Development and characterization of novel microsatellite markers for the Common Pheasant (Phasianus colchicus) using RAD-seq

Abstract Background The Common Pheasant ( Phasianus colchicus ) Linnaeus, 1758 is the most widespread pheasant in the world and widely introduced as a game bird. Increasing needs for conservation genetics and management of both wild and captive populations require permanent genetic resources, such as polymorphic microsatellites in order to genotype individuals and populations. Methods In this study, 7598 novel polymorphic microsatellites for the Common Pheasant were isolated using a RAD-seq approach at an Illumina high-throughput sequencing platform. A panel of ten novel microsatellites and three existing ones from the chicken genome were multiplexed and genotyped on a set of 90 individuals of Common Pheasants (representing nine subspecies and ten individuals each) and 10 individuals of the Green Pheasant ( P. versicolor ). Results These 13 microsatellites exhibited moderate to high levels of polymorphism, with the number of alleles per locus ranging from 2 to 8 and expected heterozygosities from 0.049 to 0.905. The first analysis of the genetic structure of subspecies/populations using a Bayesian clustering approach, implemented in STRUCTURE, showed two genetic clusters, corresponding to both the Green and the Common Pheasant, with further evidence of subpopulation structuring within the Common Pheasants. Conclusion These markers are useful genetic tools for sustainable uses and evolutionary studies in these two Phasianus pheasants and probably other closely related game birds