Investigation of MHC-B linked LEI0258 marker diversity in various chicken populations

The variable number tandem repeat (VNTR) LEI0258 is the most polymorphic marker in the chicken major histocompatibility complex (MHC) B region. Unlike other microsatellite markers, LEI0258 is characterized by R13 and R12 repeat motifs, resulting in greater allele variation across chicken breeds. The allele size of this marker can also vary due to deletions and insertions of one to several base pairs. Sanger sequencing of LEI0258 alleles allows for determining exact allele sizes (bp), elucidates its repeat motif combination patterns, reveals other polymorphisms in the non-repeating sequence region, and identifies allele size inconsistencies among populations. This study investigates LEI0258 diversity and its repeat motif and flanking sequence variation by Sanger sequencing of 621 LEI0258 alleles from Asian, African, and North American standard and commercial chickens. Eighty-eight different allele sizes (182-565 bp) were detected. Asian and African chickens exhibited more alleles than North American and commercial breeds. Eighteen shared alleles and numerous unique alleles were identified. There were 48 repeat motif combinations across the 88 allele sizes, including 16 novel combinations in Asian chickens and two in American and commercial chickens. In 26 alleles, the R13-R12 combinations consisted of a single copy of R13 with 2 to 28 R12 repeats; the remaining alleles contained various copy numbers for both R13 and R12 repeats. Moreover, the same allele size could occur with different motif combinations. Additional allele variation was observed due to single-nucleotide polymorphisms and insertions or deletions (indels) in the upstream or downstream of the LEI0258 marker. Collectively, the loss or gain of VNTRs and additional polymorphisms explain the broader allele variation in LEI0258; greater MHC diversity is observed in Asian and African chickens.