Application of NGS to develop molecular markers for monitoring and selection purposes in the context of climate change

The rapid development of NGS technologies and bioinformatic tools has paved the way for the assembly of complete genome sequences which may serve as references for the efficient development of molecular markers for different traits or the determination of species and origin of trees (Badenes et al, Front Genet 2016). Recently, we assembled draft nuclear genome scaffolds of Populus tremula x P. alba INRA 717-1B4 (submitted to PlabiPD; http://www.plabipd.de/) and the complete chloroplast and mitochondrial genomes of P. tremula (Kersten et al, PLoS One 2016) as new genome sequence resources for trees. For the development of molecular markers that differentiate species or origin of trees, we successfully applied the cost-effective "genome skimming" strategy (Pakull et al, Conserv Genet Resour 2016; Schroeder et al, PLoS One 2016) and reduced representation strategies such as RADseq (Jardine et al, Conserv Genet Resour, 2016). NGS strategies are also very useful for the development of diagnostic markers that co-segregate with a trait of interest. NGS sequencing of DNA from phenotypic pools has successfully been applied to develop a diagnostic aspen marker for sex (Pakull et al, Plant Biol 2015), a qualitative trait that is expected to be mono-or digenic. In case of polygenic quantitative traits (e.g., insect tolerance in Quercus robur, drought tolerance in Picea abies) the development of diagnostic markers or even functional markers that are causally linked to the phenotype of interest is more challenging. For this purpose, we intend to use a combination of quantitative RNAseq (stressed versus non-stressed trees) to identify candidate genes (Kersten et al, BMC Genomics 2013) with a subsequent DNAseq of selected candidate genes and their potential regulators in sets of trees representing the contrasting phenotypes. Once developed, such diagnostic markers may be applied for marker assisted selection or for monitoring purposes to cope with the effects of climate change.