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Wang Y, Gou Y, Yuan R, Zou Q, Zhang X, Zheng T, Fei K, Shi R, Zhang M, Li Y, Gong Z, Luo C, Xiong Y, Shan D, Wei C, Shen L, Tang G, Li M, Zhu L, Li X, Jiang Y. A chromosome-level genome of Chenghua pig provides new insights into the domestication and local adaptation of pigs. Int J Biol Macromol 2024; 270:131796. [PMID: 38677688 DOI: 10.1016/j.ijbiomac.2024.131796] [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: 07/26/2023] [Revised: 03/24/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
As a country with abundant genetic resources of pigs, the domestication history of pigs in China and the adaptive evolution of Chinese pig breeds at different latitudes have rarely been elucidated at the genome-wide level. To fill this gap, we first assembled a high-quality chromosome-level genome of the Chenghua pig and used it as a benchmark to analyse the genomes of 272 samples from three genera of three continents. The divergence of the three species belonging to three genera, Phacochoerus africanus, Potamochoerus porcus, and Sus scrofa, was assessed. The introgression of pig breeds redefined that the migration routes were basically from southern China to central and southwestern China, then spread to eastern China, arrived in northern China, and finally reached Europe. The domestication of pigs in China occurred ∼12,000 years ago, earlier than the available Chinese archaeological domestication evidence. In addition, FBN1 and NR6A1 were identified in our study as candidate genes related to extreme skin thickness differences in Eurasian pig breeds and adaptive evolution at different latitudes in Chinese pig breeds, respectively. Our study provides a new resource for the pig genomic pool and refines our understanding of pig genetic diversity, domestication, migration, and adaptive evolution at different latitudes.
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Affiliation(s)
- Yifei Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yuwei Gou
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Rong Yuan
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan 610081, China
| | - Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xukun Zhang
- Academy for Engineering and Technology, Fudan University, Shanghai 200433, China
| | - Ting Zheng
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Kaixin Fei
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Rui Shi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Mei Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Zhengyin Gong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Chenggang Luo
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan 610081, China
| | - Ying Xiong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Dai Shan
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Chenyang Wei
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China.
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Du H, Liu Z, Lu SY, Jiang L, Zhou L, Liu JF. Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed. BMC Genomics 2024; 25:331. [PMID: 38565992 PMCID: PMC10986048 DOI: 10.1186/s12864-024-10259-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown. RESULTS Through whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness. CONCLUSIONS Our research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.
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Affiliation(s)
- Heng Du
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Zhen Liu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Shi-Yu Lu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Li Jiang
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Lei Zhou
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China.
| | - Jian-Feng Liu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China.
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3
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Du H, Diao C, Zhuo Y, Zheng X, Hu Z, Lu S, Jin W, Zhou L, Liu JF. Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity. Genomics 2024; 116:110782. [PMID: 38176574 DOI: 10.1016/j.ygeno.2024.110782] [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: 10/03/2023] [Revised: 12/27/2023] [Accepted: 01/01/2024] [Indexed: 01/06/2024]
Abstract
There is an increasing understanding that a reference genome representing an individual cannot capture all the gene repertoire of a species. Here, we conduct a population-scale missing sequences detection of Chinese domestic pigs using whole-genome sequencing data from 534 individuals. We identify 132.41 Mb of sequences absent in the reference assembly, including eight novel genes. In particular, the breeds spread in Chinese high-altitude regions perform significantly different frequencies of new sequences in promoters than other breeds. Furthermore, we dissect the role of non-coding variants and identify a novel sequence inserted in the 3'UTR of the FMO3 gene, which may be associated with the intramuscular fat phenotype. This novel sequence could be a candidate marker for meat quality. Our study provides a comprehensive overview of the missing sequences in Chinese domestic pigs and indicates that this dataset is a valuable resource for understanding the diversity and biology of pigs.
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Affiliation(s)
- Heng Du
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Chenguang Diao
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Yue Zhuo
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xianrui Zheng
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhengzheng Hu
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shiyu Lu
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenjiao Jin
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lei Zhou
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Jian-Feng Liu
- State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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A V, Kumar A, Mahala S, Chandra Janga S, Chauhan A, Mehrotra A, Kumar De A, Ranjan Sahu A, Firdous Ahmad S, Vempadapu V, Dutt T. Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds. Gene 2024; 893:147950. [PMID: 37918549 DOI: 10.1016/j.gene.2023.147950] [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: 08/04/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.
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Affiliation(s)
- Vani A
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Amit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India.
| | - Sudarshan Mahala
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Sarath Chandra Janga
- Luddy School of Informatics, Computing, and Engineering, Indiana University, IUPUI, Indianapolis, IN, USA
| | - Anuj Chauhan
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
| | | | - Arun Kumar De
- Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Amiya Ranjan Sahu
- Central Coastal Agricultural Research Institute, Old Goa, Goa, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Varshini Vempadapu
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
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5
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Poklukar K, Mestre C, Škrlep M, Čandek-Potokar M, Ovilo C, Fontanesi L, Riquet J, Bovo S, Schiavo G, Ribani A, Muñoz M, Gallo M, Bozzi R, Charneca R, Quintanilla R, Kušec G, Mercat MJ, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Servin B. A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits. Genet Sel Evol 2023; 55:88. [PMID: 38062367 PMCID: PMC10704730 DOI: 10.1186/s12711-023-00858-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments. RESULTS Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene. CONCLUSIONS In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.
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Affiliation(s)
- Klavdija Poklukar
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000, Ljubljana, Slovenia
| | - Camille Mestre
- GenPhySE, Université de Toulouse, INRAE, INP, ENVT, 31320, Castanet-Tolosan, France
| | - Martin Škrlep
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000, Ljubljana, Slovenia
| | | | - Cristina Ovilo
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña Km. 7,5, 28040, Madrid, Spain
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRAE, INP, ENVT, 31320, Castanet-Tolosan, France
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Maria Muñoz
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña Km. 7,5, 28040, Madrid, Spain
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Rome, Italy
| | - Ricardo Bozzi
- DAGRI-Animal Science Section, Università Di Firenze, Via Delle Cascine 5, 50144, Florence, Italy
| | - Rui Charneca
- MED- Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, 7006-554, Évora, Portugal
| | - Raquel Quintanilla
- Programa de Genética y Mejora Animal, IRTA, Torre Marimon, Caldes de Montbui, 08140, Barcelona, Spain
| | - Goran Kušec
- Faculty of Agrobiotechnical Sciences, University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia
| | - Marie-José Mercat
- IFIP Institut du Porc, La Motte au Vicomte, BP 35104, 35651, Le Rheu Cedex, France
| | - Christoph Zimmer
- Bauerliche Erzeugergemeinschaft Schwäbisch Hall, Haller Str. 20, 74549, Wolpertshausen, Germany
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, 82317, Baisogala, Lithuania
| | - Jose P Araujo
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, 4990-706, Ponte de Lima, Portugal
| | - Čedomir Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, 11080, Belgrade-Zemun, Serbia
| | - Radomir Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080, Belgrade-Zemun, Serbia
| | - Danijel Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INP, ENVT, 31320, Castanet-Tolosan, France.
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6
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Benjamin NR, Crooijmans RPMA, Jordan LR, Bolt CR, Schook LB, Schachtschneider KM, Groenen MAM, Roca AL. Swine global genomic resources: insights into wild and domesticated populations. Mamm Genome 2023; 34:520-530. [PMID: 37805667 DOI: 10.1007/s00335-023-10012-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/25/2023] [Indexed: 10/09/2023]
Abstract
Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids. Collecting samples from diverse populations of suids is resource intensive and may negatively impact endangered populations. Here we catalog extensive tissue and DNA samples from suids in collections in both Europe and North America. We include samples that have previously been used for whole genome sequencing, targeted DNA sequencing, RNA sequencing, and reduced representation bisulfite sequencing (RRBS). This work provides an important centralized resource for researchers who wish to access published databases.
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Affiliation(s)
- Neal R Benjamin
- The Program in Ecology, Evolution and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Luke R Jordan
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Courtni R Bolt
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Chicago, Chicago, IL, USA
| | - Kyle M Schachtschneider
- National Center for Supercomputing Applications, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA.
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Alfred L Roca
- The Program in Ecology, Evolution and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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7
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Shen Q, Gong W, Pan X, Cai J, Jiang Y, He M, Zhao S, Li Y, Yuan X, Li J. Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs. Int J Mol Sci 2023; 24:16205. [PMID: 38003395 PMCID: PMC10671760 DOI: 10.3390/ijms242216205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs with diverse functions, and previous studies have reported that circRNAs are involved in the growth and development of pigs. However, studies about porcine circRNAs over the past few years have focused on a limited number of tissues. Based on 215 publicly available RNA sequencing (RNA-seq) samples, we conducted a comprehensive analysis of circRNAs in nine pig tissues, namely, the gallbladder, heart, liver, longissimus dorsi, lung, ovary, pituitary, skeletal muscle, and spleen. Here, we identified a total of 82,528 circRNAs and discovered 3818 novel circRNAs that were not reported in the CircAtlas database. Moreover, we obtained 492 housekeeping circRNAs and 3489 tissue-specific circRNAs. The housekeeping circRNAs were enriched in signaling pathways regulating basic biological tissue activities, such as chromatin remodeling, nuclear-transcribed mRNA catabolic process, and protein methylation. The tissue-specific circRNAs were enriched in signaling pathways related to tissue-specific functions, such as muscle system process in skeletal muscle, cilium organization in pituitary, and cortical cytoskeleton in ovary. Through weighted gene co-expression network analysis, we identified 14 modules comprising 1377 hub circRNAs. Additionally, we explored circRNA-miRNA-mRNA networks to elucidate the interaction relationships between tissue-specific circRNAs and tissue-specific genes. Furthermore, our conservation analysis revealed that 19.29% of circRNAs in pigs shared homologous positions with their counterparts in humans. In summary, this extensive profiling of housekeeping, tissue-specific, and co-expressed circRNAs provides valuable insights into understanding the molecular mechanisms of pig transcriptional expression, ultimately deepening our understanding of genetic and biological processes.
