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Poullet N, Devarieux O, Beramice D, Dantec L, Félicité Y, Feuillet D, Gourdine JL, Bambou JC. Comparative analysis of whole blood transcriptomics between European and local Caribbean pigs in response to feed restriction in a tropical climate. BMC Genomics 2023; 24:292. [PMID: 37254043 DOI: 10.1186/s12864-023-09381-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Feed restriction occurs frequently during pig growth, either due to economic reasons or stressful environmental conditions. Local breeds are suggested to have better tolerance to periods of feed restriction. However, the mechanisms underlying the response to feed restriction in different breeds is largely unknown. The aims of the present study were (1) to compare the blood transcriptome profile in response to feed restriction and refeeding of two contrasted breeds, Large White (LW), which has been selected for high performance, and Creole (CR), which is adapted to tropical conditions, and (2) to investigate the effect of a moderate feed restriction and refeeding on whole blood transcriptome. Analysis of blood transcriptome allows to study the response to feed restriction and refeeding in a dynamic way. RNAseq was performed on blood samples of growing LW and CR pigs at two time points: after 3 weeks of feed restriction and after 3 weeks of refeeding. The data was compared with samples from control animals offered the same diet on an ad libitum basis throughout the whole experiment. RESULTS In terms of performance (body weight and feed efficiency), CR pigs were less impacted by feed restriction than LW. The transcriptional response to feed restriction and refeeding between CR and LW was contrasted both in terms of number of DEGs and enriched pathways. CR demonstrated a stronger transcriptional response to feed restriction whereas LW had a stronger response to refeeding. Differences in the transcriptional response to feed restriction between CR and LW were related to cell stress response (Aldosterone Signalling, Protein ubiquitination, Unfolded Protein Signalling) whereas after refeeding, differences were linked to thermogenesis, metabolic pathways and cell proliferation (p38 MAPK, ERK/MAPK pathway). In both breeds, transcriptional changes related to the immune response were found after restriction and refeeding. CONCLUSIONS Altogether, the present study indicates that blood transcriptomics can be a useful tool to study differential genetic response to feed restriction in a dynamic way. The results indicate a differential response of blood gene expression to feed restriction and refeeding between breeds, affecting biological pathways that are in accordance with performance and thermoregulatory results.
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Affiliation(s)
- Nausicaa Poullet
- ASSET, INRAE, Petit-Bourg (Guadeloupe), ²PTEA, INRAE, Petit-Bourg (Guadeloupe), 97170, France.
| | - Orianne Devarieux
- ASSET, INRAE, Petit-Bourg (Guadeloupe), ²PTEA, INRAE, Petit-Bourg (Guadeloupe), 97170, France
| | | | | | - Yoann Félicité
- ASSET, INRAE, Petit-Bourg (Guadeloupe), ²PTEA, INRAE, Petit-Bourg (Guadeloupe), 97170, France
| | - Dalila Feuillet
- ASSET, INRAE, Petit-Bourg (Guadeloupe), ²PTEA, INRAE, Petit-Bourg (Guadeloupe), 97170, France
| | - Jean-Luc Gourdine
- ASSET, INRAE, Petit-Bourg (Guadeloupe), ²PTEA, INRAE, Petit-Bourg (Guadeloupe), 97170, France
| | - Jean-Christophe Bambou
- ASSET, INRAE, Petit-Bourg (Guadeloupe), ²PTEA, INRAE, Petit-Bourg (Guadeloupe), 97170, France
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Suárez-Mesa R, Ros-Freixedes R, Laghouaouta H, Pena RN, Hernández-Ortiz B, Rondón-Barragán I, Estany J. Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing. Trop Anim Health Prod 2023; 55:154. [PMID: 37041265 PMCID: PMC10089996 DOI: 10.1007/s11250-023-03557-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.
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Affiliation(s)
- Rafael Suárez-Mesa
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Houda Laghouaouta
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Byron Hernández-Ortiz
- Research and Innovation Group in Animal Health and Welfare Germplasm Animal Bank, Agrosavia, Bogotá, 250047, Colombia
| | - Iang Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia
| | - Joan Estany
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
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Introduced, Mixed, and Peripheral: Conservation of Mitochondrial-DNA Lineages in the Wild Boar (Sus scrofa L.) Population in the Urals. DIVERSITY 2022. [DOI: 10.3390/d14110916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Translocations and introductions are important events that allow organisms to overcome natural barriers. The genetic background of colonization success and genetic consequences of the establishment of populations in new environments are of great interest for predicting species’ colonization success. The wild boar has been introduced into many parts of the world. We analyzed sequences of the mitochondrial-DNA control region in the wild boars introduced into the Ural region and compared them with sequences from founder populations (from Europe, the Caucasus, Central Asia, and the Far East). We found that the introduced population has high genetic diversity. Haplotypes from all the major phylogenetic clades were detected in the analyzed group of the animals from the Urals. In this group, no haplotypes identical to Far Eastern sequences were detectable despite a large number of founders from that region. The contribution of lineages originating from Eastern Europe was greater than expected from the proportions (%) of European and Asian animals in the founder populations. This is the first study on the genetic diversity and structure of a wild boar population of mixed origin at the northern periphery of this species’ geographical range.
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4
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Invasion and spatial distribution of wild pigs (Sus scrofa L.) in Brazil. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02872-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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5
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Tang H, Ouyang J, Liu S, Xiong Y, Wu Y, Wang L, Wang C, Yan X, Shen Y, Chen H. Population structure of 3907 worldwide pigs and the introgression of Chinese indigenous pigs by European pigs. Anim Genet 2022; 53:599-612. [PMID: 35735069 DOI: 10.1111/age.13234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 05/25/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
With the improvement in sequencing technology and the decrease in sequencing cost, increasing amounts of genomic data for pigs have been uploaded to public databases. However, no researchers have to date integrated all currently available data to uncover the global genetic status of pigs. Meanwhile, little is known about the introgression from European to Chinese pigs and its underlying influences. Therefore, we integrated the effective genotype data of 3907 pigs from 193 populations worldwide using population genetic analysis, gene flow analysis and a sharing-IBD study. These findings illustrate not only the population structure of 59 Chinese native breeds and others but also the amounts of gene flow and introgression that have occurred between Western and Chinese pigs. In addition, we demonstrate the presence of introgressed European haplotypes in Chinese indigenous breeds and identify relevant introgressed regions that contain genes associated with growth and feed efficiency. Moreover, we compare the introgression patterns of Western and Chinese pigs and further discuss possible explanations for why the level of introgression differs between Chinese pig breeds and Western modern breeds. Collectively, this study provides a fine global population structure analysis of pigs and presents evidence of European pigs being interbred with local breeds in China.
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Affiliation(s)
- Hongbo Tang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Jing Ouyang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Siyu Liu
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yanpeng Xiong
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yongfei Wu
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Luping Wang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Cong Wang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xueming Yan
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yangyang Shen
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Hao Chen
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
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6
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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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7
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Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar. BIOLOGY 2022; 11:biology11020203. [PMID: 35205070 PMCID: PMC8869248 DOI: 10.3390/biology11020203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 02/04/2023]
Abstract
The wild boar is the wild ancestor of the domestic pig and one of the most common species of ungulates. At the beginning of the 20th century, the wild boar was practically exterminated in the European part of Russia. In the period 1935-1988, 7705 boars were caught in various regions of the European part of Russia, the Far East, Ukraine, Belarus, Kyrgyzstan, Kazakhstan, Latvia, Lithuania, Estonia, Tajikistan and resettled in the territory of Russia. Asian and European wild boars dwell the territory of Russia. The aim of our research was to study the genetic diversity and structure of wild boar populations in different regions of Russia using genome-wide genotyping. We have determined the genetic distances, population structure, parameters of genetic diversity and significantly expanded our understanding of the genetic state of the Russian wild boar. For the first time, we calculated autozygosity of the wild boar of the European and Asian subspecies using Homozygous-by-Descent (HBD) Segments analysis, which is important in terms of population recovery. We also found evidence of hybridization between Russian wild boar and domestic pigs. A group of European wild boars showed introgression of the Asian boar into population. The mean level of the inbreeding coefficient in European wild boar was higher than in Asian wild boar, and combined groups of the European boar had higher inbreeding coefficient than Russian wild boars. These results obtained can be used in population management.
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8
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Bonneau M, Poullet N, Beramice D, Dantec L, Canario L, Gourdine JL. Behavior Comparison During Chronic Heat Stress in Large White and Creole Pigs Using Image-Analysis. FRONTIERS IN ANIMAL SCIENCE 2021. [DOI: 10.3389/fanim.2021.784376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Behavior is a good indicator of animal welfare, especially in challenging environments. However, few studies have investigated how pig behavior changes during heat stress. The current study is a proof-of-concept using Convolutional Neural Network (CNN) models to monitor pig behavior in order to investigate the differences in behavioral response to heat stress of two contrasted breeds: Large White (LW), selected for high performance, and Creole (CR), adapted to tropical conditions. A total of 6 slaughter pigs (3 CR and 3 LW; 22 weeks of age) were monitored from 8:30 to 17:30 during 54 days. Two CNN architectures were used to detect the animal (Yolo v2) and to estimate animal's posture (GoogleNet). Pig postures estimated by the neural network showed that pigs spent more time lying on their side when temperature increased. When comparing the two breeds, as temperature increases, CR pigs spent more time lying on their side than LW pigs, suggesting that they use this posture to increase thermoregulation and dissipate heat more efficiently. This study demonstrates that neural network models are an efficient tool to monitor animal behavior in an automated way, which could be particularly relevant to characterize breed adaptation to challenging environments.
