1
|
Gaspar D, Ginja C, Carolino N, Leão C, Monteiro H, Tábuas L, Branco S, Padre L, Caetano P, Romão R, Matos C, Ramos AM, Bettencourt E, Usié A. Genome-wide association study identifies genetic variants underlying footrot in Portuguese Merino sheep. BMC Genomics 2024; 25:100. [PMID: 38262937 PMCID: PMC10804546 DOI: 10.1186/s12864-023-09844-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/26/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Ovine footrot caused by Dichelobacter nodosus (D. nodosus) is a contagious disease with serious economic and welfare impacts in sheep production systems worldwide. A better understanding of the host genetic architecture regarding footrot resistance/susceptibility is crucial to develop disease control strategies that efficiently reduce infection and its severity. A genome-wide association study was performed using a customized SNP array (47,779 SNPs in total) to identify genetic variants associated to footrot resistance/susceptibility in two Portuguese native breeds, i.e. Merino Branco and Merino Preto, and a population of crossbred animals. A cohort of 1375 sheep sampled across 17 flocks, located in the Alentejo region (southern Portugal), was included in the analyses. RESULTS Phenotypes were scored from 0 (healthy) to 5 (severe footrot) based on visual inspection of feet lesions, following the Modified Egerton System. Using a linear mixed model approach, three SNPs located on chromosome 24 reached genome-wide significance after a Bonferroni correction (p < 0.05). Additionally, six genome-wide suggestive SNPs were identified each on chromosomes 2, 4, 7, 8, 9 and 15. The annotation and KEGG pathway analyses showed that these SNPs are located within regions of candidate genes such as the nonsense mediated mRNA decay associated PI3K related kinase (SMG1) (chromosome 24) and the RALY RNA binding protein like (RALYL) (chromosome 9), both involved in immunity, and the heparan sulfate proteoglycan 2 (HSPG2) (chromosome 2) and the Thrombospodin 1 (THBS1) (chromosome 7) implicated in tissue repair and wound healing processes. CONCLUSION This is the first attempt to identify molecular markers associated with footrot in Portuguese Merino sheep. These findings provide relevant information on a likely genetic association underlying footrot resistance/susceptibility and the potential candidate genes affecting this trait. Genetic selection strategies assisted on the information obtained from this study could enhance Merino sheep-breeding programs, in combination with farm management strategies, for a more effective and sustainable long-term solution for footrot control.
Collapse
Affiliation(s)
- Daniel Gaspar
- Centro de Biotecnologia Agrícola E Agro-Alimentar Do Alentejo (CEBAL)/ Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus do Varão, Campus de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - Catarina Ginja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus do Varão, Campus de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- CIISA, Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Nuno Carolino
- CIISA, Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. Universidade Técnica, 1300-477, Lisboa, Portugal
- Instituto Nacional de Investigação Agrária E Veterinária, I.P. (INIAV, I.P.), Avenida da República, Quinta Do Marquês, 2780-157, Oeiras, Portugal
- Escola Universitária Vasco da Gama, Av. José R. Sousa Fernandes 197, 3020-210, Lordemão, Coimbra, Portugal
| | - Célia Leão
- Centro de Biotecnologia Agrícola E Agro-Alimentar Do Alentejo (CEBAL)/ Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal
- Instituto Nacional de Investigação Agrária E Veterinária, I.P. (INIAV, I.P.), Avenida da República, Quinta Do Marquês, 2780-157, Oeiras, Portugal
- MED - Mediterranean Institute for Agriculture, Environment and Development and CHANGE - Global Change and Sustainability Institute, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908, Beja, Portugal
| | | | | | - Sandra Branco
- MED-Mediterranean Institute for Agriculture, Environment and Development and CHANGE - Global Change and Sustainability Institute, University of Évora, Polo da Mitra, Ap. 94, 7006-554, Évora, Portugal
- Departamento de Medicina Veterinária, Escola de Ciências E Tecnologia, Évora University, Pólo da Mitra Ap. 94, 7002-554, Évora, Portugal
| | - Ludovina Padre
- MED-Mediterranean Institute for Agriculture, Environment and Development and CHANGE - Global Change and Sustainability Institute, University of Évora, Polo da Mitra, Ap. 94, 7006-554, Évora, Portugal
| | - Pedro Caetano
- MED-Mediterranean Institute for Agriculture, Environment and Development and CHANGE - Global Change and Sustainability Institute, University of Évora, Polo da Mitra, Ap. 94, 7006-554, Évora, Portugal
| | - Ricardo Romão
- MED-Mediterranean Institute for Agriculture, Environment and Development and CHANGE - Global Change and Sustainability Institute, University of Évora, Polo da Mitra, Ap. 94, 7006-554, Évora, Portugal
| | | | - António Marcos Ramos
- Centro de Biotecnologia Agrícola E Agro-Alimentar Do Alentejo (CEBAL)/ Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal
- MED - Mediterranean Institute for Agriculture, Environment and Development and CHANGE - Global Change and Sustainability Institute, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908, Beja, Portugal
| | - Elisa Bettencourt
- MED-Mediterranean Institute for Agriculture, Environment and Development and CHANGE - Global Change and Sustainability Institute, University of Évora, Polo da Mitra, Ap. 94, 7006-554, Évora, Portugal
| | - Ana Usié
- Centro de Biotecnologia Agrícola E Agro-Alimentar Do Alentejo (CEBAL)/ Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal.
- MED - Mediterranean Institute for Agriculture, Environment and Development and CHANGE - Global Change and Sustainability Institute, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908, Beja, Portugal.
| |
Collapse
|