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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: Characterization of microsatellite loci in the SLA class I region

Authors
item Chung, H -
item McClure, Matthew

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 19, 2011
Publication Date: April 20, 2011
Repository URL: http://www.sciencedirect.com/science/article/pii/S0888754310002673
Citation: Chung, H.Y., Mcclure, M.C. 2011. Characterization of microsatellite loci in the SLA class I region. Genomics. Genomics 97(1):223-234.

Interpretive Summary: As the human major histocompatibility complex (MHC) and porcine swine leukocyte antigen (SLA) complexes share multiple paralogous regions, swine have traditionally been used as a model to identify MHC regions that are responsible for systematic immune responses in both organisms. While numerous genetic markers have been identified in the SLA region microsatellite (MS) markers have not been intensively studied in this region. This study’s aim is to identify all MS markers in the SLA class I (SLA-1) region and compare them to the human MHC region. By analyzing shotgun sequences from BAC libraries constructed from 6 miniature pigs for the SLA-1 region and SLA-1 sequences in GenBank 423 MS markers were identified. This study provides newly discovered sequence information and genetic characteristics for polymorphic MS markers in swine, which can be utilized in studies that seek to understand how allelic variation in the SLA-1 region impact immunological traits and the feasibility of using swine organs for xenotransplantation. Additionally, the MS markers identified here can be used for identifying recombination hot spots in the SLA-1 region.

Technical Abstract: This study was aimed to investigate genetic variation of repeat sequences in the Swine Leukocyte Antigen class I (SLA-1) region which is believed to be responsible for systematic immune responses. Microsatellite (MS) markers in the SLA-1 region were characterized via sequencing analysis with BAC clones generated from the National Institute of Health miniature pigs (MIPs). A total of 16 BAC clones were sequenced producing 15,228 shotgun reads, corresponding to 11.2 X sequencing coverage, that were used to construct a contig of 12.18 Mb in length. MS markers were compared with previously deposited GenBank sequences to verify the existence of 423 potential MS candidate markers in the SLA-1 region. Evaluation of these polymorphisms confirmed 59 markers in MIPs, and the combined data including sequences from GenBank revealed 155 polymorphic MS markers. One to 7 repeat units were observed, with 50% of the MS having single abundant repeat units, and 1 to 83 being observed in MIP.. Irregular repetitive patterns, insertions, and deletions of nucleotides were also detected. Five MS markers were located in the exon regions of genes FB19, DDX16, and ZNFB173, while 10 were detected in the intron regions of genes ABCF1, DDX16, and RFB30. A comparative analysis of nucleotides between species showed the average repeat size and interval length between markers was 29 bp and 2,243 bp for swine, and 44 bp and 590 bp for human, respectively. MS markers tended to cluster in a few human genomic regions versus a widely distributed pattern in swine. MS markers in this analysis will provide an alternative method for determining the SLA-1 haplotype instead of direct typing of each SLA-1 region gene, and the genetic information in the SLA-1 region will be valuable for transplantation and association studies with immunological traits.

Last Modified: 8/1/2014
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