| SLA was the most polymorphic known at present and the diversity of SLA-DQB was focused on the second exon (282bp) . Here We analysed 21 breeds of seven groups in Chinese pig by cloning sequencing. Combined with the sequences in Genbank, 77 alles were detected in 198 sequences, among them 73 new alles were gained(function alles were sixty-eight, pseudogenes were five), 1^ H^ H8 and HI2 were the shared alles between the foreign pigs and the Chinese pigs. There were disiquilibrium distribution of the alles in all breeds. Some alles were all shared in most breeds, the special HI alle(occupied 55.10%) existed in general in 11 breeds of seven groups and in the wild pigs of Yunnan and Sichuan province.We guessed there were three copies in SLA-DQB gene. Combined with the sequences of Genebank, 91 polymorphic sites were identified(include the pseudogenes ), 81 polymorphic sites were gained(exclude the pseudogenes), 77 polymorphic sites were get in Chinese pigs. The polymorphic nucleotide sites of P pleated sheet region were more than that in a helix region, but the opposite in HLA-DQB and H2-Ab. No insert or deletion was found in the detected sequences of SLA-DQB.The values of alleic diversity (H=0.93) and the nucleotide diversity (71=0.058) were revealed higher, both values of H and n were higher in the p pleated sheet region than that in a helix region in most groups except in Gaoyuan and Huabei groups. Also both values of H and n were higher in the foreign pigs than that in the Chinese pigs, as the same results between the Chinese native pigs and the wild pigs. There were ordered Huabei group(first)N Huanan, Xinan N Huazhong ^ Jianghai and Gaoyuan groups (last) by H value, while there were differently ordered as follow, Jianghai (first) .. Huanan^ Xinan N Huabek Huazhong and Gaoyuan (last) by the n value. There were the opposite position in both values between the Huabei group with Jianghai group.The allelic diversity was abundant but the nucleotide diversity was small in Huabei group, vis versa in Jianghai group. The genetic distance orders were ranked Jianghai > Xinan > Huabek Huana^ Huazhong ^ Gaoyuan within groups, the average genetic distance of the wild pig group was smaller than that in Chinese native groups. There were great genetic distance between the Jianghai and Huabei groups, and the smallest groups were detected between the Huazhong andGaoyuan groups. Hence we concluded the different rate of nucleotide substitution were positve correlated with the degree of nucleotide diversity in Chinese native subgroup, respectively.After analyzing the composition of nucleotide, the average percent value of G+C (60.8% ) was higher than that of A+T (39.2% ) ,the content of G+C (90.6%) was higher than that of A+T (9.4%) in the third condon. There were four G+C -rich parts, which have been considered to involve the intra-exon sequence exchange also in other gene evolutions. The first and second GC-rich sequences were X-like sequences, which have been shown to be a putative recombination signal, and were stably conserved in DQB genes. These X-like sequences identified in SLA-DQB were found to encode the first turning point of the beta-pleated sheet and the boundary between the beta-pleated sheet and the alpha helix. There were five types (three new) and three types (two new) X-like sequences(the alpha-like sequences act as putative breakpoints) in GCi and GCii region, respectively. We also found the fourteen smallest recombination events in exon 2 of the SLA-DQB gene, there were stronger linkage disiqilibrium in some sites and up to significant level(p<0.05) or extremely significant level (p<0.01) . Using the Jukes-cantor one parameter model or the Kimura two parameters model, the average values of tranversion was higher than that of tansition, which illuminated the saturation effects about the tanversion. The tranversion values of four types were equal between T and A> T and G> A and C> C and G. The transion value between C and T was smaller than that between A and G. The transion value was higher than tranver...
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