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Glob Change Biol Bioenergy. 2016 May;8(3):670-685. Epub 2015 Jul 29.

Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology.

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Department of Plant Biology Uppsala BioCenter Swedish University of Agricultural Sciences and Linnean Center for Plant Biology P.O. Box 7043 750 07 Uppsala Sweden.
Computational and Systems Biology Department Rothamsted Research Harpenden Herts AL5 2JQ UK.
AgroEcology Department Rothamsted Research Harpenden Herts AL5 2JQ UK.
Department of Crop Production Ecology Swedish University of Agricultural Sciences and Linnean Center for Plant Biology P.O. Box 7043 750 07 Uppsala Sweden.
Department of Plant Ecology and Evolution Evolutionary Biology Centre Uppsala University 752 36 Uppsala Sweden.


Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnäs, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (G × E) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation (Radj2) explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR < 0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small Radj2 estimates and to considerable G × E interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).


Salix; adaptation; association mapping; candidate gene; growth; marker‐assisted selection; phenology; short‐rotation coppice; willow

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