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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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Suárez-Mesa R, Estany J, Rondón-Barragán I. Semen quality of Colombian Creole as compared to commercial pig breeds. Trop Anim Health Prod 2021; 53:129. [PMID: 33462746 DOI: 10.1007/s11250-021-02557-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
Characterization of Creole breeds is still very limited, including reproductive performance. In this research, we assessed the semen quality of three Colombian Creole breeds (Zungo, Casco de Mula and San Pedreño) relative to that of international breeds (Duroc, Belgian Landrace and Pietrain). Two doses from seven boars per breed were evaluated for sperm kinetics and membrane and acrosome integrity using computer-assisted sperm analysis (CASA) and flow cytometry, respectively. The Creole pigs showed lower (P < 0.05) volume of fluid ejaculated (185.5 mL vs 239.9 mL), and sperm concentration (340.5 × 106 vs 395.4 × 106 sperm/mL), motility (90.9% vs 95.3%) and progressive motility (63.1% vs 67.2%) than international breeds. No relevant differences between Creole and international breeds for sperm velocity traits were observed, but Creole boars had lower (P < 0.05) proportion of morphologic normal sperm (86.1% vs 90.6%) and of sperm with both intact plasma membrane and acrosome integrity (76.8% vs 87.5%). Mitochondrial membrane potential did not differ between breeds. Creole breeds in general produced less normal and motile sperm per ejaculate than international breeds (49.3 × 109 vs 81.5 × 109). Although San Pedreño had larger ejaculates than Zungo and Zungo had a greater proportion of normal and motile sperm than San Pedreño, Creole breeds did not differ in total amount of normal and motile sperm per ejaculate. The semen from Colombian Creole pigs is qualitatively acceptable, being less abundant but rich in normal and motile sperm, than that from commercial breeds. This should be considered when developing recommendations for semen use and conservation for AI in Creole pigs.
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Affiliation(s)
- Rafael Suárez-Mesa
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia
- Department of Animal Science, University of Lleida - Agrotecnio Center, 191 Rovira Roure, 25198, Lleida, Spain
| | - Joan Estany
- Department of Animal Science, University of Lleida - Agrotecnio Center, 191 Rovira Roure, 25198, Lleida, Spain
| | - Iang Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.
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11
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Ramírez-Ayala LC, Rocha D, Ramos-Onsins SE, Leno-Colorado J, Charles M, Bouchez O, Rodríguez-Valera Y, Pérez-Enciso M, Ramayo-Caldas Y. Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions. Genet Sel Evol 2021; 53:3. [PMID: 33397281 PMCID: PMC7784321 DOI: 10.1186/s12711-020-00597-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/11/2020] [Indexed: 02/01/2023] Open
Abstract
Background In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine cattle have difficulty coping with. Results In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 whole-genome sequences from six additional taurine, indicus and crossed breeds to estimate the genetic diversity, structure and accurate ancestral origin of the CHCU animals. Although CHCU animals are assumed to form a closed population, the results of our admixture analysis indicate a limited introgression of Bos indicus. We used the extended haplotype homozygosity (EHH) approach to identify regions in the genome that may have had an important role in the adaptation of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of Bos indicus, but they were not sufficient to explain adaptation of CHCU to tropical conditions by Bos indicus introgression only. EHH suggested signals of potential adaptation in genomic windows that include genes of taurine origin involved in thermogenesis (ATP9A, GABBR1, PGR, PTPN1 and UCP1) and hair development (CCHCR1 and CDSN). Within these genes, we identified single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute to some of the observed phenotypic differences between CHCU and CHFR animals. Conclusions Whole-genome data confirm that CHCU cattle are closely related to Charolais from France (CHFR) and Canada, but also reveal a limited introgression of Bos indicus genes in CHCU. We observed possible signals of recent adaptation to tropical conditions between CHCU and CHFR founder populations, which were largely independent of the Bos indicus introgression. Finally, we report candidate genes and variants that may have a functional impact and explain some of the phenotypic differences observed between CHCU and CHFR cattle.
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Affiliation(s)
- Lino C Ramírez-Ayala
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Dominique Rocha
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France
| | - Sebas E Ramos-Onsins
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Jordi Leno-Colorado
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Mathieu Charles
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France.,INRAE, SIGENAE, Jouy-En-Josas, 78350, France
| | - Olivier Bouchez
- INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, US, 1426, France
| | | | - Miguel Pérez-Enciso
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain.,Institut Català de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France. .,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes De Montbui, 08140, Spain.
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12
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Tracing selection signatures in the pig genome gives evidence for selective pressures on a unique curly hair phenotype in Mangalitza. Sci Rep 2020; 10:22142. [PMID: 33335158 PMCID: PMC7747725 DOI: 10.1038/s41598-020-79037-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/02/2020] [Indexed: 12/30/2022] Open
Abstract
Selection for desirable traits and breed-specific phenotypes has left distinctive footprints in the genome of pigs. As representative of a breed with strong selective traces aiming for robustness, health and performance, the Mangalitza pig, a native curly-haired pig breed from Hungary, was investigated in this study. Whole genome sequencing and SNP chip genotyping was performed to detect runs of homozygosity (ROH) in Mangalitza and Mangalitza-crossbreeds. We identified breed specific ROH regions harboring genes associated with the development of the curly hair type and further characteristics of this breed. Further analysis of two matings of Mangalitza with straight-coated pig breeds confirmed an autosomal dominant inheritance of curly hair. Subsequent scanning of the genome for variant effects on this trait revealed two variants potentially affecting hair follicle development and differentiation. Validation in a large sample set as well as in imputed SNP data confirmed these variants to be Mangalitza-specific. Herein, we demonstrated how strong artificial selection has shaped the genome in Mangalitza pigs and left traces in the form of selection signatures. This knowledge on genomic variation promoting unique phenotypes like curly hair provides an important resource for futures studies unraveling genetic effects for special characteristics in livestock.
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13
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Fyda TJ, Spencer C, Jastroch M, Gaudry MJ. Disruption of thermogenic UCP1 predated the divergence of pigs and peccaries. J Exp Biol 2020; 223:jeb223974. [PMID: 32620708 DOI: 10.1242/jeb.223974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022]
Abstract
Uncoupling protein 1 (UCP1) governs non-shivering thermogenesis in brown adipose tissue. It has been estimated that pigs lost UCP1 ∼20 million years ago (MYA), dictating cold intolerance among piglets. Our current understanding of the root causes of UCP1 loss are, however, incomplete. Thus, examination of additional species can shed light on these fundamental evolutionary questions. Here, we investigated UCP1 in the Chacoan peccary (Catagonus wagneri), a member of the Tayassuid lineage that diverged from pigs during the late Eocene-mid Oligocene. Exons 1 and 2 have been deleted in peccary UCP1 and the remaining exons display additional inactivating mutations. A common nonsense mutation in exon 6 revealed that UCP1 was pseudogenized in a shared ancestor of pigs and peccaries. Our selection pressure analyses indicate that the inactivation occurred 36.2-44.3 MYA during the mid-late Eocene, which is much earlier than previously thought. Importantly, pseudogenized UCP1 provides the molecular rationale for cold sensitivity and current tropical biogeography of extant peccaries.
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Affiliation(s)
- Thomas Jacob Fyda
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Connor Spencer
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Martin Jastroch
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael J Gaudry
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, SE-106 91 Stockholm, Sweden
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14
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Silva EC, McManus C, Piovezan U, Faria DA, Souza CA, Caetano AR, Paiva SR. Phylogeography of feral Monteiro pig in the Brazilian Pantanal Ecosystem. Genetica 2020; 148:183-193. [PMID: 32770285 DOI: 10.1007/s10709-020-00099-y] [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: 09/12/2019] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
The Monteiro is a feral pig found in the Brazilian Pantanal ecosystem. The goal of this research is to generate data and knolewdge related to animal populations wich can be used for management and development of an in vitro conservation program for animal resourses at Pantanal ecosystem. The present study evaluated animals sampled from 10 distinct locations within the region, using 19 microsatellite markers (N = 189) and the control region of mitochondrial DNA (mtDNA) (N = 392). Low genetic differences were found between populations with the microsatellite data. The FST range was between 0.009 and 0.063 (p-value < 0.05). The Mantel test corroborated with previous results, as low correlations between genetic and geographic distances were observed (r2 = 0.2309, p = 0.06). Bayesian analysis for genetic structure identification placed the Monteiro pigs into three main clusters (MOB, Pop 1 and all others Pantanal populations). Most of the Monteiro pigs share a single European haplotype as seen by mtDNA analyses. This haplotype is not exclusive, as it is shared with other swine populations (commercial and other locally adapted breeds). Monteiro populations from different geographic locations within Pantanal are not isolated and can be considered as a large unique population. Since animals roam freely to seek food and water, or even due to seasonal flooding of their habitat, the Monteiro populations presented absence of major genetic structure and evidence of high gene flow. These results can be used to create a management plan and in situ and ex situ conservation program for conservation and use of the Monteiro breed in the Pantanal ecosystem.
