Identifying and testing marker–trait associations for growth and phenology in three pine species:Implications for genomic prediction

In tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker-trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 SNPs from three closely related pine species (Pinus sylvestris, Pinus uncinata and Pinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial of P. sylvestris and the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376, p < 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204, p = 0.034; 2018: r = 0.205, p = 0.034-0.037) and negatively associated with budburst timing at the other (YA: r = -0.202, p = 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments

Does cooperation mean kinship between spatially discrete ant nests?

Procter, D., J. Cottrell, K. Watts, S. A'Hara, M. Hofreiter and E. J. H. Robinson (in press). "" Ecology and Evolutio

Do non-native conifer plantations provide benefits for a native forest specialist, the wood ant Formica lugubris?

AbstractRecent increases in plantation forestry are starting to reverse the global decline in forest cover, in some areas of the world. Britain has practiced afforestation, primarily with non-native conifers, for over a century. It is unclear whether these new plantations have the potential to support native forest species.We quantify afforestation across the North York Moors National Park, UK, deriving a chronology of afforestation from historic maps at six time points from 1854 to 2013. We map the location of current wood ant (Formica lugubris) nests and set their distribution in the context of historic forest cover. We use these nest locations and the features of the habitat in which they occur to model the suitability of recently established conifer plantations for wood ants using MaxEnt. We determine whether non-native conifers offer suitable habitat for a forest specialist species, and assess the lag between establishment of conifer plantations and colonisation by wood ants from historic woodland fragments.Forest cover increased by 229% over 160years and is now dominated by non-native conifer plantations. Our survey data show that current wood ant populations extend hundreds of metres from where forest was in the past, demonstrating geographical population expansions into newly formed forest, comprised of non-native conifer plantations. Both our data and model reveal that the recently planted non-native conifer plantations are a suitable habitat for this forest specialist species. Our model reveals that Formica lugubris has not yet spread through all available suitable habitat due to very poor dispersal ability, displaying a severe lag behind the availability of habitat.Managers should not assume that unoccupied habitat is unsuitable nor should they expect to see immediate colonisation of plantations. Future forest creation should be targeted close to existing forests to facilitate colonisation of forest specialists

Spring phenology shows genetic variation among and within populations in seedlings of Scots pine (Pinus sylvestris L.) in the Scottish Highlands

Background: Genetic differentiation in phenotypic traits is often observed among forest tree populations, but less is known about patterns of adaptive variation within populations. Such variation is expected to enhance the survival likelihood of extant populations under climate change. Aims: Scots pine (Pinus sylvestris) occurs over a spatially and temporally heterogeneous landscape in Scotland. Our goal was to examine whether populations had differentiated genetically in timing of bud flush in response to spatial heterogeneity and whether variation was also maintained within populations. Methods: Two common-garden studies, involving maternal families of seedlings from 21 native pinewoods, were established and variation in the trait was measured at the beginning of the second growing season. Results: Populations showed genetic differences in the trait correlated with the length of growing season at their site of origin, but the majority of variation was observed within populations. Populations also differed in their levels of variation in the trait; a pattern that may be influenced by spatial variation in the extent of temporal climate variability. Conclusions: Our findings suggest that populations have adapted to their home environments and that they also have substantial ability to adapt in situ to changes in growing season length

Phenotypic trait variation in a long-term multisite common garden experiment of Scots pine in Scotland

Multisite common garden experiments, exposing common pools of genetic diversity to a range of environments, allow quantification of plastic and genetic components of trait variation. For tree species, such studies must be long term as they typically only express mature traits after many years. As well as evaluating standing genetic diversity, these experiments provide an ongoing test of genetic variation against changing environmental conditions and form a vital resource for understanding how species respond to abiotic and biotic variation. Finally, quantitative assessments of phenotypic variation are essential to pair with rapidly accumulating genomic data to advance understanding of the genetic basis of trait variation, and its interaction with climatic change. We describe a multisite, population-progeny, common garden experiment of the economically and ecologically important tree species, Scots pine, collected from across its native range in Scotland and grown in three contrasting environments. Phenotypic traits, including height, stem diameter and budburst were measured over 14 growing seasons from nursery to field site. The datasets presented have a wide range of applications

