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Azziz G, Giménez M, Carballo C, Espino N, Barlocco N, Batista S. Characterization of the fecal microbiota of Pampa Rocha pigs, a genetic resource endemic to eastern Uruguay. Heliyon 2023; 9:e16643. [PMID: 37303559 PMCID: PMC10248110 DOI: 10.1016/j.heliyon.2023.e16643] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023] Open
Abstract
Pampa Rocha (PR) is a breed of pig that emerged in eastern Uruguay during the 18th century. They represent an important resource for non-intensive production using purebred or crossbred animals. However, productive activities have been oriented towards intensive production using commercial breeds, abandoning, except by some academic and educational institutions, the promotion of this creole breed. Thus, a population of few animals is still maintained, which could be in danger of disappearing. This work focuses on the fecal microbiota of these animals, which is related to the animal genetic background but also to their grazing capacity and resistance to weather. The structure and diversity of bacterial communities in the intestines of four PR adult females and of other breeds, including crosses, reared under non-grazing conditions, were analyzed and compared. Results obtained indicate that PR fecal microbiota is clearly different from those of other animals analyzed. Some sequences, corresponding to particular groups apparently related to the consumption of fiber, were strongly associated with PR pigs.
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Affiliation(s)
- Gastón Azziz
- Laboratorio de Microbiología, Facultad de Agronomía, UdelaR, Montevideo, Uruguay
| | - Matías Giménez
- Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Cecilia Carballo
- Unidad de Producción de Cerdos, Centro Regional Sur, Facultad de Agronomía, UdelaR, Canelones, Uruguay
| | - Nandy Espino
- Unidad de Producción de Cerdos, Centro Regional Sur, Facultad de Agronomía, UdelaR, Canelones, Uruguay
| | - Nelson Barlocco
- Unidad de Producción de Cerdos, Centro Regional Sur, Facultad de Agronomía, UdelaR, Canelones, Uruguay
| | - Silvia Batista
- Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
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Giantsis IA, Antonopoulou D, Dekolis N, Zaralis K, Avdi M. Origin, demographics, inbreeding, phylogenetics, and phenogenetics of Karamaniko breed, a major common ancestor of the autochthonous Greek sheep. Trop Anim Health Prod 2022; 54:73. [PMID: 35072809 DOI: 10.1007/s11250-022-03081-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 11/22/2021] [Accepted: 01/20/2022] [Indexed: 11/24/2022]
Abstract
Greece has a long history in autochthonous sheep, the genetic ancestry of which has been associated with four subtypes known to inhabit Greece at the end of the nineteenth century. Among them, the Karamaniko breed is still surviving, however endangered. This study was designed in order to (a) determine the phylogenetic status, (b) to evaluate the levels of inbreeding, and (c) to assess the genetic basis of coat color of Karamaniko breed. For these purposes, the mitochondrial cyt b gene was sequenced, the AFLP methodology was applied, and the MC1R was genotyped, respectively, in 72 female sheep from the Karamaniko breed. Four different novel cyt b haplotypes were defined and three MC1R genotypes were scored, whereas inbreeding levels estimated using AFLPs by the means of relatedness coefficient (r) were 0.287, with gene diversity at the levels of 0.105. Phylogenetic analysis indicated an eastern Asian tropical and subtropical origin of the Karamaniko breed, close with breeds originating from central Turkey, or a clustering within western European or Mediterranean sheep, mirroring a recent genetic divergence, with a non-random spread towards the formation of lowland breeds. The MC1R genotypes were all associated with the white coat color, in which selective breeding has probably been based on traditional morphological characters. Finally, levels of inbreeding do not constitute an indication for a particular mating plan to prevent unpleasant phenomena such as inbreeding depression, probably because of the special attention paid by the farmers towards the avoidance of relative recurrent mating.
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Affiliation(s)
- Ioannis A Giantsis
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece.
