The swine leukocyte antigen (SLA) nomenclature system: 2014 update

C.S. Ho, S. Essler, A. Ando, C. Rogel-Gaillard, J.H. Lee, L. Schook, D. Smith, J. Lunney
34th International Society for Animal Genetics Conference, July 28 - August 1, 2014, Xi'an, China


The swine leukocyte antigen (SLA) system is among the most well characterized MHC systems. The mtDNA D-loop region and ATP6-Arg gene were sequenced to determine the inheritance background of Kazahk horse from China and Kazahkstan. Results demonstrated that haplotype diversity and nucleotide diversity of D-loop region were both higher than those of ATP6-Arg gene.There was no significant difference in Hd and Pi between horses from the two countries. In comparison, in the nps7974-9963 sequences data with 81 sequences from GenBank representing18 major haplogroups of wrold horses, we found that Kazakh horses composed of 13 majorhaplogroups, accounting for 72% of all horse haplogroups, in which seven haplogroups' frequencies were higher than 5%, indicating an abundant maternal hereditary background of Kazakh horses. The inheritance character was almost the same except for differences in some haplogroups' frequencies. Haplogroups C, N and R were only found in Kazahkstan horsepopulations, but haplogroup frequency was lower than 5%; while haplogroup J exclusively was observed in Xinjiang horse populaitons, with frequence higher than 5%. The frequencies of haplogroups L and O in Kazahkstan horses were 14% and 16%, respectively; in contrast, those two values were both less than 5% for Xinjiang horses. Multiple sequences alignment was conducted with the D-loop data of Kazahk horse and additional 388 accessions retrieved from GenBank representing other horses, such as Fell, Highland and Shetland horse from Europe; Mesenskaya, Vayatskaya and Orlov horse from Russia; Mongolian horse and Yakutian horse. Furthermore, NJ phylogenetic tree was reconstructed with the alignment.The phlogeny revealed that Kazakh horse from Xinjiang and Kazakhstan were closely related, and they further differences was observed between Baicheng and Aheqi chicken populations. The genetic distance between Tashikuergan chicken breed and Baicheng, Hejing, Aehqi chicken breed were larger than that of between Baicheng, Hejing and Aehqi chicken breed pairs. Nei's analyses revealed that the lowest genetic distance was between Baicheng and Aheqi chicken breeds; genetic distance between Tashikuergan and the other chicken breeds were much larger. UPGMA tree inferred from Nei's genetic distance demonstrated that Tashikuergan chickens formed a single branch and sister to the branch comprised of the other three chicken breeds. Baicheng and Aheqi chicken breeds were clustered together, indicating a more close relationship between them. Tashikuergan is a county located in the Pamirs. It is hypothesized that due to the relative geographic isolation from the outside world, the genetic exchange of Taxkuergan with other chicken breeds was much rare, leading to a relative lower genetic diversity and farther genetic distance with other chicken breeds, and then gradually evolved into a more independent breed