Genetic and evolutionary characteristics of the major histocompatibility complex class II β-chain genes of a large colony of captive king penguins (Aptenodytes patagonicus).

Major histocompatibility complex class II beta (MHC-class IIB) genes are highly polymorphic and play important roles in immune function, making them valuable DNA markers for efficient animal breeding and conservation management programs. However, MHC genetic information on king penguins (Aptenodytes patagonicus; Appa) in captivity remains limited. Here, we developed a Next Generation Sequencing (NGS)-based genotyping method to characterize MHC class IIB (Appa-CIIB) polymorphisms in 99 king penguins housed at Adventure World (Wakayama, Japan), identifying 72 novel Appa-CIIB alleles, each encoding a distinct amino acid sequence. Phylogenetic analysis classified these alleles into two major and one minor lineage, with peptide-binding regions in the main lineages showing signatures of positive selection. Thirty-four Appa-CIIB haplotypes composed of one to three Appa-CIIB loci, were inferred using individual management records (IMRs) from 123 individuals. Pedigree analysis revealed that 114 individuals belonged to a single extended family encompassing up to five generations, with the founders representing the first generation. Despite over 30 years of captive maintenance, population genetic analyses indicated that this population has retained high genetic diversity. The identification of multiple Appa-CIIB loci and copy number variations suggests that the Appa-CIIB region has undergone gene duplication and recombination events during evolution. These findings provide valuable insights into the genetics and evolutionary characteristics of Appa-CIIB genes and offer a practical framework for managing king penguin gene diversity in captivity, supporting future breeding programs that minimize inbreeding depression and maintain healthy populations.