1
|
Sveistiene R, Tapio M. SNPs in Sheep: Characterization of Lithuanian Sheep Populations. Animals (Basel) 2021; 11:ani11092651. [PMID: 34573614 PMCID: PMC8467540 DOI: 10.3390/ani11092651] [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: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/05/2021] [Indexed: 11/16/2022] Open
Abstract
In Lithuania, there are two recognised native sheep breeds: old native Lithuanian Coarsewooled and Lithuanian Blackface. In addition, in 2005, primitive Heidschnucke-type Skudde sheep were imported to Lithuania and were argued to possibly represent a lost Lithuanian sheep type. The aim of the study was to investigate the genetic variation in the two Lithuanian native sheep breeds, compare them with the imported Skudde sheep and establish the historical patterns of admixture and the genetic relatedness of Lithuanian sheep to British, Central European and Nordic sheep breeds included in the SheepHapMap study. In total, 72 individuals, representing two Lithuanian native and imported Skudde sheep breeds, were genotyped using a Neogen 12K Illumina Infinium chip. The population analysis was carried out by model-based clustering, principal component analysis and neighbour net analysis, and showed similar patterns for the Lithuanian sheep populations. Lithuanian Coarsewooled and Skudde in Lithuania have unique divergence and possibly some shared ancestry, while the Lithuanian Blackface conforms to a modern synthetic breed. The study clearly showed that the Coarsewooled and the Skudde breeds are distinct from each other. Historical data strongly suggest that the Coarsewooled breed represents a local breed, while the Skudde origin is less directly linked to the geographical area of modern-day Lithuania. Within the modern-day Lithuanian context, the Lithuanian Coarsewooled sheep is very important historical sheep type for conservation.
Collapse
Affiliation(s)
- Ruta Sveistiene
- Animal Science Institute, Lithuanian University of Health Sciences, 82317 Baisogala, Lithuania
- Correspondence: ; Tel.: +370-61214095
| | - Miika Tapio
- Natural Resources Institute Finland, 00790 Helsinki, Finland;
| |
Collapse
|
2
|
An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds. Animals (Basel) 2021; 11:ani11072016. [PMID: 34359144 PMCID: PMC8300386 DOI: 10.3390/ani11072016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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.
Collapse
|
3
|
Placental Characteristics Classification of Various Native Turkish Sheep Breeds. Animals (Basel) 2021; 11:ani11040930. [PMID: 33805958 PMCID: PMC8064391 DOI: 10.3390/ani11040930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The aim of this study was to classify placental characteristics of Akkaraman, Morkaraman, Karayaka, Awassi, Malya, and Bafra native sheep breeds using the hierarchical clustering method. As a result, six breeds were separated into three clusters: the first cluster consisted of Bafra, Karayaka, and Awassi breeds; the second consisted of Akkaraman and Malya breeds; and the third cluster included only the Morkaraman breed. Abstract The aim of this study was to classify placental characteristics of Akkaraman, Morkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds using the hierarchical clustering method. In total, 240 individual data records were used as experimental material. Placental characteristics such as total cotyledon surface area, small and large cotyledon length, small cotyledon depth, etc. were used as explanatory variables to classify the breeds’ characteristics. Hierarchical clustering was used with the nearest neighbour method with Euclidean distance in order to classify the sheep breeds’ variations. As a result, six breeds were separated into three clusters: the first cluster consisted of Bafra, Karayaka, and Awassi breeds; the second consisted of Akkaraman and Malya breeds; and the third cluster included only the Morkaraman breed. Bafra and Karayaka were pointed as the nearest breeds, with a similarity of 98.7% in terms of placental characteristics. The similarity rate of the Akkaraman and Malya breeds was at a level of 97.5%, whereas it was 96.8% for Bafra, Karayaka, and Awassi breeds. The similarity of Akkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds was estimated as 95.7%. The overall similarity was found to be at a level of 93.2% among sheep breeds. The outcomes of the study might be useful as a selection tool for reproductivity and can be used to select the breed to be reared.