| | - Danai Antonopoulou
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece.,Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Dekolis
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Zaralis
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece
| | - Melpomeni Avdi
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Bhattacharjee U, Sen A, Sharma I. A retrospective study reveals the Porcine circovirus-2f genotype predominant in the indigenous pig population of North-eastern India. Infect Genet Evol 2021; 96:105100. [PMID: 34619393 DOI: 10.1016/j.meegid.2021.105100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Porcine circovirus-2 (PCV2) is a widespread virus and presents sub-clinically in most of the swineherd. Globally, eight genotypes of PCV2 have been identified that is PCV2a to 2h. To determine the region-wide genotype distribution of PCV2 infection, with additional reference to indigenous breeds, a total of 1314 pig's clinical samples from the eight states of North-eastern India between 2011 and 2014; were analyzed. The overall prevalence rate of PCV2 in this region was 28.2% (370/1314) by PCR. The state-wise PCR based PCV2 prevalence rate was: Tripura (20.8%), Nagaland (25.0%), Meghalaya (25.8%), Assam (32.1%), Sikkim (32.6%), Manipur (33.3%), Mizoram (36.7%) and Arunachal Pradesh (42.3%). Subsequently, a total of 29 complete genomes of PCV2 were amplified and sequenced from these PCV2 positive samples. The phylogenetic tree represents that the 29 PCV2 isolates of this study were divided into four distinct genetic groups; PCV2a, PCV2b, PCV2d, and PCV2f. Among these, 14 PCV2 strains were classified as PCV2f, 13 classified as PCV2d, and one isolate of each classified as PCV2a and PCV2b. All the 14 PCV2f strains appeared from indigenous pigs of this region. Based on the date of collection, the present study further describes that the PCV2f genotypes circulate in the indigenous pigs' population back in 2011. The amino acid residues and the atomic coordinate structure (3D model) of PCV2f capsid protein represents similarity to PCV2d capsid protein support the efficacy of the existing PCV2 vaccine against the PCV2f. The observation of this study helps to understand the genotype distribution of PCV2 and stands as a reference for future molecular epidemiological studies in North-eastern India.
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Affiliation(s)
- Uttaran Bhattacharjee
- Department of Microbiology, Assam University, Silchar, Assam, India; Division of Animal Health, Indian Council of Agricultural Research-Research Complex for North-Eastern Hill Region (ICAR-RC for NEH Region), Umiam, Barapani, Meghalaya, India
| | - Arnab Sen
- Division of Animal Health, Indian Council of Agricultural Research-Research Complex for North-Eastern Hill Region (ICAR-RC for NEH Region), Umiam, Barapani, Meghalaya, India
| | - Indu Sharma
- Department of Microbiology, Assam University, Silchar, Assam, India.
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Joller S, Bertschinger F, Kump E, Spiri A, von Rotz A, Schweizer-Gorgas D, Drögemüller C, Flury C. Crossed beaks in a local Swiss chicken breed. BMC Vet Res 2018; 14:68. [PMID: 29506524 PMCID: PMC5838925 DOI: 10.1186/s12917-018-1398-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Crossed beaks have been reported to occur in Appenzeller Barthuhn, a local Swiss chicken breed. The assumed causes for this beak deformity which are also seen in other bird species including domestic chickens, range from environmental influences to genetic factors. The aim of this project was to characterize the prevalence, the phenotype, and the underlying genetics of crossed beaks in Appenzeller Barthuhn chickens. RESULTS The estimated prevalence of 7% crossed beaks in Appenzeller Barthuhn was significantly higher compared to two other local Swiss chicken breeds. A breeding trial showed significantly higher prevalence of offspring with deformed beaks from mating of affected parents compared to mating of non-affected parents. Examination of 77 Appenzeller Barthuhn chickens with crossed beaks showed a variable phenotype presentation. The deviation of the beak from the median plane through the head ranged from 1° to 61°. In more than 60% of the cases, the upper and lower beak were bent in the same direction, whereas the remaining cases showed different forms of crossed beaks. Computed tomographic scans and bone maceration of the head of two chickens with crossed beaks revealed that the maxilla and the mandibula were affected, while other parts of the skull appeared to be normal. The gene LOC426217, a member of the keratin family, was postulated as a candidate gene for beak deformity in domestic chickens. Sequencing of the coding region revealed two significantly associated synonymous variants for crossed beaks in Appenzeller Barthuhn chickens. A genome-wide association study and a comparative analysis of runs of homozygosity based on high-density SNP array genotyping data of 53 cases and 102 controls showed no evidence of association. CONCLUSIONS The findings suggest a hereditary cause of crossed beaks in Appenzeller Barthuhn chickens. However, the observed variation in the phenotype, together with the inconclusive molecular genetic results indicates the need for additional research to unravel the genetic architecture of this beak deformity.
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Affiliation(s)
- Sara Joller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Flurina Bertschinger
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Astrid Spiri
- Züchterverein für ursprüngliches Nutzgeflügel, Neukirch an der Thur, Switzerland
| | - Alois von Rotz
- Divison of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
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