The BALB/c inbred mouse strain is one of the most commonly used for immunological studies and is an animal model for natural killer (NK) cell function during pathogen infection and tumorigenesis. To understand better NK cell function in this strain, the complete BALB/c Ly49 haplotype was deduced. The BALB/c haplotype spans approximately 300 kb with a gene order and content of Ly49q, e, x, i, g, l, c, and a. Functional BALB/c alleles of Ly49q and e were isolated and found to be conserved. The BALB/c cluster represents a minimal haplotype as it contains many fewer functional genes than the 129 or B6 mouse strains. The small number of BALB/c Ly49 genes is due mainly to an absent group of genes (relative to B6 and 129) between Ly49x and i, although other smaller deletions are present. These gene deletions provide a genetic basis for the lack of certain Ly49-associated NK cell functions in this mouse strain. Finally, the mapping of a third Ly49 haplotype reveals that the basic murine Ly49 repertoire is composed of three framework gene pairs (Ly49q and e, Ly49i and g, and Ly49c and a) that are interspersed with variable numbers of strain-specific Ly49.
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