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Aminou O, Badaoui B, Machmoum M, Piro M. Evaluation of the effectiveness of single nucleotide polymorphisms compared to microsatellite markers for parentage verification in Moroccan horses. Anim Genet 2024; 55:404-409. [PMID: 38383954 DOI: 10.1111/age.13408] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024]
Abstract
The International Society for Animal Genetics (ISAG) currently advocates for a transition towards single nucleotide polymorphism (SNP) markers as a potential alternative for equine parentage verification. To ascertain the efficacy of this transition, it is imperative to evaluate the performance of parentage testing using SNPs in juxtaposition with short tandem repeats (STRs). As per ISAG's recommendation, we used an equine genotyping-by-sequencing panel with 144 SNPs for this purpose. Equine parentage is currently realized using 16 microsatellites (STRs) excluding the LEX3 marker. In this study, 1074 horses were genotyped using the 144 SNPs panel, including 432 foals, 414 mares, and 228 stallions, from five different breeds: 293 Arabians, 167 Barbs, 189 Thoroughbreds, 73 Anglo-Arabians, and 352 Arabian-Barbs. As a result, two SNPs markers were eliminated from the panel system due to inconsistent amplification across all examined individuals leaving 142 SNPs markers for analysis. A comparative analysis between SNPs and STRs markers revealed that the mean expected heterozygosity was 0.457 for SNPs and 0.76 for STRs, while the mean observed heterozygosity stood at 0.472 for SNPs and 0.72 for STRs. Furthermore, the probability of identity was calculated to be 5.722 × 10-57 for SNPs and 1.25 × 10-15 for STRs markers. In alignment with the Hardy-Weinberg equilibrium in polyploids test, 110 out of the total SNPs were consistent with the Hardy-Weinberg equilibrium in polyploids test (p > 0.05). Employing both SNPs and STRs markers, the mean polymorphic information content was discerned to be 0.351 for SNPs and 0.72 for STRs. The cumulative exclusion probabilities for SNP markers exceeded 99.99%, indicating that the 142 SNPs panel might be adequate for parentage testing. In contrast, when utilizing STRs markers, the combined average exclusion probabilities for one and both parents were determined to be 99.8% and 99.9%, respectively. Our comprehensive study underscores the potential of SNPs in equine parentage verification, especially when compared to STRs in terms of exclusion probabilities. As a corollary, the application of SNPs for parentage verification and identification can significantly contribute to the conservation initiative for the five Moroccan horse breeds. Nonetheless, further research is required to address and replace the deficient SNPs within the panel.
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Affiliation(s)
- O Aminou
- Veterinary Genetic Analysis Laboratory, Hassan II Agronomic and Veterinary Institute, Rabat, Morocco
| | - B Badaoui
- Biodiversity, Ecology and Genome Laboratory, Mohammed V University, Faculty of Sciences, Rabat, Morocco
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - M Machmoum
- Veterinary Genetic Analysis Laboratory, Hassan II Agronomic and Veterinary Institute, Rabat, Morocco
| | - M Piro
- Veterinary Genetic Analysis Laboratory, Hassan II Agronomic and Veterinary Institute, Rabat, Morocco
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Wagner-Ballon O, Badaoui B, Brignoli A, Le Priol J, Roussel M. Evaluation of whole-blood conservation reagents for Hematoflow-based WBC differential count: Unsatisfactory results. Int J Lab Hematol 2017; 39:e127-e131. [PMID: 28656600 DOI: 10.1111/ijlh.12697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- O Wagner-Ballon
- Département d'Hématologie et d'Immunologie biologiques, Hôpitaux universitaires Henri Mondor, Creteil, France.,UPEC, Creteil, France
| | - B Badaoui
- Département d'Hématologie et d'Immunologie biologiques, Hôpitaux universitaires Henri Mondor, Creteil, France.,UPEC, Creteil, France
| | - A Brignoli
- Département d'Hématologie et d'Immunologie biologiques, Hôpitaux universitaires Henri Mondor, Creteil, France
| | - J Le Priol
- Laboratoire d'Hématologie, Pôle de Biologie, CHU Rennes, Rennes, France
| | - M Roussel
- Laboratoire d'Hématologie, Pôle de Biologie, CHU Rennes, Rennes, France.,EFS Bretagne, Equipe Labellisée Ligue Contre le Cancer, INSERM, UMR U1236, Université Rennes 1, Rennes, France
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Badaoui B, Manunza A, Castelló A, D'Andrea M, Pilla F, Capote J, Jordana J, Ferrando A, Martínez A, Cabrera B, Delgado JV, Landi V, Gómez M, Pons A, El Ouni M, Vidal O, Amills M. Technical note: Advantages and limitations of authenticating Palmera goat dairy products by pyrosequencing the melanocortin 1 receptor (MC1R) gene. J Dairy Sci 2014; 97:7293-7. [PMID: 25200789 DOI: 10.3168/jds.2014-8316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/23/2014] [Indexed: 11/19/2022]
Abstract
