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Zhao QB, López-Cortegano E, Oyelami FO, Zhang Z, Ma PP, Wang QS, Pan YC. Conservation Priorities Analysis of Chinese Indigenous Pig Breeds in the Taihu Lake Region. Front Genet 2021; 12:558873. [PMID: 33747032 PMCID: PMC7966724 DOI: 10.3389/fgene.2021.558873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022] Open
Abstract
Most indigenous pig resources are known to originate from China. Thus, establishing conservation priorities for these local breeds is very essential, especially in the case of limited conservation funds. Therefore, in this study, we analyzed 445 individuals belonging to six indigenous breeds from the Taihu Lake Region, using a total of 131,300 SNPs. In order to determine the long-term guidelines for the management of these breeds, we analyzed the level of diversity in the metapopulation following a partition of diversity within and between breed subpopulations, using both measures of genic and allelic diversity. From the study, we found that the middle Meishan (MMS) pig population contributes the most (22%) to the total gene diversity while the Jiaxing black (JX) pig population contributes the most (27%) to the gene diversity between subpopulations. Most importantly, when we consider one breed is removed from the meta-population, the first two breeds prioritized should be JX pig breed and Fengjing pig breed followed by small Meishan (SMS), Mizhu (MI), and Erhualian (EH) if we pay more attention to the gene diversity between subpopulations. However, if the priority focus is on the total gene diversity, then the first breed to be prioritized would be the Shawutou (SW) pig breed followed by JX, MI, EH, and Fengjing (FJ). Furthermore, we noted that if conservation priority is to be based on the allelic diversity between subpopulations, then the MI breed should be the most prioritized breed followed by SW, Erhuanlian, and MMS. Summarily, our data show that different breeds have different contributions to the gene and allelic diversity within subpopulations as well as between subpopulations. Our study provides a basis for setting conservation priorities for indigenous pig breeds with a focus on different priority criteria.
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Affiliation(s)
- Qing-Bo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Eugenio López-Cortegano
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Favour Oluwapelumi Oyelami
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Pei-Pei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qi-Shan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yu-Chun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
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Kierkegaard LS, Groeneveld LF, Kettunen A, Berg P. The status and need for characterization of Nordic animal genetic resources. ACTA AGR SCAND A-AN 2020. [DOI: 10.1080/09064702.2020.1722216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | | | - Anne Kettunen
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Nofima AS, Ås, Norway
| | - Peer Berg
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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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] [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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Poulsen NA, Rosengaard AK, Szekeres BD, Gregersen VR, Jensen HB, Larsen LB. Protein heterogeneity of bovine β-casein in Danish dairy breeds and association of rare β-casein F with milk coagulation properties. ACTA AGR SCAND A-AN 2017. [DOI: 10.1080/09064702.2017.1342858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- N. A. Poulsen
- Department of Food Science, Aarhus University, Tjele, Denmark
| | | | - B. D. Szekeres
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - V. R. Gregersen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - H. B. Jensen
- Department of Food Science, Aarhus University, Tjele, Denmark
| | - L. B. Larsen
- Department of Food Science, Aarhus University, Tjele, Denmark
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Iso-Touru T, Tapio M, Vilkki J, Kiseleva T, Ammosov I, Ivanova Z, Popov R, Ozerov M, Kantanen J. Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe. Anim Genet 2016; 47:647-657. [DOI: 10.1111/age.12473] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 12/31/2022]
Affiliation(s)
- T. Iso-Touru
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
| | - M. Tapio
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
| | - J. Vilkki
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
| | - T. Kiseleva
- All-Russian Research Institute for Farm Animal Genetics and Breeding; Russian Academy of Sciences; 55-a Moskovskoe Shosse St. Petersburg-Pushkin 199601 Russia
| | - I. Ammosov
- Board of Agricultural Office of Eveno-Bytantaj Region; Batagay-Alyta 678580 The Sakha Republic (Yakutsk) Russia
| | - Z. Ivanova
- Yakutian Research Institute of Agriculture; Yakutsk Sakha 677007 Russia
| | - R. Popov
- Yakutian Research Institute of Agriculture; Yakutsk Sakha 677007 Russia
| | - M. Ozerov
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
- Department of Biology; University of Turku; Turku 20014 Finland
| | - J. Kantanen
- Green Technology; Natural Resources Institute Finland (Luke); Jokioinen 31600 Finland
- Department of Environmental and Biological Sciences; University of Eastern Finland; PO Box 1627 Kuopio 70211 Finland
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Abstract
Most donkey and local horse breeds are vulnerable to extinction as mechanization of agriculture progress throughout the world. The present study analyzed the pedigree and herd records of the donkey Asinina de Miranda breed (RAM), identifying genealogical and human factors that may affect the breed genetic diversity in the future and suggesting suitable strategies to breed preservation, early on the conservation program. The breeding rate was very low, with a ratio of foaling/live animals of 0.23 (178/760). The estimated number of founders and ancestors contributing to the reference population was 128 and 121. The number of founder herds in the reference population was 64, with an effective number of founder herds for the reference population of 7.6. The mean age of herd owners was 65.50 ± 0.884 years, with a negative association among the herd size and owner's age (P<0.001). In contrast, the size of the herd and the ownership of a male were both positively associated (P<0.001) with the herd number of in-born foals. Both the owners' age and the herd location (RAM home region v. dispersal region) were negatively associated with the foaling number (P<0.001). The main identified risk factors were: low breeding rates; low number of males and their unequal contribution to the genetic pool; unequal contribution of the herds to genetic pool; and advanced age of herd owners.