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Affiliation(s)
- Elizabete C Silva
- Faculdade de Agronomia E Medicina Veterinária, Instituto Central de Ciências, Campus Darcy Ribeiro, Universidade de Brasília, Asa Norte, Brasilia, DF, 70910-900, Brazil
| | - Concepta McManus
- Departamento de Ciências Fisiológicas, Instituto de Biologia, Campus Darcy Ribeiro, Universidade de Brasilia, Asa Norte, Brasilia, DF, 70910-900, Brazil
| | - Ubiratan Piovezan
- Embrapa Tabuleiros Costeiros, Av. Beira Mar, 3250 - Jardins, Aracaju, SE, 49025-040, Brazil
| | - Danielle A Faria
- Faculdade de Agronomia E Medicina Veterinária, Instituto Central de Ciências, Campus Darcy Ribeiro, Universidade de Brasília, Asa Norte, Brasilia, DF, 70910-900, Brazil
| | - Carla A Souza
- La Trobe University, Plenty Rd & Kingsbury Dr., Bundoora, VIC, 3086, Australia
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos E Biotecnologia, Final W5 Norte, Brasília, DF, 70770-917, Brazil
| | - Samuel R Paiva
- Embrapa Recursos Genéticos E Biotecnologia, Final W5 Norte, Brasília, DF, 70770-917, Brazil.
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15
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Pasupa K, Rathasamuth W, Tongsima S. Discovery of significant porcine SNPs for swine breed identification by a hybrid of information gain, genetic algorithm, and frequency feature selection technique. BMC Bioinformatics 2020; 21:216. [PMID: 32456608 PMCID: PMC7251909 DOI: 10.1186/s12859-020-3471-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 03/25/2020] [Indexed: 11/21/2022] Open
Abstract
Background The number of porcine Single Nucleotide Polymorphisms (SNPs) used in genetic association studies is very large, suitable for statistical testing. However, in breed classification problem, one needs to have a much smaller porcine-classifying SNPs (PCSNPs) set that could accurately classify pigs into different breeds. This study attempted to find such PCSNPs by using several combinations of feature selection and classification methods. We experimented with different combinations of feature selection methods including information gain, conventional as well as modified genetic algorithms, and our developed frequency feature selection method in combination with a common classification method, Support Vector Machine, to evaluate the method’s performance. Experiments were conducted on a comprehensive data set containing SNPs from native pigs from America, Europe, Africa, and Asia including Chinese breeds, Vietnamese breeds, and hybrid breeds from Thailand. Results The best combination of feature selection methods—information gain, modified genetic algorithm, and frequency feature selection hybrid—was able to reduce the number of possible PCSNPs to only 1.62% (164 PCSNPs) of the total number of SNPs (10,210 SNPs) while maintaining a high classification accuracy (95.12%). Moreover, the near-identical performance of this PCSNPs set to those of bigger data sets as well as even the entire data set. Moreover, most PCSNPs were well-matched to a set of 94 genes in the PANTHER pathway, conforming to a suggestion by the Porcine Genomic Sequencing Initiative. Conclusions The best hybrid method truly provided a sufficiently small number of porcine SNPs that accurately classified swine breeds.
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Affiliation(s)
- Kitsuchart Pasupa
- Faculty of Information Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand.
| | - Wanthanee Rathasamuth
- Faculty of Information Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Khong Luang, 12120, Thailand
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16
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Hlongwane NL, Hadebe K, Soma P, Dzomba EF, Muchadeyi FC. Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa. Front Genet 2020; 11:344. [PMID: 32457791 PMCID: PMC7221027 DOI: 10.3389/fgene.2020.00344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%-98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise F ST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise F ST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.
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Affiliation(s)
- Nompilo Lucia Hlongwane
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
| | - Khanyisile Hadebe
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Pranisha Soma
- Animal Production Institute, Agricultural Research Council, Irene, South Africa
| | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
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17
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Lee SH, Seo DW, Cho ES, Choi BH, Kim YM, Hong JK, Han HD, Jung YB, Kim DJ, Choi TJ, Lee SH. Genetic Diversity and Ancestral Study for Korean Native Pigs Using 60K SNP Chip. Animals (Basel) 2020; 10:ani10050760. [PMID: 32349346 PMCID: PMC7277343 DOI: 10.3390/ani10050760] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 01/08/2023] Open
Abstract
Simple Summary Assessing and understanding the genetic resources of indigenous livestock populations is necessary to address issues associated with conservation and domestic supply, etc. This study examined the Korean native pig (KNP; Sus scrofa coreanus), which is among the native porcine breeds in South Korea, in terms of its overall genetic diversity and ancestry. According to 60K single-nucleotide polymorphism (SNP) BeadChip analyses, the KNP pig showed similarity to Western breeds than to Chinese breeds. This conclusion runs contrary to popular belief as a Chinese origin of KNP pigs, as suggested by previous historical and genetic studies. We also describe the possibility of potential biases in the analysis results. Abstract The Korean native pig (KNP; Sus scrofa coreanus) is an indigenous porcine breed in South Korea considered as a valuable but dwindling genetic resource. Studies using diverse methodologies and genetic markers suggest that this population originated from the Manchu province of Northeastern China and migrated approximately 3000 years ago into the Korean peninsula. This study aimed to verify those findings by performing diversity and ancestral analyses using the 60K single-nucleotide polymorphism (SNP) BeadChip on 891 pigs of 47 breeds worldwide. We also performed principal component analysis (PCA), ancestry analyses, phylogenetic tree analysis using SNPhylo, and linkage disequilibrium analysis. Furthermore, we generated heatmap, obtained Nei’s genetic distance and FST values, and explored the heterozygosity of commercial and native Korean pigs. The results demonstrated that KNP pigs are more closely related to European breeds than to Chinese breeds. In addition, as previous studies have suggested, our admixture analyses indicated that KNP pigs showed distinguishable genetic structure.
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Affiliation(s)
- Soo Hyun Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (S.H.L.); (D.W.S.)
| | - Dong Won Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (S.H.L.); (D.W.S.)
| | - Eun Seok Cho
- Swine Science division, National Institute of Animal Science, RDA, Seonghwan 31000, Korea; (E.S.C.); (Y.M.K.); (J.K.H.)
| | - Bong Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, WanJu 55365, Korea;
| | - Yong Min Kim
- Swine Science division, National Institute of Animal Science, RDA, Seonghwan 31000, Korea; (E.S.C.); (Y.M.K.); (J.K.H.)
| | - Joon Ki Hong
- Swine Science division, National Institute of Animal Science, RDA, Seonghwan 31000, Korea; (E.S.C.); (Y.M.K.); (J.K.H.)
| | - Hyo Dong Han
- Research and Development Division, Korea Institute for Animal Products Quality Evaluation, Areumseo-gil 21, Sejong 30100, Korea; (H.D.H.); (Y.B.J.); (D.J.K.)
| | - Yeon Bok Jung
- Research and Development Division, Korea Institute for Animal Products Quality Evaluation, Areumseo-gil 21, Sejong 30100, Korea; (H.D.H.); (Y.B.J.); (D.J.K.)
| | - Dong Jun Kim
- Research and Development Division, Korea Institute for Animal Products Quality Evaluation, Areumseo-gil 21, Sejong 30100, Korea; (H.D.H.); (Y.B.J.); (D.J.K.)
| | - Tae Jeong Choi
- Swine Science division, National Institute of Animal Science, RDA, Seonghwan 31000, Korea; (E.S.C.); (Y.M.K.); (J.K.H.)
- Correspondence: (T.J.C.); (S.H.L.); Tel.: +82-42-821-5878 (S.H.L.)
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (S.H.L.); (D.W.S.)
- Correspondence: (T.J.C.); (S.H.L.); Tel.: +82-42-821-5878 (S.H.L.)
