Intrabreed and interbreed variation of the BOLA-DRB3.2 gene in the Kostroma and Yaroslavl indigenous Russian cattle breeds.

Intrabreed and interbreed variation of BOLA-DRB3 exon 2 (BOLA-DRB3.2) was for the first time studied in the Kostroma and Yaroslavl cattle breeds by PCR-RFLP. These breeds are among the best Russian breeds and were developed as dairy-beef and dairy cattle, respectively. Twenty-nine alleles were observed in five Kostroma samples, and 14 of them proved unique in comparison with two Yaroslavl samples, in which 25 alleles were detected, and 10 of them were unique. The total frequency of bovine leukemia virus (BLV) resistance alleles (*11, *23, and *28) was 23.2% in the Kostroma, while the total frequency of BLV susceptibility alleles (*8, *16, *22, *24) was low, 8.4%. The frequencies were 25.8 and 30.1%, respectively, in Yaroslavl cattle. Testing Hardy-Weinberg equilibrium revealed a significant deficit of heterozygotes: the observed (H) and expected (H) heterozygosities were, respectively, 0.734 and 0.859 in Kostroma cattle and 0.613 and 0.886 in Yaroslavl cattle. The intrabreed differentiation (F) in the Kostroma (4.5%, P = 0.001) was substantially higher than in the Yaroslavl (0.5%, P = 0.158), between the two breeds was 8.2% (P = 0.001). The Bayesian clustering approach showed an intrabreed structure for each of the breeds, with the most probable number of clusters being 2 in the Kostroma and 3 in the Yaroslavl. The structure observed in the Kostroma remained the same when the breed was analyzed together with six additional breeds. Our data provide important clues toward the understanding of the genetic structure of indigenous breeds.