Genome Wide Associations of Growth, Phenology, and Plasticity Traits in Willow [Salix viminalis (L.)]

Abstract

The short rotation biomass crop willow ( Salix genera) has been of interest for bioenergy but recently also for biofuel production. For a faster development of new varieties molecular markers could be used as selection tool in an early stage of the breeding cycle. To identify markers associated with growth traits, genome-wide association mapping was conducted using a population of 291 Salix viminalis accessions collected across Europe and Russia and a large set of genotyping-by-sequencing markers. The accessions were vegetatively propagated and planted in replicated field experiments, one in Southern Sweden and one in Central Sweden. Phenology data, including bud burst and leaf senescence, as well as different growth traits were collected and measured repeatedly between 2010 and 2017 at both field environments. A value of the plasticity for each accession was calculated for all traits that were measured the same year in both environments as the normalized accession value in one environment subtracted by the corresponding value in the other environment. Broad-sense accession heritabilities and narrow-sense chip heritabilities ranged from 0.68 to 0.95 and 0.45 to 0.99, respectively for phenology traits and from 0.56 to 0.85 and 0.24 to 0.97 for growth traits indicating a considerable genetic component for most traits. Population structure and kinship between accessions were taken into account in the association analyses. In total, 39 marker-trait associations were found where four were specifically connected to plasticity and interestingly one particular marker was associated to several different plasticity growth traits. Otherwise association consistency was poor, possibly due to accession by environment interactions which were demonstrated by the low structure adjusted accession correlations across environments (ranging from 0.40 to 0.58). However, one marker association with biomass fresh weight was repeatedly observed in the same environment over two harvest years. For some traits where several associations were found, the markers jointly explained over 20% of the accession variation. The result from this study using a population of unrelated accessions has given useful information about marker-trait associations especially highlighting marker-plasticity associations and genotype-by-environment interactions as important factors to take account of in future strategies of Salix breeding.

Genetic variation of biomass recalcitrance in a natural Salix viminalis (L.) population

“…Therefore, these particular associations should be interpreted with skepticism as they may be due to a specific population substructure that our analysis, despite our efforts, was unable to account for. This particular phenomenon was also seen in a previous GWAS on this population [16].…”

“…For the main shoot of each plant, fresh weight (MSW) and wood density were measured. Whole plant fresh weight (FW) and number of shoots on the plant (NSh), which were recorded in 2017 for an earlier study [16], were also included in analyses within the present study (Fig. 1; Table 1).…”

“…For the 291 clones for which DNA sampling, preparation, and genotyping were successful, 1,555,795 sequence sites showing polymorphisms (single-nucleotide polymorphisms, SNPs; and single-nucleotide indels, SNIs) were identified and merged by TASSEL 4.3.7. The merged genotype data are stored at a publicly available repository [45].…”

“…The GBS polymorphism data were thereafter merged with older genotyping data (1290 SNPs) previously developed for the study population [34]. Polymorphic sites were then filtered using VCFtools 0.1.12b based on data completeness and on minor allele frequency (MAF) depending on downstream use (see [16] for details). To reduce the number of sites produced by erroneous merging of paralogous sequences, all polymorphisms with an apparent heterozygosity above 70% were removed using a custom Perl script.…”

Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate

“…Hence, now more than ever it is essential to explore changing abiotic (Chakhchar et al, 2017;Alcaide et al, 2019b) and biotic (Meyer et al, 2016) interactions. Rampant phenotypic plasticity (Berlin et al, 2017;Hallingback et al, 2019) to climate gradients is presumed in trees, arguing resilience to variability throughout their long lives. Still, forests adaptability should also be assessed in the light of spatially varying local environmental selective pressures (Savolainen et al, 2013), and trees' genetic and evolutionary potentials (Howe and Brunner, 2005).…”