Estimating inbreeding in an inbred line of Japanese quail (Coturnix Japonica) using pedigree and microsatellite analyses

Accurately estimating the level of inbreeding in a population is essential because inbreeding reduces fitness, fertility, viability, hatchability, and other production traits in populations. Inbreeding has been estimated by analyses of pedigrees and genetic markers. The objective of this study was to evaluate the accuracy of the two methods in an inbred line of Japanese quail. The inbred line was derived from a random bred (QO) line and maintained for 17 generations by pedigreed matings of brothers to groups of sisters. Data from analysis of 14 microsatellite markers, GUJ0001, GUJ0024, GUJ0030, GUJ0034, GUJ0040, GUJ0044, GUJ0057, GUJ0059, GUJ0060, GUJ0065, GUJ0068, GUJ0070, GUJ0071, and GUJ0085, were obtained. Pedigree data were used to calculate the inbreeding coefficient (FIT), which is the level of inbreeding based on a reference ancestor. From the microsatellite locus data, the population differentiation (Fst) of the two lines caused by inbreeding was calculated as Fst=1-(He(inb)/He(rand)), where He(inb) and He(rand) are the expected heterozygosity of the inbred and the random bred lines, respectively. The Fit was then calculated as Fit = Fis+(1 -Fis)*Fst, where Fis is the level of inbreeding within the inbred line. The heterozygosity observed by analysis of the microsatellite markers of the randombred and inbred lines was 0.430 and 0.207, respectively, and the number of alleles was 3.29 and 1.93, respectively, demonstrating that genetic diversity was reduced in the inbred line. The Fit of the inbred line from the pedigree and microsatellite marker analyses was 0.687 (±0.069) and 0.567 (±0.329), respectively. These results suggest that pedigree analysis seems to be more accurate than microsatellite marker analyses without multi-generation genotyping for estimating inbreeding in an inbred line of Japanese quail. Further studies will be required to investigate reasons for the high standard deviation of microsatellite marker analyses.Medicine, Faculty ofMedical Genetics, Department ofGraduat