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18
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Muñoz M, García-Casco JM, Alves E, Benítez R, Barragán C, Caraballo C, Fernández AI, García F, Núñez Y, Óvilo C, Fernández A, Rodríguez C, Silió L. Development of a 64 SNV panel for breed authentication in Iberian pigs and their derived meat products. Meat Sci 2020; 167:108152. [PMID: 32361066 DOI: 10.1016/j.meatsci.2020.108152] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/07/2020] [Accepted: 04/14/2020] [Indexed: 11/19/2022]
Abstract
Spanish legislation regulates the labelling of Iberian pig meat and dry-cured products, which are labelled as "Ibérico" or "100% Ibérico" when they come from Duroc x Iberian crossbred or Iberian purebred pigs. Although the analytical authentication of breed origin is not mandatory, a genetic diagnostic tool is demanded by producers and consumers. We have designed a 64 Single Nucleotide Variant genotyping panel displaying extreme allelic frequencies between Duroc and Iberian purebred samples. Average proportions of Iberian alleles of 0.99, 0.01, 0.77 and 0.48 were estimated by admixture clustering analysis of known origin samples, for Iberian and Duroc purebred, 75% Iberian and 50% Iberian classes, respectively. A supervised analysis with 1419 samples showed some overlapping between contiguous classes, but the calculated degrees of separability ranged from 0.800 to 0.996, exceeding the threshold value (0.70) for considering suitable for prediction. Therefore, this panel is a useful genetic tool to infer purebred or crossbred Iberian origin of live animals, meat and dry-cured products.
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Affiliation(s)
- M Muñoz
- Centro de I+D en Cerdo Ibérico INIA-Zafra, 06300 Zafra, Badajoz, Spain; Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain.
| | - J M García-Casco
- Centro de I+D en Cerdo Ibérico INIA-Zafra, 06300 Zafra, Badajoz, Spain; Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - E Alves
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - R Benítez
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - C Barragán
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - C Caraballo
- Centro de I+D en Cerdo Ibérico INIA-Zafra, 06300 Zafra, Badajoz, Spain
| | - A I Fernández
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - F García
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - Y Núñez
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - C Óvilo
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - A Fernández
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - C Rodríguez
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
| | - L Silió
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain
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Lukić B, Ferenčaković M, Šalamon D, Čačić M, Orehovački V, Iacolina L, Curik I, Cubric-Curik V. Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds. Front Genet 2020; 11:261. [PMID: 32296459 PMCID: PMC7136467 DOI: 10.3389/fgene.2020.00261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
The majority of the nearly 400 existing local pig breeds are adapted to specific environments and human needs. The demand for large production quantities and the industrialized pig production have caused a rapid decline of many local pig breeds in recent decades. Black Slavonian pig and Turopolje pig, the latter highly threatened, are the two Croatian local indigenous breeds typically grown in extensive or semi-intensive systems. In order to guide a long-term breeding program to prevent the disappearance of these breeds, we analyzed their genetic diversity, inbreeding level and relationship with other local breeds across the world, as well as modern breeds and several wild populations, using high throughput genomic data obtained using the Illumina Infinium PorcineSNP60 v2 BeadChip. Multidimensional scaling analysis positioned Black Slavonian pigs close to the UK/North American breeds, while the Turopolje pig clustered within the Mediterranean breeds. Turopolje pig showed a very high inbreeding level (FROH>4Mb = 0.400 and FROH>8Mb = 0.332) that considerably exceeded the level of full-sib mating, while Black Slavonian pig showed much lower inbreeding (FROH>4Mb = 0.098 and FROH>8Mb = 0.074), indicating a planned mating strategy. In Croatian local breeds we identified several genome regions showing adaptive selection signals that were not present in commercial breeds. The results obtained in this study reflect the current genetic status and breeding management of the two Croatian indigenous local breeds. Given the small populations of both breeds, a controlled management activity has been implemented in Black Slavonian pigs since their commercial value has been recognized. In contrast, the extremely high inbreeding level observed in Turopolje pig argues for an urgent conservation plan with a long-term, diversity-oriented breeding program.
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Affiliation(s)
- Boris Lukić
- Department for Animal Production and Biotechnology, Faculty of Agrobiotechnical Sciences Osijek, J.J. Strossmayer University of Osijek, Osijek, Croatia
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Dragica Šalamon
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Mato Čačić
- Ministry of Agriculture, Zagreb, Croatia
| | | | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department for Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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20
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Smyser TJ, Tabak MA, Slootmaker C, Robeson MS, Miller RS, Bosse M, Megens HJ, Groenen MAM, Paiva SR, de Faria DA, Blackburn HD, Schmit BS, Piaggio AJ. Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine. Mol Ecol 2020; 29:1103-1119. [PMID: 32080922 DOI: 10.1111/mec.15392] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 01/13/2023]
Abstract
Invasive alien species are a significant threat to both economic and ecological systems. Identifying the processes that give rise to invasive populations is essential for implementing effective control strategies. We conducted an ancestry analysis of invasive feral swine (Sus scrofa, Linnaeus, 1758), a highly destructive ungulate that is widely distributed throughout the contiguous United States, to describe introduction pathways, sources of newly emergent populations and processes contributing to an ongoing invasion. Comparisons of high-density single nucleotide polymorphism genotypes for 6,566 invasive feral swine to a comprehensive reference set of S. scrofa revealed that the vast majority of feral swine were of mixed ancestry, with dominant genetic associations to Western heritage breeds of domestic pig and European populations of wild boar. Further, the rapid expansion of invasive feral swine over the past 30 years was attributable to secondary introductions from established populations of admixed ancestry as opposed to direct introductions of domestic breeds or wild boar. Spatially widespread genetic associations of invasive feral swine to European wild boar deviated strongly from historical S. scrofa introduction pressure, which was largely restricted to domestic pigs with infrequent, localized wild boar releases. The deviation between historical introduction pressure and contemporary genetic ancestry suggests wild boar-hybridization may contribute to differential fitness in the environment and heightened invasive potential for individuals of admixed domestic pig-wild boar ancestry.
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Affiliation(s)
- Timothy J Smyser
- National Wildlife Research Center, United States Department of Agriculture, Wildlife Services, Fort Collins, CO, USA
| | - Michael A Tabak
- Center for Epidemiology and Animal Health, United States Department of Agriculture, Veterinary Services, Fort Collins, CO, USA.,Quantitative Science Consulting, Laramie, WY, USA
| | - Chris Slootmaker
- National Wildlife Research Center, United States Department of Agriculture, Wildlife Services, Fort Collins, CO, USA
| | - Michael S Robeson
- National Wildlife Research Center, United States Department of Agriculture, Wildlife Services, Fort Collins, CO, USA.,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Ryan S Miller
- Center for Epidemiology and Animal Health, United States Department of Agriculture, Veterinary Services, Fort Collins, CO, USA
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Samuel Rezende Paiva
- Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, USA
| | - Danielle Assis de Faria
- Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, USA
| | - Harvey D Blackburn
- Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, USA
| | - Brandon S Schmit
- National Wildlife Disease Program, United States Department of Agriculture, Fort Collins, CO, USA
| | - Antoinette J Piaggio
- National Wildlife Research Center, United States Department of Agriculture, Wildlife Services, Fort Collins, CO, USA
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21
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Wang J, Liu C, Chen J, Bai Y, Wang K, Wang Y, Fang M. Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds. Genes (Basel) 2020; 11:E275. [PMID: 32143300 PMCID: PMC7140852 DOI: 10.3390/genes11030275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 12/27/2022] Open
Abstract
Genetic variations introduced via introgression from Western to Chinese pigs have contributed to the performance of Chinese breeds in traits such as growth rate and feed conversion efficiency. However, little is known about the underlying genomic changes that occurred during introgression and the types of traits affected by introgression. To address these questions, 525 animals were characterized using an SNP array to detect genomic regions that had been introgressed from European to indigenous Chinese breeds. The functions of genes located in introgressed regions were also investigated. Our data show that five out of six indigenous Chinese breeds show evidence of introgression from Western pigs, and eight introgressed genome regions are shared by five of the Chinese breeds. A region located on chr13: 12.8-13.1 M was affected by both introgression and artificial selection, and this region contains the glucose absorption related gene, OXSM, and the sensory related gene, NGLY. The results provide a foundation for understanding introgression from Western to indigenous Chinese pigs.
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Affiliation(s)
- Jue Wang
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (J.W.)
| | - Chengkun Liu
- Berry Genomics Corporation, Beijing 102206, China;
| | - Jie Chen
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (J.W.)
| | - Ying Bai
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China;
| | - Kejun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China;
| | - Yubei Wang
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (J.W.)
| | - Meiying Fang
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (J.W.)
