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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] [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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Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data. Genes (Basel) 2022; 13:genes13122310. [PMID: 36553577 PMCID: PMC9777694 DOI: 10.3390/genes13122310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable germplasm resource for improving the quality of the pig breeding industry. In this study, 24 AQ pigs that were distantly blood-related and 6 Asian Wild Boar (AWB) were selected for 10× deep-genome resequencing. The signatures of the selection were analyzed to explore the genetic basis of their germplasm characteristics and to identify excellent germplasm-related functional genes based on NGS data. A total of 49,289,052 SNPs and 6,186,123 indels were detected across the genome in 30 pigs. Most of the genetic variations were synonym mutations and existed in the intergenic region. We identified 275 selected regions (top 1%) harboring 85 genes by applying a crossover approach based on genetic differentiation (FST) and polymorphism levels (π ratio). Some genes were found to be positively selected in AQ pigs' breeding. The SMPD4 and DDX18 genes were involved in the immune response to pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The BCL6 and P2RX6 genes were involved in biological regulation of immune T cells and phagocytes. The SLC7A4 and SPACA4 genes were related to reproductive performance. The MSTN and HIF1A genes were related to fat deposition and muscle development. Moreover, 138 overlapping regions were detected in selected regions and ROH islands of AQ pigs. Additionally, we found that the QTLs with the most overlapping regions were related to back fat thickness, meat color, pH value, fatty acid content, immune cells, parasitic immunity, and bacterial immunity. Based on functional enrichment analysis and QTLs mapping, we conducted further research on the molecular genetic basis of germplasm traits (disease resistance and excellent meat quality). These results are a reliable resource for conserving germplasm resources and exploiting molecular markers of AQ pigs.
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Rodriguez VR, Maffioly JI, Zdanovicz LA, Fabre RM, Barrandeguy ME, García MV, Lagadari M. Genetic diversity of meat quality related genes in Argentinean pigs. Vet Anim Sci 2022; 15:100237. [PMID: 35169654 PMCID: PMC8829130 DOI: 10.1016/j.vas.2022.100237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Genetic diversity and phylogenetic relationships within local pigs in southern Benin. Trop Anim Health Prod 2021; 53:434. [PMID: 34387779 DOI: 10.1007/s11250-021-02857-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
The current context of climate change requires the conservation of local zoogenetic resources already very well adapted to the traditional breeding system, rough feeding, and heat and cold stress. This study assessed genetic diversity in local pigs in southern Benin, as a prerequisite for their sustainable use and sustainable management in Benin. A total of 69 individuals including 54 local pigs, 7 Large-White, and 8 hybrids (local pigs × Bush-pig) were genotyped by using 17 microsatellite markers. On the average, 8.94 alleles were detected per locus. Average expected and observed heterozygosities were respectively 0.51 and 0.46. Polymorphic information content was 0.61, and genetic diversity was 0.53. A phylogenetic tree gathered local pigs into three genetic clusters. Genetic structural analyses revealed introgression of Large-White's genes into the local pig's genome. Three groups were identified: hybrids (subpopulation 1), a mixture of Large-White and local pigs (subpopulation 2), and only local pigs (subpopulation 3). Symmetrical allelic distances were higher between subpopulations 1 and 2 (0.787) and then 1 and 3 (0.713). The same trend was detected for genetic distances between pairs of subpopulations. Genetic differentiation between subpopulations 2 and 3 was very weak as a consequence of high gene flow (10.82). Molecular variance analysis showed that 77% of genetic diversity within populations was related to variability between the individuals. These results showed that local pigs in southern Benin are threatened by genetic erosion and suggest prompt actions to implement sustainable conservation strategies.
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Revidatti MA, Gama LT, Martin Burriel I, Cortés Gardyn O, Cappello Villada JS, Carolino MI, Cañón FJ, Ginja C, Sponenberg P, Vicente AP, Zaragoza P, Delgado JV, Martínez A. On the origins of American Criollo pigs: A common genetic background with a lasting Iberian signature. PLoS One 2021; 16:e0251879. [PMID: 34014971 PMCID: PMC8136715 DOI: 10.1371/journal.pone.0251879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/05/2021] [Indexed: 11/18/2022] Open
Abstract
American Criollo pigs are thought to descend mainly from those imported from the Iberian Peninsula starting in the late 15th century. Criollo pigs subsequently expanded throughout the Americas, adapting to very diverse environments, and possibly receiving influences from other origins. With the intensification of agriculture in the mid-20th century, cosmopolitan breeds largely replaced Criollo pigs, and the few remaining are mostly maintained by rural communities in marginal areas where they still play an important socio-economic and cultural role. In this study, we used 24 microsatellite markers in samples from 1715 pigs representing 46 breeds with worldwide distribution, including 17 American Criollo breeds, with the major focus of investigating their genetic diversity, structure and breed relationships. We also included representatives of the Iberian, Local British, Hungarian, Chinese and Commercial breeds, as well as Wild Boar, in order to investigate their possible influence in the genetic composition of Criollos. Our results show that, when compared with the other breeds, Criollo pigs present higher levels of genetic diversity, both in terms of allelic diversity and expected heterozygosity. The various analyses indicate that breed differentiation overall explains nearly 21% of the total genetic diversity. Criollo breeds showed their own identity and shared a common genetic background, tending to cluster together in various analyses, even though they differ from each other. A close relationship of Criollos with Iberian breeds was revealed by all the different analyses, and the contribution of Iberian breeds, particularly of the Celtic breeds, is still present in various Criollo breeds. No influence of Chinese breeds was detected on Criollos, but a few were influenced by Commercial breeds or by wild pigs. Our results confirm the uniqueness of American Criollo pigs and the role that Iberian breeds have played in their development.
