| MHC is a chromosomal region consisting of a group of closely linked loci, which are highly polymorphic, and play a central role in the immune system. In this research, five Chinese yellow cattle breeds, which were En-shi cattle, Qin-chuan cattle, Wan-nan cattle, Wenling-Gaofeng cattle and Yan-bian cattle were studied for the molecular genetic diversity in MHC-DQB*exon2, DRB3*exon2 and their upstream regulatory region by DNA sequencing.1. 127 DQB*exon2 alleles were found in Chinese yellow cattle. The number of alleles was 36, 42, 35, 40 and 42 respectively in En-shi cattle, Qin-chuan cattle, Wan-nan cattle, Wenling-Gaofeng cattle and Yan-bian cattle. 87 new alleles were found. Five alleles in which stop-code existed were pseudogenes, so the functional new alleles were 82. 19 alleles of them were accessed by GenBank and nominated by BoLA nomenclature committee.259 DRB3*exon2 alleles were found in Chinese yellow cattle. The number of alleles was 67, 72, 64, and 77 respectively in Qin-chuan cattle, Wan-nan cattle, Wenling-Gaofeng cattle and Yan-bian cattle. 131 new alleles were found among them. 11 alleles in which stop-code existed were pseudogenes, so the functional new alleles were 120.2. 85 (79Pi+6S) polymorphic sites were found in 127 DQB*exon2 alleles, which were 31.48% of the full length. The number of polymorphic sites was 76 (65Pi+ 11S) , 71 (68 Pi+3S ) , 68 (60 Pi+85) , 72 (61 Pi+11S) and 76 (67Pi+9S) respectively in En-shi cattle, Qin-chuan cattle, Wan-nan cattle, Wenling-Gaofeng cattle and Yan-bian cattle. 59 polymorphic sites were shared with the 5 breeds, which were 69.41 % of all polymorphic sites.87 (69Pi+18S) polymorphic sites were found in 259 DRB3*exon2 alleles, which were 32.46% of the full length. The number of polymorphic sites was 63 (60 Pi+3S) , 69 (58Pi+11S) , 68 (57Pi+11S) and 68 (59Pi+9S) respectively in Qin-chuan cattle, Wan-nan cattle, Wenling-Gaofeng cattle and Yan-bian cattle. 57 polymorphic sites were shared with the 4 breeds, which were 65.52% of all polymorphic sites, and the variable types were almost same between breeds.Both BoL4~DQB*exon2 alleles and DRB3*exon2 alleles contained higher proportions of non-synonymous substitutions in the peptide-binding sites (PBS) than in the non-peptide-binding sites.3. Compare the amino acid sequences of 127 DQB*exon2 alleles, 41 (40 Pi+1S) variable sites were found. The number of variable sites was 40 (36Pi+4S) ,37 (36Pi+1S) ,36 (34Pi+2S) ,37(34 Pi+3S) , 39 (36 Pi+3S ) respectively in En-shi cattle, Qin-chuan cattle, Wan-nan cattle, Wenling-Gaofeng cattle and Yan-bian cattle. Compare the component of amino acid among 5 breeds, the results of x 2text indicated that 13th, 77th, 86th sites were significant difference (p<0.05), 28th, 75th sites were very significant difference (p<0.01). These variable sites included three PBSS.The number of amino acid variable sites of 259 DRB3*exon2 alleles was 47 ( 37 Pi +10S ) . there were 32 (31 Pi+lS) ,38 (31 Pi+7S) ,34 (30Pi+4S) ,37 (34PS+3S) respectively in Qin-chuan cattle, Wan-nan cattle, Wenling-Gaofeng cattle and Yan-bian cattle. Compare the component of aminoacid among 4 breeds, the results of x 2text indicated that 13th. 25th, 48th, 61th, 67th. 67th, 70th, 74thsites were significant difference (p<0.05), 11th 8th. 37th, 44th, 57th, 59th, 60th. 63th. 75th,94th sites were very significant difference (p<0.01) . These variable sites included eight PBSs.4. Twenty-eight DQB-URR alleles were found in upstream regulatory region out of thirty-five BoLA-DQB*exon2 alleles. Each DQB*exon2 alleles had two URR alleles, except Q-19, Q-36 and Q-38, which had only one URR allele respectively.Twelve DRB-URR alleles were found in upstream regulatory region out of eighteen BoLA-DRB3*exon2 alleles. Each DRB3*exon2 alleles had only one allele, except R-03, R-05, R-06, R-17, R-18, which had two URR alleles respectively.5. Regulatory elements including W box X box , Y box CCAAT box and TATA-like box, which were associated with the expression of genes were found in both 28 BoLA-DQB...
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