author(s)
MS Thakur, Amit Kumar Jha and Akhilesh Pandey

abstract
Multiple sequence alignment of exon-2 MHC B-Lβ (class II) gene sequence of each of the Cobb, Kadaknath and Cari-Vishal revealed variations at 91 sites with consensus sequence. Kadaknath had a total of 20 base variations comprising 13 transversions and 7 substitutions at nucleotide sites. The least nucleotide variation was observed in Cobb i.e. at 2 nucleotide sites. The variation found in Cari-Vishal was at 21 sites in nucleotide sequence when compared with consensus sequence. The genetic relatedness in terms of per cent identity was found to be 91.5, 91.1 and 90.8 between Kadaknath and Cobb, Kadaknath and Cari-Vishal and Cobb with Cari-Vishal, respectively. The phylogenetic analysis for flanking region of MHC B-Lβ II gene revealed two major clusters. The first cluster consisted of Cari-Vishal, Cobb, Red Jungle Fowl, Chinese indigenous and Hebei chickens. The Kadaknath breed was found in a separate second cluster. Among all the three genetic groups, Kadaknath breed was found to have more genetic divergence indicating that this breed is genetically distinct from the other chicken breed included under study.