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Ginja C, Gama LT, Cortes O, Delgado JV, Dunner S, García D, Landi V, Martín-Burriel I, Martínez-Martínez A, Penedo MCT, Rodellar C, Zaragoza P, Cañon J. Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers. Genet Sel Evol 2013; 45:35. [PMID: 24079454 PMCID: PMC3851275 DOI: 10.1186/1297-9686-45-35] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 08/22/2013] [Indexed: 11/10/2022] Open
Abstract
Background Determining the value of livestock breeds is essential to define conservation priorities, manage genetic diversity and allocate funds. Within- and between-breed genetic diversity need to be assessed to preserve the highest intra-specific variability. Information on genetic diversity and risk status is still lacking for many Creole cattle breeds from the Americas, despite their distinct evolutionary trajectories and adaptation to extreme environmental conditions. Methods A comprehensive genetic analysis of 67 Iberoamerican cattle breeds was carried out with 19 FAO-recommended microsatellites to assess conservation priorities. Contributions to global diversity were investigated using alternative methods, with different weights given to the within- and between-breed components of genetic diversity. Information on Iberoamerican plus 15 worldwide cattle breeds was used to investigate the contribution of geographical breed groups to global genetic diversity. Results Overall, Creole cattle breeds showed a high level of genetic diversity with the highest level found in breeds admixed with zebu cattle, which were clearly differentiated from all other breeds. Within-breed kinships revealed seven highly inbred Creole breeds for which measures are needed to avoid further genetic erosion. However, if contribution to heterozygosity was the only criterion considered, some of these breeds had the lowest priority for conservation decisions. The Weitzman approach prioritized highly differentiated breeds, such as Guabalá, Romosinuano, Cr. Patagonico, Siboney and Caracú, while kinship-based methods prioritized mainly zebu-related breeds. With the combined approaches, breed ranking depended on the weights given to the within- and between-breed components of diversity. Overall, the Creole groups of breeds were generally assigned a higher priority for conservation than the European groups of breeds. Conclusions Conservation priorities differed significantly according to the weight given to within- and between-breed genetic diversity. Thus, when establishing conservation programs, it is necessary to also take into account other features. Creole cattle and local isolated breeds retain a high level of genetic diversity. The development of sustainable breeding and crossbreeding programs for Creole breeds, and the added value resulting from their products should be taken into consideration to ensure their long-term survival.
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Affiliation(s)
- Catarina Ginja
- Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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Wellmann R, Hartwig S, Bennewitz J. Optimum contribution selection for conserved populations with historic migration. Genet Sel Evol 2012; 44:34. [PMID: 23153196 PMCID: PMC3807754 DOI: 10.1186/1297-9686-44-34] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 10/17/2012] [Indexed: 11/11/2022] Open
Abstract
Background In recent decades, local varieties of domesticated animal species have been frequently crossed with economically superior breeds which has resulted in considerable genetic contributions from migrants. Optimum contribution selection by maximizing gene diversity while constraining breeding values of the offspring or vice versa could eventually lead to the extinction of local breeds with historic migration because maximization of gene diversity or breeding values would be achieved by maximization of migrant contributions. Therefore, other objective functions are needed for these breeds. Results Different objective functions and side constraints were compared with respect to their ability to reduce migrant contributions, to increase the genome equivalents originating from native founders, and to conserve gene diversity. Additionally, a new method for monitoring the development of effective size for breeds with incomplete pedigree records was applied. Approaches were compared for Vorderwald cattle, Hinterwald cattle, and Limpurg cattle. Migrant contributions could be substantially decreased for these three breeds, but the potential to increase the native genome equivalents is limited. Conclusions The most promising approach was constraining migrant contributions while maximizing the conditional probability that two alleles randomly chosen from the offspring population are not identical by descent, given that both descend from native founders.