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Affiliation(s)
- Qingpeng Shen
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Wentao Gong
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Xiangchun Pan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Jiali Cai
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Yao Jiang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA 6149, Australia
| | - Mingran He
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Shanghui Zhao
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Yipeng Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Xiaolong Yuan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Jiaqi Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
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8
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Sun L, Qu K, Liu Y, Ma X, Chen N, Zhang J, Huang B, Lei C. Assessing genomic diversity and selective pressures in Bashan cattle by whole-genome sequencing data. Anim Biotechnol 2023; 34:835-846. [PMID: 34762022 DOI: 10.1080/10495398.2021.1998094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Specific ecological environments and domestication have continuously influenced the physiological characteristics of Chinese indigenous cattle. Among them, Bashan cattle belongs to one of the indigenous breeds. However, the genomic diversity of Bashan cattle is still unknown. Published whole-genome sequencing (WGS) data of 13 Bashan cattle and 48 worldwide cattle were used to investigate the genetic composition and selection characteristics of Bashan cattle. The population structure analysis revealed that Bashan cattle harbored ancestries with East Asian taurine and Chinese indicine. Genetic diversity analysis implied the relatively high genomic diversity in Bashan cattle. Through the identification of containing >5 nsSNPs or frameshift mutations genes in Bashan cattle, a large number of pathways related to sensory perception were discovered. CLR, θπ ratio, FST, and XP-EHH methods were used to detect the candidate signatures of positive selection in Bashan cattle. Among the identified genes, most of the enriched signal pathways were related to environmental information processing, biological systems, and metabolism. We mainly reported genes related to the nervous system (HCN1, KATNA1, FSTL1, GRIK2, and CPLX2), immune (CD244, SLAMF1, LY9, and CD48), and reproduction (AKR1C1, AKR1C3, AKR1C4, and TUSC3). Our findings will be significant in understanding the molecular basis underlying phenotypic variation of breed-related traits and improving productivity in Bashan cattle.
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Affiliation(s)
- Luyang Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Yangkai Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohui Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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9
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Walker LR, Vu HL, Montooth KL, Ciobanu DC. Functional and evolutionary analysis of host Synaptogyrin-2 in porcine circovirus type 2 susceptibility. PLoS Genet 2023; 19:e1011029. [PMID: 38011217 PMCID: PMC10703400 DOI: 10.1371/journal.pgen.1011029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/07/2023] [Accepted: 10/24/2023] [Indexed: 11/29/2023] Open
Abstract
Mammalian evolution has been influenced by viruses for millions of years, leaving signatures of adaptive evolution within genes encoding for viral interacting proteins. Synaptogyrin-2 (SYNGR2) is a transmembrane protein implicated in promoting bacterial and viral infections. A genome-wide association study of pigs experimentally infected with porcine circovirus type 2b (PCV2b) uncovered a missense mutation (SYNGR2 p.Arg63Cys) associated with viral load. In this study, CRISPR/Cas9-mediated gene editing of the porcine kidney 15 (PK15, wtSYNGR2+p.63Arg) cell line generated clones homozygous for the favorable SYNGR2 p.63Cys allele (emSYNGR2+p.63Cys). Infection of edited clones resulted in decreased PCV2 replication compared to wildtype PK15 (P<0.05), with consistent effects across genetically distinct PCV2b and PCV2d isolates. Sequence analyses of wild and domestic pigs (n>700) revealed the favorable SYNGR2 p.63Cys allele is unique to domestic pigs and more predominant in European than Asian breeds. A haplotype defined by the SYNGR2 p.63Cys allele was likely derived from an ancestral haplotype nearly fixed within European (0.977) but absent from Asian wild boar. We hypothesize that the SYNGR2 p.63Cys allele arose post-domestication in ancestral European swine. Decreased genetic diversity in homozygotes for the SYNGR2 p.63Cys allele compared to SYNGR2 p.63Arg, corroborates a rapid increase in frequency of SYGNR2 p.63Cys via positive selection. Signatures of adaptive evolution across mammalian species were also identified within SYNGR2 intraluminal loop domains, coinciding with the location of SYNGR2 p.Arg63Cys. Therefore, SYNGR2 may reflect a novel component of the host-virus evolutionary arms race across mammals with SYNGR2 p.Arg63Cys representing a species-specific example of putative adaptive evolution.
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Affiliation(s)
- Lianna R. Walker
- Animal Science Department, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Hiep L. Vu
- Animal Science Department, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Kristi L. Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Daniel C. Ciobanu
- Animal Science Department, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
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10
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Fabbri G, Molinaro L, Mucci N, Pagani L, Scandura M. Anthropogenic hybridization and its influence on the adaptive potential of the Sardinian wild boar (Sus scrofa meridionalis). J Appl Genet 2023; 64:521-530. [PMID: 37369962 PMCID: PMC10457222 DOI: 10.1007/s13353-023-00763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
The wild boar (Sus scrofa meridionalis) arrived in Sardinia with the first human settlers in the early Neolithic with the potential to hybridize with the domestic pig (S. s. domesticus) throughout its evolution on the island. In this paper, we investigated the possible microevolutionary effects of such introgressive hybridization on the present wild boar population, comparing Sardinian wild specimens with several commercial pig breeds and Sardinian local pigs, along with a putatively unadmixed wild boar population from Central Italy, all genotyped with a medium density SNP chip. We first aimed at identifying hybrids in the population using different approaches, then examined genomic regions enriched for domestic alleles in the hybrid group, and finally we applied two methods to find regions under positive selection to possibly highlight instances of domestic adaptive introgression into a wild population. We found three hybrids within the Sardinian sample (3.1% out of the whole dataset). We reported 11 significant windows under positive selection with a method that looks for overly differentiated loci in the target population, compared with other two populations. We also identified 82 genomic regions with signs of selection in the domestic pig but not in the wild boar, two of which overlapped with genomic regions enriched for domestic alleles in the hybrid pool. Genes in these regions can be linked with reproductive success. Given our results, domestic introgression does not seem to be pervasive in the Sardinian wild boar. Nevertheless, we suggest monitoring the possible spread of advantageous domestic alleles in the coming years.
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Affiliation(s)
- Giulia Fabbri
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2A, 07100, Sassari, Italy.
| | - Ludovica Molinaro
- Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell'Emilia, Bologna, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131, Padua, Italy
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2A, 07100, Sassari, Italy
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11
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Wang L, Piao Y, Guo F, Wei J, Chen Y, Dai X, Zhang X. Current progress of pig models for liver cancer research. Biomed Pharmacother 2023; 165:115256. [PMID: 37536038 DOI: 10.1016/j.biopha.2023.115256] [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: 05/17/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
Preclinical trials play critical roles in assessing the safety and efficiency of novel therapeutic strategies for human diseases including live cancer. However, most therapeutic strategies that were proved to be effective in preclinical cancer models failed in human clinical trials due to the lack of appropriate disease animal models. Therefore, it is of importance and urgent to develop a precise animal model for preclinical cancer research. Liver cancer is one of the most frequently diagnosed cancers with low 5-year survival rate. Recently, porcine attracted increasing attentions as animal model in biomedical research. Porcine liver cancer model may provide a promising platform for biomedical research due to their similarities to human being in body size, anatomical characteristics, physiology and pathophysiology. In this review, we comprehensively summarized and discussed the advantages and disadvantages, rationale, current status and progress of pig models for liver cancer research.
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Affiliation(s)
- Luyao Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, China; National-Local Joint Engineering Laboratory of Animal Models for Human Disease, First Hospital of Jilin University, Changchun, China
| | - Yuexian Piao
- Invasive Technology Nursing Platform, First Hospital of Jilin University, Changchun, China
| | - Fucheng Guo
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, China; National-Local Joint Engineering Laboratory of Animal Models for Human Disease, First Hospital of Jilin University, Changchun, China
| | - Jiarui Wei
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, China; National-Local Joint Engineering Laboratory of Animal Models for Human Disease, First Hospital of Jilin University, Changchun, China
| | - Yurong Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, China; National-Local Joint Engineering Laboratory of Animal Models for Human Disease, First Hospital of Jilin University, Changchun, China
| | - Xiangpeng Dai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, China; National-Local Joint Engineering Laboratory of Animal Models for Human Disease, First Hospital of Jilin University, Changchun, China.
| | - Xiaoling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, China; National-Local Joint Engineering Laboratory of Animal Models for Human Disease, First Hospital of Jilin University, Changchun, China.
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12
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Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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13
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Tong X, Chen D, Hu J, Lin S, Ling Z, Ai H, Zhang Z, Huang L. Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences. Nat Commun 2023; 14:5126. [PMID: 37612277 PMCID: PMC10447580 DOI: 10.1038/s41467-023-40434-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/27/2023] [Indexed: 08/25/2023] Open
Abstract
High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retrieve 207 resequencing datasets, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures, amounting to 1096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genomic selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.
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Affiliation(s)
- Xinkai Tong
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
- College of Life Sciences, Jiangxi Normal University, NanChang, Jiangxi Province, PR China
| | - Dong Chen
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Jianchao Hu
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Shiyao Lin
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Ziqi Ling
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Huashui Ai
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China
| | - Zhiyan Zhang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China.
| | - Lusheng Huang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, PR China.
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14
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Razmaitė V, Šiukščius A, Marašinskienė Š. Cranial Morphology of Lithuanian Indigenous Wattle Pigs and Their Hybrids with Wild Boar. Animals (Basel) 2023; 13:ani13091453. [PMID: 37174490 PMCID: PMC10177289 DOI: 10.3390/ani13091453] [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: 03/15/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
The diversity of domestic pig breeds and their hybridization increases the variety of phenotypes expressed in hybrids. The aim of this study was to quantify the differences of cranial morphologies between local Lithuanian Indigenous Wattle pigs and theirhybrids with wild boar. A total of sixteen craniometric measurements were performed on the lateral, ventral and dorsal sides of 71 skulls of Lithuanian Indigenous Wattle pigs and their hybrids, including 1/4 wild boar (WB), 1/2 wild boar and 3/4 wild boar genotypes. The weight of the skull was affected by the genotype, live weight and sex of the animal. The size of the skull, particularly related to skull length parameters, increased consistently with the increase of the wild boar proportion in the hybrids. However, the Sus scrofa genotype did not affect the skull height. Clear discrimination was possible between the local Lithuanian breed pigs and their hybrids with different proportions of wild boar and between individual groups of hybrids. The most correct classification was determined on the basis of the overall and length parameters of the crania. This could contribute to better management and utilization of hybrids.
