Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus

TLDR: The power of the now well established DArT marker platform in combination with Illumina short read sequencing to generate a linkage map for a segregating outcrossed F1 population derived from E. grandis BRASUZ1, the donor of the Eucalyptus reference genome is assessed.

Abstract: Background Wider genome coverage and higher throughput genotyping methods have become increasingly important to meet the resolution and speed necessary for a variety of applications in genomics and molecular breeding of forest trees. Developed more than 10 years ago [1], the Diversity Arrays Technology (DArT) has experienced an increasing interest worldwide for it has efficiently satisfied the requirements of throughput, genome coverage and inter-specific transferability for over 40 different plant species to date, including Eucalyptus[2] and recently Pinus (Dione Alves-Freitas, this meeting). DArT is based on genome complexity reduction using restriction enzymes, followed by hybridization to microarrays to simultaneously assay hundreds to thousands of markers across a genome. Genome complexity reduction for genotyping has now been taken to another level when combined to next generation sequencing (NGS) technologies. Such a strategy has been used for rapid SNP discovery in different organisms [3], and proposed as a way to genotype with RAD (Restriction-associated DNA) sequencing [4]and recently by a similar method generally termed GbS (Genotyping-by-Sequencing)[5]. In this work we assessed the power of the now well established DArT marker platform in combination with Illumina short read sequencing to generate a linkage map for a segregating outcrossed F1 population derived from E. grandis BRASUZ1, the donor of the Eucalyptus reference genome.