, L ^a,b   Ibanez Escriche N ^a   Quintanilla, R ^a   Noguera, J L ^a  

^a IRTA   (Spain)

^b UNIVERSITY OF ZARAGOZA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FOUNDER EFFECT; GENETIC LOAD; INBREEDING DEPRESSION; LONGEVITY; NONHUMAN; RECESSIVE INHERITANCE; SWINE; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; COMPARATIVE STUDY; FEMALE; GENETIC SELECTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; INBREEDING; MALE; MONTE CARLO METHOD; PHYSIOLOGY; PROBABILITY; PROPORTIONAL HAZARDS MODEL; STATISTICAL MODEL;

ANIMALIA;

ANIMALS; BAYES THEOREM; FEMALE; FOUNDER EFFECT; GENETIC LOAD; INBREEDING; LIKELIHOOD FUNCTIONS; LONGEVITY; MALE; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PROPORTIONAL HAZARDS MODELS; SELECTION (GENETICS); SUS SCROFA;

EID: 63449133423     PISSN: 00166723     EISSN: 14695073     Source Type: Journal    
DOI: 10.1017/S0016672308009907     Document Type: Article

References (59)

1. Allison, P. D. (1995). Survival Analysis Using the SAS® System: A Practical Guide. Cary, NC: SAS Institute.
2. Brandt, H., von Brevern, N. & Glodek, P. (1999). Factors affecting survival rate of crossbred sows in weaner production. Livestock Production Science 57, 127-135.
3. Casellas, J. (2007). Bayesian inference in a piecewise Weibull proportional hazards model with unknown change points. Journal of Animal Breeding and Genetics 124, 176-184.
4. Casellas, J., Tarrés, J., Piedrafita, J. & Varona, L. (2006). Parametric bootstrap for testing model fitting in the proportional hazards framework: An application to the survival analysis of Bruna dels Pirineus beef calves. Journal of Animal Science 84, 2609-2616.
5. Casellas, J., Piedrafita, J., Caja, G. & Varona, L. (2009). Bayesian analysis of founder-specific inbreeding depression on birth weight in Ripollesa lambs. Journal of Animal Science, under review.
6. Cox, D. R. (1972). Regression models and life tables (with discussion). Journal of the Royal Statistical Society, Series B 34, 187-220.
7. Damgaard, L. H. & Korsgaard, I. R. (2006). A bivariate quantitative genetic model for a linear Gaussian trait and a survival trait. Genetics Selection Evolution 38, 45-64.
8. Ducrocq, V., Quaasm, R. L., Pollak, E. J. & Casella, G. (1988). Length of productive life of dairy cows. 1. Justification of a Weibull model. Journal of Dairy Science 71, 3061-3070.
9. Falconer, D. S. & Mackay, T. F. C (1996). Introduction to Quantitative Genetics. Harlow, Essex, UK: Longman.
10. Farkas, J., Curik, I., Csató, L., Csörnyei, Z., Baumung, R. & Nagy, I. (2007). Bayesian inference of inbreeding effects on litter size and gestation length in Hungarian Landrace and Hungarian Large White pigs. Livestock Science 112, 109-114.
11. Fernández, A., Rodrigáñez, J., Toro, M. A., Rodríguez, M. C. & Silió, L. (2002). Inbreeding effects on the parameters of the growth function in three strains of Iberian pigs. Journal of Animal Science 80, 2267-2275.
12. Fernández de Sevilla, X., Fàbrega, E., Tibau, J. & Casellas, J. (2008). Effect of leg conformation on survivability of Duroc, Landrace and Large White sows. Journal of Animal Science, 86, 2392-2400.
13. Fox, C. W., Scheibly, K. L., Wallin, W. G., Hitchcock, L. J., Stillwell, R. C. & Smith, B. P. (2006). The genetic architecture of life span and mortality rates: Gender and species differences in inbreeding load of two seed-feeding beetles. Genetics 174, 763-773.
14. Galal, E. S. E., Afifi, E. A., El-Kimary, I. S., Ahmad, I. A. & Shawar, A. F. (1981). Lamb survival as affected by inbreeding and cross-breeding. Journal of Agricultural Science 96, 1-5.
15. Gelfand, A. & Smith, A. F. M. (1990). Sampling based approaches to calculating marginal densities. Journal of the American Statistical Association 85, 398-409.
16. Gulisija, D., Gianola, D., Weigel, K. A. & Toro, M. A. (2006). Between-founder heterogeneity in inbreeding depression for production in Jersey cows. Livestock Production Science 104, 244-253.
17. Hastings, W. K. (1970). Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57, 97-109.