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Affiliation(s)
- Violeta Razmaitė
- Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, 82317 Baisogala, Lithuania
| | - Artūras Šiukščius
- Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, 82317 Baisogala, Lithuania
| | - Šarūnė Marašinskienė
- Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, 82317 Baisogala, Lithuania
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15
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Petrelli S, Buglione M, Rivieccio E, Ricca E, Baccigalupi L, Scala G, Fulgione D. Reprogramming of the gut microbiota following feralization in Sus scrofa. Anim Microbiome 2023; 5:14. [PMID: 36823657 PMCID: PMC9951470 DOI: 10.1186/s42523-023-00235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Wild boar has experienced several evolutionary trajectories from which domestic (under artificial selection) and the feral pig (under natural selection) originated. Strong adaptation deeply affects feral population's morphology and physiology, including the microbiota community. The gut microbiota is generally recognized to play a crucial role in maintaining host health and metabolism. To date, it is unclear whether feral populations' phylogeny, development stages or lifestyle have the greatest impact in shaping the gut microbiota, as well as how this can confer adaptability to new environments. Here, in order to deepen this point, we characterized the gut microbiota of feral population discriminating between juvenile and adult samples, and we compared it to the microbiota structure of wild boar and domestic pig as the references. Gut microbiota composition was estimated through the sequencing of the partial 16S rRNA gene by DNA metabarcoding and High Throughput Sequencing on DNA extracted from fecal samples. RESULTS The comparison of microbiota communities among the three forms showed significant differences. The feral form seems to carry some bacteria of both domestic pigs, derived from its ancestral condition, and wild boars, probably as a sign of a recent re-adaptation strategy to the natural environment. In addition, interestingly, feral pigs show some exclusive bacterial taxa, also suggesting an innovative nature of the evolutionary trajectories and an ecological segregation in feral populations, as already observed for other traits. CONCLUSIONS The feral pig showed a significant change between juvenile and adult microbiota suggesting an influence of the wild environment in which these populations segregate. However, it is important to underline that we certainly cannot overlook that these variations in the structure of the microbiota also depended on the different development stages of the animal, which in fact influence the composition of the intestinal microbiota. Concluding, the feral pigs represent a new actor living in the same geographical space as the wild boars, in which its gut microbial structure suggests that it is mainly the result of environmental segregation, most different from its closest relative. This gives rise to interesting fields of exploration regarding the changed ecological complexity and the consequent evolutionary destiny of the animal communities involved in this phenomenon.
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Affiliation(s)
- Simona Petrelli
- grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, NA Italy
| | - Maria Buglione
- grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, NA Italy
| | - Eleonora Rivieccio
- grid.4691.a0000 0001 0790 385XDepartment of Humanities, University of Naples Federico II, Via Porta Di Massa 1, 80133 Naples, Italy
| | - Ezio Ricca
- grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, NA Italy ,grid.4691.a0000 0001 0790 385XTask Force On Microbiome Studies, University of Naples Federico II, 80100 Naples, NA Italy
| | - Loredana Baccigalupi
- grid.4691.a0000 0001 0790 385XDepartment of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, NA Italy
| | - Giovanni Scala
- grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, NA Italy
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126, Naples, NA, Italy. .,Task Force On Microbiome Studies, University of Naples Federico II, 80100, Naples, NA, Italy.
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16
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Lowe JWE. Humanising and dehumanising pigs in genomic and transplantation research. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:66. [PMID: 36417007 PMCID: PMC9684229 DOI: 10.1007/s40656-022-00545-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Biologists who work on the pig (Sus scrofa) take advantage of its similarity to humans by constructing the inferential and material means to traffic data, information and knowledge across the species barrier. Their research has been funded due to its perceived value for agriculture and medicine. Improving selective breeding practices, for instance, has been a driver of genomics research. The pig is also an animal model for biomedical research and practice, and is proposed as a source of organs for cross-species transplantation: xenotransplantation. Genomics research has informed transplantation biology, which has itself motivated developments in genomics. Both have generated models of correspondences between the genomes of pigs and humans. Concerning genomics, I detail how researchers traverse species boundaries to develop representations of the pig genome, alongside ensuring that such representations are sufficiently porcine. In transplantation biology, the representations of the genomes of humans and pigs are used to detect and investigate immunologically-pertinent differences between the two species. These key differences can then be removed, to 'humanise' donor pigs so that they can become a safe and effective source of organs. In both of these endeavours, there is a tension between practices that 'humanise' the pig (or representations thereof) through using resources from human genomics, and the need to 'dehumanise' the pig to maintain distinctions for legal, ethical and scientific reasons. This paper assesses the ways in which this tension has been managed, observing the differences between its realisations across comparative pig genomics and transplantation biology, and considering the consequences of this.
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Affiliation(s)
- James W E Lowe
- Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons' Hall, High School Yards, Edinburgh, EH1 1LZ, UK.
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17
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Xie HB, Yan C, Adeola AC, Wang K, Huang CP, Xu MM, Qiu Q, Yin X, Fan CY, Ma YF, Yin TT, Gao Y, Deng JK, Okeyoyin AO, Oluwole OO, Omotosho O, Okoro VMO, Omitogun OG, Dawuda PM, Olaogun SC, Nneji LM, Ayoola AO, Sanke OJ, Luka PD, Okoth E, Lekolool I, Mijele D, Bishop RP, Han J, Wang W, Peng MS, Zhang YP. African Suid Genomes Provide Insights into the Local Adaptation to Diverse African Environments. Mol Biol Evol 2022; 39:6840307. [PMID: 36413509 PMCID: PMC9733430 DOI: 10.1093/molbev/msac256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/21/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
African wild suids consist of several endemic species that represent ancient members of the family Suidae and have colonized diverse habitats on the African continent. However, limited genomic resources for African wild suids hinder our understanding of their evolution and genetic diversity. In this study, we assembled high-quality genomes of a common warthog (Phacochoerus africanus), a red river hog (Potamochoerus porcus), as well as an East Asian Diannan small-ear pig (Sus scrofa). Phylogenetic analysis showed that common warthog and red river hog diverged from their common ancestor around the Miocene/Pliocene boundary, putatively predating their entry into Africa. We detected species-specific selective signals associated with sensory perception and interferon signaling pathways in common warthog and red river hog, respectively, which contributed to their local adaptation to savannah and tropical rainforest environments, respectively. The structural variation and evolving signals in genes involved in T-cell immunity, viral infection, and lymphoid development were identified in their ancestral lineage. Our results provide new insights into the evolutionary histories and divergent genetic adaptations of African suids.
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Affiliation(s)
| | | | | | | | | | - Ming-Min Xu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710129, China
| | - Xue Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Chen-Yu Fan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yun-Fei Ma
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Jia-Kun Deng
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Agboola O Okeyoyin
- National Park Service Headquarter, Federal Capital Territory, Abuja 900108, Nigeria
| | - Olufunke O Oluwole
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Oladipo Omotosho
- Department of Veterinary Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Victor M O Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri 460114, Nigeria
| | - Ofelia G Omitogun
- Department of Animal Sciences, Obafemi Awolowo University, Ile-Ife 220282, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi 970001, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming 650204, China
| | - Adeola O Ayoola
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming 650204, China
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660213, Nigeria
| | - Pam D Luka
- National Veterinary Research Institute, Vom 930103, Nigeria
| | - Edward Okoth
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | | | | | - Richard P Bishop
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | | | - Wen Wang
- Corresponding authors: E-mails: ; ; ;
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18
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The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111893. [PMID: 36431028 PMCID: PMC9695872 DOI: 10.3390/life12111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
For more than a decade, next-generation sequencing (NGS) has been emerging as the mainstay of agrigenomics research. High-throughput technologies have made it feasible to facilitate research at the scale and cost required for using this data in livestock research. Scale frameworks of sequencing for agricultural and livestock improvement, management, and conservation are partly attributable to innovative informatics methodologies and advancements in sequencing practices. Genome-wide sequence-based investigations are often conducted worldwide, and several databases have been created to discover the connections between worldwide scientific accomplishments. Such studies are beginning to provide revolutionary insights into a new era of genomic prediction and selection capabilities of various domesticated livestock species. In this concise review, we provide selected examples of the current state of sequencing methods, many of which are already being used in animal genomic studies, and summarize the state of the positive attributes of genome-based research for cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa domesticus), horses (Equus caballus), chickens (Gallus gallus domesticus), and ducks (Anas platyrhyncos). This review also emphasizes the advantageous features of sequencing technologies in monitoring and detecting infectious zoonotic diseases. In the coming years, the continued advancement of sequencing technologies in livestock agrigenomics will significantly influence the sustained momentum toward regulatory approaches that encourage innovation to ensure continued access to a safe, abundant, and affordable food supplies for future generations.
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19
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Current Analytical Methods and Research Trends Are Used to Identify Domestic Pig and Wild Boar DNA in Meat and Meat Products. Genes (Basel) 2022; 13:genes13101825. [PMID: 36292710 PMCID: PMC9601671 DOI: 10.3390/genes13101825] [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: 09/11/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/04/2022] Open
Abstract
The pig, one of the most important livestock species, is a meaningful source of global meat production. It is necessary, however, to prove whether a food product that a discerning customer selects in a store is actually made from pork or venison, or does not contain it at all. The problem of food authenticity is widespread worldwide, and cases of meat adulteration have accelerated the development of food and the identification methods of feed species. It is worth noting that several different molecular biology techniques can identify a porcine component. However, the precise differentiation between wild boar and a domestic pig in meat products is still challenging. This paper presents the current state of knowledge concerning the species identification of the domestic pig and wild boar DNA in meat and its products.
