Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành y học dành cho các bạn tham khảo đề tài: High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species | Grattapaglia et al. BMC Plant Biology 2011 11 65 http 1471-2229 11 65 BMC Plant Biology RESEARCH ARTICLE Open Access High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus assay success polymorphism and transferability across species 13 1 Dario Grattapaglia Orzenil B Silva-Junior Matias Kirst Bruno Marco de Lima Danielle A Faria and Georgios J Pappas Jr1 2 Abstract Background High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology GGGT . This issue becomes exacerbated when attempting to transfer SNPs across species a scarcely explored topic in plants and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger 454 database with 1 164 695 ESTs and the preliminary draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints 93 of them provided high quality genotype calls and 71 of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus .
