Hostname: page-component-78c5997874-mlc7c Total loading time: 0 Render date: 2024-11-19T17:30:03.310Z Has data issue: false hasContentIssue false
  • English
  • Français

Empirical Bayes factor analyses of quantitative trait loci for gestation length in Iberian × Meishan F2 sows

Published online by Cambridge University Press:  01 February 2008

J. Casellas ,
L. Varona ,
G. Muñoz ,
O. Ramírez ,
C. Barragán ,
A. Tomás ,
M. Martínez-Giner ,
C. Óvilo ,
A. Sánchez  and
J. L. Noguera
...Show all authors
J. Casellas*
Affiliation:
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
L. Varona
Affiliation:
Genètica i Millora Animal, IRTA-Lleida, 25198 Lleida, Spain
G. Muñoz
Affiliation:
Departamento de Mejora Genética Animal, SGIT-INIA, 28040 Madrid, Spain
O. Ramírez
Affiliation:
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
C. Barragán
Affiliation:
Departamento de Mejora Genética Animal, SGIT-INIA, 28040 Madrid, Spain
A. Tomás
Affiliation:
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
M. Martínez-Giner
Affiliation:
Genètica i Millora Animal, IRTA-Lleida, 25198 Lleida, Spain
C. Óvilo
Affiliation:
Departamento de Mejora Genética Animal, SGIT-INIA, 28040 Madrid, Spain
A. Sánchez
Affiliation:
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
J. L. Noguera
Affiliation:
Genètica i Millora Animal, IRTA-Lleida, 25198 Lleida, Spain
M. C. Rodríguez
Affiliation:
Departamento de Mejora Genética Animal, SGIT-INIA, 28040 Madrid, Spain
*
E-mail: [email protected]
Get access

Abstract

The aim of this study was to investigate chromosomal regions affecting gestation length in sows. An experimental F2 cross between Iberian and Meishan pig breeds was used for this purpose and we genotyped 119 markers covering the 18 porcine autosomal chromosomes. Within this context, we have developed a new empirical Bayes factor (BF) approach to compare between nested models, with and without the quantitative trait loci (QTL) effect, and after including the location of the QTL as an unknown parameter in the model. This empirical BF can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null QTL effects. Linkage analyses were performed in each chromosome using an animal model to account for infinitesimal genetic effects. Initially, three QTL were detected at chromosomes 6, 8 and 11 although, after correcting for multiple testing, only the additive QTL located in cM 110 of chromosome 8 remained. For this QTL, the allelic effect of substitution of the Iberian allele increased gestation length in 0.521 days, with a highest posterior density region at 95% ranged between 0.121 and 0.972 days. Although future studies are necessary to confirm if detected QTL is relevant and segregating in commercial pig populations, a hot-spot on the genetic regulation of gestation length in pigs seems to be located in chromosome 8.

Keywords

Bayes factorgestation lengthpigsquantitative trait loci
Type
Full Paper
Information
animal , Volume 2 , Issue 2 , February 2008 , pp. 177 - 183
Copyright
Copyright © The Animal Consortium 2008