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20
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Horsburgh KA, Gosling AL, Cochrane EE, Kirch PV, Swift JA, McCoy MD. Origins of Polynesian Pigs Revealed by Mitochondrial Whole Genome Ancient DNA. Animals (Basel) 2022; 12:ani12182469. [PMID: 36139328 PMCID: PMC9495175 DOI: 10.3390/ani12182469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/22/2022] Open
Abstract
Simple Summary Retracing the ancient human migration routes in the remote islands of the Pacific relies on robust models of the origins and spread of animals that were commensal to long-distance ocean voyages. Domestic pigs (Sus scrofa) in Polynesia belong to a rare mitochondrial DNA group whose geographic origins are disputed. We report new complete genome ancient DNA that suggests all founding populations of pigs in Polynesia, first settled by people about 2800–700 years ago, can be traced back to northern peninsular Southeast Asia. Abstract Domestic pigs (Sus scrofa) were first transported to Polynesia through a series of long-distance voyages ultimately linked to the Neolithic expansion of Austronesian-speaking people out of Asia. The descendants of the founding pigs belong to a rare mtDNA group referred to as the “Pacific Clade” that may have originated in peninsular or island Southeast Asia. We report the first whole genome mtDNA from domestic pigs from any of the remote islands of the Pacific. In this brief report, we describe the close link we discovered between ancient mtDNA from archaeological specimens from across Polynesia and from that of modern pigs in northern peninsular Southeast Asia, specifically southern China’s Yunnan Province. More complete mtDNA coverage in commensal animals is necessary to improve our picture of the settlement of Polynesia (ca. 2800–700 years before the present) and specify the route, or routes, that pigs took from northern peninsular Southeast Asia.
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Affiliation(s)
- K. Ann Horsburgh
- Department of Anthropology, Southern Methodist University, Dallas, TX 75205, USA
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg 2000, South Africa
- Correspondence:
| | - Anna L. Gosling
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - Ethan E. Cochrane
- Anthropology, School of Social Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Patrick V. Kirch
- Department of Anthropology, University of Hawaii at Mānoa, Honolulu, HI 96822, USA
| | | | - Mark D. McCoy
- Department of Anthropology, Southern Methodist University, Dallas, TX 75205, USA
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21
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Panigrahi M, Kumar H, Saravanan KA, Rajawat D, Sonejita Nayak S, Ghildiyal K, Kaisa K, Parida S, Bhushan B, Dutt T. Trajectory of livestock genomics in South Asia: A comprehensive review. Gene 2022; 843:146808. [PMID: 35973570 DOI: 10.1016/j.gene.2022.146808] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kaiho Kaisa
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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22
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Berghöfer J, Khaveh N, Mundlos S, Metzger J. Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs. BMC Genomics 2022; 23:564. [PMID: 35933356 PMCID: PMC9357325 DOI: 10.1186/s12864-022-08801-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH regions within groups or populations displaying potential signatures of selection requires high-quality SNP data as well as carefully adjusted ROH-defining parameters. In this study, we used a simultaneous testing of rule- and model-based approaches to perform strategic ROH calling in genomic data from different pig populations to detect genomic regions under selection for specific phenotypes. RESULTS Our ROH analysis using a rule-based approach offered by PLINK, as well as a model-based approach run by RZooRoH demonstrated a high efficiency of both methods. It underlined the importance of providing a high-quality SNP set as input as well as adjusting parameters based on dataset and population for ROH calling. Particularly, ROHs ≤ 20 kb were called in a high frequency by both tools, but to some extent covered different gene sets in subsequent analysis of ROH regions common for investigated pig groups. Phenotype associated ROH analysis resulted in regions under potential selection characterizing heritage pig breeds, known to harbour a long-established breeding history. In particular, the selection focus on fitness-related traits was underlined by various ROHs harbouring disease resistance or tolerance-associated genes. Moreover, we identified potential selection signatures associated with ear morphology, which confirmed known candidate genes as well as uncovered a missense mutation in the ABCA6 gene potentially supporting ear cartilage formation. CONCLUSIONS The results of this study highlight the strengths and unique features of rule- and model-based approaches as well as demonstrate their potential for ROH analysis in animal populations. We provide a workflow for ROH detection, evaluating the major steps from filtering for high-quality SNP sets to intersecting ROH regions. Formula-based estimations defining ROHs for rule-based method show its limits, particularly for efficient detection of smaller ROHs. Moreover, we emphasize the role of ROH detection for the identification of potential footprints of selection in pigs, displaying their breed-specific characteristics or favourable phenotypes.
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Affiliation(s)
- Jan Berghöfer
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Nadia Khaveh
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Stefan Mundlos
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Charité-Universitätsmedizin Berlin, BCRT, Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Julia Metzger
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany.
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23
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Zheng M, Guo T, Yang B, Zhang Z, Huang L. Origin, evolution, and tissue-specific functions of the porcine repetitive element 1. Genet Sel Evol 2022; 54:54. [PMID: 35896967 PMCID: PMC9327148 DOI: 10.1186/s12711-022-00745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Background The porcine repetitive element 1 (PRE1) is the most abundant short interspersed nuclear element (SINE) in the Sus scrofa genome and it has been suggested that some PRE1 can have regulatory functions. The million copies of PRE1 in the porcine genome have accumulated abundant CpG dinucleotides and unique structural variations, such as direct repeats and patterns of sequence degeneration. The aims of this study were to analyse these structural variations to trace the origin and evolutionary pattern of PRE1 and to investigate potential methylation-related functions of PRE1 based on methylation patterns of PRE1 CpG dinucleotides in different tissues. Results We investigated the evolutionary trajectory of PRE1 and found that PRE1 originated from the ancestral CHRS-S1 family through three main successive partial duplications. We found that the partial duplications and deletions of PRE1 were likely due to RNA splicing events during retrotransposition. Functionally, correlation analysis showed that the methylation levels of 103 and 261 proximal PRE1 were, respectively, negatively and positively correlated with the expression levels of neighboring genes (Spearman correlation, P < 0.01). Further epigenomic analysis revealed that, in the testis, demethylation of proximal PRE1 in the HORMAD1 and HACD3 genes had tissue-specific enhancer and promoter functions, while in the muscle, methylation of proximal PRE1 repeats in the TCEA3 gene had an enhancer function. Conclusions The characteristic sequences of PRE1 reflect unique patterns of origin and evolution and provide a structural basis for diverse regulatory functions. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00745-3.
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Affiliation(s)
- Min Zheng
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Tianfu Guo
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
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24
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Garcia-Erill G, Jørgensen CHF, Muwanika VB, Wang X, Rasmussen MS, de Jong YA, Gaubert P, Olayemi A, Salmona J, Butynski TM, Bertola LD, Siegismund HR, Albrechtsen A, Heller R. Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes. Mol Biol Evol 2022; 39:6627297. [PMID: 35779009 PMCID: PMC9250280 DOI: 10.1093/molbev/msac134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
African wild pigs have a contentious evolutionary and biogeographic history. Until recently, desert warthog (Phacochoerus aethiopicus) and common warthog (P. africanus) were considered a single species. Molecular evidence surprisingly suggested they diverged at least 4.4 million years ago, and possibly outside of Africa. We sequenced the first whole-genomes of four desert warthogs and 35 common warthogs from throughout their range. We show that these two species diverged much later than previously estimated, 400,000–1,700,000 years ago depending on assumptions of gene flow. This brings it into agreement with the paleontological record. We found that the common warthog originated in western Africa and subsequently colonized eastern and southern Africa. During this range expansion, the common warthog interbred with the desert warthog, presumably in eastern Africa, underlining this region’s importance in African biogeography. We found that immune system–related genes may have adaptively introgressed into common warthogs, indicating that resistance to novel diseases was one of the most potent drivers of evolution as common warthogs expanded their range. Hence, we solve some of the key controversies surrounding warthog evolution and reveal a complex evolutionary history involving range expansion, introgression, and adaptation to new diseases.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Christian H F Jørgensen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Vincent B Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Xi Wang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Malthe S Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Yvonne A de Jong
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Philippe Gaubert
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria
| | - Jordi Salmona
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Thomas M Butynski
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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25
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ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature 2022; 606:358-367. [PMID: 35477154 PMCID: PMC9157047 DOI: 10.1038/s41586-022-04769-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/19/2022] [Indexed: 12/12/2022]
Abstract
The composition of the intestinal microbiome varies considerably between individuals and is correlated with health1. Understanding the extent to which, and how, host genetics contributes to this variation is essential yet has proved to be difficult, as few associations have been replicated, particularly in humans2. Here we study the effect of host genotype on the composition of the intestinal microbiota in a large mosaic pig population. We show that, under conditions of exacerbated genetic diversity and environmental uniformity, microbiota composition and the abundance of specific taxa are heritable. We map a quantitative trait locus affecting the abundance of Erysipelotrichaceae species and show that it is caused by a 2.3 kb deletion in the gene encoding N-acetyl-galactosaminyl-transferase that underpins the ABO blood group in humans. We show that this deletion is a ≥3.5-million-year-old trans-species polymorphism under balancing selection. We demonstrate that it decreases the concentrations of N-acetyl-galactosamine in the gut, and thereby reduces the abundance of Erysipelotrichaceae that can import and catabolize N-acetyl-galactosamine. Our results provide very strong evidence for an effect of the host genotype on the abundance of specific bacteria in the intestine combined with insights into the molecular mechanisms that underpin this association. Our data pave the way towards identifying the same effect in rural human populations. The host blood-type-associated ABO genotype affects the abundance of specific bacteria in the pig intestine.