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22
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Ramos-Canché ME, Aguilar-Urquizo E, Chay-Canul AJ, Piñeiro-Vázquez ÁT, Velázquez-Madrazo PA, Magaña Magaña MA, Toledo-López V, Sanginés-García JR. Dietary levels of energy and protein on productive performance and carcass traits of growing female Mexican hairless pigs. Anim Feed Sci Technol 2020. [DOI: 10.1016/j.anifeedsci.2019.114269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Acosta DB, Figueroa CE, Fernández GP, Carpinetti BN, Merino ML. Genetic diversity and phylogenetic relationships in feral pig populations from Argentina. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Gourdine JL, Riquet J, Rosé R, Poullet N, Giorgi M, Billon Y, Renaudeau D, Gilbert H. Genotype by environment interactions for performance and thermoregulation responses in growing pigs1,2. J Anim Sci 2019; 97:3699-3713. [PMID: 31351442 PMCID: PMC6735898 DOI: 10.1093/jas/skz245] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/18/2019] [Indexed: 01/21/2023] Open
Abstract
Heat stress affects pig health, welfare, and production, and thus the economic viability of the pig sector in many countries. Breeding for heat tolerance is a complex issue, increasingly important due to climate change and the development of pig production in tropical areas. Characterizing genetic determinism of heat tolerance would help building selection schemes dedicated to high performance in tropical areas. The main objective of our study was to estimate the genetic parameters for production and thermoregulation traits in two highly related growing pig populations reared in temperate (TEMP) or tropical humid (TROP) environment. Pigs came from a backcross population between Large White (LW, heat sensitive) and Creole (CR, heat tolerant) pigs. Phenotypic data were obtained on a total of 1,297 pigs using the same procedures in both environments, for body weight (BW, at weeks 11 and 23), daily feed intake (ADFI), backfat thickness (BFT, at weeks 19 and 23), cutaneous temperature (CT, at weeks 19 and 23), and rectal temperature (RT, at weeks 19, 21, and 23). Feed conversion ratio (FCR) and residual feed intake (RFI) were computed for the whole test period (11 to 23 wk). Criteria comparing the fits to the data revealed genotype × environment (G × E) interactions for most traits but not for FCR. The variance components were obtained using two different methods, a restricted maximum likelihood method and a Bayesian Markov chain Monte Carlo method, considering that traits are either similar or different in each environment. Regardless of the method, heritability estimates for production traits were moderate to high, except for FCR (lower than 0.18). Heritability estimates for RT were low to moderate, ranging from 0.04 to 0.34. The genetic correlations of each trait between environments generally differed from 1, except for FCR and ADG. For most thermoregulation traits, they also did not differ significantly from zero, suggesting that the main genetic bases of heat tolerance may vary in different environment. Within environments, the unfavorable genetic correlations between production traits and RT suggest an antagonism between the ability to maintain inner temperature and the ability to increase ADFI and ADG. However, greater RT were also associated to leaner pigs and better feed efficiency. Nevertheless, due to large inaccuracies of these estimations, larger cohorts would be needed to decide about the best breeding schemes to choose for tropical pig production.
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Affiliation(s)
| | - Juliette Riquet
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, Castanet Tolosan, France
| | | | | | | | | | | | - Hélène Gilbert
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, Castanet Tolosan, France
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Assessing Sus scrofa diversity among continental United States, and Pacific islands populations using molecular markers from a gene banks collection. Sci Rep 2019; 9:3173. [PMID: 30816173 PMCID: PMC6395668 DOI: 10.1038/s41598-019-39309-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 01/07/2019] [Indexed: 11/11/2022] Open
Abstract
Human migration and trade facilitated domesticated livestock movement, gene flow and development of diverse populations upon which agriculture is based. In addition, varying USA ecological conditions has led to a diverse set of livestock populations to utilize. Quantifying genetic diversity of these populations is incomplete. This paper quantifies genetic diversity captured by the National Animal Germplasm Program and explores genetic structure and differences among 19 pig populations (feral populations from Pacific islands, continental US, and Chinese breeds) using 70,231 SNP from 500 animal samples. Among continental US breeds Fis was consistently low suggesting genetic variability is sufficiently available for breeders to use. A unique population structure using principal component analysis illustrated clear distinctions between Duroc, Yorkshire, Hampshire, breeds of Chinese origin, and feral Pacific Island populations were identified. Five Y chromosome haplotypes were evaluated and demonstrated migration patterns from European, central Asia, and potentially Polynesian waves of gene flow. Quantifying diversity and potential origin of Pacific populations provides insight for future uses, and the need for preservation. Viewing gene bank holdings in context of diversity measures we found a lack of inbreeding within breeds, suggesting the collection represents a wide sampling of individual breeds.
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Mastrangelo S, Ciani E, Ajmone Marsan P, Bagnato A, Battaglini L, Bozzi R, Carta A, Catillo G, Cassandro M, Casu S, Ciampolini R, Crepaldi P, D'Andrea M, Di Gerlando R, Fontanesi L, Longeri M, Macciotta NP, Mantovani R, Marletta D, Matassino D, Mele M, Pagnacco G, Pieramati C, Portolano B, Sarti FM, Tolone M, Pilla F. Conservation status and historical relatedness of Italian cattle breeds. Genet Sel Evol 2018; 50:35. [PMID: 29940848 PMCID: PMC6019226 DOI: 10.1186/s12711-018-0406-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 06/11/2018] [Indexed: 01/30/2023] Open
Abstract
Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. Conclusions This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource. Electronic supplementary material The online version of this article (10.1186/s12711-018-0406-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy.
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124, Bari, Italy
| | | | - Alessandro Bagnato
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Luca Battaglini
- Dipartimento di Scienze Agrarie Forestali e Alimentari, University of Torino, 10095, Grugliasco, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, University of Firenze, 50144, Florence, Italy
| | - Antonello Carta
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015, Monterotondo, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Sara Casu
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, University of Pisa, 56100, Pisa, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Luca Fontanesi
- Dipartimento di Scienze e tecnologie Agroalimentari, University of Bologna, 40127, Bologna, Italy
| | - Maria Longeri
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Roberto Mantovani
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione, Ambiente, University of Catania, 95125, Catania, Italy
| | - Donato Matassino
- Divulgazione e Applicazione di Biotecniche Innovative, Consorzio per la Sperimentazione, 82100, Benevento, Italy
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, 56124, Pisa, Italy
| | - Giulio Pagnacco
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Camillo Pieramati
- Dipartimento di Medicina Veterinaria, University of Perugia, 06126, Perugia, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari, Ambientali, University of Perugia, 06121, Perugia, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, University of Molise, 86100, Campobasso, Italy.,Centro Risorse Bio-Culturali e Sviluppo Locale, University of Molise, 86100, Campobasso, Italy
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Queirós J, Alves PC, Vicente J, Gortázar C, de la Fuente J. Genome-wide associations identify novel candidate loci associated with genetic susceptibility to tuberculosis in wild boar. Sci Rep 2018; 8:1980. [PMID: 29386541 PMCID: PMC5792637 DOI: 10.1038/s41598-018-20158-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/12/2018] [Indexed: 12/23/2022] Open
Abstract
Tuberculosis (TB) affects a wide range of host species worldwide. Understanding host-pathogen co-evolution remains a global challenge owing to complex interactions among host genetic factors, pathogen traits and environmental conditions. We used an endemic wild boar population that had undergone a huge increase in Mycobacterium bovis infection prevalence, from 45% in 2002/06 to 83% in 2009/12, to understand the effects of host genetics on host TB outcomes and disease dynamics. Host genomic variation was characterized using a high-density single nucleotide polymorphism (SNP) array, while host TB phenotype was assessed using both gross pathology and mycobacterial culture. Two complementary genome-wide association (GWAS) analyses were conducted: (i) infected-uninfected; and (ii) 2002/06–2009/12. The SNPs with the highest allelic frequency differences between time-periods and TB outcomes were identified and validated in a large dataset. In addition, we quantified the expression levels of some of their closest genes. These analyses highlighted various SNPs (i.e. rs81465339, rs81394585, rs81423166) and some of the closest genes (i.e. LOC102164072, BDNF/NT-3, NTRK2, CDH8, IGSF21) as candidates for host genetic susceptibility. In addition to TB-driven selection, our findings outline the putative role of demographic events in shaping genomic variation in natural populations and how population crashes and drift may impact host genetic susceptibility to TB over time.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, R. Monte-Crasto, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal. .,SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Paulo Célio Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, R. Monte-Crasto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| | - Joaquín Vicente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - Christian Gortázar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
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28
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Cesconeto RJ, Joost S, McManus CM, Paiva SR, Cobuci JA, Braccini J. Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups. Ecol Evol 2017; 7:9544-9556. [PMID: 29187988 PMCID: PMC5696410 DOI: 10.1002/ece3.3323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 11/27/2022] Open
Abstract
Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as FST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in both methods, with a Kappa value of 0.073 (95% CI: 0.011-0.134). The frequency of these markers indicated a clear north-south country division that reflects Brazilian environmental differences in temperature, solar radiation, and precipitation. Global spatial territory correlation for environmental variables corroborates this finding (average Moran's I = 0.89, range from 0.55 to 0.97). The distribution of alleles over the territory was not strongly correlated with the breed/genetic groups. These results are congruent with previous mtDNA studies and should be used to direct germplasm collection for the National gene bank.
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Affiliation(s)
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG)School of Architecture, Civil and Environmental Engineering (ENAC)Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | | | | | - Jaime Araujo Cobuci
- Universidade Federal do Rio Grande do SulPorto AlegreRio Grande do SulBrazil
| | - Jose Braccini
- Universidade Federal do Rio Grande do SulPorto AlegreRio Grande do SulBrazil
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29
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Chen M, Su G, Fu J, Zhang Q, Wang A, Sandø Lund M, Guldbrandtsen B. Population admixture in Chinese and European Sus scrofa. Sci Rep 2017; 7:13178. [PMID: 29030577 PMCID: PMC5640611 DOI: 10.1038/s41598-017-13127-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/18/2017] [Indexed: 11/30/2022] Open
Abstract
Relationships between different populations were investigated using Porcine 60 K data from 1,135 domestic pigs and wild boars across Europe and China. The results indicate that most European breeds have been introgressed with Chinese ancestry, but the extent of introgression varies considerably among breeds. Moreover, the main source of this introgression is pigs from South China, closely related to Bamaxiang and Dongshan pigs. Contributions from East and Central Chinese pig breeds are also detectable. Phylogeny reconstruction places European wild boars among European domestic breeds. Coalescent simulations indicate that this may be the result of gene flow from European wild boars to European domestic pigs. These results will facilitate further genomic studies such as genome-wide association studies, selection signature detection and genomic prediction.
