Four haplotypes identified at the MHC locus on chromosome 19. (A) Haplotype A is found on Zv8 chromosome AB and is formed by alignment of 5 bacterial artificial chromosomes: AL672176, AL672164, AL672185, AL672151, and AL672216. Haplotype B is found on Zv8 chromosome 19 and is formed by alignment of 2 bacterial artificial chromosomes (BX927188 and BX510994) and 6 pieces of shotgun sequences from Zv8_scaffold2271. MHC class I U genes are in red, and flanking genes are in black. Haplotype A contains 4 MHC class I U genes and 18 flanking genes, whereas haplotype B contains 2 MHC class I U genes and 17 flanking genes. Both haplotypes are defined by the same flanking genes, such as col11a2, daxx, and flot1, in a region 350 kb in length. The megabase pair (Mb) positions under the haplotypes are from Ensembl Zebrafish genome browser. Haplotypes C and D are identified by direct sequencing of PCR amplified DNA sequences and are defined by the 2 MHC class I U genes (LOC751750 and mhc1uxa2) that independently segregated in the family of F1 siblings. (B) MHC genotypes for the wild-type AB male and Tg(β-actin:GFP) female parents are shown, as well as the 4 genotypes identified in their F1 progeny.