A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls.

The objectives of this study were to characterize the genetic variability of village chickens from three agro-ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of French slow-growing chickens. Two populations of wild red jungle fowls were also genotyped to compare the range of diversity between domestic and wild fowls. A genetic diversity analysis was conducted both within and between populations. Multivariate redundancy analyses were performed to assess the relative influence of geographical location among Algerian ecotypes. The results showed a high genetic variability within the Algerian population, with 184 alleles and a mean number of 8.09 alleles per locus. The values of heterozygosity (He and Ho) ranged from 0.55 to 0.62 in Algerian ecotypes and were smaller than values found in Jungle fowl populations and higher than values found in commercial populations. Although the structuring analysis of genotypes did not reveal clear subpopulations within Algerian ecotypes, the supervised approach using geographical data showed a significant (p < 0.01) differentiation between the three ecotypes which was mainly due to altitude. Thus, the genetic diversity of Algerian ecotypes may be under the influence of two factors with contradictory effects: the geographical location and climatic conditions may induce some differentiation, whereas the high level of exchanges and gene flow may suppress it. Evidence of gene flow between commercial and Algerian local populations was observed, which may be due to unrecorded crossing with commercial chickens. Chicken ecotypes from western Algeria are characterized by a high genetic diversity and must be safeguarded as an important reservoir of genetic diversity.

An insight into population structure and gene flow within pure-bred cats.

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.

Vietnamese chickens: a gate towards Asian genetic diversity.

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.

Revealing fine scale subpopulation structure in the Vietnamese H'Mong cattle breed for conservation purposes.

BACKGROUND: During the last decades, there has been an acceleration of the loss of domestic animal biodiversity. For conservation purposes, the genetic diversity of the H'Mong cattle, an indigenous local breed was studied. Single-nucleotide polymorphisms (SNP) of the SRY gene and mtDNA D-Loop sequence were analysed to clarify the origin of the breed. The genetic diversity was assessed through genetic data with twenty-five FAO microsatellites, and morphometric data with five body measurements from 408 animals sampled from eight districts of the Ha Giang province. RESULTS: The SRY genes were all of the zebu type. Among the 27 mtDNA haplotypes, 12 haplotypes were of the taurine type and the remaining 15 of the zebu type. This indicates female taurine introgression in the zebu H'Mong. The observed and expected heterozygosity ranged from 0.616 to 0.673 and from 0.681 to 0.729 respectively according to district, with low genetic differentiation (F ST = 0.0076). Multivariate analysis on morphometric and genetic data shows a separation of districts into two groups following a south-west/north-east cline and admixture analysis confirmed the two clusters, but no differentiation of taurine introgression between clusters was observed. A possible admixture with the Yellow cattle breed from a neighbouring province was suggested through genetic data and householder interviews. CONCLUSIONS: In this study we demonstrate the interest of fine-scale sampling for the study of genetic structure of local breeds. Such a study allows avoiding erroneous conservation policies and on the contrary, proposes measures for conserving and limiting crossbreeding between the H'Mong and the Yellow cattle breeds.

Genetic and morphometric characterization of a local Vietnamese swamp buffalo population.

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.

Genetic diversity of dog breeds: between-breed diversity, breed assignation and conservation approaches.

Genetic relationships between 61 dog breeds were investigated, using a sampling of 1514 animals and a panel of 21 microsatellite markers. Based on the results from distance-based and Bayesian methods, breed constituted the main genetic structure, while groups including genetically close breeds showed a very weak structure. Depending on the method used, between 85.7% and 98.3% of dogs could be assigned to their breed, with large variations according to the breed. However, breed heterozygosity influenced assignment results differently according to the method used. Within-breed and between-breed diversity variations when breeds were removed were highly negatively correlated (r = -0.963, P < 0.0001), because of the genetic structure of the breed set.

Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data.

The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37-0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator (r = 0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier.

Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations.

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.

Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds.

French and Asian subsets of chicken breeds were first analysed using 22 microsatellites and then compared to the AVIANDIV European set using 14 loci. Positive correlations were observed between F(IT) or F(ST) and typological values or variance of markers using the multivariate analysis mcoa. The first axis of the multivariate representation separated Asian from European breeds, revealing breeds with Asian ancestor. Using all or 14 loci, correct assignation rate was always higher than 93%. The Weitzman index and the aggregate diversity D were calculated using 22 loci within French and Asian breeds. The French breed Coucou de Rennes and the Hua-Tung breed seemed to contribute the most to the global diversity of each subset. This approach on French-only breeds and then on French with AVIANDIV domestic breeds (14 loci) showed that the Marans breed contributed the most. The AVIANDIV framework could be useful to evaluate the genetic diversity of local breeds and to help in connecting national and regional conservation policies.

Genetic variability in French dog breeds assessed by pedigree data.

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.

Large extent of mitochondrial DNA transfer from Oreochromis aureus to O. niloticus in West Africa.

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.

Mitochondrial DNA differentiation among East and West African Nile tilapia populations

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.