Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs
Crespo-Piazuelo, Daniel (Centre de Recerca en Agrigenòmica)
Criado Mesas, Lourdes (Centre de Recerca en Agrigenòmica)
Revilla Sánchez, Manuel (Centre de Recerca en Agrigenòmica)
Castelló Farré, Anna (Centre de Recerca en Agrigenòmica)
Fernández Ávila, Ana Isabel (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (Espanya))
Folch, Josep M. (Centre de Recerca en Agrigenòmica)
Ballester Devis, Maria (Institut de Recerca i Tecnologia Agroalimentàries)

Date:	2019
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)).
Grants:	Ministerio de Economía y Competitividad AGL2014-56369-C2 Ministerio de Economía y Competitividad AGL2017-82641-R Agència de Gestió d'Ajuts Universitaris i de Recerca ECO2014-1788 Agència de Gestió d'Ajuts Universitaris i de Recerca ECO2013-1639 Ministerio de Economía y Competitividad RYC-2013-12573 Ministerio de Economía y Competitividad SEV2015-0533
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Genome-wide association studies
Published in:	PloS one, Vol. 14, Núm. 6 (June 2019) , art. e0218862, ISSN 1932-6203

DOI: 10.1371/journal.pone.0218862
PMID: 31246983

17 p, 1.9 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles