Performance and Applications of the "EucHIP60K.BR" for High Throughput Genotyping Across Thirteen Species of Eucalyptus

High throughput, high quality, affordable genotyping systems have become a key tool to advance applications in genetics and molecular breeding of eucalypts. We have developed a 60,000 SNP Infinium chip (EucHIP60K.br), by a multi-species SNP discovery strategy. Chip performance was assessed based on standard genotype clustering quality parameters, inheritance in pedigrees, reproducibility in blindly replicated samples and polymorphism within and across all the main eucalypt plantation species. Over 15,000 samples including thirteen different Eucalyptus species, hybrids, and close genera have been successfully genotyped to date. Genotype reproducibility has been >99.99%, while call rates ≥80% and ≥95% have been obtained for 55,786 (92%) and 45,680 (76%) SNPs respectively, providing robust genome-wide coverage. Between 29,000 and 33,000 SNPs were polymorphic (MAF>0.01) in each one of the four species that make up >90% of eucalypt planted forests worldwide (E. grandis, E. urophylla, E. camaldulensis, E. globulus), with 15,033 SNPs simultaneously polymorphic in all four. The SNP frequency spectrum revealed a large proportion of polymorphic SNPs with rare alleles (MAF <0.01) suggesting that SNP ascertainment bias was minimized from the deliberate multi-species SNP discovery from deep sequencing a large panel of individuals. These constraints avoided strong selection on common SNPs in any species in particular, favoring sampling SNPs across the range such that the final selection better approximated random sampling. Chip data have now allowed the analysis of chromosome-specific and genome-wide linkage disequilibrium, identification of ancestry informative SNPs and powerful GWAS and Genomic Selection analyses. Results of such applications will be presented.