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26
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Maigrot AL, Hillmann E, Briefer EF. Cross-species discrimination of vocal expression of emotional valence by Equidae and Suidae. BMC Biol 2022; 20:106. [PMID: 35606806 PMCID: PMC9128205 DOI: 10.1186/s12915-022-01311-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 04/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Discrimination and perception of emotion expression regulate interactions between conspecifics and can lead to emotional contagion (state matching between producer and receiver) or to more complex forms of empathy (e.g., sympathetic concern). Empathy processes are enhanced by familiarity and physical similarity between partners. Since heterospecifics can also be familiar with each other to some extent, discrimination/perception of emotions and, as a result, emotional contagion could also occur between species. RESULTS Here, we investigated if four species belonging to two ungulate Families, Equidae (domestic and Przewalski's horses) and Suidae (pigs and wild boars), can discriminate between vocalizations of opposite emotional valence (positive or negative), produced not only by conspecifics, but also closely related heterospecifics and humans. To this aim, we played back to individuals of these four species, which were all habituated to humans, vocalizations from a unique set of recordings for which the valence associated with vocal production was known. We found that domestic and Przewalski's horses, as well as pigs, but not wild boars, reacted more strongly when the first vocalization played was negative compared to positive, regardless of the species broadcasted. CONCLUSIONS Domestic horses, Przewalski's horses and pigs thus seem to discriminate between positive and negative vocalizations produced not only by conspecifics, but also by heterospecifics, including humans. In addition, we found an absence of difference between the strength of reaction of the four species to the calls of conspecifics and closely related heterospecifics, which could be related to similarities in the general structure of their vocalization. Overall, our results suggest that phylogeny and domestication have played a role in cross-species discrimination/perception of emotions.
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Affiliation(s)
- Anne-Laure Maigrot
- Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland.,Division of Animal Welfare, Veterinary Public Health Institute, Vetsuisse Faculty, University of Bern, Länggassstrasse 120, 3012, Bern, Switzerland.,Swiss National Stud Farm, Agroscope, Les Longs-Prés, 1580, Avenches, Switzerland
| | - Edna Hillmann
- Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland.,Animal Husbandry and Ethology, Albrecht Daniel Thaer-Institut, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany
| | - Elodie F Briefer
- Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland. .,Centre for Proper Housing of Ruminants and Pigs, Federal Food Safety and Veterinary Office, Agroscope, Tänikon, 8356, Ettenhausen, Switzerland. .,Department of Biology, Behavioral Ecology Group, Section for Ecology & Evolution, University of Copenhagen, 2100, Copenhagen Ø, Denmark.
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27
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Chen JQ, Zhang MP, Tong XK, Li JQ, Zhang Z, Huang F, Du HP, Zhou M, Ai HS, Huang LS. Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds. Zool Res 2022; 43:423-441. [PMID: 35437972 PMCID: PMC9113972 DOI: 10.24272/j.issn.2095-8137.2021.379] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/12/2022] [Indexed: 11/21/2022] Open
Abstract
In pig-to-human xenotransplantation, the transmission risk of porcine endogenous retroviruses (PERVs) is of great concern. However, the distribution of PERVs in pig genomes, their genetic variation among Eurasian pigs, and their evolutionary history remain unclear. We scanned PERVs in the current pig reference genome (assembly Build 11.1), and identified 36 long complete or near-complete PERVs (lcPERVs) and 23 short incomplete PERVs (siPERVs). Besides three known PERVs (PERV-A, -B, and -C), four novel types (PERV-JX1, -JX2, -JX3, and -JX4) were detected in this study. According to evolutionary analyses, the newly discovered PERVs were more ancient, and PERV-Bs probably experienced a bottleneck ~0.5 million years ago (Ma). By analyzing 63 high-quality porcine whole-genome resequencing data, we found that the PERV copy numbers in Chinese pigs were lower (32.0±4.0) than in Western pigs (49.1±6.5). Additionally, the PERV sequence diversity was lower in Chinese pigs than in Western pigs. Regarding the lcPERV copy numbers, PERV-A and -JX2 in Western pigs were higher than in Chinese pigs. Notably, Bama Xiang (BMX) pigs had the lowest PERV copy number (27.8±5.1), and a BMX individual had no PERV-C and the lowest PERV copy number (23), suggesting that BMX pigs were more suitable for screening and/or modification as xenograft donors. Furthermore, we identified 451 PERV transposon insertion polymorphisms (TIPs), of which 86 were shared by all 10 Chinese and Western pig breeds. Our findings provide systematic insights into the genomic distribution, variation, evolution, and possible biological function of PERVs.
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Affiliation(s)
- Jia-Qi Chen
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Ming-Peng Zhang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Xin-Kai Tong
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Jing-Quan Li
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Zhou Zhang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Fei Huang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Hui-Peng Du
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Meng Zhou
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Hua-Shui Ai
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China. E-mail:
| | - Lu-Sheng Huang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China. E-mail:
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Chen J, Zhong J, He X, Li X, Ni P, Safner T, Šprem N, Han J. The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications. Anim Genet 2022; 53:281-292. [PMID: 35238061 PMCID: PMC9314987 DOI: 10.1111/age.13181] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/12/2022] [Accepted: 02/12/2022] [Indexed: 02/05/2023]
Abstract
The rapid progress of sequencing technology has greatly facilitated the de novo genome assembly of pig breeds. However, the assembly of the wild boar genome is still lacking, hampering our understanding of chromosomal and genomic evolution during domestication from wild boars into domestic pigs. Here, we sequenced and de novo assembled a European wild boar genome (ASM2165605v1) using the long‐range information provided by 10× Linked‐Reads sequencing. We achieved a high‐quality assembly with contig N50 of 26.09 Mb. Additionally, 1.64% of the contigs (222) with lengths from 107.65 kb to 75.36 Mb covered 90.3% of the total genome size of ASM2165605v1 (~2.5 Gb). Mapping analysis revealed that the contigs can fill 24.73% (93/376) of the gaps present in the orthologous regions of the updated pig reference genome (Sscrofa11.1). We further improved the contigs into chromosome level with a reference‐assistant scaffolding method. Using the ‘assembly‐to‐assembly’ approach, we identified intra‐chromosomal large structural variations (SVs, length >1 kb) between ASM2165605v1 and Sscrofa11.1 assemblies. Interestingly, we found that the number of SV events on the X chromosome deviated significantly from the linear models fitting autosomes (R2 > 0.64, p < 0.001). Specifically, deletions and insertions were deficient on the X chromosome by 66.14 and 58.41% respectively, whereas duplications and inversions were excessive on the X chromosome by 71.96 and 107.61% respectively. We further used the large segmental duplications (SDs, >1 kb) events as a proxy to understand the large‐scale inter‐chromosomal evolution, by resolving parental‐derived relationships for SD pairs. We revealed a significant excess of SD movements from the X chromosome to autosomes (p < 0.001), consistent with the expectation of meiotic sex chromosome inactivation. Enrichment analyses indicated that the genes within derived SD copies on autosomes were significantly related to biological processes involving nervous system, lipid biosynthesis and sperm motility (p < 0.01). Together, our analyses of the de novo assembly of ASM2165605v1 provides insight into the SVs between European wild boar and domestic pig, in addition to the ongoing process of meiotic sex chromosome inactivation in driving inter‐chromosomal interaction between the sex chromosome and autosomes.
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Affiliation(s)
- Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Zhong
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xuefei He
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoyu Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Pan Ni
- Animal Husbandry and Veterinary Institute of Keqiao District, Shaoxing, Zhejiang, China
| | - Toni Safner
- Faculty of Agriculture, University of Zagreb, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, (CoE CroP-BioDiv), Zagreb, Croatia
| | - Nikica Šprem
- Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Jianlin Han
- International Livestock Research Institute, Nairobi, Kenya.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhang M, Yang Q, Ai H, Huang L. Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1040-1052. [PMID: 35181533 DOI: 10.1016/j.gpb.2022.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 12/20/2021] [Accepted: 02/09/2022] [Indexed: 12/30/2022]
Abstract
The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history. Herein, we estimated the de novo mutation rate of pigs as 3.6 × 10-9 per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation. Using this mutation rate, we re-investigated the evolutionary history of pigs. The estimated divergence time of ∼ 10 kiloyears ago (KYA) between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological evidence. However, other divergence events inferred here were not as ancient as previously described. Our estimates suggested that Sus speciation occurred ∼ 1.36 million years ago (MYA); European wild pigs split from Asian wild pigs only ∼ 219 KYA; and south and north Chinese wild pigs split ∼ 25 KYA. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao plain, North China, approximately 20 KYA, supporting the possibly independent domestication in North China along the middle Yellow River. We also found that the maximum effective population size of pigs was ∼ 6 times larger than the previous estimate. An archaic migration from other Sus species originating ∼ 2 MYA to European pigs was detected during western colonization of pigs; this interfered with the previous demographic inference. Our de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.
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Affiliation(s)
- Mingpeng Zhang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qiang Yang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Huashui Ai
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China.
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30
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Zhao P, Du H, Jiang L, Zheng X, Feng W, Diao C, Zhou L, Liu GE, Zhang H, Chamba Y, Zhang Q, Li B, Liu JF. PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene. Genome Biol Evol 2021; 12:1751-1764. [PMID: 33151306 PMCID: PMC7643367 DOI: 10.1093/gbe/evaa142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 12/22/2022] Open
Abstract
Introgression events and population admixture occurred among Sus species across the Eurasian mainland in the Middle Pleistocene, which reflects the local adaption of different populations and contributes to evolutionary novelty. Previous findings on these population introgressions were largely based on extensive genome-wide single-nucleotide polymorphism information, ignoring structural variants (SVs) as an important alternative resource of genetic variations. Here, we profiled the genome-wide SVs and explored the formation of pattern-related SVs, indicating that PRE1-SS is a recently active subfamily that was strongly associated with introgression events in multiple Asian and European pig populations. As reflected by the three different combination haplotypes from two specific patterns and known phylogenetic relationships in Eurasian boars, we identified the Asian Northern wild pigs as having experienced introgression from European wild boars around 0.5–0.2 Ma and having received latitude-related selection. During further exploration of the influence of pattern-related SVs on gene functions, we found substantial sequence changes in 199 intron regions of 54 genes and 3 exon regions of 3 genes (HDX, TRO, and SMIM1), implying that the pattern-related SVs were highly related to positive selection and adaption of pigs. Our findings revealed novel introgression events in Eurasian wild boars, providing a timeline of population admixture and divergence across the Eurasian mainland in the Middle Pleistocene.
