Genetic Divergence in Domestic Japanese Quail Inferred from Mitochondrial DNA D-Loop and Microsatellite Markers

Mikiharu Nakano,Tzen-Yuh Chiang,Mitsuo Nunome,Makoto Mizutani,Ryo Tadano,Shinji Takahashi,Akira Fujiwara,Keijiro Nirasawa,Tomohiro Kono,Takaharu Kawashima,Ryoka Kawahara-Miki,Yoichi Matsuda

doi:10.1371/journal.pone.0169978

Abstract

To assess the genetic diversity of domestic Japanese quail (Coturnix japonica) populations, and their genetic relationships, we examined mitochondrial DNA (mtDNA) D-loop sequences and microsatellite markers for 19 Japanese quail populations. The populations included nine laboratory lines established in Japan (LWC, Quv, RWN, WE, AWE, AMRP, rb-TKP, NIES-L, and W), six meat-type quail lines reimported from Western countries (JD, JW, Estonia, NIES-Br, NIES-Fr, and NIES-Hn), one commercial population in Japan, and three wild quail populations collected from three Asian areas. The phylogenetic tree of mtDNA D-loop sequences revealed two distinct haplotype groups, Dloop-Group1 and Dloop-Group2. Dloop-Group1 included a dominant haplotype representing most of the quail populations, including wild quail. Dloop-Group2 was composed of minor haplotypes found in several laboratory lines, two meat-type lines, and a few individuals in commercial and wild quail populations. Taking the breeding histories of domestic populations into consideration, these results suggest that domestic quail populations may have derived from two sources, i.e., domestic populations established before and after World War II in Japan. A discriminant analysis of principal components and a Bayesian clustering analysis with microsatellite markers indicated that the domestic populations are clustered into four genetic groups. The two major groups were Microsat-Group1, which contained WE, and four WE-derived laboratory lines (LWC, Quv, RWN, and AWE), and Microsat-Group2 consisting of NIES-L, JD, JW, Estonia, NIES-Br, NIES-Fr, NIES-Hn, W, and commercial and wild populations. The remaining two lines (AMRP and rb-TKP) were each clustered into a separate clade. This hierarchical genetic difference between domestic quail populations is attributed to the genetic background derived from two different genetic sources—the pre-war and post-war populations—which is well supported by their breeding histories.

Highlights

Japanese quail (Coturnix japonica, Phasianidae) is an important animal species in poultry production
19 Japanese quail populations were used, including nine laboratory lines established in Japan, six laboratory lines derived from meat-type quail populations that were reimported from Western countries, one commercial population in Japan, and three wild quail populations collected from three Asian areas, (S1 and S2 Tables, S1 Fig)
The Estonia and NIES-Fr lines retained the haplotypes of Dloop-Group2 (JqD2 and JqD3), which were possibly derived from the pre-war population, and these lines are apparently distinct from the other lines clustered into Microsat-Group2 in the pairwise FST network and the Bayesian clustering at K = 8. These results suggest that some quail populations clustered into Microsat-Group2, such as Estonia and NIES-Fr, initially retained the genetic background of both pre-war and post-war populations, and the genetic contribution of the pre-war population decreased over time during some selective breeding process, such as backcrossing with quail derived from the post-war population

Summary

Introduction

Japanese quail (Coturnix japonica, Phasianidae) is an important animal species in poultry production Owing to their high growth and egg-laying rates, Japanese quail have been preferentially bred worldwide, including selective breeding to improve egg and meat production, since the beginning of the 20th century [1]. Some laboratory lines of Japanese quail are considered to have been established from game bird populations in the United States during the mid-20th century [7,12]. The commercial use of this species for egg and meat production began around 1910 in Japan [10,13] and became active in the 1930s [14] During this period, Japanese quail was selected for various characteristics, such as body size and plumage color, in Japan [12]. Most domestic Japanese quail that are bred worldwide today are likely descendants of populations that were re-established in Japan after the war [15,16,17]

Methods

Results

Conclusion