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Affiliation(s)
- Maria Antonia Revidatti
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Luis T. Gama
- Centre for Interdisciplinary Research for Animal Health, Faculdade de Medicina Veterinaria, Universidade de Lisboa, Lisbon, Portugal
| | - Inmaculada Martin Burriel
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Oscar Cortés Gardyn
- Departamento de Producción Animal, Facultad de Veterinaria, Madrid, Spain
- * E-mail:
| | - Juan Sebastian Cappello Villada
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - María Inés Carolino
- Instituto Nacional Investigação Agrária e Veterinária, Vale de Santarém, Portugal
| | | | - Catarina Ginja
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Philip Sponenberg
- Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Antonio P. Vicente
- Escola Superior Agrária, Instituto Politécnico de Santarém, Santarém, Portugal
| | - Pilar Zaragoza
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Juan Vicente Delgado
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Amparo Martínez
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
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Canales Vergara AM, Landi V, Delgado Bermejo JV, Martínez AM, Cervantes Acosta P, Pons Barros A, Bigi D, Sponenberg P, Helal M, Banabazi MH, Camacho Vallejo ME. Design and development of a multiplex microsatellite panel for the genetic characterisation and diversity assessment of domestic turkey ( Meleagris gallopavo gallopavo). ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1745695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | - Vincenzo Landi
- Animal Breeding Consulting S.L. Parque Científico Tecnológico de Córdoba c/Astrónoma Cecilia Payne, Córdoba, España
| | | | - Amparo Martínez Martínez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Cordoba, Spain
- Animal Breeding Consulting S.L. Parque Científico Tecnológico de Córdoba c/Astrónoma Cecilia Payne, Córdoba, España
| | | | | | - Daniele Bigi
- Department of Agricultural and Food Sciences, Università di Bologna, Bologna, Italy
| | - Phillip Sponenberg
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Mostafa Helal
- Department of Animal Production, Cairo University, Giza, Egypt
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), Karaj, Iran
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Svishcheva G, Babayan O, Lkhasaranov B, Tsendsuren A, Abdurasulov A, Stolpovsky Y. Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle. Animals (Basel) 2020; 10:E1493. [PMID: 32846979 PMCID: PMC7552156 DOI: 10.3390/ani10091493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 12/03/2022] Open
Abstract
We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes.
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Affiliation(s)
- Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga Babayan
- Gordiz Ltd., Skolkovo Innovation Centre, 121205 Moscow, Russia
| | | | - Ariuntuul Tsendsuren
- Institute of General and Experimental Biology, The Mongolian Academy of Sciences, Ulaanbaatar 210351, Mongolia
| | - Abdugani Abdurasulov
- Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, 723500 Osh, Kyrgyzstan
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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Pardo E, Maya H, Alvarino G. Estudio de la diversidad genética del cerdo doméstico en el departamento de Córdoba (Colombia) utilizando marcadores microsatélites. REVISTA DE LA FACULTAD DE MEDICINA VETERINARIA Y DE ZOOTECNIA 2015. [DOI: 10.15446/rfmvz.v62n3.54939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
<p>En este estudio se analizaron los niveles de diversidad y estructura genética de 161 cerdos domésticos pertenecientes a tres poblaciones del departamento de Córdoba, mediante 20 marcadores microsatélites. Todos los microsatélites utilizados resultaron polimórficos. Para todos los <em>loci</em>, el valor promedio de la heterocigosidad esperada fue mayor al valor promedio de la heterocigosidad observada, lo cual puede sugerir una posible endogamia en el sistema de apareamiento. El índice F<sub>ST</sub> (0,12 ± 0,08) mostró un 88% de la varianza en las frecuencias alélicas reportadas dentro de cada población y solo el 12% de la varianza atribuible a diferencias entre poblaciones. Los valores de F<sub>IS</sub> (0,079) y F<sub>IT</sub> (0,13), indican deficiencia de heterocigotos dentro de cada población y a nivel global. Desviaciones significativas del equilibrio Hardy-Weinberg (*P<0,05) fueron observadas en ocho de los marcadores utilizados. El árbol Neighbor-Joining obtenido reveló que Momil estuvo más estrechamente relacionada con Cereté, mientras Tierralta se mostró más alejada. El análisis de componentes principales (ACoP) genera la individualización geográfica de cada población, siendo distante la población de Tierralta de las poblaciones Momil y Cereté, resultados similares a los obtenidos con la metodología Neighbor-Joining. El programa Structure con un K = 3, confirma la existencia de tres grupos o poblaciones distintas, generándose un patrón filogeográfico observado en la relación entre Momil, Cereté y Tierralta. Es importante señalar que son 3 grupos raciales diferentes, valiosos y deben conservarse.</p>
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