Collapse
|
4
|
Xia Q, Wang X, Pan Z, Zhang R, Wei C, Chu M, Di R. Genetic diversity and phylogenetic relationship of nine sheep populations based on microsatellite markers. Arch Anim Breed 2021; 64:7-16. [PMID: 34084899 PMCID: PMC8160997 DOI: 10.5194/aab-64-7-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/02/2020] [Indexed: 11/11/2022] Open
Abstract
The objective of this study was to assess the genetic diversity and
phylogenetic relationship of nine sheep populations, including two famous
high prolific populations and seven popular mutton populations raised in
China. Overall, these sheep populations in this study exhibited a rich
genetic diversity. Both the expected heterozygosity and Nei's unbiased gene
diversity ranged from 0.64 to 0.75, with the lowest value found in Dorset sheep (DST) and
the highest in Hu sheep (HUS) and Ba Han sheep (BAS). The polymorphic information content (PIC) varied between 0.59 in DST and 0.71 in HUS and BAS. Specifically, for
individual breeds, the small-tail Han sheep (STH) and the four introduced populations did not
display the expected diversity; therefore more attention should be paid to
the maintenance of diversity during management of these populations. The
results of un-weighted pair-group method (UPGMA) phylogenetic tree and structure analysis indicated that the
nine investigated populations can be divided into two groups. Suffolk (SUF) and DST
were clustered in one group, and the other group can be further divided into
three clusters: German Mutton Merino (GMM)–BAS–Bamei Mutton sheep (BAM), HUS–STH and Du Han (DOS)–Dorper (DOP). This clustering result is
consistent with sheep breeding history. TreeMix analysis also hinted at the
possible gene flow from GMM to SUF. Together, an in-depth view of genetic
diversity and genetic relationship will have important implications for
breed-specific management.
Collapse
Affiliation(s)
- Qing Xia
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Zhangyuan Pan
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Rensen Zhang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Caihong Wei
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Ran Di
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| |
Collapse
|
5
|
Bordin F, Dalvit C, Caldon M, Zulian L, Colamonico R, Trincanato S, Mock B, Reale S, Mutinelli F, Granato A. Genetic variability following selection for scrapie resistance in six autochthonous sheep breeds in the province of Bolzano (northern Italy). J Anim Breed Genet 2020; 137:395-406. [PMID: 32314834 DOI: 10.1111/jbg.12478] [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: 01/14/2020] [Revised: 03/17/2020] [Accepted: 03/22/2020] [Indexed: 11/28/2022]
Abstract
Scrapie is an ovine transmissible spongiform encephalopathy, and its susceptibility is associated with polymorphisms in the prion protein gene (PRNP). Genetic selection is currently the most effective mean for eradication of the susceptible VRQ allele in favour of resistant ARR allele. Maintenance of genetic diversity should be one of the major objectives in breeding programmes, especially in endangered breeds, and genetic information are an excellent alternative to pedigree data where these information are missing. The aim of our study was to determine changes of genetic variability in six native sheep breeds from autonomous province of Bolzano, northern Italy, following simulation of scrapie selection scenarios. A total of 684 rams were investigated for PRNP polymorphisms and for 10 microsatellite loci to estimate genetic variability. Across all loci, a total of 163 alleles were detected with a mean of 10.4 alleles per locus. Average observed (Ho) and unbiased expected (uHe) heterozygosity overall loci were 0.74 and 0.78, respectively, showing a statistically significant deviation from Hardy-Weinberg equilibrium (HWE) in all breeds. This heterozygosity deficit was confirmed by a positive fixation index (Fis), determining a moderate inbreeding in each breed. Simulating a soft selection, where only rams having at least a VRQ allele should be excluded from reproduction, Ho, uHe and Fis values remained almost unchanged, indicating that genetic variability should not be affected by the removal of these individuals. With a mild selection scenario, considering only rams with at least one ARR allele, we observed a decrease in the mean alleles per breed (8.9) and the maintenance of heterozygosity deficiency, except for two breeds, where it was any longer significant. These results showed that selection strategies allowing use of heterozygous as well homozygous ARR rams might be the right compromise to improve resistance to scrapie and to do not dramatically affect genetic variability of these breeds.
Collapse
Affiliation(s)
- Fulvio Bordin
- Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Chiara Dalvit
- Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Mauro Caldon
- Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Laura Zulian
- Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Rosa Colamonico
- Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | | | - Barbara Mock
- Verband der Südtiroler Kleintierzüchter, Bolzano, Italy
| | - Stefano Reale
- Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy
| | - Franco Mutinelli
- Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Anna Granato
- Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| |
Collapse
|
6
|
Duruz S, Flury C, Matasci G, Joerin F, Widmer I, Joost S. A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON). PLoS One 2017; 12:e0176362. [PMID: 28453561 PMCID: PMC5408993 DOI: 10.1371/journal.pone.0176362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/10/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs. METHODOLOGY/WEB PORTAL IMPLEMENTATION The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch. RESULTS/SIGNIFICANCE GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland.
