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Plant J. 2019 Jun 5. doi: 10.1111/tpj.14429. [Epub ahead of print]

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

Author information

1
Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Parallellvägen 21, Umeå, 907 36, Sweden.
2
Section of Population Epigenetics and Epigenomics, Centre of Life and Food Sciences Weihenstephan, Technische Universität München, Lichtenbergstr. 2a, München, 85748, Germany.
3
Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland.
4
Department of Mathematical Sciences, Biocenter Oulu, University of Oulu, Pentti Kaiteran katu 1, Oulu, Finland.
5
Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 4-6, Umeå, 907 36, Sweden.
6
Uppsala Multidisciplinary Centre for Advanced Computational Science, Uppsala University, Lägerhyddsvägen 2, Uppsala, 752 37, Sweden.
7
RISE Bioeconomy, Drottning Kristinas väg 61, SE-114 86, Stockholm, Sweden.
8
Skogforsk, Ekebo 2250, SE-268 90, Svalöv, Sweden.
9
Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Kåbovägen 4, Uppsala, 752 36, Sweden.
10
IIC, Rosenlundsgatan 48B, SE-118 63, Stockholm, Sweden.

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.

KEYWORDS:

Norway spruce; candidate genes; functional trait mapping; genome-wide association mapping; sequence capture; single nucleotide polymorphisms

PMID:
31166032
DOI:
10.1111/tpj.14429

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