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Affiliation(s)
- Minhui Chen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark.,Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, China
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark.
| | - Jinluan Fu
- Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, China
| | - Qin Zhang
- Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, China
| | - Aiguo Wang
- Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, China
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
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30
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Yang B, Cui L, Perez-Enciso M, Traspov A, Crooijmans RPMA, Zinovieva N, Schook LB, Archibald A, Gatphayak K, Knorr C, Triantafyllidis A, Alexandri P, Semiadi G, Hanotte O, Dias D, Dovč P, Uimari P, Iacolina L, Scandura M, Groenen MAM, Huang L, Megens HJ. Genome-wide SNP data unveils the globalization of domesticated pigs. Genet Sel Evol 2017; 49:71. [PMID: 28934946 PMCID: PMC5609043 DOI: 10.1186/s12711-017-0345-y] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. RESULTS A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. CONCLUSIONS Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.
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Affiliation(s)
- Bin Yang
- National Key Laboratory for Pig Genetic Improvement and Production Technology, Nanchang, China
| | - Leilei Cui
- National Key Laboratory for Pig Genetic Improvement and Production Technology, Nanchang, China
| | - Miguel Perez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona Spain
- Institut Catala de Recerca i Estudis Avancats (ICREA), Carrer de Lluís Companys, Barcelona, Spain
| | - Aleksei Traspov
- All-Russian Research Institute of Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitzy, Moscow Region Russia
| | | | - Natalia Zinovieva
- All-Russian Research Institute of Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitzy, Moscow Region Russia
| | - Lawrence B. Schook
- Institute of Genomic Biology, University of Illinois, Urbana, Champaign, IL USA
| | - Alan Archibald
- Division of Genetics and Genomics, The Roslin Institute, R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - Kesinee Gatphayak
- Animal and Aquatic Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Christophe Knorr
- Division of Biotechnology and Reproduction of Livestock, Department of Animal Sciences, Georg-August-University, Göttingen, Germany
| | - Alex Triantafyllidis
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloníki, Thessaloniki, Greece
| | - Panoraia Alexandri
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloníki, Thessaloniki, Greece
| | - Gono Semiadi
- Research Centre for Biology- Zoology Division, LIPI, Bogor, Indonesia
| | - Olivier Hanotte
- School of Biology, University of Nottingham, Notttingham, UK
| | - Deodália Dias
- Faculdade de Ciências and CESAM, Universidade de Lisboa, Lisbon, Portugal
| | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Pekka Uimari
- Animal Breeding, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
- Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Massimo Scandura
- Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | | | - Lusheng Huang
- National Key Laboratory for Pig Genetic Improvement and Production Technology, Nanchang, China
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University, Wageningen, The Netherlands
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31
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Li X, Yang S, Dong K, Tang Z, Li K, Fan B, Wang Z, Liu B. Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances. Anim Genet 2017; 48:600-605. [DOI: 10.1111/age.12574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2017] [Indexed: 11/26/2022]
Affiliation(s)
- X. Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education; Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University; Wuhan Hubei 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production; Wuhan Hubei 430070 China
- Department of Agricultural, Food and Nutritional Science; University of Alberta; Edmonton AB T6G 2P5 Canada
| | - S. Yang
- College of Animal Science and Technology; Zhejiang A&F University; Lin'an Zhejiang 311300 China
| | - K. Dong
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - Z. Tang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - K. Li
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing 100193 China
| | - B. Fan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education; Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University; Wuhan Hubei 430070 China
| | - Z. Wang
- Department of Agricultural, Food and Nutritional Science; University of Alberta; Edmonton AB T6G 2P5 Canada
| | - B. Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education; Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University; Wuhan Hubei 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production; Wuhan Hubei 430070 China
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32
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Abstract
Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig (Sus scrofa) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q-value < 0.05 in Asia and Europe, respectively; five were shared across continents. In Asia, we found six significant pathways related to behavior, which involved essential neurotransmitters like dopamine and serotonin. Several significant pathways were interrelated and shared a variable percentage of genes. There were 12 genes present in >10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding processes. Purifying selection was, nevertheless, stronger in significantly differentiated pathways than in random pathways, mainly in Europe. We conclude that pathway analysis facilitates the biological interpretation of genome-wide studies. Notably, in the case of pig, behavior played an important role, among other physiological and developmental processes.
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33
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Osei-Amponsah R, Skinner BM, Adjei DO, Bauer J, Larson G, Affara NA, Sargent CA. Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis. BMC Genomics 2017; 18:193. [PMID: 28219344 PMCID: PMC5319064 DOI: 10.1186/s12864-017-3536-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/02/2017] [Indexed: 12/12/2022] Open
Abstract
Background The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R, Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping. Results The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both European and Asian genetic signatures, with differences between the geographical zones. Black coat colour is the most predominant within the breed, with black MC1R alleles of both Asian and European origin. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster closely with European pigs of commercial origin, but we identified intervals via FST analyses that may elucidate loci for ADP specific traits. Conclusions The presence of both European and Asian contributions, with differences between geographical zones probably reflects trading and colonial influences. Understanding the effects of admixture on important adaptive and economic traits of the ADP and other local breeds in Africa is critical for developing sustainable conservation programmes to prevent the decline of these genetic resources. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3536-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard Osei-Amponsah
- Animal Breeding and Genetics Research Group, Department of Animal Science, University of Ghana, P. O. Box LG 226, Legon-ACCRA, Ghana.,Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK
| | - Benjamin M Skinner
- Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK
| | - Dennis O Adjei
- Animal Breeding and Genetics Research Group, Department of Animal Science, University of Ghana, P. O. Box LG 226, Legon-ACCRA, Ghana
| | - Julien Bauer
- Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK
| | - Nabeel A Affara
- Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK
| | - Carole A Sargent
- Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK.
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Renner S, Dobenecker B, Blutke A, Zöls S, Wanke R, Ritzmann M, Wolf E. Comparative aspects of rodent and nonrodent animal models for mechanistic and translational diabetes research. Theriogenology 2016; 86:406-21. [PMID: 27180329 DOI: 10.1016/j.theriogenology.2016.04.055] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/22/2016] [Accepted: 03/14/2016] [Indexed: 12/31/2022]
Abstract
The prevalence of diabetes mellitus, which currently affects 387 million people worldwide, is permanently rising in both adults and adolescents. Despite numerous treatment options, diabetes mellitus is a progressive disease with severe comorbidities, such as nephropathy, neuropathy, and retinopathy, as well as cardiovascular disease. Therefore, animal models predictive of the efficacy and safety of novel compounds in humans are of great value to address the unmet need for improved therapeutics. Although rodent models provide important mechanistic insights, their predictive value for therapeutic outcomes in humans is limited. In recent years, the pig has gained importance for biomedical research because of its close similarity to human anatomy, physiology, size, and, in contrast to non-human primates, better ethical acceptance. In this review, anatomic, biochemical, physiological, and morphologic aspects relevant to diabetes research will be compared between different animal species, that is, mouse, rat, rabbit, pig, and non-human primates. The value of the pig as a model organism for diabetes research will be highlighted, and (dis)advantages of the currently available approaches for the generation of pig models exhibiting characteristics of metabolic syndrome or type 2 diabetes mellitus will be discussed.
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Affiliation(s)
- Simone Renner
- Gene Center and Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Diabetes Research (DZD), Helmholtz Zentrum München, Neuherberg, Germany.
| | - Britta Dobenecker
- Chair of Animal Nutrition and Dietetics, Department of Veterinary Science, LMU Munich, Munich, Germany
| | - Andreas Blutke
- Institute of Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, Germany
| | - Susanne Zöls
- Clinic for Swine, Center for Clinical Veterinary Medicine, LMU Munich, Germany
| | - Rüdiger Wanke
- Institute of Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, Germany
| | - Mathias Ritzmann
- Clinic for Swine, Center for Clinical Veterinary Medicine, LMU Munich, Germany
| | - Eckhard Wolf
- Gene Center and Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Diabetes Research (DZD), Helmholtz Zentrum München, Neuherberg, Germany
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Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information. Heredity (Edinb) 2016; 117:14-24. [PMID: 27025169 DOI: 10.1038/hdy.2016.21] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/22/2016] [Accepted: 02/02/2016] [Indexed: 01/17/2023] Open
Abstract
Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.
