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

BACKGROUND: The Japanese quail (Coturnix japonica) is an important poultry species owing to their high economic efficiency and biological advantages. The genetic diversity of farm quail populations has rarely been studied. OBJECTIVES: This study aimed to assess the genetic diversity of farm quail populations and their genetic relationships, which could provide important information for designing breeding programmes to maintain egg and/or meat production efficiency. METHODS: Molecular phylogenetic and STRUCTURE analyses were conducted for seven farm populations and six laboratory lines using 50 microsatellite markers previously developed by us. RESULTS: The genetic diversity within each farm population was relatively high despite long‐term breeding within closed colonies. However, the genetic variation between populations was absent. Twenty highly polymorphic markers, selected based on Ne, He and F(ST) values, enabled the construction of reliable phylogenetic trees and STRUCTURE plots. CONCLUSIONS: In the farm populations analysed in the present study, gene flow between genetically distant populations is needed to restore genetic diversity between farm populations, which could exploit heterosis and decrease the risk of inbreeding depression. Our findings demonstrate that these markers are useful for examining the genetic structure of farm quail populations.