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Wang F, Zha Z, He Y, Li J, Zhong Z, Xiao Q, Tan Z. Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China. Animals (Basel) 2023; 13:1835. [PMID: 37889708 PMCID: PMC10252034 DOI: 10.3390/ani13111835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 09/29/2023] Open
Abstract
Tunchang pig is one population of Hainan pig in the Hainan Province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, FST, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (SELENOV, CBR4, TNNT1, TNNT3, VPS13A, PLD3, SRFBP1, and SSPN), immune regulation (CD48, FBL, PTPRH, GNA14, LOX, SLAMF6, CALCOCO1, IRGC, and ZNF667), growth and development (SYT5, PRX, PPP1R12C, and SMG9), reproduction (LGALS13 and EPG5), vision (SLC9A8 and KCNV2), energy metabolism (ATP5G2), cell migration (EPS8L1), and olfaction (GRK3). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.
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Affiliation(s)
| | | | | | | | | | - Qian Xiao
- School of Animal Science and Technology, Hainan University, Haikou 570228, China; (F.W.)
| | - Zhen Tan
- School of Animal Science and Technology, Hainan University, Haikou 570228, China; (F.W.)
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Tiemann I, Becker S, Fournier J, Damiran D, Büscher W, Hillemacher S. Differences among domestic chicken breeds in tonic immobility responses as a measure of fearfulness. PeerJ 2023; 11:e14703. [PMID: 37033722 PMCID: PMC10081456 DOI: 10.7717/peerj.14703] [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: 02/15/2021] [Accepted: 12/15/2022] [Indexed: 04/07/2023] Open
Abstract
Background One priority for animal welfare is for animals to experience less fear, especially during human contact. For domestic animals, breeds that are less fearful may provide genetic resources to develop strains with improved welfare due to lower susceptibility to fear. Genetic predispositions inherited in these breeds might reflect the large diversity of chicken breeds. The goal of the present study was to systematically test a diverse group of chicken breeds to search for breeds that experience less fear. Methods Nineteen chicken breeds from commercial hybrid lines, native layer-type, meat-type and dual-purpose breeds, ornamental breeds as well as bantam breeds were tested in a standardized tonic immobility (TI) test. Chickens were manually restrained on their back, and the time to first head movement and first leg movement, the duration of TI, as well as the number of attempts needed to induce TI were measured. Results The TI response differed among chicken breeds (p ≤ 0.001) for naïve, mature hens. The median number of attempts required to induce TI ranged from 1 to 2 and did not differ significantly among breeds. Median durations were much more variable, with Lohmann Brown showing shortest durations (6 s, 12 s, 58 s for time to first head movement, first leg movement and total duration of TI, respectively). In contrast, medians reached the maximum of 600 s for all three measures in German Creepers. Repeated tests on the same individuals did not affect attempts needed to induce TI nor TI durations. Breeds clustered into two main groups, with layer-type native breeds and ornamental breeds having longer TI durations, and bantam, dual-purpose and meat-type native breeds having shorter TI durations. Conclusions Our findings provide evidence for substantial variation of fearfulness among breeds. This variation could be linked to the intended use during the breed's specific history. Knowledge and quantitative measurement of these behavioural responses provide the opportunity to improve welfare through selection and future breeding.
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Affiliation(s)
- Inga Tiemann
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
| | - Senta Becker
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
| | - Jocelyn Fournier
- Department of Animal & Poultry Science, University of Saskatchewan, Saskatoon, Canada
| | - Daalkhaijav Damiran
- Department of Animal & Poultry Science, University of Saskatchewan, Saskatoon, Canada
| | - Wolfgang Büscher
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
| | - Sonja Hillemacher
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
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Tian S, Li W, Zhong Z, Wang F, Xiao Q. Genome-wide re-sequencing data reveals the genetic diversity and population structure of Wenchang chicken in China. Anim Genet 2023; 54:328-337. [PMID: 36639920 DOI: 10.1111/age.13293] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/14/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023]
Abstract
Wenchang (WC) chicken, the only indigenous chicken breed listed in Chinese genetic resources in Hainan province, is well known for its excellent meat quality and is sold all over southeast Asia. In recent years, the number of WC has decreased sharply with considerable variability in the quality at market. To explore the genetic diversity and population structure of WC chickens, the whole-genome data of 235 WC individuals from three conservation farms were obtained using the Illumina 150 bp paired-end platform and used in conjunction with the sequencing data from 123 individuals from other chicken breeds (including eight Chinese indigenous chicken breeds and three foreign or commercial breeds) downloaded from a public database. A total of 12 111 532 SNPs were identified, of which 11 541 878 SNPs were identified in WC. The results of gene enrichment analyses revealed that the SNPs harbored in WC genomes are mainly related to environmental adaptation, disease resistance and meat quality traits. Genetic diversity statistics, quantified by expected heterozygosity, observed heterozygosity, linkage disequilibrium, nucleotide diversity and fixation statistics, indicated that WC displays high genetic diversity compared with other Chinese indigenous chicken breeds. Genetic structure analyses showed that each population displayed great differentiation between WC and the other breeds, indicating the uniqueness of WC. In conclusion, the results of our study provide the first genomic overview of genetic variants, genetic diversity and population structure of WC from three conservation farms. This information will be valuable for the future breeding and conservation of WC and other surveyed populations.
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Affiliation(s)
- Shuaishuai Tian
- Hainan Key Laboratory of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Wei Li
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Feifan Wang
- Hainan Key Laboratory of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Qian Xiao
- Hainan Key Laboratory of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
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Nilson SM, Gandolfi B, Grahn RA, Kurushima JD, Lipinski MJ, Randi E, Waly NE, Driscoll C, Murua Escobar H, Schuster RK, Maruyama S, Labarthe N, Chomel BB, Ghosh SK, Ozpinar H, Rah HC, Millán J, Mendes-de-Almeida F, Levy JK, Heitz E, Scherk MA, Alves PC, Decker JE, Lyons LA. Genetics of randomly bred cats support the cradle of cat domestication being in the Near East. Heredity (Edinb) 2022; 129:346-355. [PMID: 36319737 PMCID: PMC9708682 DOI: 10.1038/s41437-022-00568-4] [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: 06/14/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/04/2022] Open
Abstract
Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats' predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor's (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.
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Affiliation(s)
- Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Monika J Lipinski
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Øst, Denmark
| | - Nashwa E Waly
- Department of Animal Medicine, Faculty of Veterinary Medicine, Assuit University, 71526, Assiut, Egypt
| | | | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, 18055, Rostock, Germany
| | - Rolf K Schuster
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Soichi Maruyama
- Laboratory of Veterinary Public Health, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Norma Labarthe
- Programa de Bioética, Ética Aplicada e Saúde Coletiva, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Bruno B Chomel
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | | | - Haydar Ozpinar
- Graduate School of Health Sciences, Istanbul Gedik University, 34876, İstanbul, Turkey
| | - Hyung-Chul Rah
- Research Institute of Veterinary Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, South Korea
| | - Javier Millán
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Miguel Servet 177, 50013, Zaragoza, Spain
- Fundación ARAID, Avda. de Ranillas, 50018, Zaragoza, Spain
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Flavya Mendes-de-Almeida
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Julie K Levy
- Maddie's Shelter Medicine Program, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32608, USA
| | | | | | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Associate Lab & Faculdade de Ciências, Universidade do Porto, Campus e Vairão, 4485-661, Vila do Conde, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.
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Analysis of Family Structure and Paternity Test of Tan Sheep in Yanchi Area, China. Animals (Basel) 2022; 12:ani12223099. [PMID: 36428327 PMCID: PMC9686711 DOI: 10.3390/ani12223099] [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: 10/09/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Tan sheep is a special breed of locally protected sheep in China, one of the best quality meat sheep in the world. Due to the unclear pedigree of the rams on the Ningxia Tan sheep breeding farm, we investigated 74 rams in the field and explored a new method for family division. Genomic DNA was extracted from the blood of breeding rams. Using Plink software, GCTA tools and R language, we analyzed the genetic structure, kinship, and inbreeding coefficient of the breeding sheep, which revealed the genetic relationship between the individuals. The results showed that there was no obvious clustering phenomenon in the PCA, and the genetic background of the samples was similar. The G matrix and IBS distance matrix indicated that most individuals were far away from each other. Paternity testing identified 24 pairs of unknown parent-child pairs, and all the Tan sheep could be divided into 12 families, which provided a reference for sheep breeding. The average inbreeding coefficient based on the ROH of this population was 0.049, so there was a low degree of inbreeding and the rams in the field were able to maintain high genetic diversity. Overall, we explored a more accurate method through paternity and kinship analysis; it provides a scientific basis for pedigree construction, which has an important application value for Tan sheep breeding.
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Dementieva NV, Shcherbakov YS, Tyshchenko VI, Terletsky VP, Vakhrameev AB, Nikolaeva OA, Ryabova AE, Azovtseva AI, Mitrofanova OV, Peglivanyan GK, Reinbah NR, Griffin DK, Romanov MN. Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds. Genes (Basel) 2022; 13:genes13101876. [PMID: 36292761 PMCID: PMC9601448 DOI: 10.3390/genes13101876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.
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Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence: (N.V.D.); (M.N.R.)
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Anatoly B. Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anna E. Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Grigoriy K. Peglivanyan
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia R. Reinbah
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence: (N.V.D.); (M.N.R.)
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Chebo C, Betsha S, Melesse A. Chicken genetic diversity, improvement strategies and impacts on egg productivity in Ethiopia: a review. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2067020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chencha Chebo
- Department of Animal Science, Arba Minch University, College of Agricultural Sciences, Arba Minch, Ethiopia
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
| | - Simret Betsha
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
| | - Aberra Melesse
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
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