Abstract
BackgroundCryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, both from an animal welfare point of view as well as for economic reasons. The aim of this genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) that are strongly associated with these congenital defects. Genotypes were available for 2570 Large White (LW) and 2272 Landrace (LR) pigs. Breeding values were estimated based on 1 359 765 purebred and crossbred male offspring, using a binary trait animal model. Estimated breeding values were deregressed (DEBV) and taken as the response variable in the GWAS.ResultsHeritability estimates were equal to 0.26 ± 0.02 for cryptorchidism and to 0.31 ± 0.01 for scrotal/inguinal hernia. Seven and 31 distinct QTL regions were associated with cryptorchidism in the LW and LR datasets, respectively. The top SNP per region explained between 0.96% and 1.10% and between 0.48% and 2.77% of the total variance of cryptorchidism incidence in the LW and LR populations, respectively. Five distinct QTL regions associated with scrotal/inguinal hernia were detected in both LW and LR datasets. The top SNP per region explained between 1.22% and 1.60% and between 1.15% and 1.46% of the total variance of scrotal/inguinal hernia incidence in the LW and LR populations, respectively. For each trait, we identified one overlapping region between the LW and LR datasets, i.e. a region on SSC8 (Sus scrofa chromosome) between 65 and 73 Mb for cryptorchidism and a region on SSC13 between 34 and 37 Mb for scrotal/inguinal hernia.ConclusionsThe use of DEBV in combination with a binary trait model was a powerful approach to detect regions associated with difficult traits such as cryptorchidism and scrotal/inguinal hernia that have a low incidence and for which affected animals are generally not available for genotyping. Several novel QTL regions were detected for cryptorchidism and scrotal/inguinal hernia, and for several previously known QTL regions, the confidence interval was narrowed down.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0096-6) contains supplementary material, which is available to authorized users.
Highlights
Cryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs
The use of DEBV obtained with a binary trait model was considered to be a powerful approach for traits like cryptorchidism and hernia, which have a low incidence and for which affected animals are generally not genotyped [10]
The incidence of cryptorchidism was lower in Large White (LW) than in LR pigs (0.14 vs. 0.33%), while the incidence of hernia was slightly higher in LW than in LR pigs (0.42% vs. 0.34%) (Table 1)
Summary
Cryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, both from an animal welfare point of view as well as for economic reasons The aim of this genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) that are strongly associated with these congenital defects. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, both from an animal welfare point of view and for economic reasons. To obtain “phenotypes” of the genotyped animals, we applied a pedigree-based method to calculate estimated breeding values (EBV) These EBV were subsequently deregressed (DEBV) and used as response variable in the GWAS analysis. Our aim was to identify single nucleotide polymorphisms (SNPs) associated with cryptorchidism and hernia using DEBV
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