Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce

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http://hdl.handle.net/10138/305763

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Baison , J , Vidalis , A , Zhou , L , Chen , Z-Q , Li , Z , Sillanpää , M J , Bernhardsson , C , Scofield , D , Forsberg , N , Grahn , T , Olsson , L , Karlsson , B , Wu , H , Ingvarsson , P K , Lundqvist , S-O , Niittylae , T & Garcia-Gil , M R 2019 , ' Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce ' , Plant Journal , vol. 100 , no. 1 , pp. 83-100 . https://doi.org/10.1111/tpj.14429

Title: Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce
Author: Baison, John; Vidalis, Amaryllis; Zhou, Linghua; Chen, Zhi-Qiang; Li, Zitong; Sillanpää, Mikko J.; Bernhardsson, Carolina; Scofield, Douglas; Forsberg, Nils; Grahn, Thomas; Olsson, Lars; Karlsson, Bo; Wu, Harry; Ingvarsson, Pär K.; Lundqvist, Sven-Olof; Niittylae, Totte; Garcia-Gil, M. Rosario
Contributor: University of Helsinki, Ecological Genetics Research Unit
Date: 2019-10
Language: eng
Number of pages: 18
Belongs to series: Plant Journal
ISSN: 0960-7412
URI: http://hdl.handle.net/10138/305763
Abstract: Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.
Subject: candidate genes
functional trait mapping
genome-wide association mapping
Norway spruce
sequence capture
single nucleotide polymorphisms
QUANTITATIVE TRAIT LOCI
PINUS-TAEDA L.
GENETIC ARCHITECTURE
QUALITY TRAITS
CELLULOSE BIOSYNTHESIS
LINKAGE DISEQUILIBRIUM
COMPLEX TRAITS
FOREST TREES
GROWTH
POPULUS
1181 Ecology, evolutionary biology
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