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Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Maryland
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yangzom Chamba
- College of Animal Science and Technology, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
| | - Qin Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, PR China
| | - Bugao Li
- Department of Animal Sciences and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
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31
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Mehrotra A, Bhushan B, A K, Singh A, Panda S, Bhati M, Panigrahi M, Dutt T, Mishra BP, Pausch H, Kumar A. Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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De AK, Sawhney S, Ponraj P, Muthiyan R, Muniswamy K, Ravi SK, Malakar D, Alyethodi RR, Mondal S, Sunder J, Banik S, Kundu A, Bhattacharya D. Maternal lineage of Nicobari pig ( Sus scrofa nicobaricus) correlated with migration of Nicobarese, a native tribal population of Andaman and Nicobar Islands, India. Anim Biotechnol 2021; 34:156-165. [PMID: 34310265 DOI: 10.1080/10495398.2021.1950742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Nicobari pig is reared by Nicobarese, a native tribal population of Andaman and Nicobar Islands. Nicobari pig has maintained its genetic identity due to geographical isolation. This communication is the first report on maternal inheritance of Nicobari pigs. DNA polymorphism data showed seven haplotypes. D-loop sequence information and mitogenome analysis were able to earmark Nicobari pigs to Asian clade. The domestication process of pigs and its expansion pattern help to understand human migration pattern. Based on this hypothesis, this communication elucidates the probable origin of Nicobarese. Earlier studies indicated that Nicobarese had genetic affinities to races distributed in China, Malaysia and Thailand. Our data on maternal inheritance of Nicobari pig correlates with the data on migration of Nicobarese. Moreover, we could establish a novel connection of Nicobarese with people of Northeastern parts of India, Philippines and Vietnam through phylogenetic signal and geographical provenance of Nicobari pig. We further concluded that migration of Nicobarese happened during Western route of migration (WRM) ∼4000 years before present. Therefore, we propose one wave hypothesis of peopling of Nicobar based on our study and existence of Ausrtroasiatic language, Mon-Khmer in these islands.
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Affiliation(s)
- Arun Kumar De
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - Sneha Sawhney
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - Perumal Ponraj
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - Ramachandran Muthiyan
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - Kangayan Muniswamy
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - Sanjay Kumar Ravi
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - Dhruba Malakar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - R R Alyethodi
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - Samiran Mondal
- Department of Veterinary Pathology, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Jai Sunder
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - Santanu Banik
- Department of Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Guwahati, India
| | - Anandamoy Kundu
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - Debasis Bhattacharya
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, India
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Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021; 11:1617. [PMID: 34072591 PMCID: PMC8230064 DOI: 10.3390/ani11061617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022] Open
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.
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Affiliation(s)
- Vivien J. Chebii
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| | - Emmanuel A. Mpolya
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
| | - Farai C. Muchadeyi
- Agricultural Research Council Biotechnology Platform (ARC-BTP), Private Bag X5, Onderstepoort 0110, South Africa;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
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34
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Donaldson B, Villagomez DAF, King WA. Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective. Animals (Basel) 2021; 11:1257. [PMID: 33925534 PMCID: PMC8146943 DOI: 10.3390/ani11051257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to produce high-quality karyotypes and reveal large-scale chromosome ectopic exchanges. Further refinements to clinical cytogenetics practices have led to the implementation of molecular cytogenetics techniques such as fluorescent in-situ hybridization (FISH), allowing for rearrangements to be visualized and breakpoints refined using fluorescently labelled painting probes. The next-generation of clinical cytogenetics include the implementation of DNA microarrays, and next-generation sequencing (NGS) technologies such as DNA sequencing to better explore tentative genome architecture changes. The implementation of these cytogenomics techniques allow the genomes of rearrangement carriers to be deciphered at the highest resolution, allowing rearrangements to be detected; breakpoints to be delineated; and, most importantly, potential gene implications of those chromosome rearrangements to be interrogated. Clinical cytogenetics has become an integral tool in the livestock industry, identifying rearrangements and allowing breeders to make informed breeding decisions.
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Affiliation(s)
- Brendan Donaldson
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | | | - W. Allan King
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Karyotekk Inc., Box 363 OVC, University of Guelph, Guelph, ON N1G 2W1, Canada
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35
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Zhang S, Zhang K, Peng X, Zhan H, Lu J, Xie S, Zhao S, Li X, Ma Y. Selective sweep analysis reveals extensive parallel selection traits between large white and Duroc pigs. Evol Appl 2020; 13:2807-2820. [PMID: 33294024 PMCID: PMC7691457 DOI: 10.1111/eva.13085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
In the process of pig genetic improvement, different commercial breeds have been bred for the same purpose, improving meat production. Most of the economic traits, such as growth and fertility, have been selected similarly despite the discrepant selection pressure, which is known as parallel selection. Here, 28 whole-genome sequencing data of Danish large white pigs with an approximately 25-fold depth each were generated, resulting in about 12 million high-quality SNPs for each individual. Combined with the sequencing data of 27 Duroc and 23 European wild boars, we investigated the parallel selection of Danish large white and Duroc pigs using two complementary methods, Fst and iHS. In total, 67 candidate regions were identified as the signatures of parallel selection. The genes in candidate regions of parallel selection were mainly associated with sensory perception, growth rate, and body size. Further functional annotation suggested that the striking consistency of the terms may be caused by the polygenetic basis of quantitative traits, and revealing the complex genetic basis of parallel selection. Besides, some unique terms were enriched in population-specific selection regions, such as the limb development-related terms enriched in Duroc-specific selection regions, suggesting unique selections of breed-specific selected traits. These results will help us better understand the parallel selection process of different breeds. Moreover, we identified several potential causal SNPs that may contribute to the pig genetic breeding process.
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Affiliation(s)
- Saixian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Kaili Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Xia Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Huiwen Zhan
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Jiahui Lu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
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Cai Z, Sarup P, Ostersen T, Nielsen B, Fredholm M, Karlskov-Mortensen P, Sørensen P, Jensen J, Guldbrandtsen B, Lund MS, Christensen OF, Sahana G. Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds. J Anim Sci 2020; 98:5873883. [PMID: 32687196 DOI: 10.1093/jas/skaa229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/14/2020] [Indexed: 01/04/2023] Open
Abstract
Whole-genome sequencing of 217 animals from three Danish commercial pig breeds (Duroc, Landrace [LL], and Yorkshire [YY]) was performed. Twenty-six million single-nucleotide polymorphisms (SNPs) and 8 million insertions or deletions (indels) were uncovered. Among the SNPs, 493,099 variants were located in coding sequences, and 29,430 were predicted to have a high functional impact such as gain or loss of stop codon. Using the whole-genome sequence dataset as the reference, the imputation accuracy for pigs genotyped with high-density SNP chips was examined. The overall average imputation accuracy for all biallelic variants (SNP and indel) was 0.69, while it was 0.83 for variants with minor allele frequency > 0.1. This study provides whole-genome reference data to impute SNP chip-genotyped animals for further studies to fine map quantitative trait loci as well as improving the prediction accuracy in genomic selection. Signatures of selection were identified both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during breed development or subsequent divergent selection. However, the fixation indices did not indicate a strong divergence among these three breeds. In LL and YY, the integrated haplotype score identified genomic regions under recent selection. These regions contained genes for olfactory receptors and oxidoreductases. Olfactory receptor genes that might have played a major role in the domestication were previously reported to have been under selection in several species including cattle and swine.
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Affiliation(s)
- Zexi Cai
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
| | - Pernille Sarup
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
| | - Tage Ostersen
- SEGES Danish Pig Research Centre, Copenhagen, Denmark
| | | | - Merete Fredholm
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Peter Sørensen
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
| | - Ole Fredslund Christensen
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
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Improving read alignment through the generation of alternative reference via iterative strategy. Sci Rep 2020; 10:18712. [PMID: 33127969 PMCID: PMC7599232 DOI: 10.1038/s41598-020-74526-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 09/30/2020] [Indexed: 11/08/2022] Open
Abstract
There is generally one standard reference sequence for each species. When extensive variations exist in other breeds of the species, it can lead to ambiguous alignment and inaccurate variant calling and, in turn, compromise the accuracy of downstream analysis. Here, with the help of the FPGA hardware platform, we present a method that generates an alternative reference via an iterative strategy to improve the read alignment for breeds that are genetically distant to the reference breed. Compared to the published reference genomes, by using the alternative reference sequences we built, the mapping rates of Chinese indigenous pigs and chickens were improved by 0.61-1.68% and 0.09-0.45%, respectively. These sequences also enable researchers to recover highly variable regions that could be missed using public reference sequences. We also determined that the optimal number of iterations needed to generate alternative reference sequences were seven and five for pigs and chickens, respectively. Our results show that, for genetically distant breeds, generating an alternative reference sequence can facilitate read alignment and variant calling and improve the accuracy of downstream analyses.
