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_o) and expected (H_e) heterozygosities were, respectively, 0.734 and 0.859 in Kostroma cattle and 0.613 and 0.886 in Yaroslavl cattle. The intrabreed differentiation (F_ST) 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.

BOLA -DRB3外显子2（BOLA-DRB3.2的近交和近交变异））首次通过PCR-RFLP在Kostroma和Yaroslavl牛品种中进行了研究。这些品种是俄罗斯最好的品种之一，分别被开发为奶牛和奶牛。在五个Kostroma样本中观察到29个等位基因，与两个Yaroslavl样本相比，其中14个被证明是独特的，其中两个Yaroslavl样本被检测到25个等位基因，其中10个是独特的。牛白血病病毒（BLV）耐药等位基因（* 11，* 23和* 28）的总频率在Kostroma中为23.2％，而BLV易感性等位基因的总频率（* 8，* 16，* 22，* 24 ）低至8.4％。雅罗斯拉夫尔牛的频率分别为25.8％和30.1％。测试Hardy-Weinberg平衡表明杂合子明显不足：观察到的（H _o）和预期的（H _o）_e）科斯特罗马牛的杂合度分别为0.734和0.859，雅罗斯拉夫尔牛的杂合度分别为0.613和0.886。科斯特罗马（4.5％，P  = 0.001）的种内分化（F _ST）明显高于雅罗斯拉夫尔（Yaroslavl）（0.5％，P  = 0.158），两个品种之间的内部分化为（8.2％（P  = 0.001））。贝叶斯聚类方法显示了每个品种的内部结构，最可能的簇数在科斯特罗马（Kostroma）为2个，在雅罗斯拉夫尔（Yaroslavl）为3个。当与另外六个品种一起分析该品种时，在科斯特罗马中观察到的结构保持不变。我们的数据为了解土著品种的遗传结构提供了重要线索。