Abstract. The genetic diversity at major histocompatibility complex (MHC) in indigenous chicken breeds of India
(Ghagus and Nicobari) in comparison with the White Leghorn (WLH) breed was
investigated by genotyping the MHC-linked LEI0258 marker. Altogether 38 alleles
and 96 genotypes were observed among three breeds. The observed and
effective alleles were highest in Ghagus (23, 8.3) followed by Nicobari (14,
3.2) and WLH (10 and 2.2) breeds. The size of alleles ranged from 193 to 489 bp in Ghagus, 193 to 552 bp in Nicobari and 241 to 565 bp in the WLH breed. The
number of private alleles was also highest in Ghagus (18) followed by
Nicobari (8) and WLH (5) breeds. The most frequent allele was 261 bp in WLH
(66 %), 343 bp in Nicobari (50.4 %) and 309 bp in the Ghagus (28.15 %)
breed. Observed and expected heterozygosities were highest in Ghagus (0.83,
0.88) followed by Nicobari (0.58, 0.68) and WLH (0.53, 0.54). The genetic
distance (Nei) between Ghagus and Nicobari breeds (2.24) was higher as
compared to that of Ghagus and WLH (1.23) and that between Nicobari and WLH
breeds (0.89). Association analysis revealed significant influence of MHC
alleles on body weight, egg production in Ghagus and WLH breeds and antibody
titres to Newcastle disease vaccine in the Nicobari breed.