WP4

In species with large, highly complex genomes, the limitation of marker density may preclude accurate pedigree reconstruction and sufficient accuracy of genomic prediction. In a comparative study between Douglas fir and Interior spruce, the authors concluded that a substantial increase in accuracy of genomic prediction requires a dramatic increase in marker density, which remains prohibitive despite the constant advances in genotyping technology and conifer genome assemblies. We will fill this gap by developing a panel of Single Sequence Repeats (SSRs). SSRs are highly polymorphic markers, which translates into a higher power of resolution at a much lower marker density compared to Single Nucleotide Polymorphisms (SNPs). Recent developments in RNA-Seq technology permits high-throughput SSR genotyping, however, the application of genome-wide SSRs genotyping in genetic studies remains scarce. Furthermore, in SNPchip genotyping, even based on a large number of pre-tested spotted markers, on average, half of the spotted markers do not deliver reliable data.