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38
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Zhang M, Li Z, Li J, Huang T, Peng G, Tang W, Yi G, Zhang L, Song Y, Liu T, Hu X, Ren L, Liu H, Butler JE, Han H, Zhao Y. Revisiting the Pig IGHC Gene Locus in Different Breeds Uncovers Nine Distinct IGHG Genes. THE JOURNAL OF IMMUNOLOGY 2020; 205:2137-2145. [PMID: 32929042 DOI: 10.4049/jimmunol.1901483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/13/2020] [Indexed: 11/19/2022]
Abstract
IgG subclass diversification is common in placental mammals. It has been well documented in humans and mice that different IgG subclasses, with diversified functions, synergistically regulate humoral immunity. However, our knowledge on the genomic and functional diversification of IgG subclasses in the pig, a mammalian species with high agricultural and biomedical importance, is incomplete. Using bacterial artificial chromosome sequencing and newly assembled genomes generated by the PacBio sequencing approach, we characterized and mapped the IgH C region gene locus in three indigenous Chinese breeds (Erhualian, Xiang, and Luchuan) and compared them to that of Duroc. Our data revealed that IGHG genes in Chinese pigs differ from the Duroc, whereas the IGHM, IGHD, IGHA, and IGHE genes were all single copy and highly conserved in the pig breeds examined. Most striking were differences in numbers of IGHG genes: there are seven genes in Erhualian pigs, six in the Duroc, but only five in Xiang pigs. Phylogenetic analysis suggested that all reported porcine IGHG genes could be classified into nine subclasses: IGHG1, IGHG2a, IGHG2b, IGHG2c, IGHG3, IGHG4, IGHG5a, IGHG5b, and IGHG5c. Using sequence information, we developed a mouse mAb specific for IgG3. This study offers a starting point to investigate the structure-function relationship of IgG subclasses in pigs.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Zhenrong Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jingying Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Tian Huang
- School of Life Sciences, Henan University, Kaifeng 475004, People's Republic of China
| | - Gaochuang Peng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Wenda Tang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Guoqiang Yi
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, People's Republic of China
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China; and
| | - Yu Song
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Tianran Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China; and
| | - John E Butler
- Department of Microbiology, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China;
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China;
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39
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Ramos L, Lunney JK, Gonzalez-Juarrero M. Neonatal and infant immunity for tuberculosis vaccine development: importance of age-matched animal models. Dis Model Mech 2020; 13:dmm045740. [PMID: 32988990 PMCID: PMC7520460 DOI: 10.1242/dmm.045740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Neonatal and infant immunity differs from that of adults in both the innate and adaptive arms, which are critical contributors to immune-mediated clearance of infection and memory responses elicited during vaccination. The tuberculosis (TB) research community has openly admitted to a vacuum of knowledge about neonatal and infant immune responses to Mycobacterium tuberculosis (Mtb) infection, especially in the functional and phenotypic attributes of memory T cell responses elicited by the only available vaccine for TB, the Bacillus Calmette-Guérin (BCG) vaccine. Although BCG vaccination has variable efficacy in preventing pulmonary TB during adolescence and adulthood, 80% of endemic TB countries still administer BCG at birth because it has a good safety profile and protects children from severe forms of TB. As such, new vaccines must work in conjunction with BCG at birth and, thus, it is essential to understand how BCG shapes the immune system during the first months of life. However, many aspects of the neonatal and infant immune response elicited by vaccination with BCG remain unknown, as only a handful of studies have followed BCG responses in infants. Furthermore, most animal models currently used to study TB vaccine candidates rely on adult-aged animals. This presents unique challenges when transitioning to human trials in neonates or infants. In this Review, we focus on vaccine development in the field of TB and compare the relative utility of animal models used thus far to study neonatal and infant immunity. We encourage the development of neonatal animal models for TB, especially the use of pigs.
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Affiliation(s)
- Laylaa Ramos
- Mycobacteria Research Laboratories, Microbiology Immunology and Pathology Department, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA Building 1040, Room 103, Beltsville, MD 20705, USA
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Microbiology Immunology and Pathology Department, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
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Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O'Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience 2020; 9:5858065. [PMID: 32543654 PMCID: PMC7448572 DOI: 10.1093/gigascience/giaa051] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 01/05/2023] Open
Abstract
Background The domestic pig (Sus scrofa) is important both as a food source and
as a biomedical model given its similarity in size, anatomy, physiology, metabolism,
pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a
purebred Duroc female pig established using older clone-based sequencing methods was
incomplete, and unresolved redundancies, short-range order and orientation errors, and
associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created
with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the
same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0).
Both assemblies are of substantially higher (>90-fold) continuity and accuracy than
Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read
assemblies provide an unprecedented view of the genetic make-up of this important
agricultural and biomedical model species. We propose that the improved Duroc assembly
(Sscrofa11.1) become the reference genome for genomic research in pigs.
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Affiliation(s)
- Amanda Warr
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Nabeel Affara
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Hamid Beiki
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Lel Eory
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Heather A Finlayson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Carlos G Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Richard Hall
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | | | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.,Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane QLD 4104, Australia
| | - Osagie Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kristi Kim
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Haibou Liu
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Nancy Manchanda
- Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Dan J Nonneman
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Gary A Rohrer
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | - Laurie A Rund
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Carole A Sargent
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | | | - Ben M Skinner
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Richard Talbot
- Edinburgh Genomics, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Elizabeth Tseng
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Christopher K Tuggle
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA.,Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Timothy P L Smith
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
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41
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Huang M, Yang B, Chen H, Zhang H, Wu Z, Ai H, Ren J, Huang L. The fine-scale genetic structure and selection signals of Chinese indigenous pigs. Evol Appl 2020; 13:458-475. [PMID: 31993089 PMCID: PMC6976964 DOI: 10.1111/eva.12887] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 01/24/2023] Open
Abstract
Genome-wide SNP profiling has yielded insights into the genetic structure of China indigenous pigs, but has focused on a limited number of populations. Here, we present an analysis of population structure and signals of positive selection in 42 Chinese pig populations that represent the most extensive pig phenotypic diversity in China, using genotype data of 1.1 million SNPs on customized Beadchips. This unravels the fine-scale genetic diversity, phylogenic relationships, and population structure of these populations, which shows remarkably concordance between genetic clusters and geography with few exceptions. We also reveal the genetic contribution to North Chinese pigs from European modern pigs. Furthermore, we identify possible targets of selection in the Tibetan pig, including the well-characterized hypoxia gene (EPAS1) and several previously unrecognized candidates. Intriguingly, the selected haplotype in the EPAS1 gene is associated with higher hemoglobin contents in Tibetan pigs, which is different from the protective role of EPAS1 in the high-altitude adaptation in Tibetan dogs and their owners. Additionally, we present evidence for the causality between EDNRB variants and the two-end-black (TEB) coat color phenotype in all Chinese pig populations except the Jinhua pig. We hypothesize that distinct targets have been independently selected for the formation of the TEB phenotype in Chinese pigs of different geographic origins. This highlights the importance of characterizing population-specific genetic determinants for heritable phenotype in diverse pig populations.
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Affiliation(s)
- Min Huang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Hui Zhang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Zhongping Wu
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
- Present address:
College of Animal ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
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42
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Thomas F, Giraudeau M, Dheilly NM, Gouzerh F, Boutry J, Beckmann C, Biro PA, Hamede R, Abadie J, Labrut S, Bieuville M, Misse D, Bramwell G, Schultz A, Le Loc'h G, Vincze O, Roche B, Renaud F, Russell T, Ujvari B. Rare and unique adaptations to cancer in domesticated species: An untapped resource? Evol Appl 2020. [DOI: 10.1111/eva.12920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Frédéric Thomas
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Mathieu Giraudeau
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences Stony Brook University Stony Brook NY USA
| | - Flora Gouzerh
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Justine Boutry
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Christa Beckmann
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
- School of Science Western Sydney UniversityParramatta NSW Australia
| | - Peter A. Biro
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
| | - Rodrigo Hamede
- School of Natural Sciences University of Tasmania Hobart TAS Australia
| | | | | | - Margaux Bieuville
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Dorothée Misse
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Georgina Bramwell
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
| | - Aaron Schultz
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
| | - Guillaume Le Loc'h
- Clinique des NAC et de la Faune Sauvage, UMR IHAP École Nationale Vétérinaire de Toulouse Toulouse France
| | - Orsolya Vincze
- Hungarian Department of Biology and Ecology Evolutionary Ecology Group Babeş‐Bolyai University Cluj‐Napoca Romania
- Department of Tisza Research MTA Centre for Ecological Research‐DRI Debrecen Hungary
| | - Benjamin Roche
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
- Unité mixte Internationale de Modélisation Mathématique et Informatique des Systèmes Complexes UMI IRD/Sorbonne UniversitéUMMISCO Bondy France
| | - François Renaud
- CREECUMR IRD 224‐CNRS 5290‐Université de Montpellier Montpellier France
| | - Tracey Russell
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
| | - Beata Ujvari
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds VIC Australia
- School of Natural Sciences University of Tasmania Hobart TAS Australia
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43
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Cañás Bottos L. Race and Process: Certifying IberianPigs and Invisibilising Humans. NORSK ANTROPOLOGISK TIDSSKRIFT 2020. [DOI: 10.18261/issn.1504-2898-2019-03-04-06] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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44
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Porcine models for studying complications and organ crosstalk in diabetes mellitus. Cell Tissue Res 2020; 380:341-378. [PMID: 31932949 DOI: 10.1007/s00441-019-03158-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/28/2019] [Indexed: 02/06/2023]
Abstract
The worldwide prevalence of diabetes mellitus and obesity is rapidly increasing not only in adults but also in children and adolescents. Diabetes is associated with macrovascular complications increasing the risk for cardiovascular disease and stroke, as well as microvascular complications leading to diabetic nephropathy, retinopathy and neuropathy. Animal models are essential for studying disease mechanisms and for developing and testing diagnostic procedures and therapeutic strategies. Rodent models are most widely used but have limitations in translational research. Porcine models have the potential to bridge the gap between basic studies and clinical trials in human patients. This article provides an overview of concepts for the development of porcine models for diabetes and obesity research, with a focus on genetically engineered models. Diabetes-associated ocular, cardiovascular and renal alterations observed in diabetic pig models are summarized and their similarities with complications in diabetic patients are discussed. Systematic multi-organ biobanking of porcine models of diabetes and obesity and molecular profiling of representative tissue samples on different levels, e.g., on the transcriptome, proteome, or metabolome level, is proposed as a strategy for discovering tissue-specific pathomechanisms and their molecular key drivers using systems biology tools. This is exemplified by a recent study providing multi-omics insights into functional changes of the liver in a transgenic pig model for insulin-deficient diabetes mellitus. Collectively, these approaches will provide a better understanding of organ crosstalk in diabetes mellitus and eventually reveal new molecular targets for the prevention, early diagnosis and treatment of diabetes mellitus and its associated complications.
