Genetic control of tracheid properties in Norway spruce wood

Through the use of genome-wide association (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such an effort in Norway spruce (Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 high quality Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a LASSO based association mapping method using a functional multi-locus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). Expression of the identified candidate genes was examined using publicly available spruce databases. The analysis have provided 31 loci and 26 mostly novel candidate genes, majority of which showing specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among most promising candidates, the analysis identified Picea abies BIG GRAIN 2 (PabBG2) with predicted function in auxin transport and sensitivity, and MA_373300g0010 - similar to wall-associated receptor kinases (WAKs), both associated to cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce. The presence of many traits with several significant QTLs supports the notion that the majority of these traits are polygenic in nature.