The present study was conducted to evaluate the genetic diversity and relationships of 9 native Japanese long-tailed chicken breeds (Shoukoku, Koeyoshi, Kurokashiwa, Minohiki, Ohiki, Onagadori, Satsumadori, Toumaru, and Toutenkou) together with 2 commercial breeds (White Leghorn and White Plymouth Rock), using 40 polymorphic microsatellite markers covering 23 linkage groups. The 8 breeds mentioned, except for Shoukoku and 2 commercial breeds, were believed to be descendants derived from crossings of the ancestor of Shoukoku and some other breeds. Three to 14 alleles per locus were detected across all the breeds. The mean number of alleles per locus, the mean unbiased expected heterozygosity, and the mean polymorphic information content ranged from 2.60 (Minohiki) to 4.07 (Shoukoku), from 0.293 (Koeyoshi) to 0.545 (Satsumadori), and from 0.250 (Koeyoshi) to 0.478 (Satsumadori), respectively. The mean fixation coefficient of subpopulation within the total population of 9 Japanese long-tailed breeds showed that approximately 38% of the genetic variation was caused by breed differences and 62% was due to differences among individuals. Toumaru had the largest number of breed-specific alleles with relatively high (>20%) frequency. In the phylogenetic tree of 11 breeds constructed by the neighbor-joining method from modified Cavalli-Sforza chord genetic distance measure, White Leghorn and White Plymouth Rock clustered together apart from the Japanese breeds. Among the Japanese long-tailed breeds, Toumaru, Kurokashiwa, and Koeyoshi showed relatively far distance from the other breeds. The Ohiki, Onagadori, Shoukoku, and Toutenkou were grouped into the same branch. Minohiki and Satsumadori were also clustered together. Kurokashiwa was not genetically close to Shoukoku, differing from a traditional hypothsis. It was confirmed in the present study that the microsatellite is a suitable tool to evaluate genetic diversity and relationships in chicken breeds.

The aims of the current study were to assess genetic diversity, conduct genetic characterization, and evaluate usefulness of an individual assignment test for 12 commercial chicken lines using 40 microsatellite markers. A total of 268 distinct alleles were observed across the 12 lines, and 42 of the 268 alleles (15.7%) were unique to only 1 line. Mean observed heterozygosity within a line ranged from 0.295 to 0.664, and the highest value was obtained from 1 of the White Plymouth Rock lines. Significant deviations from the Hardy-Weinberg equilibrium were observed at several locus-line combinations, showing excess of heterozygotes in many cases. As a whole, genetic differences among the lines estimated by the fixation index were high at 29.8%, whereas higher genetic similarity was observed among White Leghorn lines despite their different breeding histories. Assignment test could correctly allocate individuals at the line level to their origins, with a high accuracy (96.6%). Individual-based genetic characterization would be a usable step to conserve chicken genetic resources. Here, guidelines for future breeding and management of these lines by the poultry industry are provided.

Next-generation sequencing technologies permit rapid and cost-effective identification of numerous putative microsatellite loci. Here, from the genome sequences of Japanese quail, we developed microsatellite markers containing dinucleotide repeats and employed these for characterisation of genetic diversity and population structure. A total of 385 individuals from 12 experimental and one wild-derived Japanese quail lines were genotyped with newly developed autosomal markers. The maximum number of alleles, expected heterozygosity and polymorphic information content (PIC) per locus were 10, 0.80 and 0.77 respectively. Approximately half of the markers were highly informative (PIC ≥ 0.50). The mean number of alleles per locus and observed heterozygosity within a line were in the range of 1.3-4.1 and 0.11-0.53 respectively. Compared with the wild-derived line, genetic diversity levels were low in the experimental lines. Genetic differentiation (FST ) between all pairs of the lines ranged from 0.13 to 0.83. Genetic clustering analyses based on multilocus genotypes of individuals showed that most individuals formed clearly defined clusters corresponding to the origins of the lines. These results suggest that Japanese quail experimental lines are highly structured. Microsatellite markers developed in this study may be effective for future genetic studies of Japanese quail.

A wide diversity of domesticated chicken breeds exist due to artificial selection on the basis of human interests. Miniature variants (bantams) are eminently illustrative of the large changes from ancestral junglefowls. In this report, the genetic characterization of seven Japanese miniature chicken breeds and varieties, together with institute-kept Red Junglefowl, was conducted by means of typing 40 microsatellites located on 21 autosomes. We drew focus to genetic differentiation between the miniature chicken breeds and Red Junglefowl in particular. A total of 305 alleles were identified: 27 of these alleles (8.9%) were unique to the Red Junglefowl with high frequencies (>20%). Significantly high genetic differences (F(ST)) were obtained between Red Junglefowl and all other breeds with a range of 0.3901-0.5128. Individual clustering (constructed from combinations of the proportion of shared alleles and the neighbour-joining method) indicated high genetic divergence among breeds including Red Junglefowl. There were also individual assignments on the basis of the Bayesian and distance-based approaches. The microsatellite differences in the miniature chicken breeds compared to the presumed wild ancestor reflected the phenotypic diversity among them, indicating that each of these miniature chicken breeds is a unique gene pool.

The Onagadori is a distinguished chicken breed that is characterized by an extremely long tail in the male. In this breed, three different plumage colour varieties have been developed (black-breasted white, black-breasted red and white) in which the black-breasted white is believed to be the original colour of the Onagadori, based on historical records. To establish a conservation strategy, 176 birds were genotyped for autosomal microsatellites. Significant genetic distinctness was found between the original (black-breasted white) and two derivative varieties (F(ST) = 0.091 and 0.093). At the same time, a Bayesian model-based clustering revealed that the majority of individuals belonging to the black-breasted red and white varieties had an extremely low proportion of the genome shared with the original type (black-breasted white). This suggests that derivative varieties were created by crossing with other breeds, with low introgression of the original-type genome. We propose that the three plumage colour varieties should be treated as separate genetic units in a conservation programme.