Global diversity and genetic contributions of chicken populations from African, Asian and European regions.

Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (FST ) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour-Net genetic clustering and structure analysis revealed two main groups of Asian and north-west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north-west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds.

Lyimo CM ，Weigend A ，Msoffe PL ，Eding H ，Simianer H ，Weigend S ... -  《-》

Genetic diversity and conservation of South African indigenous chicken populations.

In this study, we compare the level and distribution of genetic variation between South African conserved and village chicken populations using microsatellite markers. In addition, diversity in South African chickens was compared to that of a reference data set consisting of other African and purebred commercial lines. Three chicken populations Venda, Ovambo and Eastern Cape and four conserved flocks of the Venda, Ovambo, Naked Neck and Potchefstroom Koekoek from the Poultry Breeding Resource Unit of the Agricultural Research Council were genotyped at 29 autosomal microsatellite loci. All markers were polymorphic. Village chicken populations were more diverse than conservation flocks. structure software was used to cluster individuals to a predefined number of 2 ≤ K ≤ 6 clusters. The most probable clustering was found at K = 5 (95% identical runs). At this level of differentiation, the four conservation flocks separated as four independent clusters, while the three village chicken populations together formed another cluster. Thus, cluster analysis indicated a clear subdivision of each of the conservation flocks that were different from the three village chicken populations. The contribution of each South African chicken populations to the total diversity of the chickens studied was determined by calculating the optimal core set contributions based on Marker estimated kinship. Safe set analysis was carried out using bootstrapped kinship values calculated to relate the added genetic diversity of seven South African chicken populations to a set of reference populations consisting of other African and purebred commercial broiler and layer chickens. In both core set and the safe set analyses, village chicken populations scored slightly higher to the reference set compared to conservation flocks. Overall, the present study demonstrated that the conservation flocks of South African chickens displayed considerable genetic variability that is different from that of the assumed founder populations (village chickens).

Mtileni BJ ，Muchadeyi FC ，Maiwashe A ，Groeneveld E ，Groeneveld LF ，Dzama K ，Weigend S ... -  《-》

Genetic diversity within chicken populations from different continents and management histories.

Intra-population variation was assessed in 1970 chickens from 64 populations using 29 autosomal microsatellites. On average, 95% of the loci were polymorphic across populations. In 1456 (c. 83%) of the 1763 combinations of populations and polymorphic loci, no departure from Hardy-Weinberg equilibrium was observed. On average, there were 11.4 alleles per locus and 3.6 alleles per population across loci. Within populations, the average observed heterozygote frequency was 0.46, with a range between 0.20 and 0.64. Dagu, a Chinese population, and the Red Jungle Fowl (Gallus gallus gallus) had the highest average heterozygote frequencies at 0.64 and 0.63 respectively. An inbred line used as a reference population for comparison showed the lowest average of observed heterozygote frequency (0.05), followed by the European population Hamburger Lackhuhn, whose average observed heterozygote frequency was 0.20. A total of 32 private alleles (alleles detected in only one population) for 20 loci were found in 18 populations. H'mong chickens, a Vietnamese population, carried the largest number of private alleles at five, followed by the Red Jungle Fowl with four private alleles. Genetic diversity within populations was low in the NW European fancy breeds and high in the non-commercial Asian populations, in agreement with population management history.

Granevitze Z ，Hillel J ，Chen GH ，Cuc NT ，Feldman M ，Eding H ，Weigend S ... -  《-》

East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis.

Understanding the complex origin of domesticated populations is of vital importance for understanding, preserving and exploiting breed genetic diversity. Here, we aim to assess Asian contributions to European traditional breeds and western commercial chickens for mitochondrial genetic diversity. To this end, a 365-bp fragment of the chicken mtDNA D-loop region of 16 Dutch fancy breeds (113 individuals) was surveyed, comprising almost the entire breed diversity of The Netherlands. We also sequenced the same fragment for 160 commercial birds representing all important commercial types from multiple commercial companies that together represent more than 50% of the worldwide commercial value. We identified 20 different haplotypes. The haplotypes clustered into five clades. The commonest clade (E-clade) supposedly originates from the Indian subcontinent. In addition, both in commercial chicken and Dutch fancy breeds, many haplotypes were found with a clear East Asian origin. However, the erratic occurrence of many different East Asian mitochondrial clades indicates that there were many independent instances where breeders used imported exotic chickens for enhancing local breeds. Nucleotide diversity and haplotype diversity analyses showed the influence of the introgression of East Asian chicken on genetic diversity. All populations that had haplotypes of multiple origin displayed high inferred diversity, as opposed to most populations that had only a single mitochondrial haplotype signature. Most fancy breeds were found to have a much lower within-population diversity compared to broilers and layers, although this is not the case for mitochondrial estimates in fancy breeds that have multiple origin haplotypes.

Dana N ，Megens HJ ，Crooijmans RP ，Hanotte O ，Mwacharo J ，Groenen MA ，van Arendonk JA ... -  《-》

Genetic diversity of local Yunnan chicken breeds and their relationships with Red Junglefowl.

Yunnan is situated in the Southwest China and encompasses regions having high biodiversity, including habitats for several ancestral species of domestic animals such as chicken. Domestic chickens in Yunnan were kept by peoples of varied ethnic and economic backgrounds living in highly varied geographic environments. To identify the genetic background of Yunnan domestic chickens and their relationships with Red Junglefowl, we applied 28 widely used microsatellite DNA markers to genotype 340 birds from 7 chicken breeds and Red Junglefowl indigenous to Yunnan. Among a total of 342 alleles identified, 121 (35.4%) were breed specific, with Red Junglefowl harboring most microsatellite alleles (23). High levels of heterozygosity were observed within populations indicated by a mean unbiased HE value of 0.663, which was higher than the reported for most populations elsewhere. The FIS value of domestic populations ranged from -0.098-0.005, indicating a lack of inbreeding among these populations. A high proportion of significant departures (89) from the 224 HWE tests for each locus in each population reflected an excess of heterozygosity and population substructure. Individual assignment tests, high FST values (0.1757-0.3015), and Nei's DA genetic distances (0.4232-0.6950) indicated clear differentiation among these populations. These observations, along with the close genetic distance between indigenous domestic populations and Red Junglefowl, were consistent with the primitive and ancestral state of Yunnan indigenous chickens. Protecting the unique variants of these indigenous poultry varieties from contamination with commercial breeds might provide values for improving modern agricultural livestock and breeding programs. Thus, the current study may benefit breeding management and conservation efforts.

Huo JL ，Wu GS ，Chen T ，Huo HL ，Yuan F ，Liu LX ，Ge CR ，Miao YW ... -  《Genetics and Molecular Research》