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Evelyne M, Nguyen Van D, Amelyne D, Nguyen Hoang T, Duc LD, Nassim M, Dinh TV, Frédéric F. High-resolution genomic analysis of four local Vietnamese chicken breeds. J Anim Breed Genet 2022; 139:583-595. [PMID: 35665968 DOI: 10.1111/jbg.12723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 05/07/2022] [Indexed: 11/29/2022]
Abstract
In Vietnam, local chicken breeds account for over 70% of the national poultry population. Although these breeds are abundant, their productivity is low and their use is threatened by the extensive importation of foreign productive breeds. In this context, conservation programmes targeting several emblematic breeds have been established. The goal of these programmes was to characterize endangered breeds and maintain a pool of characteristic birds for preserving their genetic heritage. To contribute to these programmes, we comprehensively characterized four Vietnamese local chicken breeds (Dong Tao, Ho, Mia and Mong) at the genomic level using high-density single-nucleotide polymorphism (SNP) genotyping. Despite originating in geographically close areas, Dong Tao and Ho were evidently different from each other as well as from Mong and Mia, which shared a more recent common ancestor. The genomic inbreeding coefficient revealed high homozygosity amongst the four breeds (10%-20%). The observation of clear differentiation at the genomic level supported the presence of distinct breeds; nonetheless, the occurrence of crossbred birds in a presumably purebred sample demonstrated the need to apply genomic tools to unambiguously assign the birds to the correct breed. Moreover, the occurrence of substantial inbreeding and the presence of subgroups in certain breeds warranted attention to create future nuclei for use in the conservation of these local breeds.
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Affiliation(s)
- Moyse Evelyne
- Biostatistics & Bioinformatics, FARAH-PAD, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
| | - Duy Nguyen Van
- Biostatistics & Bioinformatics, FARAH-PAD, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium.,Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Dor Amelyne
- Biostatistics & Bioinformatics, FARAH-PAD, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
| | - Thinh Nguyen Hoang
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Luc Do Duc
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Moula Nassim
- Biostatistics & Bioinformatics, FARAH-PAD, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
| | - Ton Vu Dinh
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Farnir Frédéric
- Biostatistics & Bioinformatics, FARAH-PAD, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
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Nguyen TH, Nguyen CX, Luu MQ, Nguyen AT, Bui DH, Pham DK, Do DN. Mathematical models to describe the growth curves of Vietnamese Ri chicken. BRAZ J BIOL 2021; 83:e249756. [PMID: 34755795 DOI: 10.1590/1519-6984.249756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
Ri chicken is the most popular backyard chicken breed in Vietnam, but little is known about the growth curve of this breed. This study compared the performances of models with three parameters (Gompertz, Brody, and Logistic) and models containing four parameters (Richards, Bridges, and Janoschek) for describing the growth of Ri chicken. The bodyweight of Ri chicken was recorded weekly from week 1 to week 19. Growth models were fitted using minpack.lm package in R software and Akaike's information criterion (AIC), Bayesian information criterion (BIC), and root mean square error (RMSE) were used for model comparison. Based on these criteria, the models having four parameters showed better performance than the ones with three parameters, and the Richards model was the best one for males and females. The lowest and highest value of asymmetric weights (α) were obtained by Bridges and Brody models for each of sexes, respectively. Age and weight estimated by the Richard model were 8.46 and 7.51 weeks and 696.88 and 487.58 g for males and for females, respectively. Differences in the growth curves were observed between males and female chicken. Overall, the results suggested using the Richards model for describing the growth curve of Ri chickens. Further studies on the genetics and genomics of the obtained growth parameters are required before using them for the genetic improvement of Ri chickens.
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Affiliation(s)
- T H Nguyen
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - C X Nguyen
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - M Q Luu
- Ministry of Science and Technology, Hanoi, Vietnam
| | - A T Nguyen
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - D H Bui
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - D K Pham
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - D N Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Canada
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Samaraweera AM, Liyanage R, Ibrahim MN, Okeyo AM, Han J, Silva P. High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers. Front Genet 2021; 12:723706. [PMID: 34650594 PMCID: PMC8505892 DOI: 10.3389/fgene.2021.723706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (F IS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative F IS were observed. The positive F IS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.
