Genetic differentiation among White Leghorn lines: application of individual-based clustering approaches

Genetic differentiations among White Leghorn lines were quantified based on allele frequencies of 40 microsatellite loci. In the survey among 7 lines, a considerable degree of differentiation was estimated between each pair of lines; genetic differentiation index (pairwise F(ST)) ranged from 0.0706 to 0.2590. Furthermore, 2 genetic clustering analyses of individuals, a neighbor-joining approach based on interindividual distances and the Bayesian procedure, which can assign individuals to the origins of their lines based on information on multilocus genotypes, were applied to a pairwise comparison of line differentiation. In the clustering approaches between the lowest differentiated line pair (pairwise F(ST) = 0.0706), individuals from 2 different line origins could not be separated into 2 distinct clusters, which indicates that the genetic boundary of these lines is ambiguous. On the other hand, between the highest differentiated pair (pairwise F(ST) = 0.2590), all individuals could be strictly clustered into 2 distinct groups, consistent with the origins of their lines. In the clustering based on interindividual distances, firm separations of individuals were observed in only relatively highly differentiated pairs of lines. Furthermore, in the Bayesian procedure, even in pairs with a relatively low differentiation, individuals from 2 lines formed 2 distinct clusters according to their origins. The results of the present study suggest that chicken lines possess considerable genetic differentiation despite their common breed origin. These clustering approaches at the individual level may be useful for the genetic identification and characterization of poultry stocks.