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 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).
Highlights
In the cultivation of trees and shrubs for biomass production, fast and stable growth is a highly desirable trait
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)
The accessions were genotyped using 1536 single nucleotide polymorphism (SNP) markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments
Summary
In the cultivation of trees and shrubs for biomass production, fast and stable growth is a highly desirable trait. The plant material needs to be genetically adapted to the environment at the site where. Transitions is highly influenced by a combination of temperature and photoperiodic cues (Cannell, 1990; Fracheboud et al, 2009) The plant integrates these onto developmental switches in a delicate trade-off between the competitive advantage of early and longer growth versus possible damage from low/freezing temperatures in spring and autumn (Savage & Cavender-Bares, 2013). For the development of such selection tools, a dissection of the relevant traits by, for example, quantitative trait locus (QTL) linkage mapping or by association mapping is first required (Savolainen et al, 2013; Hanley & Karp, 2014)
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