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Affiliation(s)
- Amali Malshani Samaraweera
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla, Sri Lanka
| | - Ranga Liyanage
- Postgraduate Institute of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - Ally Mwai Okeyo
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Pradeepa Silva
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
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Nguyen Hoang T, Do HTT, Bui DH, Pham DK, Hoang TA, Do DN. Evaluation of non-linear growth curve models in the Vietnamese indigenous Mia chicken. Anim Sci J 2021; 92:e13483. [PMID: 33462943 DOI: 10.1111/asj.13483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 12/31/2022]
Abstract
Understanding of animal growth is important for the improvement of management and feeding practices; however, little is known about the growth curve in Vietnamese indigenous chicken. This study was performed to determine the most appropriate models for describing the growth curve of Vietnamese Mia chicken. The study evaluated the performances of the Logistic, Gompertz, Richards, and Bridges models of body weights in 224 Mia chickens. Models were fitted using minpack.lm package in R software and Akaike's information criterion and Bayesian information criterion were used for model comparison. Based on these criteria, the Gompertz and Bridges were the best models for males and females, respectively. Estimated asymmetric weights (α) were ranged from 2,241.91 ± 14.74 (g) (Logistic) to 2,623.86 ± 30.23 (g) (Gompertz) for males and from 1,537.36 ± 10.97 (g) (Logistic) and 1,958.36 ± 72.92 (g) (Bridges) for females, respectively. The age at the inflection point was estimated from 9.32 to 10.5 weeks and from 8.51 to 9.86 weeks for males and females, respectively. In conclusion, the Gompertz model is the most suitable model for describing the growth curve of Mia chicken. The parameters obtained from growth models could help define feeding programs to meet nutritional needs from hatching to the age of maximum growth, reproduction programs, and marketing strategies.
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Affiliation(s)
- Thinh Nguyen Hoang
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Huong T T Do
- Bac Giang Agriculture and Forestry University, Bac Giang, Vietnam
| | - Doan H Bui
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Dang K Pham
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Tuan A Hoang
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Duy N Do
- Institute of Research and Development, Duy Tan University, Danang, Vietnam.,Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
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Olschewsky A, Hinrichs D. An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds. Animals (Basel) 2021; 11:2016. [PMID: 34359144 DOI: 10.3390/ani11072016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The number of local farm animal breeds is declining worldwide. However, these breeds have different degrees of genetic diversity. Measuring genetic diversity is important for the development of conservation strategies and, therefore, various genomic analysis techniques are available. The aim of the present work was to shed light on the use of these techniques in diversity studies of local breeds. In summary, a total of 133 worldwide studies that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that over time, almost all available genomic techniques were used and various diversity parameters were calculated. Therefore, the present results provide a comprehensive overview of the application of these techniques in the field of local breeds. This can provide helpful insights into the advancement of the conservation of breeds with high genetic diversity. Abstract Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.
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Pham LD, Do DN, Nam LQ, Van Ba N, Ninh PH, Thuy DP, Son PV, Thieu PC. Evaluation of genetic diversity and population structure in four indigenous duck breeds in Vietnam. Anim Biotechnol 2021; 33:1065-1072. [PMID: 33451256 DOI: 10.1080/10495398.2020.1868485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
This study characterized genetic diversity and population structure of four indigenous Vietnamese duck breeds and an exotic breed for setting the conservation priority. A total of 200 samples from four duck breeds (Sincheng, Minhhuong, Muongchieng and Bauben) and an exotic breed (Supermeat) were genotyped for fifteen microsatellite markers. The average number of alleles per locus was 14.07. A moderate genetic diversity was observed for indigenous breeds as mean of observed and expected heterozygosity as Ho = 0.50 and He = 0.57, respectively. The Bauben had the lowest values of Ho (0.41) and He (0.48) while Sincheng had the highest values of Ho (0.6) and He (0.69), respectively. The inbreeding coefficients (FIS) ranged from 0.12 to 0.16, and all breeds were significantly under heterozygote deficit. Nei's genetic distance was the shortest between Minhhuong and Muongkhieng. The discriminant analysis of principal components of studied breeds resulted in four genetic clusters. The Minhhuong and Muongkhieng breeds joined the same genetic cluster while other breeds had their own clusters. These results indicated that the possibility to combine Minhhuong and Muongkhieng for reducing the cost of conservation and suggested that conservation of the Bauben should be prioritized to avoid inbreeding depression and genetic drift.
