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Background  The quail and chicken major histocompatibility complex ( Mhc ) genomic regions have a similar overall organization but differ markedly in that the quail has an expanded number of duplicated class I, class IIB, natural killer (NK)-receptor-like, lectin-like and BG genes. Therefore, the elucidation of genetic factors that contribute to the greater  Mhc  diversity in the quail would help to establish it as a model experimental animal in the investigation of avian  Mhc  associated diseases.    Aims and approaches  The main aim here was to characterize the genetic and genomic features of the transcribed major quail  MhcIIB  ( CojaIIB ) region that is located between the  Tapasin  and  BRD2  genes, and to compare our findings to the available information for the chicken  MhcIIB  ( BLB ). We used four approaches in the study of the quail  MhcIIB  region, (1) haplotype analyses with polymorphic loci, (2) cloning and sequencing of the RT-PCR  CojaIIB  products from individuals with different haplotypes, (3) genomic sequencing of the  CojaIIB  region from the individuals with the different haplotypes, and (4) phylogenetic and duplication analysis to explain the variability of the region between the quail and the chicken.    Results  Our results show that the  Tapasin-BRD2  segment of the quail  Mhc  is highly variable in length and in gene transcription intensity and content. Haplotypic sequences were found to vary in length between 4 to 11 kb.  Tapasin-BRD2  segments contain one or two major transcribed  CojaIIBs  that were probably generated by segmental duplications involving c-type lectin-like genes and NK receptor-like genes, gene fusions between two  CojaIIBs  and transpositions between the major and minor  CojaIIB  segments. The relative evolutionary speed for generating the  MhcIIBs  genomic structures from the ancestral  BLB2  was estimated to be two times faster in the quail than in the chicken after their separation from a common ancestor. Four types of genomic rearrangement elements (GRE), composed of simple tandem repeats (STR), were identified in the  MhcIIB  genomic segment located between the  Tapasin-BRD2  genes. The GREs have many more STR numbers in the quail than in the chicken that displays strong linkage disequilibrium.    Conclusion  This study suggests that the  Mhc  classIIB region has a flexible genomic structure generated by rearrangement elements and rapid SNP accumulation probably as a consequence of the quail adapting to environmental conditions and pathogens during its migratory history after its divergence from the chicken.

The major histocompatibility complex (Mhc) class IIB region has greater genomic structural flexibility and diversity in the quail than the chicken