Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens
Poultry play an important role in the agriculture of many African countries. The majority of chickens in sub-Saharan Africa are indigenous, raised in villages under semi-scavenging conditions. Vaccinations and biosecurity measures rarely apply, and infectious diseases remain a major cause of mortali...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Frontiers Media
2020
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/110306 |
| _version_ | 1855524724348551168 |
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| author | Banos, Giorgios Lindsay, V. Desta, T.T. Bettridge, Judy M. Sánchez Molano, E. Vallejo Trujillo, Adriana Matika, O. Dessie, Tadelle Wigley, P. Christley, Robert M. Kaiser, P. Hanotte, Olivier H. Psifidi, A. |
| author_browse | Banos, Giorgios Bettridge, Judy M. Christley, Robert M. Dessie, Tadelle Desta, T.T. Hanotte, Olivier H. Kaiser, P. Lindsay, V. Matika, O. Psifidi, A. Sánchez Molano, E. Vallejo Trujillo, Adriana Wigley, P. |
| author_facet | Banos, Giorgios Lindsay, V. Desta, T.T. Bettridge, Judy M. Sánchez Molano, E. Vallejo Trujillo, Adriana Matika, O. Dessie, Tadelle Wigley, P. Christley, Robert M. Kaiser, P. Hanotte, Olivier H. Psifidi, A. |
| author_sort | Banos, Giorgios |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Poultry play an important role in the agriculture of many African countries. The majority of chickens in sub-Saharan Africa are indigenous, raised in villages under semi-scavenging conditions. Vaccinations and biosecurity measures rarely apply, and infectious diseases remain a major cause of mortality and reduced productivity. Genomic selection for disease resistance offers a potentially sustainable solution but this requires sufficient numbers of individual birds with genomic and phenotypic data, which is often a challenge to collect in the small populations of indigenous chicken ecotypes. The use of information across-ecotypes presents an attractive possibility to increase the relevant numbers and the accuracy of genomic selection. In this study, we performed a joint analysis of two distinct Ethiopian indigenous chicken ecotypes to investigate the genomic architecture of important health and productivity traits and explore the feasibility of conducting genomic selection across-ecotype. Phenotypic traits considered were antibody response to Infectious Bursal Disease (IBDV), Marek's Disease (MDV), Fowl Cholera (PM) and Fowl Typhoid (SG), resistance to Eimeria and cestode parasitism, and productivity (body weight and body condition score (BCS)). Combined data from the two chicken ecotypes, Horro (n=384) and Jarso (n=376), were jointly analysed for genetic parameter estimation, genome-wide association studies (GWAS), genomic breeding value (GEBVs) calculation, genomic predictions, whole-genome sequencing (WGS), and pathways analyses. Estimates of across-ecotype heritability were significant and moderate in magnitude (0.22-0.47) for all traits except for SG and BCS. GWAS identified several significant genomic associations with health and productivity traits. The WGS analysis revealed putative candidate genes and mutations for IBDV (TOLLIP, ANGPTL5, BCL9, THEMIS2), MDV (GRM7), SG (MAP3K21), Eimeria (TOM1L1) and cestodes (TNFAIP1, ATG9A, NOS2) parasitism, which warrant further investigation. Reliability of GEBVs increased compared to within-ecotype calculations but accuracy of genomic prediction did not, probably because the genetic distance between the two ecotypes offset the benefit from increased sample size. However, for some traits genomic prediction was only feasible in across-ecotype analysis. Our results generally underpin the potential of genomic selection to enhance health and productivity across-ecotypes. Future studies should establish the required minimum sample size and genetic similarity between ecotypes to ensure accurate joint genomic selection. |
| format | Journal Article |
| id | CGSpace110306 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1103062024-10-03T07:40:51Z Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens Banos, Giorgios Lindsay, V. Desta, T.T. Bettridge, Judy M. Sánchez Molano, E. Vallejo Trujillo, Adriana Matika, O. Dessie, Tadelle Wigley, P. Christley, Robert M. Kaiser, P. Hanotte, Olivier H. Psifidi, A. chickens genetics indigenous breeds poultry animal diseases animal breeding Poultry play an important role in the agriculture of many African countries. The majority of chickens in sub-Saharan Africa are indigenous, raised in villages under semi-scavenging conditions. Vaccinations and biosecurity measures rarely apply, and infectious diseases remain a major cause of mortality and reduced productivity. Genomic selection for disease resistance offers a potentially sustainable solution but this requires sufficient numbers of individual birds with genomic and phenotypic data, which is often a challenge to collect in the small populations of indigenous chicken ecotypes. The use of information across-ecotypes presents an attractive possibility to increase the relevant numbers and the accuracy of genomic selection. In this study, we performed a joint analysis of two distinct Ethiopian indigenous chicken ecotypes to investigate the genomic architecture of important health and productivity traits and explore the feasibility of conducting genomic selection across-ecotype. Phenotypic traits considered were antibody response to Infectious Bursal Disease (IBDV), Marek's Disease (MDV), Fowl Cholera (PM) and Fowl Typhoid (SG), resistance to Eimeria and cestode parasitism, and productivity (body weight and body condition score (BCS)). Combined data from the two chicken ecotypes, Horro (n=384) and Jarso (n=376), were jointly analysed for genetic parameter estimation, genome-wide association studies (GWAS), genomic breeding value (GEBVs) calculation, genomic predictions, whole-genome sequencing (WGS), and pathways analyses. Estimates of across-ecotype heritability were significant and moderate in magnitude (0.22-0.47) for all traits except for SG and BCS. GWAS identified several significant genomic associations with health and productivity traits. The WGS analysis revealed putative candidate genes and mutations for IBDV (TOLLIP, ANGPTL5, BCL9, THEMIS2), MDV (GRM7), SG (MAP3K21), Eimeria (TOM1L1) and cestodes (TNFAIP1, ATG9A, NOS2) parasitism, which warrant further investigation. Reliability of GEBVs increased compared to within-ecotype calculations but accuracy of genomic prediction did not, probably because the genetic distance between the two ecotypes offset the benefit from increased sample size. However, for some traits genomic prediction was only feasible in across-ecotype analysis. Our results generally underpin the potential of genomic selection to enhance health and productivity across-ecotypes. Future studies should establish the required minimum sample size and genetic similarity between ecotypes to ensure accurate joint genomic selection. 2020-10-09 2020-11-26T08:42:41Z 2020-11-26T08:42:41Z Journal Article https://hdl.handle.net/10568/110306 en Open Access Frontiers Media Banos, G., Lindsay, V., Desta, T.T., Bettridge, J., Sanchez-Molano, E., Vallejo-Trujillo, A., Matika, O., Dessie, T., Wigley, P., Christley, R.M., Kaiser, P., Hanotte, O. and Psifidi, A. 2020. Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens. Frontiers in Genetics 11:543890. |
| spellingShingle | chickens genetics indigenous breeds poultry animal diseases animal breeding Banos, Giorgios Lindsay, V. Desta, T.T. Bettridge, Judy M. Sánchez Molano, E. Vallejo Trujillo, Adriana Matika, O. Dessie, Tadelle Wigley, P. Christley, Robert M. Kaiser, P. Hanotte, Olivier H. Psifidi, A. Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens |
| title | Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens |
| title_full | Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens |
| title_fullStr | Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens |
| title_full_unstemmed | Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens |
| title_short | Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens |
| title_sort | integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous african chickens |
| topic | chickens genetics indigenous breeds poultry animal diseases animal breeding |
| url | https://hdl.handle.net/10568/110306 |
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