Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes.

Androniki Psifidi,Judy Bettridge,Olivier Hanotte,Oswald Matika,Pete Kaiser,Paul Wigley,Rob Christley,Takele T. Desta,Georgios Banos,David A. Hume,Tadelle Dessie

doi:10.1186/s12711-016-0252-7

Abstract

BackgroundThe majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems. Although they are generally resilient to disease challenge, routine vaccination and biosecurity measures are rarely applied and infectious diseases remain a major cause of mortality and reduced productivity. Management and genetic improvement programmes are hampered by lack of routine data recording. Selective breeding based on genomic technologies may provide the means to enhance sustainability. In this study, we investigated the genetic architecture of antibody response to four major infectious diseases [infectious bursal disease (IBDV), Marek’s disease (MDV), fowl typhoid (SG), fowl cholera (PM)] and resistance to Eimeria and cestode parasitism, along with two production traits [body weight and body condition score (BCS)] in two distinct indigenous Ethiopian chicken ecotypes. We conducted variance component analyses, genome-wide association studies, and pathway and selective sweep analyses.ResultsThe large majority of birds was found to have antibody titres for all pathogens and were infected with both parasites, suggesting almost universal exposure. We derived significant moderate to high heritabilities for IBDV, MDV and PM antibody titres, cestodes infestation, body weight and BCS. We identified single nucleotide polymorphisms (SNPs) with genome-wide significance for each trait. Based on these associations, we identified for each trait, pathways, networks and functional gene clusters that include plausible candidate genes. Selective sweep analyses revealed a locus on chromosome 18 associated with viral antibody titres and resistance to Eimeria parasitism that is within a positive selection signal. We found no significant genetic correlations between production, immune and disease traits, implying that selection for altered antibody response and/or disease resistance will not affect production.ConclusionsWe confirmed the presence of genetic variability and identified SNPs significantly associated with immune, disease and production traits in indigenous village chickens. Results underpin the feasibility of concomitant genetic improvement for enhanced antibody response, resistance to parasitism and productivity within and across indigenous chicken ecotypes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0252-7) contains supplementary material, which is available to authorized users.

Highlights

The majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems
The mean infectious bursal disease virus (IBDV) antibody titre was higher for Horro birds, whereas Mareks’ disease virus (MDV), serovar Galinarum (SG) and Pasteurella multocida (PM) antibody titres were similar for birds from the two regions
We identified genome-wide significant single nucleotide polymorphisms (SNPs) for antibody titres to IBDV (P-values 2.82 × 10−8 to 2.55 × 10−8) and cestodes (4.03 × 10−8 to 1.80 × 10−11) in both ecotypes but on different chromosomes

Summary

Introduction

The majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems. They are generally resilient to disease challenge, routine vaccination and biosecurity measures are rarely applied and infectious diseases remain a major cause of mortality and reduced productivity. The first results demonstrated the presence of considerable genetic variation in performance traits and strongly suggested that productivity improvement with selective breeding should be possible [9, 11,12,13] These selection programmes are yet to consider genetic resistance to major infectious diseases, which could potentially be genetically correlated with production traits [14]. Other studies in sheep [18] have shown that more genetically resistant animals may have greater growth; studies in pigs [19] have shown that animals selected for increased feed efficiency may be less affected by porcine reproductive and respiratory syndrome (PRRS) infection

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Conclusion