Inferring the breed of origin of dairy products can be achieved through molecular analysis of genetic markers with a population-specific pattern of segregation. The goal of the current work was to generate such markers in goats by resequencing several pigmentation genes [melanocortin 1 receptor (MC1R), v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT), tyrosinase (TYR), and tyrosinase-related protein 2 (TYRP2)]. This experiment revealed 10 single nucleotide polymorphisms (SNP), including 5 missense mutations and 1 nonsense mutation. These markers were genotyped in 560 goats from 18 breeds originally from Italy, the Iberian Peninsula, the Canary Islands, and North Africa. Although the majority of SNP segregated at moderate frequencies in all populations (including 2 additional markers that were used as a source of information), we identified a c.764G>A SNP in MC1R that displayed highly divergent allelic frequencies in the Palmera breed compared with the Majorera and Tinerfeña breeds from the Canary Islands. Thus, we optimized a pyrosequencing-based technique that allowed us to estimate, very accurately, the allele frequencies of this marker in complex DNA mixtures from different individuals. Once validated, we applied this method to generating breed-specific DNA profiles that made it possible to detect fraudulent cheeses in which Palmero cheese was manufactured with milk from Majorera goats. One limitation of this approach, however, is that it cannot be used to detect illegal manufacturing where Palmero dairy products are produced by mixing milk from Palmera and Majorera goats, because the c.764G>A SNP segregates in both breeds.
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Affiliation(s)
- B Badaoui
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - A Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - A Castelló
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - M D'Andrea
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Via de Sanctis, 86100 Campobasso, Italy
| | - F Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Via de Sanctis, 86100 Campobasso, Italy
| | - J Capote
- Instituto Canario de Investigaciones Agrarias, La Laguna 38108, Tenerife, Spain
| | - J Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - A Ferrando
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - A Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - B Cabrera
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - J V Delgado
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - V Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - M Gómez
- Servicio de Ganadería, Diputación Foral de Bizkaia, 48014 Bilbao, Spain
| | - A Pons
- Unitat de Races Autòctones, Servei de Millora Agrària, (SEMILLA-SAU), Son Ferriol 07198, Spain
| | - M El Ouni
- Livestock & Wildlife Laboratory, Arid Land Institute Medenine, 4119 Médenine, Tunisia
| | - O Vidal
- Departament de Biologia, Universitat de Girona, Girona 17071, Spain
| | - M Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Salama A, Caja G, Hamzaoui S, Badaoui B, Castro-Costa A, Façanha D, Guilhermino M, Bozzi R. Different levels of response to heat stress in dairy goats. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2013.11.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Martínez A, Ferrando A, Manunza A, Gómez M, Landi V, Jordana J, Capote J, Badaoui B, Vidal O, Delgado J, Amills M. Inferring the demographic history of a highly endangered goat breed through the analysis of nuclear and mitochondrial genetic signatures. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Cánovas E, Quintanilla R, Badaoui B, Porredón C, Gallardo D, Pena R, Díaz I, Amills M. Pig HDL-binding protein (HDLBP) genotype is associated with intramuscular fat percentage. Livest Sci 2009. [DOI: 10.1016/j.livsci.2009.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ramírez O, Ojeda A, Tomàs A, Gallardo D, Huang LS, Folch JM, Clop A, Sánchez A, Badaoui B, Hanotte O, Galman-Omitogun O, Makuza SM, Soto H, Cadillo J, Kelly L, Cho IC, Yeghoyan S, Pérez-Enciso M, Amills M. Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds. Mol Biol Evol 2009; 26:2061-72. [PMID: 19535739 DOI: 10.1093/molbev/msp118] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite, and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populations. The analysis of nuclear markers evidenced the existence of a close genetic relationship between Near Eastern and European wild boars making it difficult to infer their relative contributions to the gene pool of modern European breeds. Moreover, we have shown that European and Far Eastern pig populations have contributed maternal and paternal lineages to the foundation of African and South American breeds. Although West African pigs from Nigeria and Benin exclusively harbored European alleles, Far Eastern and European genetic signatures of similar intensity were detected in swine breeds from Eastern Africa. This region seems to have been a major point of entry of livestock species in the African continent as a result of the Indian Ocean trade. Finally, South American creole breeds had essentially a European ancestry although Asian Y-chromosome and mitochondrial haplotypes were found in a few Nicaraguan pigs. The existence of Spanish and Portuguese commercial routes linking Asia with America might have favored the introduction of Far Eastern breeds into this continent.