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45
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McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019; 17:98. [PMID: 31791340 PMCID: PMC6889691 DOI: 10.1186/s12915-019-0724-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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46
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D'Alessandro E, Giosa D, Sapienza I, Giuffrè L, Cigliano RA, Romeo O, Zumbo A. Whole genome SNPs discovery in Nero Siciliano pig. Genet Mol Biol 2019; 42:594-602. [PMID: 31188930 PMCID: PMC6905442 DOI: 10.1590/1678-4685-gmb-2018-0169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 01/04/2019] [Indexed: 11/24/2022] Open
Abstract
Autochthonous pig breeds represent an important genetic reserve to be utilized mainly for the production of typical products. To explore its genetic variability, here we present for the first time whole genome sequencing data and SNPs discovered in a male domestic Nero Siciliano pig compared to the last pig reference genome Sus scrofa11.1.A total of 346.8 million paired reads were generated by sequencing. After quality control, 99.03% of the reads were mapped to the reference genome, and over 11 million variants were detected.Additionally, we evaluated sequence diversity in 21 fitness-related loci selected based on their biological function and/or their proximity to relevant QTLs. We focused on genes that have been related to environmental adaptation and reproductive traits in previous studies regarding local breeds. A total of 6,747 variants were identified resulting in a rate of 1 variant every ~276 bases. Among these variants 1,132 were novel to the dbSNP151 database. This study represents a first step in the genetic characterization of Nero Siciliano pig and also provides a platform for future comparative studies between this and other swine breeds.
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Affiliation(s)
- Enrico D'Alessandro
- Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy
| | - Domenico Giosa
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Irene Sapienza
- Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy
| | - Letterio Giuffrè
- Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy
| | | | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy.,Scientific Institute for Research, Hospitalization and Health Care (IRCCS) - Centro Neurolesi "Bonino-Pulejo", Messina, Italy
| | - Alessandro Zumbo
- Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy
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47
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Jennings J, Sang Y. Porcine Interferon Complex and Co-Evolution with Increasing Viral Pressure after Domestication. Viruses 2019; 11:v11060555. [PMID: 31208045 PMCID: PMC6631851 DOI: 10.3390/v11060555] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/16/2022] Open
Abstract
Consisting of nearly 60 functional genes, porcine interferon (IFN)-complex represents an evolutionary surge of IFN evolution in domestic ungulate species. To compare with humans and mice, each of these species contains about 20 IFN functional genes, which are better characterized using the conventional IFN-α/β subtypes as examples. Porcine IFN-complex thus represents an optimal model for studying IFN evolution that resulted from increasing viral pressure during domestication and industrialization. We hypothesize and justify that porcine IFN-complex may extend its functionality in antiviral and immunomodulatory activity due to its superior molecular diversity. Furthermore, these unconventional IFNs could even confer some functional and signaling novelty beyond that of the well-studied IFN-α/β subtypes. Investigations into porcine IFN-complex will further our understanding of IFN biology and promote IFN-based therapeutic designs to confront swine viral diseases.
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Affiliation(s)
- Jordan Jennings
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA.
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA.
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Grahofer A, Letko A, Häfliger IM, Jagannathan V, Ducos A, Richard O, Peter V, Nathues H, Drögemüller C. Chromosomal imbalance in pigs showing a syndromic form of cleft palate. BMC Genomics 2019; 20:349. [PMID: 31068123 PMCID: PMC6505205 DOI: 10.1186/s12864-019-5711-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/17/2019] [Indexed: 11/23/2022] Open
Abstract
Background Palatoschisis or cleft palate is a known anomaly in pigs resulting in their death. However, little is known about its aetiology. A detailed description of the phenotype was derived from necropsy and by computed tomography revealing that all 20 cases also exhibited hypodontia and renal cysts. Furthermore, a genetic origin was assumed due to dominant inheritance as all 20 recorded cases were confirmed offspring of a single boar. Results Single nucleotide variant (SNV) genotyping data were used to map the defect in the porcine genome and led to the detection of a chromosomal imbalance in the affected offspring. Whole genome sequencing of an affected piglet and a normal full sib was used to identify a chromosomal translocation and to fine map the breakpoints in the genome. Finally, we proved that the boar, which sired the malformed piglets, carried a balanced translocation. The detected translocation of Mb-sized segments of chromosome 8 and 14 had not been previously observed during karyotyping. All affected offspring were shown to be carriers of a partial trisomy of chromosome 14 including the FGFR2 gene, which is associated with various dominant inherited craniofacial dysostosis syndromes in man, and partial monosomy of chromosome 8 containing MSX1 known to be associated with tooth agenesis and orofacial clefts in other species. Conclusions This study illustrates the usefulness of recently established genomic resources in pigs. In this study, the application of genome-wide genotyping and sequencing methods allowed the identification of the responsible boar and the genetic cause of the observed defect. By implementing systematic surveillance, it is possible to identify genetic defects at an early stage and avoid further distribution of congenital disorders. Electronic supplementary material The online version of this article (10.1186/s12864-019-5711-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Grahofer
- Clinic for Swine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, CH-3012, Bern, Switzerland
| | - Anna Letko
- Institute of Genetics, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, CH-3012, Bern, Switzerland
| | - Irene Monika Häfliger
- Institute of Genetics, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, CH-3012, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, CH-3012, Bern, Switzerland
| | - Alain Ducos
- GenPhyse, INRA, INPT, ENVT, Université de Toulouse, 31320, Castanet-Tolosan, France
| | - Olivia Richard
- Institute of Animal Pathology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012, Bern, Switzerland
| | - Vanessa Peter
- Division of Clinical Radiology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Länggassstrasse 128, 3012 CH-, Bern, Switzerland
| | - Heiko Nathues
- Clinic for Swine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, CH-3012, Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, CH-3012, Bern, Switzerland.
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49
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Liang Z, Bu L, Qin Y, Peng Y, Yang R, Zhao Y. Selection of Optimal Ancestry Informative Markers for Classification and Ancestry Proportion Estimation in Pigs. Front Genet 2019; 10:183. [PMID: 30915106 PMCID: PMC6421339 DOI: 10.3389/fgene.2019.00183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/19/2019] [Indexed: 12/26/2022] Open
Abstract
Using small sets of ancestry informative markers (AIMs) constitutes a cost-effective method to accurately estimate the ancestry proportions of individuals. This study aimed to generate a small and effective number of AIMs from ∼60 K single nucleotide polymorphism (SNP) data of porcine and estimate three ancestry proportions [East China pig (ECHP), South China pig (SCHP), and European commercial pig (EUCP)] from Asian breeds and European domestic breeds. A total of 186 samples of 10 pure breeds were divided into three groups: ECHP, SCHP, and EUCP. Using these samples and a one-vs.-rest SVM classifier, we found that using only seven AIMs could completely separate the three groups. Subsequently, we utilized supervised ADMIXTURE to calculate ancestry proportions and found that the 129 AIMs performed well on ancestry estimates when pseudo admixed individuals were used. Furthermore, another 969 samples of 61 populations were applied to evaluate the performance of the 129 AIMs. We also observed that the 129 AIMs were highly correlated with estimates using ∼60 K SNP data for three ancestry components: ECHP (Pearson correlation coefficient (r) = 0.94), SCHP (r = 0.94), and EUCP (r = 0.99). Our results provided an example of using a small number of pig AIMs for classifications and estimating ancestry proportions with high accuracy and in a cost-effective manner.
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Affiliation(s)
- Zuoxiang Liang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lina Bu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yidi Qin
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yebo Peng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ruifei Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yiqiang Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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50
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Bunning H, Wall E, Chagunda MGG, Banos G, Simm G. Heterosis in cattle crossbreeding schemes in tropical regions: meta-analysis of effects of breed combination, trait type, and climate on level of heterosis. J Anim Sci 2019; 97:29-34. [PMID: 30346552 PMCID: PMC6313114 DOI: 10.1093/jas/sky406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/15/2018] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to investigate the effects of animal trait, breed combination, and climate on the expressed levels of heterosis in crossbreeding schemes using tropical cattle. A meta-analysis of 42 studies was carried out with 518 heterosis estimates. In total, 62.5% of estimates were found to be significantly different from zero, the majority of which (89.8%) were beneficial for the studied trait. Trait and breed combination were shown to have a significant effect on the size of heterosis (P < 0.001 and P = 0.044, respectively). However, climate did not have a significant effect. Health, longevity, and milk production traits showed the highest heterosis (31.84 ± 10.73%, 35.13 ± 14.35%, and 35.15 ± 3.29%, respectively), whereas fertility, growth, and maternal traits showed moderate heterosis (12.02 ± 4.10%, 12.25 ± 2.69%, and 15.69 ± 3.26%, respectively). Crosses between breeds from different types showed moderate to high heterosis ranging from 9.95 ± 4.53% to 19.53 ± 3.62%, whereas crosses between breeds from the same type did not express heterosis that was significantly different from zero. These results show that heterosis has significant and favorable impact on productivity of cattle farming in tropical production systems, particularly in terms of fitness but also milk production traits.
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Affiliation(s)
- Harriet Bunning
- Animal & Veterinary Sciences, Scotland's Rural College, King's Buildings, West Mains Road, Edinburgh, UK.,Global Academy of Agriculture and Food Security, University of Edinburgh, Edinburgh, UK
| | - Eileen Wall
- Animal & Veterinary Sciences, Scotland's Rural College, King's Buildings, West Mains Road, Edinburgh, UK
| | - Mizeck G G Chagunda
- Department of Animal Breeding and Husbandry in the Tropics and Subtropics, University of Hohenheim, Stuttgart, Germany
| | - Georgios Banos
- Animal & Veterinary Sciences, Scotland's Rural College, King's Buildings, West Mains Road, Edinburgh, UK.,The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Geoff Simm
- Global Academy of Agriculture and Food Security, University of Edinburgh, Edinburgh, UK
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