Collapse
Affiliation(s)
- Solange Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Giona Matasci
- Institute of Earth Surface Dynamics, Faculty of Geosciences and Environment, University of Lausanne, Lausanne, Switzerland
| | - Florent Joerin
- Institut de Géomatique, Génie d’Environnement et Construction (G2C), Haute-Ecole d’Ingénierie et de Gestion du Canton de Vaud (HEIG-VD), Yverdon-les-Bains, Switzerland
| | - Ivo Widmer
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| |
Collapse
|
7
|
E GX, Zhong T, Ma YH, Gao HJ, He JN, Liu N, Zhao YJ, Zhang JH, Huang YF. Conservation genetics in Chinese sheep: diversity of fourteen indigenous sheep (Ovis aries) using microsatellite markers. Ecol Evol 2016; 6:810-7. [PMID: 26865968 PMCID: PMC4739567 DOI: 10.1002/ece3.1891] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 11/13/2015] [Accepted: 11/23/2015] [Indexed: 11/10/2022] Open
Abstract
The domestic sheep (Ovis aries) has been an economically and culturally important farm animal species since its domestication around the world. A wide array of sheep breeds with abundant phenotypic diversity exists including domestication and selection as well as the indigenous breeds may harbor specific features as a result of adaptation to their environment. The objective of this study was to investigate the population structure of indigenous sheep in a large geographic location of the Chinese mainland. Six microsatellites were genotyped for 611 individuals from 14 populations. The mean number of alleles (±SD) ranged from 7.00 ± 3.69 in Gangba sheep to 10.50 ± 4.23 in Tibetan sheep. The observed heterozygote frequency (±SD) within a population ranged from 0.58 ± 0.03 in Gangba sheep to 0.71 ± 0.03 in Zazakh sheep and Minxian black fur sheep. In addition, there was a low pairwise difference among the Minxian black fur sheep, Mongolian sheep, Gansu alpine merino, and Lanzhou fat-tailed sheep. Bayesian analysis with the program STRUCTURE showed support for 3 clusters, revealing a vague genetic clustering pattern with geographic location. The results of the current study inferred high genetic diversity within these native sheep in the Chinese mainland.
Collapse
Affiliation(s)
- Guang-Xin E
- College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization Southwest University Chongqing 400716 China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan province Sichuan Agricultural University Chengdu Sichuan 625014 China
| | - Yue-Hui Ma
- Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS) Beijing 100193 China
| | - Hui-Jiang Gao
- Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS) Beijing 100193 China
| | - Jian-Ning He
- College of Animal Science and Technology Qingdao Agricultural University Qingdao 266109 China
| | - Nan Liu
- College of Animal Science and Technology Qingdao Agricultural University Qingdao 266109 China
| | - Yong-Ju Zhao
- College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization Southwest University Chongqing 400716 China
| | - Jia-Hua Zhang
- College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization Southwest University Chongqing 400716 China
| | - Yong-Fu Huang
- College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization Southwest University Chongqing 400716 China
| |
Collapse
|
8
|
Abstract
Domestic animals represent an extremely useful model for linking genotypic and phenotypic variation. One approach involves identifying allele frequency differences between populations, using F(ST), to detect selective sweeps. While simple to calculate, FST may generate false positives due to aspects of population history. This prompted the development of hapFLK, a metric that measures haplotype differentiation while accounting for the genetic relationship between populations. The focus of this paper was to apply hapFLK in sheep with available SNP50 genotypes. The hapFLK approach identified a known selective sweep on chromosome 10 with high precision. Further, five regions were identified centered on genes with strong evidence for positive selection (COL1A2, NCAPG, LCORL, and RXFP2). Estimation of global F(ST) revealed many more genomic regions, providing empirical data in support of published simulation-based results concerning elevated type I error associated with F(ST) when it is being used to characterize sweep regions. The findings, while conducted using sheep SNP data, are likely to be applicable across those domestic animal species that have undergone artificial selection for desirable phenotypic traits.
Collapse
|
9
|
Leroy G, Danchin-Burge C, Palhière I, SanCristobal M, Nédélec Y, Verrier E, Rognon X. How do introgression events shape the partitioning of diversity among breeds: a case study in sheep. Genet Sel Evol 2015; 47:48. [PMID: 26080856 PMCID: PMC4470023 DOI: 10.1186/s12711-015-0131-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 06/01/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND From domestication to the current pattern of differentiation, domestic species have been influenced by reticulate evolution with multiple events of migration, introgression, and isolation; this has resulted in a very large number of breeds. In order to manage these breeds and their genetic diversity, one must know the current genetic structure of the populations and the relationships among these. This paper presents the results of a genetic diversity analysis on an almost exhaustive sample of the sheep breeds reared in France. Molecular characterization was performed with a set of 21 microsatellite markers on a collection of 49 breeds that include five breed types: meat, hardy meat, dairy, high prolificacy and patrimonial breeds. RESULTS Values of expected heterozygosity ranged from 0.48 to 0.76 depending on the breed, with specialized meat breeds exhibiting the lowest values. Neighbor-Net, multidimensional analysis or clustering approaches revealed a clear differentiation of the meat breeds compared to the other breed types. Moreover, the group that clustered meat breeds included all the breeds that originated from the United Kingdom (UK) and those that originated from crossbreeding between UK breeds and French local breeds. We also highlighted old genetic introgression events that were related to the diffusion of Merino rams to improve wool production. As a result of these introgression events, especially that regarding the UK breeds, the breeds that were clustered in the 'meat type cluster' exhibited the lowest contribution to total diversity. That means that similar allelic combinations could be observed in different breeds of this group. CONCLUSIONS The genetic differentiation pattern of the sheep breeds reared in France results from a combination of factors, i.e. geographical origin, historic gene flow, and breed use. The Merino influence is weaker than that of UK breeds, which is consistent with how sheep use changed radically at the end of 19(th) century when wool-producing animals (Merino-like) were replaced by meat-producing breeds. These results are highly relevant to monitor and manage the genetic diversity of sheep and can be used to set priorities in conservation programs when needed.
