Research note: Identification of SNP-based haplotypes for the A, D, E, I, and L alloantigen systems in the chicken reference genome line UCD-001

Allelic variation in chicken red blood cell alloantigens has multiple associations with production traits or disease resistance. Recent studies have identified the gene and chromosomal location for chicken alloantigen genes A, D, E, I, and L. Haplotypes (specific SNP combinations) within each gene were identified to distinguish the serological variants found within the different blood systems. The objective of this study was to characterize alloantigen alleles in Line UCD-001, an inbred line of Jungle fowl, which is the original reference sequence for the chicken genome. The B blood group, the chicken MHC, was the only alloantigen system having known serological and SNP types, with UCD-001 typing as serological B^Q and DNA-based BSNP-A09A. Genome sequence and DNA samples from the original UCD-001 reference bird, plus an additional 10 UCD-001 birds, were used to identify five additional alloantigen system alleles within UCD-001. The alloantigen genes and their SNP types for the A and the linked E systems are complement component 4 binding protein, membrane, C4BPM-H12, and Fc fragment of IgA and IgM receptor, FCAMR-H01, respectively. Neither of these SNP types corresponded to alleles previously characterized by serology. Alloantigen D was identified as CD99 whose SNP haplotype, CD99-H06, corresponded to the D³ serological allele. The I system, equivalent to the human RHCE blood group locus, was heterozygous in the reference population. Both RHCE-H01, the I⁸ serological allele, and RHCE-H06, previously unidentified by serology, were present in UCD-001. The ABCE1 gene, ATP-binding cassette subfamily E member 1, is alloantigen L with UCD-001 containing the ABCE1-H01 haplotype consistent with the L¹ serological allele. Identifying the alloantigen genotypes of this important inbred line will facilitate studies of alloantigen effects through line crosses to produce progeny segregating for alloantigen alleles or through comparisons with other stocks.