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Mahammi FZ, Gaouar SBS, Laloë D, Faugeras R, Tabet-Aoul N, Rognon X, Tixier-Boichard M, Saidi-Mehtar N. A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls. J Anim Breed Genet 2015; 133:59-70. [DOI: 10.1111/jbg.12151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/04/2015] [Indexed: 11/29/2022]
Affiliation(s)
- F. Z. Mahammi
- Laboratoire de Génétique Moléculaire et Cellulaire; Université des Sciences et de la Technologie d'Oran-Mohamed BOUDIAF (USTO-MB); Oran Algérie
| | - S. B. S. Gaouar
- Laboratoire de Génétique Moléculaire et Cellulaire; Université des Sciences et de la Technologie d'Oran-Mohamed BOUDIAF (USTO-MB); Oran Algérie
- Département de biologie; Université de Tlemcen; Algérie
| | - D. Laloë
- INRA; UMR1313 Génétique Animale et Biologie Intégrative; Jouy-en-Josas France
| | - R. Faugeras
- INRA; Laboratoire d'analyses génétiques pour les espèces animales (LABOGENA); Jouy-en-Josas France
| | - N. Tabet-Aoul
- Département de Biotechnologie; Université d'Oran Es-Senia; Oran Algérie
| | - X. Rognon
- INRA; UMR1313 Génétique Animale et Biologie Intégrative; Jouy-en-Josas France
- AgroParisTech; UMR1313 Génétique Animale et Biologie Intégrative; Paris France
| | - M. Tixier-Boichard
- INRA; UMR1313 Génétique Animale et Biologie Intégrative; Jouy-en-Josas France
| | - N. Saidi-Mehtar
- Laboratoire de Génétique Moléculaire et Cellulaire; Université des Sciences et de la Technologie d'Oran-Mohamed BOUDIAF (USTO-MB); Oran Algérie
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Leroy G, Vernet E, Pautet MB, Rognon X. An insight into population structure and gene flow within pure-bred cats. J Anim Breed Genet 2013; 131:53-60. [PMID: 25099789 DOI: 10.1111/jbg.12043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 10/29/2012] [Accepted: 04/27/2013] [Indexed: 11/27/2022]
Abstract
Investigation of genetic structure on the basis of pedigree information requires indicators adapted to the specific context of the populations studied. On the basis of pedigree-based estimates of diversity, we analysed genetic diversity, mating practices and gene flow among eight cat populations raised in France, five of them being single breeds and three consisting of breed groups with varieties that may interbreed. When computed on the basis of coancestry rate, effective population sizes ranged from 127 to 1406, while the contribution of founders from other breeds ranged from 0.7 to 16.4%. In the five breeds, FIS ranged between 0.96 and 1.83%, with this result being related to mating practices such as close inbreeding (on average 5% of individuals being inbred within two generations). Within the three groups of varieties studied, FIT ranged from 1.59 to 3%, while FST¯ values were estimated between 0.04 and 0.91%, which was linked to various amounts of gene exchanges between subpopulations at the parental level. The results indicate that cat breeds constitute populations submitted to low selection intensity, contrasting with relatively high individual inbreeding level caused by close inbreeding practices.
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Affiliation(s)
- G Leroy
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Paris, France; UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
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Fotsa JC, Poné Kamdem D, Rognon X, Tixier-Boichard M, Fomunyam D, Choupamom J, Tchoumboué J, Manjeli Y, Bordas A. Etudes Comparees de la Croissance des Poules Locales (Gallus Gallus) Et D’une Souche Label Au Cameroun. ACTA ACUST UNITED AC 2011. [DOI: 10.4314/bahpa.v58i4.64235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Berthouly-Salazar C, Rognon X, Van TN, Gély M, Chi CV, Tixier-Boichard M, Bed'Hom B, Bruneau N, Verrier E, Maillard JC, Michaux JR. Vietnamese chickens: a gate towards Asian genetic diversity. BMC Genet 2010; 11:53. [PMID: 20565868 PMCID: PMC2897773 DOI: 10.1186/1471-2156-11-53] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 06/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. RESULTS A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69).The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. CONCLUSIONS In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation.