Collapse
Affiliation(s)
- Grégoire Leroy
- AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, F-75231, Paris 05, France. .,INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352, Jouy-en-Josas, France.
| | | | - Isabelle Palhière
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31326, Castanet-Tolosan, France. .,Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31076, Toulouse, France. .,Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31326, Castanet-Tolosan, France.
| | - Magali SanCristobal
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31326, Castanet-Tolosan, France. .,Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31076, Toulouse, France. .,Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d'Élevage, F-31326, Castanet-Tolosan, France.
| | - Yann Nédélec
- AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, F-75231, Paris 05, France. .,INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352, Jouy-en-Josas, France.
| | - Etienne Verrier
- AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, F-75231, Paris 05, France. .,INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352, Jouy-en-Josas, France.
| | - Xavier Rognon
- AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, F-75231, Paris 05, France. .,INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78352, Jouy-en-Josas, France.
| |
Collapse
|
10
|
Fine-scale population structure analysis of seven local Swiss sheep breeds using genome-wide SNP data. ACTA ACUST UNITED AC 2014. [DOI: 10.1017/s2078633614000253] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
11
|
Wei C, Lu J, Xu L, Liu G, Wang Z, Zhao F, Zhang L, Han X, Du L, Liu C. Genetic structure of Chinese indigenous goats and the special geographical structure in the Southwest China as a geographic barrier driving the fragmentation of a large population. PLoS One 2014; 9:e94435. [PMID: 24718092 PMCID: PMC3981790 DOI: 10.1371/journal.pone.0094435] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 03/17/2014] [Indexed: 01/02/2023] Open
Abstract
Background China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demograogic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers. Methodology/Principal Findings Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (HS of 0.644) and high population diversity at the species level (HT value of 0.737) were estimated. Significant moderate population differentiation was detected (FST value of 0.129). Significant excess homozygosity (FIS of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China. Conclusions/Significance Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human’s migration history throughout China. This study provides a fundamental genetic profile for the conservation of these populations and better to understand the domestication process and origin of Chinese goats.
Collapse
Affiliation(s)
- Caihong Wei
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Jian Lu
- National Center of Preservation & Utilization of Genetic Resources of Animal, National Animal Husbandry Service, Beijing, People’s Republic of China
| | - Lingyang Xu
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Gang Liu
- National Center of Preservation & Utilization of Genetic Resources of Animal, National Animal Husbandry Service, Beijing, People’s Republic of China
| | - Zhigang Wang
- National Center of Preservation & Utilization of Genetic Resources of Animal, National Animal Husbandry Service, Beijing, People’s Republic of China
| | - Fuping Zhao
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Li Zhang
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Xu Han
- National Center of Preservation & Utilization of Genetic Resources of Animal, National Animal Husbandry Service, Beijing, People’s Republic of China
| | - Lixin Du
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- * E-mail: (LD); (CL)
| | - Chousheng Liu
- National Center of Preservation & Utilization of Genetic Resources of Animal, National Animal Husbandry Service, Beijing, People’s Republic of China
- * E-mail: (LD); (CL)
| |
Collapse
|
12
|
Zhong T, Han J, Guo J, Zhao Q, Fu B, He X, Jeon J, Guan W, Ma Y. Genetic diversity of Chinese indigenous sheep breeds inferred from microsatellite markers. Small Rumin Res 2010. [DOI: 10.1016/j.smallrumres.2010.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
13
|
Álvarez I, Gutiérrez J, Royo L, Fernández I, Goyache F. Quantifying diversity losses due to selection for scrapie resistance in three endangered Spanish sheep breeds using microsatellite information. Prev Vet Med 2009; 91:172-8. [PMID: 19625092 DOI: 10.1016/j.prevetmed.2009.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 06/01/2009] [Accepted: 06/21/2009] [Indexed: 10/20/2022]
|