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Affiliation(s)
- O Ramírez
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Caravaca F, Carrizosa J, Urrutia B, Baena F, Jordana J, Amills M, Badaoui B, Sánchez A, Angiolillo A, Serradilla J. Short communication: Effect of αS1-casein (CSN1S1) and κ-casein (CSN3) genotypes on milk composition in Murciano-Granadina goats. J Dairy Sci 2009; 92:2960-4. [DOI: 10.3168/jds.2008-1510] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Amills M, Ramírez O, Tomàs A, Badaoui B, Marmi J, Acosta J, Sànchez A, Capote J. Mitochondrial DNA diversity and origins of South and Central American goats. Anim Genet 2009; 40:315-22. [DOI: 10.1111/j.1365-2052.2008.01837.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Badaoui B, Serradilla JM, Tomàs A, Urrutia B, Ares JL, Carrizosa J, Sànchez A, Jordana J, Amills M. Short communication: Identification of two polymorphisms in the goat lipoprotein lipase gene and their association with milk production traits. J Dairy Sci 2007; 90:3012-7. [PMID: 17517743 DOI: 10.3168/jds.2006-409] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lipoprotein lipase (LPL) is a glycoprotein that plays a central role in plasma triglyceride metabolism by hydrolyzing triglyceride-rich chylomicrons and very low density lipoproteins. The activity of milk LPL has been shown to differ among several goat breeds, suggesting the existence of a genetic polymorphism influencing the functional properties of this enzyme. We have characterized the complete coding sequence of the goat LPL gene in 18 individuals belonging to 3 breeds. The coding region of the goat LPL cDNA was 1,437 bp long and encoded a protein of 478 amino acids. Moreover, we have identified 2 single nucleotide polymorphisms (SNP) including a G50C missense mutation, which involved a Ser-->Thr amino acid replacement at position 17 of the signal peptide, and a C2094T substitution in the 3' untranslated region. A univariate mixed model was used to evaluate the association between LPL genotypes and milk production and composition in 130 Murciano-Granadina goats. The G50C SNP was suggestively associated with milk fat content and tended to affect the milk dry weight basis. The C2094T SNP was not associated with any of the measured traits.
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Affiliation(s)
- B Badaoui
- Departament de Ciència Animal, Facultat de Veterinària, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain
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Badaoui B, Serradilla JM, Tomàs A, Urrutia B, Ares JL, Carrizosa J, Sànchez A, Jordana J, Amills M. Goat acetyl-coenzyme A carboxylase alpha: molecular characterization, polymorphism, and association with milk traits. J Dairy Sci 2007; 90:1039-43. [PMID: 17235183 DOI: 10.3168/jds.s0022-0302(07)71590-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Acetyl-coenzyme A carboxylase alpha (ACACA), the major regulatory enzyme of fatty acid biosynthesis, catalyzes the conversion of acetyl-CoA to malonyl-CoA. We have sequenced 5.5 kb of the goat ACACA cDNA in 18 individuals. The translated cDNA sequence encodes 1,832 AA and shares a high AA identity (99%) with the ovine and bovine ACACA orthologous sequences. One silent single nucleotide polymorphism was identified at exon 45 (C5493T). The genotyping of this polymorphism in 4 goat breeds, Murciano-Granadina, Teramana, Majorera, and Malagueña, showed that it was segregating in all 4 breeds at variable frequencies. In addition, a mixed animal model was used to evaluate the association of C5493T genotypes with milk traits. Results from this study show that the C5493T mutation was suggestively associated with fat yield, lactose content, and somatic cell count.
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Affiliation(s)
- B Badaoui
- Departament de Ciència Animal, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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