Abstract
Almost 10,000 single nucleotide polymorphisms (SNPs) had been identified in the RT1 complex, the major histocompatibility complex of the rat, but less than ∼0.5% have been characterized. In the context of the incomplete characterization of most SNPs, simple sequence length polymorphism (SSLP) marker development is still valuable for understanding the involvement of genes in the RT1 in controlling disease susceptibility, since SSLPs are user-friendly and cost-effective genetic markers in rat genome analysis. In this study, we developed a set of 67 SSLP markers, including 57 novel markers, to cover the entire RT1 complex and then created genetic profiles across 67 rat strains. These markers are located almost every 50 kb in the RT1 complex and show comparable polymorphism; the average number of alleles was 8.04 ± 3.44 and the average polymorphic rate was 71 ± 23%. Interestingly, markers failing to amplify polymerase chain reaction products were highly observed in all strains except for BN/SsNHsd, which suggests the existence of highly variable genomic sequences or genomic rearrangements in the RT1 region across rat strains. Based on the phylogenic tree and individual genotyping data, we identified 28 SSLP marker haplotypes in the RT1 region that roughly consisted of three genomic regions. These findings provided new insight into the genomic organization of the RT1 complex and we recognized the need of additional RT1 genome sequences in different strains. Owing to the accuracy and ease of determination, PCR-based SSLP genotyping could replace serological typing in genetic analyses and characterization of rat major histocompatibility.
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Acknowledgements
We are grateful to the National BioResource Project for the Rat in Japan for providing the genomic DNA of 67 rat inbred strains. This work was supported in part by Grants-in-aid for Scientific Research from the Japan Society for the Promotion of Science (18300141 to TK and 20240042 to TS) and a Grant-in-aid for Cancer Research from the Ministry of Health, Labour and Welfare.
Author contributions
YT generated data and wrote the manuscript. TK designed the experiment and wrote the manuscript. TT performed initial phylogenic analysis. SN prepared the samples. BV, TM, and NM contributed material and discussion. TS designed the experiment, revised the manuscript, and supervised the project.
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An erratum to this article can be found at http://dx.doi.org/10.1007/s00251-009-0370-2
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251_2008_352_MOESM1_ESM.xls
ESM Table 1 Genetic profiles of the RT1 in the 67 rat strains (XLS 87.5 kb)
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ESM Table 2 Polymorphic rate (in percent) between all possible pairs of the 67 rat strains (XLS 89 kb)
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ESM Fig. 1 Recombination rate of the examined RT1 region among rat inbred strains. Each data point indicates the factor of the recombination rate between two adjacent markers compared to background recombination. Calculated with PHASE 2.1 (1,000 iterations; thinning interval = 1; burn-in = 100; command line parameter –k999 –l8) (Doc 66 kb)
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Takagi, Y., Kuramoto, T., Voigt, B. et al. An informative set of SSLP markers and genomic profiles in the rat MHC, the RT1 complex. Immunogenetics 61, 189–197 (2009). https://doi.org/10.1007/s00251-008-0352-9
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DOI: https://doi.org/10.1007/s00251-008-0352-9