18. Kaplan, E. L. & Meier, P. (1958). Nonparametric estimation from incomplete observations. Journal of the American Statistical Association 53, 457-481.
19. Lacy, R. C., Alaks, G. & Walsh, A. (1996). Hierarchical analysis of inbreed depression in Peromyscus polionotus. Evolution 50, 2187-2200.
20. Le Cozler, Y. L., Dagorn, J., Lindberg, E. J., Aumaitre, A. & Dourmand, Y. J. (1998). Effect of age at first farrowing and herd management on long-term productivity of sows. Livestock Production Science 53 135-142.
21. López-Serrano, M., Reinsch, N., Looft, H. & Kalm, E. (2000). Genetic correlations of growth, backfat thickness and exterior with stayability in Large White and Landrace sows. Livestock Production Science 62, 121-131.
22. Malécot, G. (1948). Les Mathématiques de l'Hérédité Paris: Masson.
23. MacKinnon, K. M. (2003). Analysis of inbreeding in a closed population of crossbred sheep. M.Sc. Thesis, Virginia Polytechnic Institute and State University.
24. Mc Parland, S., Kearney, J. F., Rath, M. & Berry, D. P. (2007) Inbreeding effects on milk production, calving performance, fertility, and conformation in Irish Holstein-Friesians. Journal of Dairy Science 90, 4411-4419.
25. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953). Equations of state calculations by fast computing machines. Journal of Chemical Physics 21, 1087-1092.
26. Miglior, F., Burnside, E. B. & Kennedy, B. W. (1995). Production traits of Holstein cattle: Estimation of nonadditive genetic variance components and inbreeding depression. Journal of Dairy Science 78, 1174-1180.
27. Nguyen, H. T., Rogers, G. S. & Walker, E. A. (1984). Estimation in change-point hazard rate models. Biometrika 71, 299-304.
28. Noura, A. A. & Read, K. L. Q. (1990). Proportional hazards changepoint models in survival analysis. Applied Statistics 39, 241-253.
29. Noguera, J. L., Varona, L., Babot, D. & Estany, J. (2002a). Multivariate analysis of litter size for multiple parities with production traits in pigs: I. Bayesian variance component estimation. Journal of Animal Science 80, 2540-2547.
30. Noguera, J. L., Varona, L., Babot, D. & Estany, J. (2002b). Multivariate analysis of litter size for multiple parities with production traits in pigs: II. Response to selection for litter size and correlated response to production traits. Journal of Animal Science 80, 2548-2555.
31. Norberg, E. & Sørensen, A. C. (2007). Inbreeding trend and inbreeding depression in the Danish populations of Texel, Shropshire, and Oxford Down. Journal of Animal Science 85, 299-304.
32. Pannell, J. R. (2008). Consequences of inbreeding depression due to sex-linked loci for the maintenance of males and outcrossing in branchiopod crustaceans. Genetics Research 90, 73-84.
33. Pariacote, F., Van Vleck, L. D. & MacNeil, M. D. (1998). Effects of inbreeding and heterozygosity on preweaning traits in a closed population of Herefords under selection. Journal of Animal Science 76, 1303-1310.
34. Raftery, A. E. & Lewis, S. M. (1992). How many iterations in the Gibbs sampler? In Bayesian Statistics IV (ed. J. M. Bernardo, J. O. Berger, A. P. Dawid & A. F. M. Smith), pp. 763-773. Oxford, UK: Oxford University Press.
35. Rathje, T. A. (2000). Strategies to manage inbreeding accumulation in swine breeding company nucleus herds: Some case studies. Journal of Animal Science 79 (e-suppl. 1), E1-E8.
36. Robinson, G. K. (1991). That BLUP is a good thing: The estimation of random effects. Statistical Science 6, 15-51.
37. Rodrigáñez, J., Toro, M. A., Rodriguez, M. C. & Silió, L. (1998). Effect of founder allele survival and inbreeding depression on litter size in closed line of Large White pigs. Animal Science 67, 573-582.
38. Sahu, S. K. & Chai, H. S. (2005). A New Skew-elliptical Distribution and its Properties. Working Paper M05/19. Southampton, UK: Southampton Statistical Sciences Research Institute, University of Southampton. Available at http://eprints.soton.ac.uk/18180/01/ s3ri-workingpaperm05-19.pdf
