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Background  The aim of this work was to study the effects on litter size of variants of the porcine genes  RBP4 ,  ESR1  and  IGF2 , currently used in genetic tests for different purposes. Moreover, we investigated a possible effect of the interaction between  RBP4 - Msp I and  ESR1-Pvu II polymorphisms. The  IGF2 -intron3-G3072A polymorphism is actually used to select lean growth, but other possible effects of this polymorphism on reproductive traits need to be evaluated.    Methods  Detection of polymorphisms in the genomic and cDNA sequences of  RBP4  gene was carried out.  RBP4 - Msp I and  IGF2 -intron3-G3072A were genotyped in a hyperprolific Chinese-European line (Tai-Zumu) and three new  RBP4  polymorphisms were genotyped in different pig breeds. A bivariate animal model was implemented in association analyses considering the number of piglets born alive at early (NBA 12 ) and later parities (NBA 3+  ) as different traits. A joint analysis of  RBP4 - Msp I and  ESR1-Pvu II was performed to test their possible interaction. In the  IGF2  analysis, paternal or maternal imprinting effects were also considered.    Results  Four different  RBP4  haplotypes were detected (TGAC, GGAG, GAAG and GATG) in different pig breeds and wild boars. A significant interaction effect between  RBP4-Msp I and  ESR1-Pvu II polymorphisms of 0.61 ± 0.29 piglets was detected on NBA 3+ . The  IGF2  analysis revealed a significant increase on NBA 3+  of 0.74 ± 0.37 piglets for the paternally inherited allele A.    Conclusions  All the analyzed pig and wild boar populations shared one of the four detected  RBP4  haplotypes. This suggests an ancestral origin of the quoted haplotype. The joint use of  RBP4-Msp I and  ESR1-Pvu II polymorphisms could be implemented to select for higher prolificacy in the Tai-Zumu line. In this population, the paternal allele  IGF2 -intron3-3072A increased litter size from the third parity. The non-additive effects on litter size reported here should be tested before implementation in other pig breeding schemes.

Non-additive effects of RBP4, ESR1 and IGF2 polymorphisms on litter size at different parities in a Chinese-European porcine line