Abstract
The selection in commercial swine breeds for meat-production efficiency has been increasing among the past decades, reducing the intramuscular fat content, which has changed the sensorial and technological properties of pork. Through processes of natural adaptation and selective breeding, the accumulation of mutations has driven the genetic divergence between pig breeds. The most common and well-studied mutations are single-nucleotide polymorphisms (SNPs). However, insertions and deletions (indels) usually represents a fifth part of the detected mutations and should also be considered for animal breeding. In the present study, three different programs (Dindel, SAMtools mpileup, and GATK) were used to detect indels from Whole Genome Sequencing data of Iberian boars and Landrace sows. A total of 1,928,746 indels were found in common with the three programs. The VEP tool predicted that 1,289 indels may have a high impact on protein sequence and function. Ten indels inside genes related with lipid metabolism were genotyped in pigs from three different backcrosses with Iberian origin, obtaining different allelic frequencies on each backcross. Genome-Wide Association Studies performed in the Longissimus dorsi muscle found an association between an indel located in the C1q and TNF related 12 (C1QTNF12) gene and the amount of eicosadienoic acid (C20:2(n-6)).
Highlights
Pork is one of the world’s most produced meat
Genetic selection has notably improved meat-production efficiency in commercial pig breeds. This artificial selection had the unwanted drawback of reducing the pork sensorial and technological properties of meat. These modifications were driven by the reduction of intramuscular fat (IMF) content and fatty acid (FA) composition changes [1]
Dindel was the program that detected the highest number of indels (3,380,221) as opposed to SAMtools mpileup and Genome Analysis Toolkit (GATK) (2,749,596 and 2,957,377, respectively)
Summary
Pork is one of the world’s most produced meat. Selective breeding in pigs has been developed in parallel to the increase and intensification of this productive sector. Genetic selection has notably improved meat-production efficiency in commercial pig breeds. This artificial selection had the unwanted drawback of reducing the pork sensorial and technological properties of meat. These modifications were driven by the reduction of intramuscular fat (IMF) content and fatty acid (FA) composition changes [1].
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