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Traspov A, Deng W, Kostyunina O, Ji J, Shatokhin K, Lugovoy S, Zinovieva N, Yang B, Huang L. Population structure and genome characterization of local pig breeds in Russia, Belorussia, Kazakhstan and Ukraine. Genet Sel Evol 2016; 48:16. [PMID: 26932452 PMCID: PMC4772533 DOI: 10.1186/s12711-016-0196-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It is generally accepted that domestication of pigs took place in multiple locations across Eurasia; the breeds that originated in Europe and Asia have been well studied. However, the genetic structure of pig breeds from Russia, Belorussia, Kazakhstan and Ukraine, which represent large geographical areas and diverse climatic zones in Eurasia, remains largely unknown. RESULTS This study provides the first genomic survey of 170 pigs representing 13 breeds from Russia, Belorussia, Kazakhstan and Ukraine; 288 pigs from six Chinese and seven European breeds were also included for comparison. Our findings show that the 13 novel breeds tested derived mainly from European pigs through the complex admixture of Large White, Landrace, Duroc, Hampshire and other breeds, and that they display no geographic structure based on genetic distance. We also found a considerable Asian contribution to the miniature Siberian pigs (Minisib breed) from Russia. Apart from the Minisib, Urzhum, Ukrainian Spotted Steppe and Ukrainian White Steppe breeds, which may have undergone intensive inbreeding, the breeds included in this study showed relatively high genetic diversity and low levels of homozygosity compared to the Chinese indigenous pig breeds. CONCLUSIONS This study provides the first genomic overview of the population structure and genetic diversity of 13 representative pig breeds from Russia, Belorussia, Kazakhstan and Ukraine; this information will be useful for the preservation and management of these breeds.
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Affiliation(s)
- Aleksei Traspov
- L.K. Ernst Institute for Animal Husbandry, Dubrovitzy 60, Podolsk district, Moscow region, Russia, 142132.
| | - Wenjiang Deng
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
| | - Olga Kostyunina
- L.K. Ernst Institute for Animal Husbandry, Dubrovitzy 60, Podolsk district, Moscow region, Russia, 142132.
| | - Jiuxiu Ji
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
| | - Kirill Shatokhin
- Siberian Research Institute for Animal Husbandry, Russian Agricultural Academy, Novosibirsk, Russia, 63050.
| | - Sergey Lugovoy
- Mykolayiv National Agrarian University, 9, Paryzka Komuna Str., Mykolayiv, 54020, Ukraine.
| | - Natalia Zinovieva
- L.K. Ernst Institute for Animal Husbandry, Dubrovitzy 60, Podolsk district, Moscow region, Russia, 142132.
| | - Bin Yang
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
| | - Lusheng Huang
- National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
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Frantz L, Meijaard E, Gongora J, Haile J, Groenen MA, Larson G. The Evolution of Suidae. Annu Rev Anim Biosci 2016; 4:61-85. [DOI: 10.1146/annurev-animal-021815-111155] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Laurent Frantz
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Erik Meijaard
- IUCN/SSC Wild Pig Specialist Group, Jakarta 15412, Indonesia
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT 0200, Australia
| | - Jaime Gongora
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - James Haile
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Martien A.M. Groenen
- Animal Breeding and Genomics Centre, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
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Revidatti MA, Delgado Bermejo JV, Gama LT, Landi Periati V, Ginja C, Alvarez LA, Vega-Pla JL, Martínez AM. Genetic characterization of local Criollo pig breeds from the Americas using microsatellite markers. J Anim Sci 2015; 92:4823-32. [PMID: 25349337 DOI: 10.2527/jas.2014-7848] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Little is known about local Criollo pig genetic resources and relationships among the various populations. In this paper, genetic diversity and relationships among 17 Criollo pig populations from 11 American countries were assessed with 24 microsatellite markers. Heterozygosities, F-statistics, and genetic distances were estimated, and multivariate, genetic structure and admixture analyses were performed. The overall means for genetic variability parameters based on the 24 microsatellite markers were the following: mean number of alleles per locus of 6.25 ± 2.3; effective number of alleles per locus of 3.33 ± 1.56; allelic richness per locus of 4.61 ± 1.37; expected and observed heterozygosity of 0.62 ± 0.04 and 0.57 ± 0.02, respectively; within-population inbreeding coefficient of 0.089; and proportion of genetic variability accounted for by differences among breeds of 0.11 ± 0.01. Genetic differences were not significantly associated with the geographical location to which breeds were assigned or their country of origin. Still, the NeighborNet dendrogram depicted the clustering by geographic origin of several South American breeds (Criollo Boliviano, Criollo of northeastern Argentina wet, and Criollo of northeastern Argentina dry), but some unexpected results were also observed, such as the grouping of breeds from countries as distant as El Salvador, Mexico, Ecuador, and Cuba. The results of genetic structure and admixture analyses indicated that the most likely number of ancestral populations was 11, and most breeds clustered separately when this was the number of predefined populations, with the exception of some closely related breeds that shared the same cluster and others that were admixed. These results indicate that Criollo pigs represent important reservoirs of pig genetic diversity useful for local development as well as for the pig industry.
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Affiliation(s)
- M A Revidatti
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional del Nordeste, 3400 Corrientes, Argentina
| | - J V Delgado Bermejo
- Departamento de Genética, Campus de Excelencia Internacional, Universidad de Córdoba, 14071 Córdoba, Spain
| | - L T Gama
- CIISA- Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - V Landi Periati
- Departamento de Genética, Campus de Excelencia Internacional, Universidad de Córdoba, 14071 Córdoba, Spain
| | - C Ginja
- Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal The names and of scientists working with the BioPig Consortium are listed at http://biopig.jimdo.com/investigadores
| | - L A Alvarez
- Universidad Nacional de Colombia, Sede Palmira, CR 32 no. 12-00 Chapinero, Palmira, Valle del Cauca, Colombia. AA 237
| | - J L Vega-Pla
- Laboratorio de Investigación Aplicada, Cría Caballar de las Fuerzas Armadas, 14080 Córdoba, Spain
| | - A M Martínez
- Departamento de Genética, Campus de Excelencia Internacional, Universidad de Córdoba, 14071 Córdoba, Spain
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Bianco E, Soto HW, Vargas L, Pérez-Enciso M. The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity. Mol Ecol 2015; 24:2364-78. [DOI: 10.1111/mec.13182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/18/2015] [Accepted: 03/24/2015] [Indexed: 01/27/2023]
Affiliation(s)
- E. Bianco
- Centre for Research in Agricultural Genomics (CRAG); CSIC-IRTA-UAB-UB Consortium; 08193 Bellaterra Spain
- Department of Animal Science; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - H. W. Soto
- Escuela de Zootecnia; Universidad de Costa Rica; 10501 San José Costa Rica
| | - L. Vargas
- Sistema Nacional de Áreas de Conservación (SINAC); Ministerio de Ambiente y Energía (MINAE); Avenida 15, Calle 1, San José Costa Rica
| | - M. Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG); CSIC-IRTA-UAB-UB Consortium; 08193 Bellaterra Spain
- Department of Animal Science; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
- Institut Català de Recerca I Estudis Avançats (ICREA); Carrer de Lluís Companys 23 Barcelona 08010 Spain
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Bianco E, Nevado B, Ramos-Onsins SE, Pérez-Enciso M. A deep catalog of autosomal single nucleotide variation in the pig. PLoS One 2015; 10:e0118867. [PMID: 25789620 PMCID: PMC4366260 DOI: 10.1371/journal.pone.0118867] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/27/2014] [Indexed: 12/31/2022] Open
Abstract
A comprehensive catalog of variability in a given species is useful for many important purposes, e.g., designing high density arrays or pinpointing potential mutations of economic or physiological interest. Here we provide a genomewide, worldwide catalog of single nucleotide variants by simultaneously analyzing the shotgun sequence of 128 pigs and five suid outgroups. Despite the high SNP missing rate of some individuals (up to 88%), we retrieved over 48 million high quality variants. Of them, we were able to assess the ancestral allele of more than 39M biallelic SNPs. We found SNPs in 21,455 out of the 25,322 annotated genes in pig assembly 10.2. The annotation showed that more than 40% of the variants were novel variants, not present in dbSNP. Surprisingly, we found a large variability in transition / transversion rate along the genome, which is very well explained (R2=0.79) primarily by genome differences in in CpG content and recombination rate. The number of SNPs per window also varied but was less dependent of known factors such as gene density, missing rate or recombination (R2=0.48). When we divided the samples in four groups, Asian wild boar (ASWB), Asian domestics (ASDM), European wild boar (EUWB) and European domestics (EUDM), we found a marked correlation in allele frequencies between domestics and wild boars within Asia and within Europe, but not across continents, due to the large evolutive distance between pigs of both continents (~1.2 MYA). In general, the porcine species showed a small percentage of SNPs exclusive of each population group. EUWB and EUDM were predicted to harbor a larger fraction of potentially deleterious mutations, according to the SIFT algorithm, than Asian samples, perhaps a result of background selection being less effective due to a lower effective population size in Europe.
