High allelic variation of MHC class II alpha antigen and the role of selection in wild and cultured Sparus aurata populations

Genetic polymorphism and differentiation in wild and cultured sea bream samples were studied after amplification, cloning, and partial sequence of the major histocompatibility complex (MHC) class II alpha antigen. Forty-one alleles were detected from 43 unrelated individuals and sequence alignment of the obtained alleles revealed 28 polymorphic sites. High heterozygosity values and allelic richness were unveiled for both wild and cultured populations. The substitution pattern (d(N) /d(S) = 0.7) is not consistent with the effect of diversifying selection, indicating lower selection pressure on the a2 domain, as well as that too few advantageous non-synonymous mutations have accumulated as substrate for the diversifying selection to act. Comparison with previously published results on microsatellite markers suggests that balancing selection in MHC genes reduces the genetic drift and bottleneck effects that are common in aquaculture and which are known to reduce genetic variation at neutral markers. The present study stresses that both coding and non-coding loci should be analyzed for designing proper management strategies.