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Affiliation(s)
- Robin Wellmann
- Institute of Animal Husbandry and Animal Breeding, University of Hohenheim, D-70599 Stuttgart, Germany.
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Honda T, Sasazaki S, Oyama K, Mukai F, Nomura T. Sampling method for estimating neutral allele frequency in a pedigreed population. J Anim Breed Genet 2012; 129:226-33. [PMID: 22583327 DOI: 10.1111/j.1439-0388.2011.00968.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The estimated allele frequency at neutral DNA marker loci is a fundamental parameter for establishing a conservation scheme for a set of livestock breeds. In this study, we propose a novel 'minimum distance (MD) method' for estimating neutral allele frequencies, which minimizes the error by the use of pedigree information. Using computer simulation and actual microsatellite data for a pedigreed cattle population, the performance of the proposed method was compared with that of conventional random sampling (RND). MD manifests a promising superiority to RND, irrespective of the sample size and the depth of pedigree. It is theoretically demonstrated that the error of the estimates depends on both the sample size and the distance of founder allele frequencies between the sampled and the non-sampled individuals. MD samples individuals so as to minimize the latter source of estimation error.
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Affiliation(s)
- Takeshi Honda
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Hyogo, Japan.
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Relative breed contributions to neutral genetic diversity of a comprehensive representation of Iberian native cattle. Animal 2011; 5:1323-34. [DOI: 10.1017/s1751731111000267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Tapio I, Tapio M, Li MH, Popov R, Ivanova Z, Kantanen J. Estimation of relatedness among non-pedigreed Yakutian cryo-bank bulls using molecular data: implications for conservation and breed management. Genet Sel Evol 2010; 42:28. [PMID: 20626845 PMCID: PMC2909159 DOI: 10.1186/1297-9686-42-28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 07/13/2010] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Yakutian cattle, the last remaining native cattle breed in Siberia, are well adapted to the extreme sub-arctic conditions. Nowadays only ca. 1200 purebred animals are left in Yakutia. The semen of six Yakutian bulls was stored in a cryo-bank without any pedigree documentation because of the traditional free herding style of the population. METHODS To clarify the genetic relatedness between these bulls and to provide recommendations to use their semen in future conservation and breed management programs, we have analysed 30 autosomal microsatellites and mitochondrial DNA sequences in 60 individuals including the six for which semen has been stored. Four relatedness estimators were calculated. In addition, we assessed the value of the cryo-bank bulls for the preservation of genetic variation of the contemporary Yakutian cattle by calculating allelic and gene diversity estimates and mean molecular coancestries. RESULTS On the basis of microsatellite variability, including the Yakutian cryo-bank bulls increases the allelic variation in the contemporary population by 3% and in the male subpopulation by 13%. In terms of the mean molecular coancestries, they are less related to the contemporary cow population than the breeding bulls and therefore could be used to reduce inbreeding in the living population. Although 30 loci are insufficient to resolve definitely their relatedness categories, the data suggest four pairs of cryo-bank bulls as possible half-sibs. CONCLUSIONS Our results show that even relatively limited cryo-bank storage of semen can carry allelic variation through a bottleneck. We propose a breeding scheme based on the rotation of breeding females and the division of cryo-bank bulls into three groups. Thus, if molecular data (e.g. autosomal microsatellite genotypes) for the contemporary population are available and based on relatively small-scale laboratory analyses, it is possible to avoid serious mistakes in their use for breeding applications. The approach suggested here based on the use of Yakutian cryo-bank semen can be easily extended to cryo-bank materials of other animals in future breeding programs.
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Affiliation(s)
- Ilma Tapio
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, FI-31600 Finland
| | - Miika Tapio
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, FI-31600 Finland
| | - Meng-Hua Li
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, FI-31600 Finland
| | - Ruslan Popov
- Yakutian Research Institute of Agriculture, 677002 Yakutsk, Sakha, Russia
| | - Zoya Ivanova
- Yakutian Research Institute of Agriculture, 677002 Yakutsk, Sakha, Russia
| | - Juha Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, FI-31600 Finland
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Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 285] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
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Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
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Toro MA, Fernández J, Caballero A. Molecular characterization of breeds and its use in conservation. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.07.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gizaw S, Komen H, Windig JJ, Hanotte O, van Arendonk JA. Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity. GENETICS SELECTION EVOLUTION 2008. [DOI: 10.1051/gse:2008012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Laloë D, Jombart T, Dufour AB, Moazami-Goudarzi K. Consensus genetic structuring and typological value of markers using multiple co-inertia analysis. Genet Sel Evol 2007. [DOI: 10.1051/gse:2007021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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