Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing

Cost-effective genotyping can be achieved by sequencing PCR amplicons.
Short 3–10 base primers can arbitrarily amplify thousands of loci using
only a few primers. To improve the sequencing efficiency of the multiple
arbitrary amplicon sequencing (MAAS) approach, we designed new primers and
examined their efficiency in sequencing and genotyping. To demonstrate the
effectiveness of our method, we applied it to examine the population
structure of the small freshwater fish, medaka (Oryzias latipes). We
obtained 2,987 informative SNVs with no missing genotype calls for 67
individuals from 15 wild populations and three artificial strains. The
estimated phylogenic and population genetic structures of the wild
populations were consistent with previous studies, corroborating the
accuracy of our genotyping method. We also attempted to reconstruct the
genetic backgrounds of a commercial orange mutant strain, Himedaka, which
has caused a genetic disturbance in wild populations. Our admixture
analysis focusing on Himedaka showed that at least two wild populations
had genetically contributed to the nuclear genome of this mutant strain.
Our genotyping methods and results will be useful in quantitative
assessments of genetic disturbance by this commercially available strain.