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Alves, E, Óvilo, C, Rodríguez, C, Silió, L 2003. Mitochondrial DNA sequence variation and phylogenetic relationships of Iberian pigs and other domestic and wild pig populations. Animal Genetics 34, 319–324.CrossRefGoogle ScholarPubMed
Birchmeier, AN, Cantet, RJC, Fernando, RL, Morris, CA, Holgado, F, Jara, A, Santos-Cristal, MG 2002. Estimation of segregation variance for birth weight in beef cattle. Livestock Production Science 76, 27–35.Google Scholar
Carlin, BP, Louis, TA 1996. Bayes and empirical Bayes methods for data analysis. Chapman and Hall, New York, NY.Google Scholar
Cassady, JP, Young, LD, Leymaster, KA 2002. Heterosis and recombination effects on pig reproductive traits. Journal of Animal Science 80, 2303–2315.Google Scholar
Churchill, GA, Doerge, RW 1994. Empirical threshold values for quantitative trait mapping. Genetics 138, 963–971.CrossRefGoogle ScholarPubMed
Falconer, DS, Mackay, TFC 1996. Introduction to quantitative genetics. Longman, New York, NY.Google Scholar
García-Cortés, LA, Cabrillo, C, Moreno, C, Varona, L 2001. Hypothesis testing for the genetic background of quantitative traits. Genetics Selection Evolution 33, 3–16.Google Scholar
Gelfand, A, Smith, AFM 1990. Sampling based approaches to calculating marginal densities. Journal of the American Statistical Association 85, 398–409.CrossRefGoogle Scholar
Gilks, WR, Richardson, S, Speigelhalter, DJ 1996. Markov chain Monte Carlo in practice. Chapman and Hall, London, UK.Google Scholar
Green P, Falls K and Crooks S 1990. Documentation of CRI-MAP version 2.4. Unpublished mimeo (available at http://compgen.rutgers.edu/multimap/crimap).Google Scholar
Haley, CS, Knott, SA 1992. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69, 315–324.Google Scholar
Haley, CS, Lee, GJ 1993. Genetic-basis of prolificacy in Meishan pigs. Journal of Reproduction and Fertility 48 (suppl), 247–259.Google ScholarPubMed
Hanenberg, EHAT, Knol, EF, Merks, JWM 2001. Estimates of genetic parameters for reproduction traits at different parities in Dutch Landrace pigs. Livestock Production Science 69, 179–186.Google Scholar
Hastings, WK 1970. Monte Carlo sampling methods using Markov chains and their application. Biometrika 57, 97–109.Google Scholar
Jeffreys, H 1961. Theory of probability. Clarendon Press, Oxford, UK.Google Scholar
Kass, RE, Raftery, AE 1995. Bayes factors. Journal of the American Statistical Association 90, 773–795.CrossRefGoogle Scholar
Kijas, JMH, Wales, R, Törnsten, A, Chardon, P, Moller, M, Andersson, L 1998. Melanocortin receptor 1 (MC1R) mutations and coat colour in pigs. Genetics 150, 1177–1185.Google Scholar
King, AH, Jiang, Z, Gibson, JP, Haley, CS, Archibald, AL 2003. Mapping quantitative trait loci affecting female reproductive traits on porcine chromosome 8. Biology of Reproduction 68, 2172–2179.Google Scholar
Knol, EF, Leenhouwers, JI, Van der Lende, T 2002. Genetic aspects of piglet survival. Livestock Production Science 78, 47–55.CrossRefGoogle Scholar
Leenhouwers, JI, Van der Lende, T, Knol, EF 1999. Analysis of stillbirth in different lines of pig. Livestock Production Science 57, 243–253.Google Scholar
Leenhouwers, JI, Wissink, P, Van der Lende, T, Paridaans, H, Knol, EF 2003. Stillbirth in the pig in relation to genetic merit for farrowing survival. Journal of Animal Science 81, 2419–2424.Google Scholar
Moeller, SJ, Goodwin, RN, Johnson, RK, Mabry, JW, Baas, TJ, Robinson, OW 2004. The National Pork Producers Council Maternal Line National Genetic Evaluation Program: a comparison of six maternal genetic lines for female productivity measures over four parities. Journal of Animal Science 82, 41–53.CrossRefGoogle ScholarPubMed
Muñoz G, Fernández A, Barragán C, Silió L, Óvilo C and Rodríguez C 2005. SNP detection on LHB gene and association analysis with litter size in pigs. Proceedings of the 56th Annual Meeting of the European Association for Animal Production, June 5–8, Uppsala, Sweden.Google Scholar
Nguyen, NH, McPhee, CP, Wade, CM 2006. Genetic variation and responses in reproductive performance of sows in lines selected for growth rate under restricted feeding. Animal Science 82, 7–12.Google Scholar
Raftery, AE, Lewis, SM 1992. How many iterations in the Gibbs Sampler? In Bayesian statistics IV (ed. JM Bernardo, JO Berger, AP Dawid and AFM Smith), pp. 763–774. Oxford University Press, New York, NY.CrossRefGoogle Scholar
Ramírez, O, Blanch, M, Amills, M, Noguera, JL, Sánchez, A 2003. Polimorfismo del gen vascular-cell adhesion molecule 1 (VCAM1) porcino. Jornadas sobre Producción Animal Información técnica Económica Agraria (serie Producción Animal) 24, 447–449.Google Scholar
Ramírez O, Tomás A, Barragán C, Noguera JL, Amills M and Varona L 2005. Effects of the pig melatonin receptor 1A gene (MTNR1A) on litter size in an Iberian × Meishan F2 population. First European Congress on Pig Genomics, Lodi, Italy.Google Scholar
Rathje, TA, Rohrer, GA, Johnson, RK 1997. Evidence for quantitative trait loci affecting ovulation rate in pigs. Journal of Animal Science 75, 1486–1494.Google Scholar
Rodríguez, C, Tomás, A, Alves, E, Ramírez, O, Arqué, M, Muñoz, G, Barragán, C, Varona, L, Silió, L, Amills, M, Noguera, JL 2005. QTL mapping for teat number in an Iberian-by-Meishan pig intercross. Animal Genetics 36, 490–496.Google Scholar
Rohrer, GA, Ford, JJ, Wise, TH, Vallet, JL, Christenson, RK 1999. Identification of quantitative trait loci affecting female reproductive traits in a multigeneration Meishan-White composite swine population. Journal of Animal Science 77, 1385–1391.Google Scholar
Scott JG and Berger J 2003. An exploration of aspects of Bayesian multiple testing. Technical report, Duke University, Durham, NC.Google Scholar
Sellier, P, Ollivier, L 1982. A genetic study of splayleg in the new-born piglet. I. Multifactorial model with on threshold. Annales de Génétique et de Sélection Animale 14, 77–92.Google Scholar
Serenius, T, Sevón-Aimonen, M-L, Kause, A, Mäntysaari, EA, Mäki-Tanila, A 2004. Selection potential of different prolificacy traits in the Finnish Landrace and Large White populations. Acta Agriculturae Scandinavica, Section A – Animal Science 54, 36–43.Google Scholar
Short, TH, Rothschild, MF, Southwood, OI, McLaren, DG, De Vries, A, Van der Steen, H, Eckardt, GR, Tuggle, CK, Helm, J, Vaske, DA, Mileham, AJ, Plastow, GS 1997. Effect of the estrogen receptor locus on reproduction and production traits in four commercial pig lines. Journal of Animal Science 75, 3138–3142.Google Scholar
Spencer, HG 2002. The correlation between relatives on the supposition of genomic imprinting. Genetics 161, 411–417.CrossRefGoogle ScholarPubMed
Stephens, DA, Fisch, RD 1998. Bayesian analysis of quantitative trait locus data using reversible jump Markov chain Monte Carlo. Biometrics 54, 1334–1347.Google Scholar
Tomás, A, Casellas, J, Ramírez, O, Pérez-Enciso, M, Rodríguez, C, Noguera, JL, Sánchez, A 2006a. Polymorphisms of the porcine dopamine β-hydroxylase gene and their relation to reproduction and piglet survivability in an Iberian × Meishan F2 intercross. Animal Genetics 37, 279–282.Google Scholar
Tomás, A, Casellas, J, Ramírez, O, Muñoz, G, Noguera, JL, Sánchez, A 2006b. High amino acid variation in the intracellular domain of the pig prolactin receptor (PRLR) and its relation to ovulation rate and piglet survival traits. Journal of Animal Science 84, 1991–1998.Google Scholar
Tomás, A, Frigo, E, Casellas, J, Ramírez, O, Óvilo, C, Noguera, JL, Sánchez, A 2006c. An association study between polymorphisms of the porcine bone morphogenetic protein receptor type 1β (BMPR1B) and reproductive performance of Iberian × Meishan F2 sows. Animal Genetics 37, 297–298.CrossRefGoogle Scholar
Van der Heyde, H, De Mets, JP, Porreye, L, Henderickx, H, Calus, A, Bekaert, H, Buysse, F 1989. Influence of season, litter size, parity, gestation length, birth weight, sex and farrowing pen on frequency of congenital splayleg in piglets. Livestock Production Science 21, 143–155.Google Scholar
Varona, L, García-Cortés, LA, Pérez-Enciso, M 2001. Bayes factors for detection of quantitative trait loci. Genetics Selection Evolution 33, 133–152.CrossRefGoogle ScholarPubMed
Varona, L, Gómez-Raya, L, Rauw, WM, Ovilo, C, Clop, A, Noguera, JL 2005. The value of prior information for detection of QTL affecting longitudinal traits: an example using Von Bertalanffy growth function. Journal of Animal Breeding and Genetics 122, 37–48.Google Scholar
Wilkie, PJ, Paszek, AA, Beattie, CW, Alexander, LJ, Wheeler, MB, Schook, LB 1999. A genomic scan of porcine reproductive traits reveals possible quantitative trait loci (QTLs) for number of corpora lutea. Mammalian Genome 10, 573–578.Google Scholar
Young, LD 1995. Reproduction of F1 Meishan, Fengjing, Minzhu and Duroc gilts and sows. Journal of Animal Science 73, 711–721.CrossRefGoogle ScholarPubMed
Young, LD 1998. Reproduction of 3/4 White composite and 1/4 Duroc, 1/4 Meishan, 1/4 Fengjing, or 1/4 Minzhu gilts and sows. Journal of Animal Science 76, 1559–1567.Google Scholar
Zaleski, HM, Hacker, RR 1993. Effect of oxygen and neostigmine on stillbirth and pig viability. Journal of Animal Science 71, 298–305.Google Scholar