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Affiliation(s)
- Erica Bianco
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Universitat Autònoma de Barcelona, Department of Animal Science, Bellaterra, Spain
| | - Bruno Nevado
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Universitat Autònoma de Barcelona, Department of Animal Science, Bellaterra, Spain
| | | | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Universitat Autònoma de Barcelona, Department of Animal Science, Bellaterra, Spain
- Institut Català de Recerca I Estudis Avançats (ICREA), Carrer de Lluís Companys 23, Barcelona, Spain
- * E-mail:
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Ramírez O, Burgos-Paz W, Casas E, Ballester M, Bianco E, Olalde I, Santpere G, Novella V, Gut M, Lalueza-Fox C, Saña M, Pérez-Enciso M. Genome data from a sixteenth century pig illuminate modern breed relationships. Heredity (Edinb) 2015; 114:175-84. [PMID: 25204303 PMCID: PMC4815627 DOI: 10.1038/hdy.2014.81] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/09/2014] [Accepted: 08/06/2014] [Indexed: 01/16/2023] Open
Abstract
Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.
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Affiliation(s)
- O Ramírez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - W Burgos-Paz
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - E Casas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
| | - M Ballester
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - E Bianco
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - I Olalde
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - G Santpere
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - V Novella
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M Gut
- Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, Spain
| | - C Lalueza-Fox
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - M Saña
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Carrer de Lluís Companys 23, Barcelona, Spain
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Fernández AI, Muñoz M, Alves E, Folch JM, Noguera JL, Enciso MP, Rodríguez MDC, Silió L. Recombination of the porcine X chromosome: a high density linkage map. BMC Genet 2014; 15:148. [PMID: 25526890 PMCID: PMC4293812 DOI: 10.1186/s12863-014-0148-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/08/2014] [Indexed: 01/22/2023] Open
Abstract
Background Linkage maps are essential tools for the study of several topics in genome biology. High density linkage maps for the porcine autosomes have been constructed exploiting the high density data provided by the PorcineSNP60 BeadChip. However, a high density SSCX linkage map has not been reported up to date. The aim of the current study was to build an accurate linkage map of SSCX to provide precise estimates of recombination rates along this chromosome and creating a new tool for QTL fine mapping. Results A female-specific high density linkage map was built for SSCX using Sscrofa10.2 annotation. The total length of this chromosome was 84.61 cM; although the average recombination rate was 0.60 cM/Mb, both cold and hot recombination regions were identified. A Bayesian probabilistic to genetic groups and revealed that the animals used in the current study for linkage map construction were likely to be carriers of X chromosomes of European origin. Finally, the newly generated linkage map was used to fine-map a QTL at 16 cM for intramuscular fat content (IMF) measured on longissimus dorsi. The sulfatase isozyme S gene constitutes a functional and positional candidate gene underlying the QTL effect. Conclusions The current study presents for the first time a high density linkage map for SSCX and supports the presence of cold and hot recombination intervals along this chromosome. The large cold recombination region in the central segment of the chromosome is not likely to be due to structural differences between X chromosomes of European and Asian origin. In addition, the newly generated linkage map has allowed us to fine-map a QTL on SSCX for fat deposition. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0148-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana I Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain.
| | - María Muñoz
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain. .,The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, EH25 9RG, UK.
| | - Estefânia Alves
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain.
| | - Josep María Folch
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, 08193, Spain. .,Present Address: Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autonoma Barcelona, Bellaterra, 08193, Spain.
| | - Jose Luis Noguera
- Genètica i Millora Animal, IRTA, Av. Alcalde Rovira Roure, 191, Lleida, 25198, Spain.
| | - Miguel Pérez Enciso
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, 08193, Spain. .,Present Address: Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autonoma Barcelona, Bellaterra, 08193, Spain. .,Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.
| | | | - Luis Silió
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain.
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da Silva EC, de Jager N, Burgos-Paz W, Reverter A, Perez-Enciso M, Roura E. Characterization of the porcine nutrient and taste receptor gene repertoire in domestic and wild populations across the globe. BMC Genomics 2014; 15:1057. [PMID: 25471201 PMCID: PMC4302110 DOI: 10.1186/1471-2164-15-1057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/13/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The oral GPCR nutrient/taste receptor gene repertoire consists of the Tas1r family (sweet and umami tastes), the Tas2r family (bitter taste) as well as several other potential candidate sensors of amino acids, peptones and fatty acids. Taste/nutrient receptors play a fundamental role in survival through the identification of dietary nutrients or potentially toxic compounds. In humans and rodents some variations in taste sensitivity have been related to receptor polymorphisms. Some allelic variants, in turn, have been linked to the adaptation to specific geographical locations and dietary regimes. In contrast, the porcine taste/nutrient receptor repertoire has been only partially characterized and limited information on genetic variation across breeds and geographical location exists. The present study aims at filling this void which in turn will form the bases for future improvements in pig nutrition. RESULTS Our results show that the pig oral repertoire of taste/nutrient receptors consists of at least 28 receptor genes with significant transcription measured for 27. When compared to humans and rodents, the porcine gene sequences encoding sensors for carbohydrates, amino acids and fatty acids were highly conserved whilst the bitter taste gene family (known as Tas2rs) showed high divergence. We identified 15 porcine Tas2rs of which 13 are orthologous to human sequences. The single nucleotide polymorphism (SNP) sequence analysis using 79 pig genomes, representing 14 different breeds/populations, revealed that the Tas2r subset had higher variability (average π =2.8 × 10-3) than for non-bitter taste genes (π =1.2-1.5 × 10-3). In addition, our results show that the difference in nutrient receptor genes between Asian and European breeds accounts for only a small part of the variability, which is in contrast with previous findings involving genome wide data. CONCLUSIONS We have defined twenty-eight oral nutrient sensing related genes for the pig. The homology with the human repertoire is high for the porcine non-bitter taste gene repertoire and low for the porcine Tas2r repertoire. Our data suggests that bitter taste is a plastic trait, possibly associated with the ability of pigs to adapt to diverse environments and that may be subject to balancing selection.
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Affiliation(s)
| | | | | | | | - Miguel Perez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Bellaterra, Spain.
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Ramos-Onsins SE, Burgos-Paz W, Manunza A, Amills M. Mining the pig genome to investigate the domestication process. Heredity (Edinb) 2014; 113:471-84. [PMID: 25074569 PMCID: PMC4815588 DOI: 10.1038/hdy.2014.68] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 05/22/2014] [Accepted: 06/09/2014] [Indexed: 12/11/2022] Open
Abstract
Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication.
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Affiliation(s)
- S E Ramos-Onsins
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autònoma Barcelona, Bellaterra, Spain
| | - W Burgos-Paz
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autònoma Barcelona, Bellaterra, Spain
| | - A Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autònoma Barcelona, Bellaterra, Spain
| | - M Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autònoma Barcelona, Bellaterra, Spain
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Montenegro M, Llambí S, Castro G, Barlocco N, Vadell A, Landi V, Delgado JV, Martínez A. Genetic characterization of Uruguayan Pampa Rocha pigs with microsatellite markers. Genet Mol Biol 2014; 38:48-54. [PMID: 25983624 PMCID: PMC4415558 DOI: 10.1590/s1415-475738120140146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/25/2014] [Indexed: 12/05/2022] Open
Abstract
In this study, we genetically characterized the Uruguayan pig breed Pampa Rocha.
Genetic variability was assessed by analyzing a panel of 25 microsatellite markers
from a sample of 39 individuals. Pampa Rocha pigs showed high genetic variability
with observed and expected heterozygosities of 0.583 and 0.603, respectively. The
mean number of alleles was 5.72. Twenty-four markers were polymorphic, with 95.8% of
them in Hardy Weinberg equilibrium. The level of endogamy was low (FIS =
0.0475). A factorial analysis of correspondence was used to assess the genetic
differences between Pampa Rocha and other pig breeds; genetic distances were
calculated, and a tree was designed to reflect the distance matrix. Individuals were
also allocated into clusters. This analysis showed that the Pampa Rocha breed was
separated from the other breeds along the first and second axes. The
neighbour-joining tree generated by the genetic distances DA showed
clustering of Pampa Rocha with the Meishan breed. The allocation of individuals to
clusters showed a clear separation of Pampa Rocha pigs. These results provide
insights into the genetic variability of Pampa Rocha pigs and indicate that this
breed is a well-defined genetic entity.
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Affiliation(s)
- M Montenegro
- Department of Animal Breeding and Genetics, Veterinary School, University of the Republic, Montevideo, Uruguay
| | - S Llambí
- Department of Animal Breeding and Genetics, Veterinary School, University of the Republic, Montevideo, Uruguay
| | - G Castro
- Department of Farm Animals, Veterinary School, University of the Republic, Montevideo, Uruguay
| | - N Barlocco
- Department of Farm Animals, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - A Vadell
- Department of Farm Animals, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - V Landi
- Department of Genetics, Veterinary School, University of Cordoba, Cordoba, Spain
| | - J V Delgado
- Department of Genetics, Veterinary School, University of Cordoba, Cordoba, Spain
| | - A Martínez
- Department of Genetics, Veterinary School, University of Cordoba, Cordoba, Spain
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