Association mapping in Salix viminalis L. (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 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 (Rnormaladj2) 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 Rnormaladj2 estimates and to considerable G × E interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32–0.61).

Identification of Quantitative Trait Loci Conditioning the Main Biomass Yield Components and Resistance to Melampsora spp. in Salix viminalis × Salix schwerinii Hybrids

“…The cited authors developed QTL maps with the application of AFLP, RFLP, SNP and SSR markers. In the present experiment, a higher number of QTLs linked with plant height, shoot diameter and number of shoots per plant (11, 9 and 3 respectively) was identified than in other studies that relied on different types of markers [17,19]. The identified QTLs explained a lower percentage of variability in the analyzed traits (2.97%–16.16%) than those identified by other authors, which explained 14%–22% [17], 10%–20% [21] and 8%–42% of variability [18].…”

“…RAPD and ISSR systems are universal tools that are highly useful at various stages of breeding new plant varieties. In the existing studies, willow loci were identified mainly in analyses of biomass yield [17,18,19,20,21]. Quantitative trait loci linked with the resistance/susceptibility of Salix species to leaf rust were rarely identified, including by Rönnberg-Wästljung et al [31], Hanley et al [26] and Samils et al [22].…”

“…A few genetic maps supporting the identification of QTLs linked with various traits have been developed for the genus Salix [8,13,14,15,16,17]. In willows, most of the identified QTLs were linked with biomass yield and yield-associated traits such as plant height, shoot diameter or side branching [17,18,19,20,21]. Molecular markers linked to leaf rust resistance [22], sex [23], phenological traits [14,19], elemental composition of biomass [24], tolerance for environmental factors [18,25], and resistance to diseases and pests [22,26,27] were also identified.…”

“…In willows, most of the identified QTLs were linked with biomass yield and yield-associated traits such as plant height, shoot diameter or side branching [17,18,19,20,21]. Molecular markers linked to leaf rust resistance [22], sex [23], phenological traits [14,19], elemental composition of biomass [24], tolerance for environmental factors [18,25], and resistance to diseases and pests [22,26,27] were also identified. Quantitative trait loci associated with plant resistance also play an important role in willows, in particular in varieties intended for large-area multiannual plantations, which become increasingly susceptible to diseases with time.…”

Effects of Cutting Phenology (Non-dormant Versus Dormant) on Early Growth Performance of Three Willow Clones Grown Under Different Weed Treatments and Planting Dates

“…The rationale behind the first hypothesis presented in the study was that the non-dormant cuttings mobilize their carbohydrate reserves, which will be more depleted in non-dormant than dormant cuttings the later the planting date becomes, and that BCGDD is genetically determined and differs between willow clones [29,30]. The first hypothesis was partly supported by our results as BCGDD was significantly affected by willow clone during mid-and late planting dates (i.e., May 10 and 24, June 16).…”