Análise de associação genômica para hérnia umbilical em suínos comerciais utilizando abordagem de marcadores únicos e múltiplos

Abstract

There are several birth defects that affect pig farming worldwide, including cryptorchidism, splay legs, congenital tremor, intersexuality, anal atresia and hernias. Umbilical hernia (UH) is one of the most common congenital disabilities in pigs caused by the protrusion of the intestinal contents by the umbilical ring. The presence of hernias can cause economic losses due to the damage caused to the welfare of the animals, which results in reduced growth and poor feed conversion. Moreover, hernias can also cause damage in the moment of slaughter, contaminating the carcass if a rupture of the intestinal loops accurs. For this reason, it is essential for the pig industry, the identification of markers in the swine genome, which may be associated to umbilical hernia to be used in the selection process, preventing the occurrence of this anomaly. The development of new generation sequencing technologies has led to the identification of many single nucleotide polymorphisms (SNPs), making genome-wide association studies (GWAS) possible which involves thousands of variants across the genome used to identify those associated with traits of interest. For this type of study, several methodologies are available, such as single marker that evaluates the individual effect of each SNP and that of multiple markers, which analyzes the haplotypes. Thus, the objective of this study was to identify genomic regions associated with the development of umbilical hernia in pigs, using two statistical methodologies: single and multiple markers. A total of 325 crossbred pigs (92 cases and 233 controls), hybrids of the Agroceres Pic® genetics, from farms located in Santa Catarina State were evaluated and genotyped, using GGP Porcine Bead Chip (Neogen, Lincon, NE, EUA). Ten significant SNPs were found with the single marker analysis, comprising 23 transcripts of biological knowledge in the extension of the regions. With the multiple marker analysis, 401 SNPs were also observed distributed in 51 genomic regions, with 116 transcripts biologically known. The biological processes significantly associated with these genes were those related to the development of skeletal muscle, the occurrence of angiogenesis, as well as the recruitment of cytokines to fight inflammation and umbilical healing. According to our results, strong candidates for the development of umbilical hernia in pigs were considered according to the methodology using a single marker, the MTM1 and MTMR1 genes, according to the multiple marker methodology, the EP300, MSTN and EYA2 genes, and by both methodologies the genes GJA5, BCL9, ACP6 and WARS2. Thus, it was possible to better understand the genetic factors associated with umbilical hernia, demonstrating that genes related to the development of skeletal muscle, and processes linked to the extracellular matrix and the immune system, may be closely related to disorders that lead to predisposition of occurrence of umbilical hernia in commercial pigs.