scholarly journals Forecasting floral futures: leveraging genetic and microenvironmental data to improve seed provenancing under climate change

Author(s):  
Andhika Putra ◽  
Jian Yen ◽  
Alexandre Fournier-Level

Revegetation projects seeking to restore degraded ecosystems face a major challenge in sourcing appropriate plant material, as identifying plants adapted to future climates requires knowledge of plant performance under novel conditions. In order to support climate-resilient provenancing efforts, we develop a quantitative trait model that integrates genetic and microenvironmental variation. We train our model with multiple natural plantings of Arabidopsis thaliana and predict days-to-bolting and fecundity across the species’ European range. Model prediction accuracy was high for days-to-bolting and moderate for fecundity, with the majority of trait variation being explained by temperature variation. Concerningly, fecundity was predicted to decline under future conditions, although this response was heterogeneous across regions, and could be offset through the introduction of specific genotypes. Our study highlights the value of predictive models to aid seed provenancing and improve the success of revegetation projects.

2012 ◽  
Vol 88 (06) ◽  
pp. 708-721 ◽  
Author(s):  
M. Irfan Ashraf ◽  
Charles P.-A. Bourque ◽  
David A. MacLean ◽  
Thom Erdle ◽  
Fan-Rui Meng

Empirical growth and yield models developed from historical data are commonly used in developing long-term strategic forest management plans. Use of these models rests on an assumption that there will be no future change in the tree growing environment. However, major impacts on forest growing conditions are expected to occur with climate change. As a result, there is a pressing need for tools capable of incorporating outcomes of climate change in their predictions of forest growth and yield. Process-based models have this capability and may, therefore, help to satisfy this requirement. In this paper, we evaluate the suitability of an ecological, individual-tree-based model (JABOWA-3) in generating forest growth and yield projections for diverse forest conditions across Nova Scotia, Canada. Model prediction accuracy was analyzed statistically by comparing modelled with observed basal area and merchantable volume changes for 35 permanent sample plots (PSPs) measured over periods of at least 25 years. Generally, modelled basal area and merchantable volume agreed fairly well with observed data, yielding coefficients of determination (r2) of 0.97 and 0.94 and model efficiencies (ME) of 0.96 and 0.93, respectively. A Chi-square test was performed to assess model accuracy with respect to changes in species composition. We found that 83% of species-growth trajectories based on measured basal area were adequately modelled with JABOWA-3 (P > 0.9). Model-prediction accuracy, however, was substantially reduced for those PSPs altered by some level of disturbance. In general, JABOWA-3 is much better at providing forest yield predictions, subject to the availability of suitable climatic and soil information.


2021 ◽  
Vol 11 ◽  
Author(s):  
Muhammad Farooq ◽  
Aalt D. J. van Dijk ◽  
Harm Nijveen ◽  
Mark G. M. Aarts ◽  
Willem Kruijer ◽  
...  

Prediction of growth-related complex traits is highly important for crop breeding. Photosynthesis efficiency and biomass are direct indicators of overall plant performance and therefore even minor improvements in these traits can result in significant breeding gains. Crop breeding for complex traits has been revolutionized by technological developments in genomics and phenomics. Capitalizing on the growing availability of genomics data, genome-wide marker-based prediction models allow for efficient selection of the best parents for the next generation without the need for phenotypic information. Until now such models mostly predict the phenotype directly from the genotype and fail to make use of relevant biological knowledge. It is an open question to what extent the use of such biological knowledge is beneficial for improving genomic prediction accuracy and reliability. In this study, we explored the use of publicly available biological information for genomic prediction of photosynthetic light use efficiency (ΦPSII) and projected leaf area (PLA) in Arabidopsis thaliana. To explore the use of various types of knowledge, we mapped genomic polymorphisms to Gene Ontology (GO) terms and transcriptomics-based gene clusters, and applied these in a Genomic Feature Best Linear Unbiased Predictor (GFBLUP) model, which is an extension to the traditional Genomic BLUP (GBLUP) benchmark. Our results suggest that incorporation of prior biological knowledge can improve genomic prediction accuracy for both ΦPSII and PLA. The improvement achieved depends on the trait, type of knowledge and trait heritability. Moreover, transcriptomics offers complementary evidence to the Gene Ontology for improvement when used to define functional groups of genes. In conclusion, prior knowledge about trait-specific groups of genes can be directly translated into improved genomic prediction.


2009 ◽  
Vol 184 (1) ◽  
pp. 180-192 ◽  
Author(s):  
Artak Ghandilyan ◽  
Luis Barboza ◽  
Sébastien Tisné ◽  
Christine Granier ◽  
Matthieu Reymond ◽  
...  

Crop Science ◽  
2016 ◽  
Vol 57 (1) ◽  
pp. 444-453 ◽  
Author(s):  
Hussain Sharifi ◽  
Robert J. Hijmans ◽  
James E. Hill ◽  
Bruce A. Linquist

Author(s):  
Vasil Atanasov ◽  
Lisa Fürtauer ◽  
Thomas Nägele

Diurnal and seasonal changes of abiotic environmental factors shape plant performance and distribution. Changes of growth temperature and light intensity may vary significantly on a diurnal, but also on a weekly or seasonal scale. Hence, acclimation to a changing temperature and light regime is essential for plant survival and propagation. In the present study, we analyzed photosynthetic CO2 assimilation and metabolic regulation of the central carbohydrate metabolism in two natural accessions of Arabidopsis thaliana originating from Russia and south Italy during exposure to heat and a combination of heat and high light. Our findings indicate that it is hardly possible to predict photosynthetic capacities to fix CO2 under combined stress from single stress experiments. Further, capacities of hexose phosphorylation were found to be significantly lower in the Italian than in the Russian accession which could explain an inverted sucrose-to-hexose ratio. Together with the finding of significantly stronger accumulation of anthocyanins under heat/high light these observations indicate a central role of hexokinase activity in stabilization of photosynthetic capacities within a changing environment.


PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e20886 ◽  
Author(s):  
Rebecca A. Silady ◽  
Sigi Effgen ◽  
Maarten Koornneef ◽  
Matthieu Reymond

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