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


RESULTS
The 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.


CONCLUSIONS
We 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.
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK. androniki.psifidi@roslin.ed.ac.uk.
Androniki
http://orcid.org/0000-0003-4095-1452
A
Psifidi
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.|Scotland's Rural College, Easter Bush, Edinburgh, Midlothian, EH25 9RG, UK.
Georgios
G
Banos
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
Oswald
O
Matika
School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
Takele T
TT
Desta
Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, UK.
Judy
J
Bettridge
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
David A
DA
Hume
International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia.
Tadelle
T
Dessie
Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, UK.
Rob
R
Christley
Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, UK.
Paul
P
Wigley
School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.|International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia.
Olivier
O
Hanotte
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
Pete
P
Kaiser
Avian Dis. 1980 Apr-Jun;24(2):358-74
6254488
Bioinformatics. 2007 May 15;23(10):1294-6
17384015
J Anim Sci. 2014 Jul;92(7):2905-21
24879764
Infect Immun. 1989 Mar;57(3):711-6
2917783
Front Genet. 2012 Jun 22;3:114
22737163
Genet Res. 2005 Oct;86(2):115-25
16356285
Infect Immun. 1988 Jun;56(6):1532-7
3372019
J Virol. 2015 Mar;89(5):2469-82
25505077
Poult Sci. 1997 Feb;76(2):289-96
9057208
Poult Sci. 2006 Jun;85(6):986-98
16776466
Microbes Infect. 2002 Nov;4(14):1409-15
12475631
Trop Anim Health Prod. 2010 Oct;42(7):1519-29
20512411
PLoS One. 2011;6(7):e21872
21779344
Anim Genet. 2015 Jun;46(3):247-54
25752210
Mol Biol Rep. 2012 May;39(5):5643-50
22203480
Front Genet. 2012 Dec 14;3:261
23412643
Vet Immunol Immunopathol. 1989 Jul;21(3-4):249-60
2678727
Anim Genet. 2003 Aug;34(4):264-74
12873214
Genet Sel Evol. 2014 Feb 19;46:14
24552175
Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19226-31
23129613
Immunogenetics. 2003 Jun;55(3):133-40
12743657
Cell Mol Life Sci. 2003 Aug;60(8):1623-35
14504653
Genetics. 2008 Jul;179(3):1591-9
18622035
Am J Hum Genet. 2006 Apr;78(4):629-44
16532393
Immunology. 1993 Jul;79(3):375-80
8406566
Vet Microbiol. 1990 Jul;24(1):55-62
2219665
Trop Anim Health Prod. 2004 Jan;36(1):1-9
14979553
J Vet Med B Infect Dis Vet Public Health. 2004 Mar;51(2):61-7
15030602
Infect Immun. 2003 Nov;71(11):6641-7
14573689
Malar J. 2015 Aug 14;14:315
26271921
PLoS Biol. 2006 Mar;4(3):e72
16494531
J Bacteriol. 1997 Dec;179(24):7856-64
9401047
Genome Biol. 2003;4(5):P3
12734009
PLoS One. 2010 Jan 28;5(1):e8940
20126627
Nat Methods. 2014 Apr;11(4):407-9
24531419
Vet Microbiol. 2004 May 20;100(1-2):43-53
15135512
Infect Immun. 1991 Jan;59(1):172-80
1987031
J Appl Genet. 2013 Nov;54(4):483-7
24114202
Trop Anim Health Prod. 2001 Dec;33(6):521-37
11770206
Poult Sci. 2000 Jun;79(6):804-9
10875759
Anim Genet. 2006 Jun;37(3):269-72
16734690
Poult Sci. 1987 May;66(5):819-24
3114728
Vet Parasitol. 2016 Jul 30;225:19-28
27369571
Prev Vet Med. 2014 Nov 15;117(2):358-66
25085600
Curr Opin Plant Biol. 2003 Jun;6(3):236-46
12753973
BMC Genomics. 2009 Jan 14;10:20
19144166
Poult Sci. 2000 Aug;79(8):1082-93
10947175
Mol Genet Genomics. 2011 Mar;285(3):237-43
21279652
Avian Pathol. 2004 Feb;33(1):25-33
14681065
Poult Sci. 2004 Jun;83(6):853-9
15206609
Bioinformatics. 2014 Feb 15;30(4):523-30
24336805
J Biol Chem. 2011 Jan 28;286(4):2567-77
21078663
Am J Hum Genet. 2007 Sep;81(3):559-75
17701901
Anim Genet. 2007 Apr;38(2):174-6
17326801
J Biol Chem. 2005 Mar 4;280(9):8617-27
15611045
Poult Sci. 2002 Dec;81(12):1775-81
12512565
Mol Biol Evol. 2013 Sep;30(9):2224-34
23777627
J Mol Histol. 2014 Aug;45(4):435-45
24337566
Trop Anim Health Prod. 2011 Jan;43(1):21-8
20625931
BMC Genomics. 2013 Jan 28;14:59
23356797
Poult Sci. 2001 Jul;80(7):879-84
11469649
FEMS Microbiol Lett. 2006 Dec;265(1):1-10
17107417
Vet Immunol Immunopathol. 2009 Mar 15;128(1-3):53-9
19070366