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Affiliation(s)
- Lan Doan Pham
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Duy Ngoc Do
- Institute of Research and Development, Duy Tan University, Danang, Vietnam.,Faculty of Environmental and Chemical Engineering, Duy Tan University, Danang, Vietnam
| | - Le Quang Nam
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Nguyen Van Ba
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Pham Hai Ninh
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Doan Phuong Thuy
- Faculty of Veterinary and Animal Husbandry, BacGiang Agriculture & Forestry University, Bacgiang, Vietnam
| | - Pham Van Son
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Pham Cong Thieu
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
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Nguyen Van D, Moula N, Moyse E, Do Duc L, Vu Dinh T, Farnir F. Productive performance and egg and meat quality of two indigenous poultry breeds in Vietnam, Ho and Dong Tao, fed on commercial feed. Animals (Basel) 2020; 10:ani10030408. [PMID: 32121548 PMCID: PMC7143232 DOI: 10.3390/ani10030408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/17/2020] [Accepted: 02/21/2020] [Indexed: 11/16/2022] Open
Abstract
The objective of this work was the evaluation of the meat production and laying performances, and the meat and egg quality of two breeds of Vietnamese broiler chickens, Ho and Dong Tao, fed on a commercial diet. In a survey, we continuously recorded for 28 weeks, the data on the production performance and meat quality of 250 chicks from each breed. We investigated egg laying and egg quality using 36 Ho and 32 Dong Tao hens during 52 weeks of laying. The growth patterns were similar for the two breeds. Feed conversion ratios were also similar, and demonstrated the low efficiency of these two breeds when compared to commercial broilers. Slaughter age proved to affect several carcass yield characteristics, showing that slaughtering between 16 and 20 weeks might be better than at the usual age of 28 weeks. Yield, carcass composition and meat quality differed between the two studied breeds. The eggs production and number of embryonated eggs were low for the two breeds when compared to other breeds, with a lower hatching performance in Ho than in Dong Tao. In summary, the production performances of Ho and Dong Tao chickens were low, even when birds were fed a commercial diet. The study demonstrates the need to find ways to improve the production and reproduction performances of these animals, in order to contribute to the program of conservation and exploitation of these two breeds.
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Affiliation(s)
- Duy Nguyen Van
- Centre for Interdisciplinary Research on Rural Development, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi 100803, Vietnam;
- Fundamental and Applied Research in Animal and Health (FARAH) Department of Veterinary Management of Animal Resources, Faculty of Veterinary Medicine, University of Liege, Liege 4000, Belgium; (N.M.); (E.M.)
| | - Nassim Moula
- Fundamental and Applied Research in Animal and Health (FARAH) Department of Veterinary Management of Animal Resources, Faculty of Veterinary Medicine, University of Liege, Liege 4000, Belgium; (N.M.); (E.M.)
| | - Evelyne Moyse
- Fundamental and Applied Research in Animal and Health (FARAH) Department of Veterinary Management of Animal Resources, Faculty of Veterinary Medicine, University of Liege, Liege 4000, Belgium; (N.M.); (E.M.)
| | - Luc Do Duc
- Faculty of Animal Science, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi 100803, Vietnam;
| | - Ton Vu Dinh
- Centre for Interdisciplinary Research on Rural Development, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi 100803, Vietnam;
- Faculty of Animal Science, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi 100803, Vietnam;
- Correspondence: (T.V.D.); (F.F.)
| | - Frederic Farnir
- Fundamental and Applied Research in Animal and Health (FARAH) Department of Veterinary Management of Animal Resources, Faculty of Veterinary Medicine, University of Liege, Liege 4000, Belgium; (N.M.); (E.M.)
- Correspondence: (T.V.D.); (F.F.)