39. Sahu, S. K., Dey, D. K. & Branco, M. D. (2003). A new class of multivariate skew distributions with applications to Bayesian regression models. The Canadian Journal of Statistics 31, 129-150.
40. Sánchez, L., Toro, M. A. & García, C. (1999). Improving the efficiency of artificial selection; More selection pressure with less inbreeding. Genetics 151, 1103-1114.
41. Serenius, T. & Stalder, K. J. (2004) Genetics of length of productive life and lifetime prolificacy in the Finnish Landrace and Large White pig populations. Journal of Animal Science 82, 3111-3117.
42. Serenius, T., Stalder, K. J., Baas, T. J., Mabry, J. W., Goodwin, R. N., Johnson, R. K., Robinson, O. W., Tokach, M. & Miller, R. K. (2006). National pork producers council maternal line national genetic evaluation program: A comparison of sow longevity and trait associations with sow longevity. Journal of Animal Science 84, 2590-2595.
43. Sewalem, A., Kistemaker, G. J., Miglior, F. & Van Doormaal, B. J. (2006). Analysis of inbreeding and its relationship with functional longevity in Canadian dairy cattle. Journal of Dairy Science 89 2210-2216.
44. Spiegelhalter, 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 64, 583-639.
45. Spiegelhalter, D. J., Thomas, A., Best, N. G. & Lunn, D. (2003). WinBUGS Version 1.4 User Manual. Cambridge, UK: MRC Biostatistics Unit. Available at http://www.mrc-bsu.cam.ac.uk/bugs/
46. Sternicki, T., Szablewski, P. & Szwaczkowski, T. (2003). Inbreeding effects of lifetime in David's deer (Elaphurus davidianus, Milne Edwards 1866) population. Journal of Applied Genetics 44, 175-183.
47. Swindell, W. R. & Bouzat, J. L. (2006). Inbreeding depression and male survivorship in Drosophila: Implications for senescence theory. Genetics 172, 317-327.
48. Tarrés, J., Casellas, J. & Piedrafita, J. (2005). Genetic and environmental factors influencing mortality up to weaning of Bruna dels Pirineus beef calves in mountain areas. A survival analysis. Journal of Animal Science 83, 543-551.
49. Tarrés, J., Bidanel, J. P., Hofer, A. & Ducrocq, V. (2006). Analysis of longevity and exterior traits on Large White sows in Switzerland. Journal of Animal Science 84, 2914-2924.
50. Tholen, E., Bunter, K. L., Hermesch, S. & Graser, H.-U. 1996. The genetic foundation of fitness and reproduction traits in Australian pig populations. 2. Relationship between weaning to conception interval, farrowing interval, stayability, and other common reproduction and production traits. Australian Journal of Agricultural Research 47, 1275-1290.
51. Varona, L., Mekkawy, W., Gianola, D. & Blasco A. (2006). A whole-genome analysis using robust asymmetric distributions. Genetical Research 88, 143-151.
52. Varona, L., Ibáñez-Escriche, N., Quintanilla, R., Noguera, J. L. & Casellas, J. (2008). Bayesian analysis of quantitative traits using skewed distributions. Genetics Research 90, 179-190.
53. Vermeulen, C. J. & Bijlsma, R. (2004). Changes in mortality patterns and temperature dependence of lifespan in Drosophila melanogaster caused by inbreeding. Heredity 92, 275-281.
54. Weiner, G., Lee, G. J. & Woolliams, J. A. (1992). Effects of rapid inbreeding and of crossing of inbreeding lines on the body weight growth of sheep. Animal Production 55, 89-99.
55. Westell, R. A., Quaas, R. L. & Van Vleck, L. D. (1988). Genetic groups in an animal model. Journal of Dairy Science 71, 1310-1318.
56. Wright, S. (1922). Coefficients of inbreeding and relationship. The American Naturalist 56, 330-338.
57. Yazdi, M. H., Rydhmer, L., Ringmar-Cedererg, E., Lundeheim, N. & Johansson, K. (2000). Genetic study of longevity in Swedish Landrace sows. Livestock Production Science 63, 255-264.
58. Yazdi, M. H., Visscher, P. M., Ducrocq, V. & Thompson, R. (2002). Heritability, reliability of genetic evaluations and response to selection in proportional hazards models. Journal of Dairy Science 85, 1563-1577.
59. Zhang, M., Montooth, K. L., Wells, M. T., Clark, A. G. & Zhang, D. (2005). Mapping multiple quantitative trait loci by Bayesian classification. Genetics 169, 2305-2318.