Sexually dimorphic genetic architecture of complex traits in a large-scale F(2) cross in pigs

BACKGROUND: It is common for humans and model organisms to exhibit sexual dimorphism in a variety of complex traits. However, this phenomenon has rarely been explored in pigs. RESULTS: To investigate the genetic contribution to sexual dimorphism in complex traits in pigs, we conducted a sex-stratified analysis on 213 traits measured in 921 individuals produced by a White Duroc × Erhualian F(2) cross. Of the 213 traits examined, 102 differed significantly between the two sexes (q value <0.05), which indicates that sex is an important factor that influences a broad range of traits in pigs. We compared the estimated heritability of these 213 traits between males and females. In particular, we found that traits related to meat quality and fatty acid composition were significantly different between the two sexes, which shows that genetic factors contribute to variation in sexual dimorphic traits. Next, we performed a genome-wide association study (GWAS) in males and females separately; this approach allowed us to identify 13.6% more significant trait-SNP (single nucleotide polymorphism) associations compared to the number of associations identified in a GWAS that included both males and females. By comparing the allelic effects of SNPs in the two sexes, we identified 43 significant sexually dimorphic SNPs that were associated with 22 traits; 41 of these 43 loci were autosomal. The most significant sexually dimorphic loci were found to be associated with muscle hue angle and Minolta a* values (which are parameters that reflect the redness of meat) and were located between 9.3 and 10.7 Mb on chromosome 6. A nearby gene i.e. NUDT7 that plays an important role in heme synthesis is a strong candidate gene. CONCLUSIONS: This study illustrates that sex is an important factor that influences phenotypic values and modifies the effects of the genetic variants that underlie complex traits in pigs; it also emphasizes the importance of stratifying by sex when performing GWAS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-014-0076-2) contains supplementary material, which is available to authorized users.