Development of Genetic Markers in Eucalypt Species by Target Enrichment and Exome Sequencing

The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes governing wood property traits in three Eucalypt species (E. tereticornis, E. camaldulensis and E. grandis) used as parents in mapping populations. Ninety three genes from twelve major pathways governing xylogenesis were selected for target enrichment and exome sequencing. Probes were designed with 1 bp tilling and approximately 169700 probes were designed to capture the targeted genes. Genomic DNA was isolated from leaves, and on-array hybridization was conducted followed by sequencing using Illumina HiSeq2000. The raw sequence data were trimmed, and HQ reads were aligned to the E. grandis reference sequence. The average read coverage depth was 216X. SNP calling and InDel detection were conducted in E. tereticornis vs. E. grandis and E. camaldulensis vs. E. tereticornis. A total of 4130 SNPs and 555 polymorphic InDels were detected between E. tereticornis and E. grandis, while 4382 SNPs and 616 InDels were detected between E. camaldulensis and E. tereticornis. The maximum number of SNPs was recorded in the CesA5 gene, while the HB1 class IIIgene contained the highest number of InDels in both parental combinations. This study has provided an array of genetic markers for conducting QTL and association mapping of wood property traits in eucalypt species.