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

<p>Abstract</p> <p>Background</p> <p>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 <it>G. gallus</it>. 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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p

Balanus glandula: from North-West America to the west coast of South Africa

We report the occurrence of the North-East Pacific intertidal barnacle Balanus glandula in the south-western African shores of the Atlantic Ocean. In addition, an attempt is made to trace the origin of the South African population by comparing the distribution of haplotype groups of two molecular markers, cytochrome oxidase subunit I (COI) and elongation factor 1 (EF1-&#945;). The frequency of COI haplotypes in the South African specimens was most similar to that in specimens from Bodega Marine Laboratory and of Fort Bragg in Central California. Pairwise genetic distances demonstrated that the samples from Pillar Point were also similar to the Cape Town population. The frequency of EF1-&#945; haplotype groups from Cape Town was most similar to that of Cape Blanco, Cape Meares and Westport Jetty, and, with lower p-values, to the populations of Cape Mendocino and Heceta Head. Pairwise genetic distances demonstrated that samples from Vancouver Island, Bodega Marine Laboratory and Heceta Head were also similar to the Cape Town population. Results indicate that the population of B. glandula from South Africa is most similar to the population from the northern portion of the Oregonian faunal province. It is possible that this is the origin of the South African population. As a result of this invasion, B. glandula out-competed the native African chthamalid species, Chthamalus dentatus. Thus, C. dentatus is presently very rare on the Atlantic South African shores. Keywords: Balanus glandula, COI, competition, EF1-&#945;, haplotypes, invasion, South AfricaAfrican Journal of Marine Science 2008, 30(1): 85–9

The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity

Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60 K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes