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United States Department of Agriculture

Agricultural Research Service


item Ando, Asako
item Uenishi, Hirohide
item Kawata, Hisaki
item Tanaka, Maiko
item Flori, Lawrence
item Chardon, Patrick
item Lunney, Joan
item Kulski, Jerzy
item Inoko, Hidetoshi

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/18/2006
Publication Date: 8/20/2006
Citation: Ando, A., Uenishi, H., Kawata, H., Tanaka, M., Flori, L., Chardon, P., Lunney, J.K., Kulski, J., Inoko, H. 2006. Microsatellite diversity within the sla region of homozygous and heterozygous samples. Proceedings 30th Conference of the International Society of Animal Genetics. p.229. Available:

Interpretive Summary:

Technical Abstract: The DNA sequence of the entire SLA region (2.4 Mb) of the H01 haplotype was completed recently and is available as a reference for developing new genetic markers. On the basis of this H01 haplotype sequence, we previously developed 40 polymorphic microsatellite (MS) markers with an average distance of 59 kb between markers. To clarify the microsatellite diversity and recombination hot spots in the SLA region, we have now analyzed genetic polymorphisms of these markers in 23 SLA homozygous/heterozygous swine with 12 SLA serological haplotypes and 28 NIH homozygous/heterozygous miniature pigs with five SLA serological haplotyes including two recombinant haplotypes. Haplotype-specific patterns and allelic variations at MS loci were observed in the comparison of these different haplotypes. Some of the haplotypes were found to share large haplotype blocks extended over 2-Mb, suggesting the existence of strong linkage disequilibrium (LD) in the entire SLA region. For example all of the polymorphic markers across 2 Mb of the SLA genomic region were matched between the pigs with the H04 haplotype and the NIH pigs with the ‘d’ haplotype. On the other hand, one of the pigs with the H10 haplotype shared polymorphisms with the NIH ‘a’ haplotype across 1 Mb of genomic sequence located between the class II and III regions. In contrast, none of the first 12 SLA serological haplotypes correlated with the NIH ‘c’ haplotype. Crossing over within the class III and I regions was found within the NIH ‘g’ and ‘h’ haplotypes, respectively. Although a centromere at the class II and III junction splits the SLA complex into two segments, the influence of the centromere on the existence of LD and the crossing over rate appeared to be limited. The present haplotype comparison shows that this set of MS markers provides a fast, economical and alternative method to the direct determination of the SLA alleles based on sequencing or SNP typing for the characterization of SLA haplotypes.

Last Modified: 10/16/2017
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