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Affiliation(s)
- C Berthouly-Salazar
- CIRAD, UPR AGIRS, Campus International de Baillarguet, F-34398 Montpellier, France.
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Berthouly C, Rognon X, Nhu Van T, Berthouly A, Thanh Hoang H, Bed'Hom B, Laloë D, Vu Chi C, Verrier E, Maillard JC. Genetic and morphometric characterization of a local Vietnamese swamp buffalo population. J Anim Breed Genet 2010; 127:74-84. [PMID: 20074189 DOI: 10.1111/j.1439-0388.2009.00806.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The water buffalo plays a key role in the socio-economy of South-East Asia as it is the main draught power for paddy rice cultivation. While in the Indian subcontinent the water buffalo is the riverine type, in South-East Asia the majority of buffaloes are of the swamp type. In the poor remote northern province of Ha Giang in Vietnam, improvement of the swamp buffalo breed may be one of the best ways to increase sustainability of farming systems. Therefore, analysis of the genetic structure of the province buffalo population is a prerequisite to any conservation or improvement project. A total of 1122 animals were described for 11 body and horn measurements for morphometric characterization. From this sample set, 744 animals were genotyped for 17 microsatellite markers. Also 17 animals from southern provinces of Vietnam were genotyped as a comparative sample. The results showed that genetic diversity as well as inbreeding value in the Ha Giang was high. The F(ST) values within the province and across Vietnam were low indicating that most of the population variation is explained by individual variability. Bayesian clustering analysis did not highlight the presence of subdivided populations. These results are useful for the implementation of a conservation and improvement strategy of the swamp buffalo in order to guarantee the householders' needs for sustainability of the farming system in the Ha Giang province.
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Leroy G, Verrier E, Meriaux JC, Rognon X. Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data. Anim Genet 2009; 40:323-32. [DOI: 10.1111/j.1365-2052.2008.01842.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Leroy G, Verrier E, Meriaux JC, Rognon X. Genetic diversity of dog breeds: between-breed diversity, breed assignation and conservation approaches. Anim Genet 2009; 40:333-43. [DOI: 10.1111/j.1365-2052.2008.01843.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Berthouly C, Leroy G, Van TN, Thanh HH, Bed'Hom B, Nguyen BT, Vu CC, Monicat F, Tixier-Boichard M, Verrier E, Maillard JC, Rognon X. Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations. BMC Genet 2009; 10:1. [PMID: 19133138 PMCID: PMC2628941 DOI: 10.1186/1471-2156-10-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 01/08/2009] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED Previous studies suggested that multiple domestication events in South and South-East Asia (Yunnan and surrounding areas) and India have led to the genesis of modern domestic chickens. Ha Giang province is a northern Vietnamese region, where local chickens, such as the H'mong breed, and wild junglefowl coexist. The assumption was made that hybridisation between wild junglefowl and Ha Giang chickens may have occurred and led to the high genetic diversity previously observed. The objectives of this study were i) to clarify the genetic structure of the chicken population within the Ha Giang province and ii) to give evidence of admixture with G. gallus. A large survey of the molecular polymorphism for 18 microsatellite markers was conducted on 1082 chickens from 30 communes of the Ha Giang province (HG chickens). This dataset was combined with a previous dataset of Asian breeds, commercial lines and samples of Red junglefowl from Thailand and Vietnam (Ha Noï). Measurements of genetic diversity were estimated both within-population and between populations, and a step-by-step Bayesian approach was performed on the global data set. RESULTS The highest value for expected heterozygosity (> 0.60) was found in HG chickens and in the wild junglefowl populations from Thailand. HG chickens exhibited the highest allelic richness (mean A = 2.9). No significant genetic subdivisions of the chicken population within the Ha Giang province were found. As compared to other breeds, HG chickens clustered with wild populations. Furthermore, the neighbornet tree and the Bayesian clustering analysis showed that chickens from 4 communes were closely related to the wild ones and showed an admixture pattern. CONCLUSION In the absence of any population structuring within the province, the H'mong chicken, identified from its black phenotype, shared a common gene pool with other chickens from the Ha Giang population. The large number of alleles shared exclusively between Ha Giang chickens and junglefowl, as well as the results of a Bayesian clustering analysis, suggest that gene flow has been taking place from junglefowl to Ha Giang chickens.
