Genome-wide association study and biological pathway analysis for response to Eimeria maxima in broilers

TY - JOUR

T1 - Genome-wide association study and biological pathway analysis for response to Eimeria maxima in broilers

AU - Hamzic, Edin

AU - Buitenhuis, Albert Johannes

AU - Hérault, Frédéric

AU - Hawken, Rachel

AU - Abrahamsen, Mitchell S

AU - Servin, Bertrand

AU - Elsen, Jean-Michel

AU - Pinard-van der Laan, Marie-Hélène

AU - Bed'Hom, Bertrand

PY - 2015/11/25

Y1 - 2015/11/25

N2 - Background Coccidiosis is the most common and costly disease in the poultry industry and which caused by protozoans from the genus of Eimeria. The current control of coccidiosis, based on the use of anticoccidial drugs and vaccination, faces serious obstacles such as drug resistance and the high costs for development of efficient vaccines, respectively. Therefore, the present control programs must be expanded with complementary approaches such as the use of genetics for improvement of the host’s response to Eimeria infections. Recently, we have performed a large-scale challenge study on Cobb500 broilers using E. maxima where we investigated variability among animals in response to the challenge. Taking advantage of size and structure of the large-scale challenge study, we performed a genome-wide association study (GWAS) with the aim to identify genomic regions underlying variability of the measured traits in the response to Eimeria maxima in broilers. Furthermore, we conducted a post-GWAS functional analysis with the aim of gaining a better biological understanding of the underlying response to Eimeria maxima challenge in broilers. Results In total, we identified 22 single nucleotide polymorphisms (SNP) with q-value <0.1 distributed across five chicken chromosomes. The highly significant SNPs are associated with body weight gain (3 SNPs on GGA5, 1 SNP on GGA1 and 1 SNP on GGA3), plasma coloration measured as optical density (OD) for wavelengths in the range 465 – 510 nm (10 SNPs and all on GGA10) and percentage of β2-globulin in blood plasma (15 SNPs on GGA1 and 1 SNP on GGA2). Biological pathways related to metabolic processes, cell proliferation, and primary innate immune processes were among the most frequent significantly enriched biological pathways. Furthermore, the network-based analysis produced two networks of high confidence; one centered on large tumor suppressor kinase 1 (LATS1) and 2 (LATS2), and the second with the myosin heavy chain 6 (MYH6), which has the largest number of direct significant links. Conclusions We identified several strong candidate genes and genomic regions associated to traits measured in the response to Eimeria maxima in broilers. Furthermore, the post-GWAS functional analysis indicates that biological pathways and networks involved in tissue proliferation and repair as well as primary innate immune response might play the most important role during the early stage of Eimeria maxima infection in broilers.

AB - Background Coccidiosis is the most common and costly disease in the poultry industry and which caused by protozoans from the genus of Eimeria. The current control of coccidiosis, based on the use of anticoccidial drugs and vaccination, faces serious obstacles such as drug resistance and the high costs for development of efficient vaccines, respectively. Therefore, the present control programs must be expanded with complementary approaches such as the use of genetics for improvement of the host’s response to Eimeria infections. Recently, we have performed a large-scale challenge study on Cobb500 broilers using E. maxima where we investigated variability among animals in response to the challenge. Taking advantage of size and structure of the large-scale challenge study, we performed a genome-wide association study (GWAS) with the aim to identify genomic regions underlying variability of the measured traits in the response to Eimeria maxima in broilers. Furthermore, we conducted a post-GWAS functional analysis with the aim of gaining a better biological understanding of the underlying response to Eimeria maxima challenge in broilers. Results In total, we identified 22 single nucleotide polymorphisms (SNP) with q-value <0.1 distributed across five chicken chromosomes. The highly significant SNPs are associated with body weight gain (3 SNPs on GGA5, 1 SNP on GGA1 and 1 SNP on GGA3), plasma coloration measured as optical density (OD) for wavelengths in the range 465 – 510 nm (10 SNPs and all on GGA10) and percentage of β2-globulin in blood plasma (15 SNPs on GGA1 and 1 SNP on GGA2). Biological pathways related to metabolic processes, cell proliferation, and primary innate immune processes were among the most frequent significantly enriched biological pathways. Furthermore, the network-based analysis produced two networks of high confidence; one centered on large tumor suppressor kinase 1 (LATS1) and 2 (LATS2), and the second with the myosin heavy chain 6 (MYH6), which has the largest number of direct significant links. Conclusions We identified several strong candidate genes and genomic regions associated to traits measured in the response to Eimeria maxima in broilers. Furthermore, the post-GWAS functional analysis indicates that biological pathways and networks involved in tissue proliferation and repair as well as primary innate immune response might play the most important role during the early stage of Eimeria maxima infection in broilers.

KW - Eimeria maxima

KW - broilers

KW - GWAS

KW - chicken

KW - association mapping

KW - biological pathway analysis

KW - network-based analysis

KW - disease resilience

KW - disease resistance

U2 - 10.1186/s12711-015-0170-0

DO - 10.1186/s12711-015-0170-0

M3 - Journal article

C2 - 26607727

SN - 0999-193X

VL - 47

SP - 1

EP - 17

JO - Genetics Selection Evolution

JF - Genetics Selection Evolution

IS - 91

ER -