Genome-wide association analysis revealed novel candidate genes for body measurement traits in indigenous Gudali and crossbred Simgud in Cameroon
Abstract Background The genetic potential of Central African cattle for enhanced productivity remains largely unexplored. The absence of systematic pedigree recording and performance monitoring represent a major obstacle to implementing informed breeding strategies aimed at improving their productio...
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2025-07-01
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| author | Youchahou Poutougnigni Matenchi Evren Koban Bastanlar Matthew Hegarty |
| author_facet | Youchahou Poutougnigni Matenchi Evren Koban Bastanlar Matthew Hegarty |
| author_sort | Youchahou Poutougnigni Matenchi |
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| description | Abstract Background The genetic potential of Central African cattle for enhanced productivity remains largely unexplored. The absence of systematic pedigree recording and performance monitoring represent a major obstacle to implementing informed breeding strategies aimed at improving their production. To address this gap, we performed a genome-wide association analysis (GWAS) on a total of 856 animals genotyped with the GGP Bovine 100K array. The analysis focused on identifying genomic regions and candidate genes associated with body traits in a local Zebu (Gudali) and its crossbreed with the European Simmental (Simgud), using mixed linear models (MLM). Results The SNP-based heritability for the four body traits studied varied between 0.23 ± 0.12 for the height at wither (HAW) to 0.44 ± 0.11 for the sacrum height (SH). The genetic correlation ranged from 0.19 ± 0.14 between height at wither and ear length (EL), to 0.81 ± 0.06 between height at wither and sacrum height. For the phenotypic correlations, the ranges were 0.58 ± 0.00 between body length (BL) and ear length to 0.90 ± 0.06 between height at wither and body length. The maximum Pairwise Linkage Disequilibrium (LD), measured as squared correlation coefficient (r2) was 0.465 for Gudali, decreasing by half (0.23) at a distance of 50,708 bp. For the Simgud population the maximum LD was 0.47 halving (0.23) at 99,201 bp. Notably, we observed extended LD patterns across both the Gudali and Simgud genomes, persisting over distances greater than 1 mbp. These features hold significant potential for association analysis studies and genetic improvement initiatives. A total of 52 SNPs were identified has being associated to the considered body traits. These SNPs were mapped within or near 70 candidate genes across the genome. Among them, the ADGRD1, NDUFAF1, RTF1 and ITPKA genes exhibited a pleiotropic effect as they were associated with two or more traits. Additionally, LAMTOR5, PCDH9, BCL2, CTIF, BHLHA15, UNC5D, CNTNAP5, TMEM109, TMEM132A, and NOS1AP genes showed direct association with individual body traits. Conclusions This study identified a number of novel loci associated with pathways influencing growth and body traits, disease resistance and immunity, reproduction and milk production. Overall, the identified genes could be considered as candidate genes in any attempt to improve growth, disease resistance and production in tropical cattle raised under extensive management systems. These genes or genomic regions should be prioritized in future cattle breeding programs in Cameroon. |
| format | Article |
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| institution | DOAJ |
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| language | English |
| publishDate | 2025-07-01 |
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| spelling | doaj-art-7750aebbc7744165a12b25620c5ba2fa2025-08-20T03:04:22ZengBMCBMC Genomics1471-21642025-07-0126111810.1186/s12864-025-11865-7Genome-wide association analysis revealed novel candidate genes for body measurement traits in indigenous Gudali and crossbred Simgud in CameroonYouchahou Poutougnigni Matenchi0Evren Koban Bastanlar1Matthew Hegarty2Department of Animal Biosciences, Swedish University of Agricultural SciencesDepartment of Biology, Ege UniversityDepartment of Life Sciences, Aberystwyth UniversityAbstract Background The genetic potential of Central African cattle for enhanced productivity remains largely unexplored. The absence of systematic