Time-Dependent Changes in the Genetic Diversity and Structure of the Onagadori Breed of Chickens Based on Microsatellite DNA Polymorphisms

Abstract

To conserve the Tosa-no-Onagadori (briefly Onagadori), one of the native Japanese chicken breeds designated as a Special National Natural Treasure of Japan, time-dependent changes in genetic diversity and structure were analyzed based on 20 microsatellites. From three varieties (black-breasted white, black-breasted red, and white) of the Onagadori reared in Nankoku City, Kochi Prefecture, Japan, blood samples were collected in 1999, 2005, and 2009-2010. Significant genetic differentiation was recognized among breeders and among varieties in the whole Onagadori population, but it was not observed between years. Focusing on breeders, some populations showed decrease in allelic richness (AR) and expected heterozygosity (H_E) with advancing years. Focusing on varieties, AR of the black-breasted red variety showed significant loss from 1999 to 2010, resulting in the significant loss of AR in the whole Onagadori population. In contrast, the AR and H_E of the black-breasted white and white varieties were constant across sampling years. The D_A genetic distance among populations decreased with sampling years, and genetic homogeneity increased in the whole Onagadori population. Structure analysis supported K＝2, dividing the genetic constitution into Onagadori-specific one and the rest. In the black-breasted white variety, the birds that have Onagadori-specific genetic composition increased with time. On the contrary, in the black-breasted red and white varieties surveyed in 2009-2010, there was no bird that showed Onagadori-specific genetic background of more than 75%. To maintain the Onagadori in Nankoku City for a long term, regular monitoring of genetic diversity and systematic reproduction using excellent black-breasted white birds that have the Onagadori-specific genetic composition should be continued.