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.

Chickens display a wide spectrum of phenotypic variations in quantitative traits such as egg-related traits. Quantitative trait locus (QTL) analysis is a statistical method used to understand the relationship between phenotypic (trait measurements) and genotypic data (molecular markers). We have performed QTL analyses for egg-related traits using an original resource population based on the Japanese Large Game (Oh-Shamo) and the White Leghorn breeds of chickens. In this article, we summarize the results of our extensive QTL analyses for 11 and 66 traits for egg production and egg quality, respectively. We reveal that at least 30 QTL regions on 17 different chromosomes affect phenotypic variation in egg-related traits. Each locus had an age-specific effect on traits, and a variety in effects was also apparent, such as additive, dominance, and epistatic-interaction effects. Although genome-wide association study (GWAS) is suitable for gene-level resolution mapping of GWAS loci with additive effects, QTL mapping studies enable us to comprehensively understand genetic control, such as chromosomal regions, genetic contribution to phenotypic variance, mode of inheritance, and age-specificity of both common and rare alleles. QTL analyses also describe the relationship between genotypes and phenotypes in experimental populations. Accumulation of QTL information, including GWAS loci, is also useful for studies of population genomics approached without phenotypic data in order to validate the identified genomic signatures of positive selection. The combination of QTL studies and next-generation sequencing techniques with uncharacterized genetic resources will enhance current understanding of the relationship between genotypes and phenotypes in livestock animals.

This is the first study in which genetic variability and relationships of a large number of Japanese chicken breeds were revealed along with those of several foreign breeds by using microsatellite DNA polymorphisms. Twenty-eight breeds (34 populations) of native Japanese chickens and seven foreign breeds or varieties were analyzed. The mean number of alleles per locus, the proportion of the polymorphic loci, and the expected average heterozygosity ranged from 1.75 to 4.70, from 0.55 to 1.00, and from 0.21 to 0.67, respectively. Microsatellite alleles being unique to a particular population were detected in some populations. The D A genetic distance between populations was obtained from allele frequency for every pair of the populations to construct a neighbor-joining tree. According to the phylogenetic tree, excluding a few exceptions, native Japanese chicken breeds and foreign breeds were clearly separated from each other. Furthermore, the tree topology divided native Japanese chickens into four main classes, which was almost in accordance with the classification based on body morphology; that is, (1) Cochin type, (2) Malay type, (3) layer type, and (4) intermediate type between Malay and layer types. This is the first finding for native Japanese chickens.

We performed a quantitative trait locus (QTL) analysis to map QTLs controlling shank length, body weight, and carcass weight in a resource family of 245 F2 birds developed from a cross of the large-sized, native, Japanese cockfighting breed, Oh-Shamo (Japanese Large Game), and the White Leghorn breed of chickens. Interval mapping revealed three significant QTLs for shank length on chromosomes 1, 4 and 24 at the experiment-wise 5% level, and a suggestive shank length QTL on chromosome 27 at the experiment-wise 10% level. For body weight two QTLs, one significant and the other suggestive, were identified on chromosomes 4 and 24, respectively. As expected, QTLs for carcass weight, which was highly correlated with body weight (r = 0.95), were detected at the same chromosomal locations as the detected body weight QTLs. Interestingly, the chromosomal locations containing these body weight and carcass weight QTLs coincided with those of two of the four shank length QTLs detected. No QTL with an epistatic interaction effect was discovered for any trait. The total contribution of all detected QTLs to genetic variance was 98.4%, 27.0% and 25.9% for shank length, body weight and carcass weight, respectively, indicating that most shank length QTLs have been identified but many body weight and carcass weight QTLs have been overlooked by the present analysis because of a low coverage rate of the 88 microsatellite markers used here (approximately 46% of the whole genome).

Excessive fat deposition adversely affects poultry production. In this study, we investigated growth, fat deposition, and hepatic mRNA expression of 13 lipid metabolism-related genes in three unique breeds of meat-type chickens with distinct breed origins and genetic relationships. One was Nagoya (NAG), a native Japanese breed, whereas the others were White Plymouth Rock (WPR) and White Cornish (WC), which have been used worldwide as the parental breeds of common broiler chickens. NAG chickens were phenotypically characterized by slow growth, lean body fat, and high gizzard and liver weights. In contrast, both WC and WPR chickens were characterized by rapid growth but high percentage of subcutaneous fat and abdominal fat weight, resulting from high feed intake. Among the three breeds, WC had the highest percentage of pectoral muscle weight, whereas WPR was the most obese. Among lipid metabolism-related genes, the expression of PPARA, PPARG, and CD36 was mostly associated with obesity. These results provide basic information for quantitative trait locus (QTL) analysis related to growth and fat traits in an F2 population of the lean NAG breed and the obese WPR breed of meat-type chickens in future.