title: Association mapping inSalix viminalisL. (Salicaceae) - identification of candidate genes associated with growth and phenology.
abstract: 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 aSalix 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 theEARLY FLOWERING 3gene 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).
authors.affiliation: 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.
authors.forename: Henrik R
authors.initials: HR
authors.lastname: Hallingbäck
authors.affiliation: 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.
authors.forename: Johan
authors.initials: J
authors.lastname: Fogelqvist
authors.affiliation: Computational and Systems Biology Department Rothamsted Research Harpenden Herts AL5 2JQ UK.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Powers
authors.affiliation: AgroEcology Department Rothamsted Research Harpenden Herts AL5 2JQ UK.
authors.forename: Juan
authors.initials: J
authors.lastname: Turrion-Gomez
authors.affiliation: AgroEcology Department Rothamsted Research Harpenden Herts AL5 2JQ UK.
authors.forename: Rachel
authors.initials: R
authors.lastname: Rossiter
authors.affiliation: AgroEcology Department Rothamsted Research Harpenden Herts AL5 2JQ UK.
authors.forename: Joanna
authors.initials: J
authors.lastname: Amey
authors.affiliation: 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.
authors.forename: Tom
authors.initials: T
authors.lastname: Martin
authors.affiliation: Department of Crop Production Ecology Swedish University of Agricultural Sciences and Linnean Center for Plant Biology P.O. Box 7043 750 07 Uppsala Sweden.
authors.forename: Martin
authors.initials: M
authors.lastname: Weih
authors.affiliation: 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.
authors.forename: Niclas
authors.initials: N
authors.lastname: Gyllenstrand
authors.affiliation: AgroEcology Department Rothamsted Research Harpenden Herts AL5 2JQ UK.
authors.forename: Angela
authors.initials: A
authors.lastname: Karp
authors.affiliation: Department of Plant Ecology and Evolution Evolutionary Biology Centre Uppsala University 752 36 Uppsala Sweden.
authors.forename: Ulf
authors.initials: U
authors.lastname: Lagercrantz
authors.affiliation: AgroEcology Department Rothamsted Research Harpenden Herts AL5 2JQ UK.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hanley
authors.affiliation: 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.
authors.forename: Sofia
authors.initials: S
authors.lastname: Berlin
authors.affiliation: 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.
authors.forename: Ann-Christin
authors.initials: AC
authors.lastname: Rönnberg-Wästljung
keywords: Salix; adaptation; association mapping; candidate gene; growth; marker‐assisted selection; phenology; short‐rotation coppice; willow