Assessment of SNPs for linkage mapping in Eucalyptus: construction of a consensus SNP/microsatellite map from two unrelated pedigrees

Background High throughput genotyping of SNP (Single Nucleotide Polymorphisms) based markers has been developed for an increasing number of plant and animal species. In forest trees large scale SNP development has been approached mainly by amplicon resequencing targeting specific genes for association genetics studies. This approach, although successfully employed in conifers aided by the use of haploid tissue, is technically laborious in diploids because of the very high levels of nucleotide and indel diversity in highly heterozygous tree genomes. Direct SNP development from large in silico sequence resources developed by next-generation sequencing is now a very efficient approach for SNP development in forest trees. We have recently developed a first set of 768 SNPs assayed by the Golden Gate Genotyping Technology for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database [1]. We saw that a careful sequence quality assessment and the application of stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. With the exception of 72 SNPs specifically selected in 20 candidate genes putatively associated with relevant wood phenotypes, all remaining validated SNPs were randomly picked based solely on in silico quality. In this study we wanted to position these SNPs relative to microsatellites and assess their information content for linkage map construction. To enhance our ability of mapping SNPs we employed two eucalyptus full-sib families involving four different Eucalyptus species.