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Identification of genomic regions affecting production traits in pigs divergently selected for feed efficiency

Authors :
Juliette Riquet
Yann Labrune
Amir Aliakbari
Katia Feve
Emilie Delpuech
Hélène Gilbert
Yvon Billon
Génétique Physiologie et Systèmes d'Elevage (GenPhySE )
Ecole Nationale Vétérinaire de Toulouse (ENVT)
Institut National Polytechnique (Toulouse) (Toulouse INP)
Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP)
Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Unité Expérimentale Elevages Porcins Innovants (GenESI)
Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
ANR-08-GENM-0038,PIC_FEED,Génétique de l'efficacité alimentaire du porc en croissance(2008)
ANR-16-CE20-0003,MICROFEED,Comprendre le rôle du microbiote intestinal pour améliorer l'efficacité et la robustesse de la production porcine(2016)
Source :
Genetics Selection Evolution, Genetics Selection Evolution, BioMed Central, 2021, 53 (1), ⟨10.1186/s12711-021-00642-1⟩, Genetics Selection Evolution, Vol 53, Iss 1, Pp 1-15 (2021), Genetics, Selection, Evolution : GSE
Publication Year :
2021
Publisher :
HAL CCSD, 2021.

Abstract

Background Feed efficiency is a major driver of the sustainability of pig production systems. Understanding the biological mechanisms that underlie these agronomic traits is an important issue for environment questions and farms' economy. This study aimed at identifying genomic regions that affect residual feed intake (RFI) and other production traits in two pig lines divergently selected for RFI during nine generations (LRFI, low RFI; HRFI, high RFI). Results We built a whole dataset of 570,447 single nucleotide polymorphisms (SNPs) in 2426 pigs with records for 24 production traits after both imputation and prediction of genotypes using pedigree information. Genome-wide association studies (GWAS) were performed including both lines (global-GWAS) or each line independently (LRFI-GWAS and HRFI-GWAS). Forty-five chromosomal regions were detected in the global-GWAS, whereas 28 and 42 regions were detected in the HRFI-GWAS and LRFI-GWAS, respectively. Among these 45 regions, only 13 were shared between at least two analyses, and only one was common between the three GWAS but it affects different traits. Among the five quantitative trait loci (QTL) detected for RFI, two were close to QTL for meat quality traits and two pinpointed novel genomic regions that harbor candidate genes involved in cell proliferation and differentiation processes of gastrointestinal tissues or in lipid metabolism-related signaling pathways. In most cases, different QTL regions were detected between the three designs, which suggests a strong impact of the dataset structure on the detection power and could be due to the changes in allelic frequencies during the establishment of lines. Conclusions In addition to efficiently detecting known and new QTL regions for feed efficiency, the combination of GWAS carried out per line or simultaneously using all individuals highlighted chromosomal regions that affect production traits and presented significant changes in allelic frequencies across generations. Further analyses are needed to estimate whether these regions correspond to traces of selection or result from genetic drift. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00642-1.

Details

Language :
English
ISSN :
0999193X and 12979686
Database :
OpenAIRE
Journal :
Genetics Selection Evolution, Genetics Selection Evolution, BioMed Central, 2021, 53 (1), ⟨10.1186/s12711-021-00642-1⟩, Genetics Selection Evolution, Vol 53, Iss 1, Pp 1-15 (2021), Genetics, Selection, Evolution : GSE
Accession number :
edsair.doi.dedup.....b3562529acc9deddc996047f5a8e8f29
Full Text :
https://doi.org/10.1186/s12711-021-00642-1⟩