doi:10.1111/j.1365-2052.2006.01500.x Comparison of genetic models for analysing the effects of a PvuII polymorphism in the oestrogen receptor 1 (ESR1) gene on prolificacy in an Iberian · Meishan pig population S. Braglia* ,†,1 , O. Ramı ´rez ‡,1 , J. L. Noguera*, A. Toma´s † , C. Ovilo ¶ and L. Varona* *Area de Produccio´ Animal, Centre UdL-IRTA, Lleida, 25198, Spain. † Univ Bologna, Fac Agr, Sez Allevamenti Zootecn, Reggio Emilia, 42100 Italy. ‡ Departament de Cie` ncia Animal i dels Aliments, Facultat de Veterina` ria, UAB, Bellaterra 08193, Spain. ¶ Departamento de Mejora Gene´ tica Animal, SGIT-INIA, Madrid 28040, Spain Summary The effect of a previously reported PvuII polymorphism in oestrogen receptor 1 (ESR1) was analysed in an F 2 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 poly- morphism 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. Keywords Iberian, Meishan, oestrogen receptor, pig, prolificacy. Introduction The oestrogen receptor is a ligand-activated transcription factor composed of several domains that are important for hormone binding, DNA binding, and activating transcrip- tion (OMIM*133430). Ovarian oestrogen receptors are needed for oestrogen-induced gene activation (Schams & Berisha 2002), and their expression on the follicle has been demonstrated (Schams & Berisha 2002). In 1994, Rothschild et al. (1994, 1996) first suggested that a PvuII polymorphism in the oestrogen receptor 1 (ESR1) gene was a useful marker for increasing prolificacy in pigs. These results are supported in other populations of Meishan (Rothschild et al. 1995; Southwood et al. 1995) and Large White (Rothschild et al. 1996; Short et al. 1997) origin. Isler et al. (2002) and Van Rens et al. (2002) also confirmed the effects of the ESR1 marker in the reproductive traits of other populations. However, other studies (Drogemuller et al. 2001; Gibson et al. 2002; Noguera et al. 2003) were not able to find any statistical association between the alleles of the ESR1 gene and prolificacy. A meta-analysis performed by Alfonso (2005) showed a high and significant degree of heterogeneity among the results. Thus, the application of ESR1 genotyping for marker-assisted selection cannot be generalized across pig populations. The objective of this study was to describe the effect of the ESR1 mutation in an Iberian · Meishan population with respect to three assumptions: (1) there was a fixed causal mutation in the parental populations and the PvuII poly- morphism acts as a neutral marker, (2) there was a causal mutation in linkage disequilibrium with the ESR1 alleles and (3) there was a causal mutation in linkage disequilibrium with the ESR1 alleles within each parental population. Materials and methods Experimental design and traits analysed A three-generation intercross was generated by mating three Iberian boars from the Guadyerbas strain (Toro et al. 2000) with 18 Meishan sows (Domain du Magneraud, INRA, France). Eight F 1 boars and 97 F 1 sows were the parents of F 2 progeny at the Nova Gene`tica S. A. experi- Address for correspondence L. Varona, Area de Produccio´ Animal, Centre UdL-IRTA, Av, Rovira Roure 191, 25198, Lleida, Spain. E-mail: luis.varona@irta.es 1 These authors equally contributed to the article. Accepted for publication 4 June 2006 Ó 2006 The Authors, Journal compilation Ó 2006 International Society for Animal Genetics, Animal Genetics, 37, 454–458 454