Identification of Novel Alleles and Structural Haplotypes of Major Histocompatibility Complex Class I and DRB Genes in Domestic Cat (Felis catus) by a Newly Developed NGS-Based Genotyping Method

Masaharu Okano, Jiro Miyamae, Shingo Suzuki, Kohei Nishiya, Fumihiko Katakura, Jerzy K. Kulski, Tadaaki Moritomo, Takashi Shiina

The major histocompatibility complex (MHC) is a highly polymorphic and duplicated
genomic region that encodes transplantation and immune regulatory molecules.
Although it is well-known that particular MHC allelic polymorphisms and haplotypes
are genetically relate to immune-mediated diseases detailed information of the cat
MHC (Feline Leukocyte Antigen; FLA) genetic and haplotypic structure and diversity
is limited in comparison to humans and many other species. In this study, to better
understand the degree and types of allele and allelic haplotype diversity of FLA-class
I (FLA-I) and FLA-DRB loci in domestic cats, we identified six expressible FLA-I loci
in peripheral white blood cells by in silico estimation of the coding exons and NGSbased
amplicon sequencing using five unrelated cats. We then used a newly developed
NGS-based genotyping method to genotype and annotate 32 FLA-I and 16 FLA-DRB
sequences in two families of 20 domestic cats. A total of 14 FLA-I and seven FLA-DRB
were identified as novel polymorphic sequences. Phylogenetic analyses grouped the
sequences into six FLA-I (FLA-E/H/K, FLA-A, FLA-J, FLA-L, FLA-O and a tentatively
named FLA-E/H/K_Rec) and four FLA-DRB (FLA-DRB1, FLA-DRB3, FLA-DRB4, and
FLA-DRB5) lineages. Pedigree analysis of two cat families revealed eight distinct FLA
structural haplotypes (Class I – DRB) with five to eight FLA-I and two to three FLA-DRB
transcribed loci per haplotype. It is evident that the eight FLA haplotypes were generated
by gene duplications and deletions, and rearrangements by genetic recombination with
the accumulation and/or inheritance of novel polymorphisms. These findings are useful
for further genetic diversity analysis and disease association studies among cat breeds
and in veterinary medicine.

Frontiers in Genetics

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