Development of a high resolution whole genome radiation hybrid map for interrogating the rhesus macaque genome assembly

This study focused on the development of new genetic resources for the rhesus macaque and the improvement of technical methods that can be applied to any species. A 10,000Rad radiati on hybrid (RH) panel was generated to construct a high-resolution rhesus chromosome 5 map via conventional PCR genotyping. The map contains 218 markers, with 798 kb average inter-marker distance. The RH mapping data indicate the conservation of synteny between macaque chromosome 5 and human chromosome 4 and reveals a previously unreported telomeric inversion. Our study also suggested that the macaque 5.2X genome sequence assembly has artifacts in that the suggested small translocations from macaque chromosome 5 to chromosome 1 and 6 are likely erroneous. These observations indicate this panel is appropriate for the generation of a high-resolution whole genome RH map to verify the rhesus genome assembly. To quickly and efficiently generate a high-resolution whole genome map, the Illumina SNP array technology was adapted to the macaque RH panel. The RH clones were genotyped using the HumanCNV370-BeadArray quad-chips. The results indicate 52% of the human-based SNPs are informative for rhesus RH mapping. A comparison between macaque chromosome 5 RH data generated via Illumina BeadArray and PCR-based genotyping indicates concordance in marker retention frequencies. The generated rhesus chromosome 5 RH map contains 7,185 markers and spans 37,052 cR10,000 as compared to the 4,846 cR10,000 PCR-based map. The integrity of whole genome amplified (WGA) DNA for RH mapping was investigated also. Comparisons of the genotypes of two distinct clone passages (first and tenth passage) derived from 11 clones revealed a 46.2% drop-out of markers of the tenth passage clones. The genotype concordance between WGA and genomic DNA, and five independent WGAs from each clone suggests that the WGA DNA is both reproducible and sustainable. The WGA DNA should enable analysis of almost infinite numbers of markers and earlier RH clone passages. Overall, this work suggests that high-resolution RH maps can be developed to aid the genome sequence assembly rapidly and efficiently using RH techniques combined with WGA and SNP arrays.