pedigree recording and performance monitoring represent a major obstacle to implementing informed breeding strategies aimed at improving their production. To address this gap, we performed a genome-wide association analysis (GWAS) on a total of 856 animals genotyped with the GGP Bovine 100K array. The analysis focused on identifying genomic regions and candidate genes associated with body traits in a local Zebu (Gudali) and its crossbreed with the European Simmental (Simgud), using mixed linear models (MLM). Results The SNP-based heritability for the four body traits studied varied between 0.23 ± 0.12 for the height at wither (HAW) to 0.44 ± 0.11 for the sacrum height (SH). The genetic correlation ranged from 0.19 ± 0.14 between height at wither and ear length (EL), to 0.81 ± 0.06 between height at wither and sacrum height. For the phenotypic correlations, the ranges were 0.58 ± 0.00 between body length (BL) and ear length to 0.90 ± 0.06 between height at wither and body length. The maximum Pairwise Linkage Disequilibrium (LD), measured as squared correlation coefficient (r2) was 0.465 for Gudali, decreasing by half (0.23) at a distance of 50,708 bp. For the Simgud population the maximum LD was 0.47 halving (0.23) at 99,201 bp. Notably, we observed extended LD patterns across both the Gudali and Simgud genomes, persisting over distances greater than 1 mbp. These features hold significant potential for association analysis studies and genetic improvement initiatives. A total of 52 SNPs were identified has being associated to the considered body traits. These SNPs were mapped within or near 70 candidate genes across the genome. Among them, the ADGRD1, NDUFAF1, RTF1 and ITPKA genes exhibited a pleiotropic effect as they were associated with two or more traits. Additionally, LAMTOR5, PCDH9, BCL2, CTIF, BHLHA15, UNC5D, CNTNAP5, TMEM109, TMEM132A, and NOS1AP genes showed direct association with individual body traits. Conclusions This study identified a number of novel loci associated with pathways influencing growth and body traits, disease resistance and immunity, reproduction and milk production. Overall, the identified genes could be considered as candidate genes in any attempt to improve growth, disease resistance and production in tropical cattle raised under extensive management systems. These genes or genomic regions should be prioritized in future cattle breeding programs in Cameroon.https://doi.org/10.1186/s12864-025-11865-7GWASBody traitsMLMGudaliSimgud |
| spellingShingle | Youchahou Poutougnigni Matenchi Evren Koban Bastanlar Matthew Hegarty Genome-wide association analysis revealed novel candidate genes for body measurement traits in indigenous Gudali and crossbred Simgud in Cameroon BMC Genomics GWAS Body traits MLM Gudali Simgud |
| title | Genome-wide association analysis revealed novel candidate genes for body measurement traits in indigenous Gudali and crossbred Simgud in Cameroon |
| title_full | Genome-wide association analysis revealed novel candidate genes for body measurement traits in indigenous Gudali and crossbred Simgud in Cameroon |
| title_fullStr | Genome-wide association analysis revealed novel candidate genes for body measurement traits in indigenous Gudali and crossbred Simgud in Cameroon |
| title_full_unstemmed | Genome-wide association analysis revealed novel candidate genes for body measurement traits in indigenous Gudali and crossbred Simgud in Cameroon |
| title_short | Genome-wide association analysis revealed novel candidate genes for body measurement traits in indigenous Gudali and crossbred Simgud in Cameroon |
| title_sort | genome wide association analysis revealed novel candidate genes for body measurement traits in indigenous gudali and crossbred simgud in cameroon |
| topic | GWAS Body traits MLM Gudali Simgud |
| url | https://doi.org/10.1186/s12864-025-11865-7 |
| work_keys_str_mv | AT youchahoupoutougnignimatenchi genomewideassociationanalysisrevealednovelcandidategenesforbodymeasurementtraitsinindigenousgudaliandcrossbredsimgudincameroon AT evrenkobanbastanlar genomewideassociationanalysisrevealednovelcandidategenesforbodymeasurementtraitsinindigenousgudaliandcrossbredsimgudincameroon AT matthewhegarty genomewideassociationanalysisrevealednovelcandidategenesforbodymeasurementtraitsinindigenousgudaliandcrossbredsimgudincameroon |