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

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.

Nonsense mutation in PMEL is associated with yellowish plumage colour phenotype in Japanese quail

“…By using this difference, we performed PCR-RFLP analysis to determine genotypes at the site of mutation in F 2 offspring. Besides F 2 offspring, 10 quail strains, including L, WE, AMRP, Quv, RWN, rb-TKP, NIES-FR/French, W (Wild), JW, and Estonian, were analyzed 51 – 53 . We examined four individuals of each strain using genomic DNA that was extracted from whole blood.…”

Assessment of genetic diversity and genetic relationships of farm and laboratory quail populations in Japan using microsatellite DNA markers

“…The phylogenetic trees constructed with the 48 microsatellite markers showed very close genetic relationships among six populations from STRUCTURE analysis of 15 laboratory lines in our previous study (Nunome et al, 2017), including the NIES-Br and the wild-derived lines, showed a high genetic affinity between the NIES-Br and wildderived lines; this may explain why the AARC-BB line is also closely related to the other three AARC laboratory lines (AARC-B, AARC-C and AARC-WW) that share a common origin from the wild-derived line.…”

“…PCR amplification of the 50 microsatellite markers used in our previous study (Nunome et al, 2017) was performed using a 10-µl reaction mix containing approximately 50 ng of genomic DNA, 10 pmol of each primer and 5 µl of Taq Gold 360 Master Mix (Thermo Fisher Scientific-Applied Biosystems). The following PCR cycling conditions were used: initial denaturation at 95°C for 10 min, followed by 42 cycles at 95°C for 30 s, 50°C or 55°C for 30 s, and 72°C for 25 s, and a final extension at 72°C for 5 min.…”

“…In our previous study (Nunome et al, 2017), genetic characterisation was carried out for 19 domestic populations of Japanese quail, consisting of nine laboratory lines, six meat-type quail lines, one commercial population and three wild quail populations from East Asia, using 50 highly variable microsatellite DNA markers.…”

Mitochondrial DNA Diversity in Commercial Lines of Laying-type Japanese Quail

“… Sanchez-Donoso et al (2014) also reported that 22 of 29 (75.9%) individuals of farm quail in Spain, which have Japanese quail maternal origin, had a single haplotype "F1W1” identical to the Cj1 haplotype in the present study. Furthermore, Nunome et al (2017) reported a predominant mtDNA haplotype of the control region across various experimental lines of domestic Japanese quail. The Cj2 haplotype had a relatively high frequency (12.8%) in the present study.…”