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Winton CL, McMahon R, Hegarty MJ, McEwan NR, Davies‐Morel MCG, Morgan C, Nash DM. Genetic diversity within and between British and Irish breeds: The maternal and paternal history of native ponies. Ecol Evol 2020; 10:1352-1367. [PMID: 32076519 PMCID: PMC7029099 DOI: 10.1002/ece3.5989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 11/09/2022] Open
Abstract
The UK and Ireland have many native pony breeds with historical and cultural importance as well as being a source of uncharacterized genetic diversity. However, there is a lack of comprehensive research investigating their genetic diversity and phylogenetic interrelationships. Many studies contain a limited number of pony breeds or small sample sizes for these breeds. This may result in erroneous grouping of pony breeds that otherwise have intricate interrelationships with each other and are not evaluated correctly when placed as a token subset of a larger dataset. This is the first study that specifically investigates the genetic diversity within and between British and Irish native pony breeds using large sample numbers from locations of their native origin. This study used a panel of microsatellite markers and sequence analysis of the mitochondrial control region to analyze the genetic diversity within and between 11 pony breeds from Britain and Ireland. A large dataset was collected (a total of 485 animals were used for mtDNA analysis and 450 for microsatellite analysis), and previously published data were used to place the British and Irish ponies in a global context. The native ponies of Britain and Ireland were found to have had a complex history, and the interrelationships between the breeds were revealed. Overall, high levels of genetic diversity were maintained in native breeds, although some reduction was evident in small or isolated populations (Shetland, Carneddau, and Section C). Unusual mitochondrial diversity distribution patterns were apparent for the Carneddau and Dartmoor, although among breeds and global haplogroups there was a high degree of haplotype sharing evident, well-represented within British and Irish ponies. Ancestral maternal diversity was maintained by most populations, particularly the Fells and Welsh ponies, which exhibited rare and ancient lineages. The maternal and paternal histories of the breeds are distinct, with male-biased crossings between native breeds, and other shared influences, likely Arabs and Thoroughbreds, are apparent. The data generated herein provide valuable information to guide and implement the conservation of increasingly rare native genetic resources.
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Affiliation(s)
- Clare L. Winton
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Robert McMahon
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- Molecular HaematologyHaematology LaboratoryRoyal Infirmary of EdinburghEdinburghUK
| | - Matthew J. Hegarty
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Neil R. McEwan
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- School of Pharmacy and Life SciencesRobert Gordon UniversityAberdeenUK
| | | | - Charly Morgan
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Deborah M. Nash
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
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Di Lorenzo P, Ceccobelli S, Panella F, Attard G, Lasagna E. The role of mitochondrial DNA to determine the origin of domestic chicken. WORLD POULTRY SCI J 2015; 71:311-8. [DOI: 10.1017/s0043933915000318] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Zhang Y, Wang L, Bian Y, Wang Z, Xu Q, Chang G, Chen G. Marginal diversity analysis of conservation of Chinese domestic duck breeds. Sci Rep 2019; 9:13141. [PMID: 31511604 PMCID: PMC6739371 DOI: 10.1038/s41598-019-49652-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/29/2019] [Indexed: 11/24/2022] Open
Abstract
The present study aimed to systematically evaluate the genetic diversity of Chinese domestic duck breeds and ensure the most effective allocation and usage of conservation funds. We first performed an analysis of DNA genetic distance in 21 duck breeds by measuring short tandem repeats. Then, we calculated the extinction probability, contribution rate, and marginal diversity for each breed. The results showed that the extinction rate of the Zhongshan duck, Guangxi duck, and Ji'an duck were the highest at 0.67, 0.59, and 0.59, respectively, and that of the Linwu duck, Jinding duck, and Gaoyou duck were the lowest at 0.15, 0.18, and 0.19, respectively. The current diversity of populations was 7.72 and the expected diversity in five hundred years is 5.14 ± 1.15. The marginal diversity of the Chinese Muscovy duck was the largest (-2.20), accounting for 42.61% of the expected diversity, followed by the Guangxi duck (-0.49, 9.44%), whereas the Jinding duck was the smallest (-0.12; 2.32%). The protection potency of the Chinese Muscovy duck was the largest (0.61), followed by Guangxi duck (0.29), whereas the Jinding duck was the smallest (0.02). This study provides a reference for determining the conservation priority of Chinese domestic duck breeds or genetic resources.
