Polymorphism and Divergence in Two Willow Species, Salix viminalis L. and Salix schwerinii E. Wolf

We investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gene segments representing parts of 18 nuclear loci in 24 individuals for each species. We used coalescent simulations and estimated the split time to around 600,000 years ago and found that there is currently limited gene flow between the species. Mean intronic nucleotide diversity across gene segments was slightly higher in S. schwerinii (πi = 0.00849) than in S. viminalis (πi = 0.00655). Compared with other angiosperm trees, the two willows harbor intermediate levels of silent polymorphisms. The decay of linkage disequilibrium was slower in S. viminalis compared with S. schwerinii, and we speculate that this is due to different demographic histories as S. viminalis has been partly domesticated in Europe

High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus

<p><b>Abstract</b></p> <p>Background</p> <p><it>Salix </it>(willow) and <it>Populus </it>(poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the <it>Populus trichocarpa </it>genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya.</p> <p>Results</p> <p>We constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S₁, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S₃consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12) between orthologs than between paralogs (median: 0.37 - 0.41).</p> <p>Conclusions</p> <p>The relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary. Estimated silent substitution rates were 1.28 × 10^-9and 1.68 × 10^-9per site and year, which are close to rates found in other perennials but much lower than rates in annuals.</p

Variation of growth and phenology traits in poplars planted in clonal trials in Northern Europe-implications for breeding

The increased demand for wood to replace oil-based products with renewable products has lifted focus to the Baltic Sea region where the environment is favorable for woody biomass growth. The aim of this study was to estimate broad-sense heritabilities and genotype-by-environment (GxE) interactions in growth and phenology traits in six climatically different regions in Sweden and the Baltics. We tested the hypothesis that both bud burst and bud set have a significant effect on the early growth of selected poplar clones in Northern Europe. Provenance hybrids of Populus trichocarpa adapted to the Northern European climate were compared to reference clones with adaptation to the Central European climate. The volume index of stemwood was under low to medium genetic control with heritabilities from 0.22 to 0.75. Heritabilities for phenology traits varied between 0.31 and 0.91. Locally chosen elite clones were identified. GxE interactions were analyzed using pairwise comparisons of the trials. Three different breeding zones for poplars between the latitudes of 55 degrees N and 60 degrees N in the Baltic Sea Region were outlined. The studied provenance hybrids with origin from North America offer a great possibility to broaden the area with commercial poplar plantations in Northern Europe and further improve the collection of commercial clones to match local climates. We conclude that phenology is an important selection criterion after growth

Quantitative genetic architecture of adaptive phenology traits in the deciduous tree, Populus trichocarpa (Torr. And Gray)

In a warming climate, the ability to accurately predict and track shifting environmental conditions will be fundamental for plant survival. Environmental cues define the transitions between growth and dormancy as plants synchronise development with favourable environmental conditions, however these cues are predicted to change under future climate projections which may have profound impacts on tree survival and growth. Here, we use a quantitative genetic approach to estimate the genetic basis of spring and autumn phenology inPopulus trichocarpato determine this species capacity for climate adaptation. We measured bud burst, leaf coloration, and leaf senescence traits across two years (2017-2018) and combine these observations with measures of lifetime growth to determine how genetic correlations between phenology and growth may facilitate or constrain adaptation. Timing of transitions differed between years, although we found strong cross year genetic correlations in all traits, suggesting that genotypes respond in consistent ways to seasonal cues. Spring and autumn phenology were correlated with lifetime growth, where genotypes that burst leaves early and shed them late had the highest lifetime growth. We also identified substantial heritable variation in the timing of all phenological transitions (h(2) = 0.5-0.8) and in lifetime growth (h(2) = 0.8). The combination of additive variation and favourable genetic correlations in phenology traits suggests that populations of cultivated varieties of P. Trichocarpa may have the capability to adapt their phenology to climatic changes without negative impacts on growth

Phenotypic plasticity in Populus trichocarpa clones across environments in the Nordic-Baltic region