Seed sourcing for woodland creation in an era of uncertainty: An analysis of the options for Great Britain

In recent years, British seed sourcing practice has tended to focus on the principle that “local-is-best” for native woodland creation. However, in the face of continuing and accelerating environmental change, the suitability of this approach has been called into question. In this article, we investigate the relevance and suitability of a series of seed sourcing strategies: maintaining the status quo by continuing to source local origin seed, sourcing seed from currently warmer locations, and the addition or replacement of species. Our main findings are that there are opportunities to increase the sophistication of existing guidance and that improvements would be timely. In any case, an important consideration is the capacity for newly established populations of trees to survive immediately and amidst increasingly variable environmental conditions. The current paucity of knowledge of forest genetic resources in British populations of native tree species suggests that deviations from sourcing currently adapted planting stock are not uniformly applicable throughout the country and that any change to policy ought to be applied judiciously and only under a restricted set of circumstances

Additive and non-additive genetic variance in juvenile Sitka spruce (Picea sitchensis Bong. Carr)

Many quantitative genetic models assume that all genetic variation is additive because of a lack of data with sufficient structure and quality to determine the relative contribution of additive and non-additive variation. Here the fractions of additive (fa) and non-additive (fd) genetic variation were estimated in Sitka spruce for height, bud burst and pilodyn penetration depth. Approximately 1500 offspring were produced in each of three sib families and clonally replicated across three geographically diverse sites. Genotypes from 1525 offspring from all three families were obtained by RADseq, followed by imputation using 1630 loci segregating in all families and mapped using the newly developed linkage map of Sitka spruce. The analyses employed a new approach for estimating fa and fd, which combined all available genotypic and phenotypic data with spatial modelling for each trait and site. The consensus estimate for fa increased with age for height from 0.58 at 2 years to 0.75 at 11 years, with only small overlap in 95% support intervals (I95). The estimated fa for bud burst was 0.83 (I95=[0.78, 0.90]) and 0.84 (I95=[0.77, 0.92]) for pilodyn depth. Overall, there was no evidence of family heterogeneity for height or bud burst, or site heterogeneity for pilodyn depth, and no evidence of inbreeding depression associated with genomic homozygosity, expected if dominance variance was the major component of non-additive variance. The results offer no support for the development of sublines for crossing within the species. The models give new opportunities to assess more accurately the scale of non-additive variation

Cryptic genetic variation and adaptation to waterlogging in Caledonian Scots pine, <i>Pinus sylvestris</i> L.

Local adaptation occurs as the result of differential selection among populations. Observations made under common environmental conditions may reveal phenotypic differences between populations with an underlying genetic basis; however, exposure to a contrasting novel environment can trigger release of otherwise unobservable (cryptic) genetic variation. We conducted a waterlogging experiment on a common garden trial of Scots pine, Pinus sylvestris (L.), saplings originating from across a steep rainfall gradient in Scotland. A flood treatment was maintained for approximately 1 year; physiological responses were gauged periodically in terms of photochemical capacity as measured via chlorophyll fluorescence. During the treatment, flooded individuals experienced a reduction in photochemical capacity, Fv/Fm, this reduction being greater for material originating from drier, eastern sites. Phenotypic variance was increased under flooding, and this increase was notably smaller in saplings originating from western sites where precipitation is substantially greater and waterlogging is more common. We conclude that local adaptation has occurred with respect to waterlogging tolerance and that, under the flooding treatment, the greater increase in variability observed in populations originating from drier sites is likely to reflect a relative absence of past selection. In view of a changing climate, we note that comparatively maladapted populations may possess considerable adaptive potential, due to cryptic genetic variation, that should not be overlooked

A strategy for UK forest genetic resources: protecting the UK's unique diversity of trees and shrubs

A strategy for the UK's forest genetic resource