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Affiliation(s)
- Yang Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China.
| | - Laidi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Youqing Bian
- Jiangsu Sci-tech Demonstration Garden of Modern Animal Husbandy, Taizhou, 225300, Jiangsu, People's Republic of China
| | - Zhaoshan Wang
- Jiangsu Eco Food Company Limited, Suqian, 223600, Jiangsu, People's Republic of China
| | - Qi Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China
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Fathi M, El-Zarei M, Al-Homidan I, Abou-Emera O. Genetic diversity of Saudi native chicken breeds segregating for naked neck and frizzle genes using microsatellite markers. Asian-Australas J Anim Sci 2018; 31:1871-1880. [PMID: 29879833 PMCID: PMC6212745 DOI: 10.5713/ajas.18.0041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/07/2018] [Indexed: 11/27/2022]
Abstract
Objective Recently, there has been an increasing interest in conservation of native genetic resources of chicken on a worldwide basis. Most of the native chicken breeds are threatened by extinction or crossing with ecotypes. Methods Six Saudi native chicken breeds including black naked neck, brown frizzled, black, black barred, brown and gray were used in the current study. The aim of the current study was to evaluate genetic diversity, relationship and population structure of Saudi native chicken breeds based on 20 microsatellite markers. Results A total of 172 alleles were detected in Saudi native chicken breeds across all 20 microsatellite loci. The mean number of alleles per breed ranged from 4.35 in gray breed to 5.45 in normally feathered black with an average of 8.6 alleles. All breeds were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the brown breed (72%) and the greatest in the frizzled and black barred populations (78%). Higher estimate of expected heterozygosity (0.68) was found in both black breeds (normal and naked neck) compared to the other chicken populations. All studied breeds showed no inbreeding within breed (negative inbreeding coefficient [FIS]). The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed three main clusters, with naked neck and gray breeds in one cluster, and brown and frizzled in the second cluster leaving black barred in a separate one. Conclusion It could be concluded that the genetic information derived from the current study can be used as a guide for genetic improvement and conservation in further breeding programs. Our findings indicate that the Saudi native chicken populations have a rich genetic diversity and show a high polymorphism.
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Affiliation(s)
- Moataz Fathi
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia.,Department of Poultry Production, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra 11241, Cairo, Egypt
| | - Mohamed El-Zarei
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia.,Department of Animal Production, Faculty of Agriculture, Suez Canal University 41522, Ismailia, Egypt
| | - Ibrahim Al-Homidan
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia
| | - Osama Abou-Emera
- Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim 51452, Saudi Arabia.,Department of Poultry Breeding, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt
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Bortoluzzi C, Crooijmans RPMA, Bosse M, Hiemstra SJ, Groenen MAM, Megens HJ. The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity. Heredity (Edinb) 2018; 121:564-78. [PMID: 29588508 DOI: 10.1038/s41437-018-0072-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 11/08/2022] Open
Abstract
Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60 K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.
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Pham M, Tran X, Berthouly-salazar C, Tixier-boichard M, Chen C, Lee Y. Monitoring of genetic diversity in Taiwan conserved chickens assessed by pedigree and molecular data. Livest Sci 2016; 184:85-91. [DOI: 10.1016/j.livsci.2015.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Lyimo CM, Weigend A, Msoffe PL, Eding H, Simianer H, Weigend S. Global diversity and genetic contributions of chicken populations from African, Asian and European regions. Anim Genet 2014; 45:836-48. [DOI: 10.1111/age.12230] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2014] [Indexed: 01/15/2023]
Affiliation(s)
- C. M. Lyimo
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; 31535 Neustadt-Mariensee Germany
- Animal Breeding and Genetics Group; Department of Animal Sciences; Georg-August-Universität Göttingen; 37075 Göttingen Germany
- Sokoine University of Agriculture; PO Box 3000 Morogoro Tanzania
| | - A. Weigend
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; 31535 Neustadt-Mariensee Germany
| | - P. L. Msoffe
- Sokoine University of Agriculture; PO Box 3000 Morogoro Tanzania
- School of Biological Sciences; University of Dodoma; PO Box 259 Dodoma Tanzania
| | - H. Eding
- Animal Evaluations Unit; CRV; PO Box 454, 6800 AL Arnhem The Netherlands
| | - H. Simianer
- Animal Breeding and Genetics Group; Department of Animal Sciences; Georg-August-Universität Göttingen; 37075 Göttingen Germany
| | - S. Weigend
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; 31535 Neustadt-Mariensee Germany
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A.m. Osman S, Nishibori M. Phylogenetic Analysis of South East Asian Countries Chickens Based on Mitochondrial DNA Variations. J Poult Sci 2014; 51:248-61. [DOI: 10.2141/jpsa.0130190] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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