Diversity analysis of AvBD gene region in Japanese quail

The AvBD gene region is an important component of the innate immune system, encoding a variety of antimicrobial peptides. The AvBD region forms a multigene cluster in a specific region of the chromosome. Comparison of the AvBD gene region among various birds suggests defects, duplication, and pseudogenesis at many loci. The AvBD gene region from certain Galliform birds, namely chicken, turkey, and bobwhite quail, contains AvBD3, AvBD6, and AvBD7, and the latter shows CNV in chickens. DNA for genomic analysis was extracted from the peripheral blood of 99 randomly selected quails from six inbred lines. Nine alleles of CjAvBD1 and eight alleles of CjAvBD12 were detected, respectively. Ten haplotypes, including three that were strain-specific, were found in alleles from both the CjAvBD1 and CjAvBD12 loci. On these ten haplotypes, the nucleotide sequences of the CjAvBD region (56 to 70 kb) for seven homozygous diplotypes were determined by next-generation sequencing. These seven haplotypes contained between 12 and 16 CjAvBD genes, and were composed of 11 common loci: CjAvBD1, 2, 4, 5, 8, 9, 10, 11, 12, 13, and 14, but lacking CjAvBD3 and -7. Furthermore, up to five CNVs of CjAvBD101 were observed among the seven haplotypes. In addition, we detected amino acid substitutions causing net charge mutations that could affect antimicrobial activity, at CjAvBD4, 13, 14, and 101. These results suggest that the CjAvBD gene region is unique among Galliformes, and that its diversity results in functional variation in innate immunity.