Transition towards a bio-based society requires large amounts of woody biomass to be converted into biofuels and biomaterials. Populus species are good candidates for growth in short rotations, but there is a lack of climate-adapted plant material suitable for growth at the high latitudes of the Nordic-Baltic region. Here we studied the growth and phenology traits in 63 Populus trichocarpa clones earlier preliminary selected for growth at northern latitudes, in three different field sites; i.e. in central Sweden, eastern and western Latvia. The material showed moderate broad sense heritabilities, with high values for phenology traits, indicating opportunities for selection. Genotype x environment (g x e) interaction was identified for all traits, but the phenotypic correlation between pairs of sites provided more detailed information indicating the strength of the g x e interaction. The between-clone variation in plasticity was high, and we identified some clones showing a high and stable performance across the three sites. These clones are of particular interest for the commercial deployment and future breeding of Populus material for the Nordic-Baltic region

A calibration method for non-overlapping cameras based on mirrored phase target

A novel calibration method for non-overlapping cameras is proposed in this paper. A LCD screen is used as a phase target to display two groups of orthogonal phase-shifted sinusoidal patterns during the calibration process. Through a mirror reflection, the phase target is captured by the cameras respectively. The relations between each camera and the phase target can be obtained according the proposed algorithm. Then the relation between the cameras can be calculated by treating the phase target as an intermediate value. The proposed method is more flexible than conventional mirror-based approach, because it do not require the common identification points and is robust to out-of-focus images. Both simulation work and experimental results show the proposed calibration method has a good result in calibrating a non-overlapping cameras system

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

Background: Salix spp. are high-productivity crops potentially used for lignocellulosic biofuels such as bioethanol. In general, pretreatment is needed to facilitate the enzymatic depolymerization process. Biomass resistance to degradation, i.e., biomass recalcitrance, is a trait which can be assessed by measuring the sugar released after combined pretreatment and enzymatic hydrolysis. We have examined genetic parameters of enzymatic sugar release and other traits related to biorefnery use in a population of 286 natural Salix viminalis clones. Furthermore, we have evaluated phenotypic and genetic correlations between these traits and performed a genomewide association mapping analysis using a set of 19,411 markers. Results: Sugar release (glucose and xylose) after pretreatment and enzymatic saccharifcation proved highly variable with large genetic and phenotypic variations, and chip heritability estimates (h2 ) of 0.23–0.29. Lignin syringyl/guaiacyl (S/G) ratio and wood density were the most heritable traits (h2=0.42 and 0.59, respectively). Sugar release traits were positively correlated, phenotypically and genetically, with biomass yield and lignin S/G ratio. Association mapping revealed seven marker–trait associations below a suggestive signifcance threshold, including one marker associated with glucose release. Conclusions: We identifed lignin S/G ratio and shoot diameter as heritable traits that could be relatively easily evaluated by breeders, making them suitable proxy traits for developing low-recalcitrance varieties. One marker below the suggestive threshold for marker associations was identifed for sugar release, meriting further investigation while also highlighting the difculties in employing genomewide association mapping for complex trait

Optimized utilization of Salix-Perspectives for the genetic improvement toward sustainable biofuel value chains

Bioenergy will be one of the most important renewable energy sources in the conversion from fossil fuels to bio-based products. Short rotation coppice Salix could be a key player in this conversion since Salix has rapid growth, positive energy balance, easy to manage cultivation system with vegetative propagation of plant material and multiple harvests from the same plantation. The aim of the present paper is to provide an overview of the main challenges and key issues in willow genetic improvement toward sustainable biofuel value chains. Primarily based on results from the research project "Optimized Utilization of Salix" (OPTUS), the influence of Salix wood quality on the potential for biofuel use is discussed, followed by issues related to the conversion of Salix biomass into liquid and gaseous transportation fuels. Thereafter, the studies address genotypic influence on soil carbon sequestration in Salix plantations, as well as on soil carbon dynamics and climate change impacts. Finally, the opportunities for plant breeding are discussed using willow as a resource for sustainable biofuel production. Substantial phenotypic and genotypic variation was reported for different wood quality traits important in biological (i.e., enzymatic and anaerobic) and thermochemical conversion processes, which is a prerequisite for plant breeding. Furthermore, different Salix genotypes can affect soil carbon sequestration variably, and life cycle assessment illustrates that these differences can result in different climate mitigation potential depending on genotype. Thus, the potential of Salix plantations for sustainable biomass production and its conversion into biofuels is shown. Large genetic variation in various wood and biomass traits, important for different conversion processes and carbon sequestration, provides opportunities to enhance the sustainability of the production system via plant breeding. This includes new breeding targets in addition to traditional targets for high yield to improve biomass quality and carbon sequestration potential