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Affiliation(s)
- C Berthouly
- CIRAD, UPR AGIRs, Campus International de Baillarguet, 34398 Montpellier Cedex 05, France.
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Berthouly C, Bed'Hom B, Tixier-Boichard M, Chen CF, Lee YP, Laloë D, Legros H, Verrier E, Rognon X. Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds. Anim Genet 2008; 39:121-9. [PMID: 18366475 DOI: 10.1111/j.1365-2052.2008.01703.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- C Berthouly
- AgroParisTech, UMR1236 Génétique et Diversité Animales, 16 rue Claude Bernard, 75321 Paris Cedex 05, France.
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Abstract
Pedigree data of nine French dog breeds, namely Barbet (BAR), Basset fauve de Bretagne (BAF), Beauceron (BEN), Berger des Pyrénées (BRP), Bouledogue Français (BUF), Braque Saint-Germain (BQG), Dogue de Bordeaux (DOB), Epagneul Breton (EPB) and Montagne des Pyrénées (MOP), were analysed. The effective numbers of ancestors of dogs born from 1997 to 2001 were equal to 6.7 (BAR), 40.2 (BAF), 36.5 (BEN), 16.0 (BRP), 37.0 (BUF), 13.1 (BQG), 28.9 (DOB), 33.3 (EPB) and 34.0 (MOP). The expected contributions of the major ancestors were found to be highly unbalanced in the EPB and BRP. The average coefficient of inbreeding of dogs born from 1997 to 2001 with both parents known was equal to 12.4% (BAR), 3.9% (BAF), 5.4% (BEN), 7.2% (BRP), 3.3% (BUF), 6.0% (BQG), 4.1% (DOB), 4.5% (EPB) and 4.0% (MOP). These values were found to be significantly higher than the average coefficient of kinship between the male and the female parents of these animals, except in the BAR and BQG, revealing an usual practice of mating between related animals. The results are discussed in relation with the demographic situation and the use of each breed. The method used to class an endangered breed and the ways to preserve the genetic variability, when necessary, are evoked.
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Affiliation(s)
- G Leroy
- UMR Génétique et diversité animales, Institut national de la recherche agronomique/Institut national agronomique Paris-Grignon, 16 rue Claude Bernard, Paris cedex 05, France.
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Abstract
Introgressive hybridization has an important evolutionary significance in terms of gene diversity and speciation. Among the major groups of vertebrates, fish show a strong propensity to hybridize. In order to highlight the possible occurrence of gene flow between two tilapia species, Oreochromis niloticus and O. aureus, a comparison of allozyme and mitochondrial DNA (mtDNA) polymorphism was performed on sympatric and allopatric populations of these two species. Nuclear data were congruent with the morphological identification of O. niloticus and O. aureus populations. In opposition, the mtDNA analysis resulted in two strictly differentiated groups which did not follow the morphological and nuclear DNA classification. The first group consisted of East African O. niloticus populations and the second included all the O. aureus populations and the West African O. niloticus populations. Moreover, in some cases, the same sequences were detected in both species. These data strongly support a differential introgression of mtDNA from O. aureus to O. niloticus involving all the West African area. This work points out the risk of misinterpretation of mtDNA or nuclear DNA data when only one single class of marker is used.
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Affiliation(s)
- X Rognon
- Département des Sciences Animales, Institut National Agronomique Paris-Grignon, 16 rue Claude Bernard, 75231 Paris cedex 05, France.
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Abstract
Variation of the ND5/6 mtDNA fragment was studied in six Nile tilapia populations using PCR and RFLP analysis. The observed variation allows a strict discrimination between eastern and western African populations.
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Affiliation(s)
- X Rognon
- Departement des Sciences Animales, Institut National Agronomique Paris-Grignon, 16 rue Claude Bernard, Paris Cedex 05, 75231, France
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