Functional Multi-Locus QTL Mapping of Temporal Trends in Scots Pine Wood Traits
G3-GENES GENOMES GENETICS, 4 (12):2365-2379
Li1 Z, Hällingback H R, Abrahamsson S, Fries A, Andersson Gull B, Sillanpää M J, García-Gil M R

Abstract:
Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g. increment cores) thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-year-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTLs for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 - 9 timepoints, 91 - 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP) and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis where trend parameter estimation and QTL mapping were conducted consecutively while the second method was our Bayesian linear mixed model where trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or Bayesian framework to perform QTL inference. In total, five and four significant QTLs were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth and spiral grain angle. Four of these QTLs were represented by candidate gene SNPs thus providing promising targets for future research in QTL-mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTLs given datasets that comprised large numbers of individuals.
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