This pedigree-based method could exploit inter-family variation in addition to intra-family variation, and could aurantiamide-acetate rapidly analyze hundreds of thousands of markers. Although the genomic control procedure was used to correct for stratification, we also could see a little population stratification of some of the traits. We think the population stratification is odd and maybe caused by cryptic relatedness. Heavy linkage disequilibrium in intercross population is one of the well-known limitations in genetic studies, which makes it difficult to identify the causative gene and mutation. In order to decrease non-positive rates, Bonferroni corrections have been used for all multiple tests. It is known that one QTL could influence a multifactorial trait and most biological traits also have a complex inheritance influenced by numerous genes. In the phenotype and genetic correlation analysis in the present study, the BH, BL, CBC and RC showed high phenotype or genetic correlations with each other Tinidazole suggested significant association between the major genes responsible for these traits. This GWAS also showed that all significant SNPs associated with more than one exterior trait localized in the same region, suggesting a pleiotropic effect of QTL on SSC7. Therefore, we chose the 20 most significant SNPs for further analysis. These SNPs, which were associated with every trait, are located in the proximal region from 31.24 Mb to 36.00 Mb on SSC7. SSC7 has been previously reported to be rich in QTLs influencing exterior traits. The region from 17.05 Mb to 45.42 Mb on SSC7 has been shown to have pleiotropic and significant QTL effects on CBC and Body length, measured in a Duroc purebred population and a White Duroc 6 Erhualian F2 intercross population. In previous reports, QTLs detected in F2 populations usually defined a high percentage of phenotypic variance. Similar to these reports, the present study indicated that 18.94% and 25.48% phenotypic variance of BH and BL, respectively, were explained by QTLs, which suggests that QTLs have a major effect on BH and BL in this 4.76 Mb region.