Genetic Diversity Pattern of the MHC-LEI0258 Locus across Asian Populations of Chickens

The major histocompatibility complex (MHC) is surprisingly well associated with epidemiological and pathogenic environments, and the MHC-related microsatellite LEI0258 is a useful biomarker for indicating MHC haplotypes. In the present study, we conducted a comprehensive analysis of LEI0258 diversity in 492 Asian chickens and White Leghorns using multiple strategies to gain insight into the effectiveness of this adaptive locus for assessing the diversity and genetics of populations and the potential forces that affect MHC evolution. Comparisons between five Asian local breeds with wide geographic distributions and one commercial breed (White Leghorn chickens) revealed a total of 82 different alleles. The overall observed heterozygosity was 85.55% in Asian chickens and 30.98% in White Leghorn chickens, indicating higher LEI0258 diversity in Asian chickens than in the commercial breed. In addition, a population structure analysis of nine wild jungle fowl populations and several geographically varied Asian chicken populations revealed consistent clustering. Moreover, the results of AMOVA among jungle fowl populations suggested that most of the diversity was found among individuals within populations and within individuals. High levels of polymorphism and divergence were observed in the MHC region within and among populations, whereas limited polymorphisms and divergence were present among geographic groups. Hence, we concluded that the MHC in chickens has low intraspecific and interbreed variation and cannot be adapted as a tool to estimate diversity and migration based on drift and neutral events.