Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs

• Published in: PloS one Vol. 14; no. 6; p. e0218862
• Main Authors: Crespo-Piazuelo, Daniel, Criado-Mesas, Lourdes, Revilla, Manuel, Castelló, Anna, Fernández, Ana I., Folch, Josep M., Ballester, Maria
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 27.06.2019; Public Library of Science (PLoS)
• Subjects: Amino acid sequence; Animal breeding; Animals; Biology and Life Sciences; Computer and Information Sciences; Consortia; Diabetes; Divergence; DNA sequencing; EDTA; Fatty acids; Female; Gene expression; Gene Frequency; Gene sequencing; Genes; Genetic divergence; Genetic polymorphisms; Genome-wide association studies; Genome-Wide Association Study - veterinary; Genomes; Genomics; Genotyping Techniques - veterinary; Health aspects; High-Throughput Nucleotide Sequencing; Hogs; Inbreeding; INDEL Mutation; Lipid Metabolism; Lipids; Livestock; Male; Meat; Medicine and Health Sciences; Metabolism; Metabolites; Muscle, Skeletal - chemistry; Muscles; Mutation; Nucleotides; Obesity; Omega 6 fatty acids; Pork; Proteins; Research and Analysis Methods; Selective breeding; Sensory properties; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Studies; Suidae; Swine; Tumor necrosis factor-TNF; Whole genome sequencing; Whole Genome Sequencing - veterinary; Spain
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0218862

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)).