The genetic architecture of traits and trait responses is recognized as a key regulator of intraspecific variation in plant responses to environmental change . Patterns of G × E are sometimes attributed to architectural aspects such as pleiotropy, differential sensitivity and non-additive effects. Pleiotropy occurs when a single gene affects two apparently unrelated phenotypic traits. Differential sensitivity occurs when a gene’s effect varies depending upon the environment, and non-additive effects can occur when allelic effects at many loci confer different degrees of plasticity.Evidence for a pleiotropic linkage between flowering time and WUE has been shown in Arabidopsis; for example, early flowering genotypes showed low WUE and late flowering genotypes showed high WUE . Here, selection for one trait would constrain the direction of change in another trait and the pattern of G × E. Antagonistic pleiotropy can also occur when a particular allele may increase a trait value in one environment, but reduce it in another. Lovell et al.demonstrated a case of ‘adaptive pleiotropy’ where expression of a particular gene can result in different strategies for coping with drought; for example, escape or avoidance . While the causes of genetic correlations among traits remain poorly understood, it is apparent that intraspecific variation in agricultural and forest species responses to climate change may be strongly determined by the direction and magnitude of genetic correlations among traits. Quantitative trait loci studies, which examine sections of the genome associated with a particular trait or response, and examination of cross-environment genetic correlations have been useful tools for inferring the underlying genetic architecture of G × E. In Arabidopsis, for example, WUE and flowering time were affected by five different QTL each , although regions of the genome contained QTL for both traits suggesting a potential pleiotropic effect. In a simulation of QTL effects on maize growth, water use and yield, a QTL that accelerated leaf elongation under well-watered conditions also increased leaf area and yield,low round pots but reduced yield under stress.Pleiotropic effects on silk elongation and grain set magnified the QTL effect on yield.

Studies in trees, particularly Populus, have also provided important insight into the genetic architecture of responsiveness to eCO2. For example, Ferris et al.found that QTL for adaxial stomatal density under ambient and eCO2 were located on the same linkage group, suggesting similar patterns of genetic control across treatments. Likewise, Rae et al.found many QTL for leaf traits, which mapped to common positions in ambient and eCO2 in Populus, and Rae et al.identified QTL linked to above ground and below ground growth responses to eCO2. The identification of these QTL may allow breeders to target regions of the Populus genome, which may confer differences in genotype productivity under eCO2. Although many QTL studies have provided evidence for pleiotropic effects, more than 50% have identified QTL that lack a significant effect in another environment , suggesting that differentially sensitive QTL are a common architectural feature of G × E. Interestingly, QTL associated with differential sensitivity tend to confer lower plasticity than QTL associated with antagonistic pleiotropy . The strength and direction of cross environment genetic correlations can also provide insight into genetic architecture of traits and how traits may respond to abiotic stress . In Brassica rapa, for instance, genotypes with low WUE under well-watered conditions had high WUE under drought , indicating possible antagonistic gene action. These findings call attention to the role of genetic architecture in influencing patterns of G × E and emphasize the importance of integrating knowledge of trait genetic architecture into physiological studies of agricultural and forest species responses to climate change.Gene expression studies have provided critical insight into the function of specific genes and regulatory networks during drought and heat stress . Additionally, there has been increasing recognition of the importance of carbohydrate-mediated gene expression during stress , with carbon sink size and activity regulating photosynthetic activity via gene expression and sugar-mediated regulation of photosynthetic enzymes . Genes associated with metabolic functions are often up-regulated under C depletion, and the sensitivity of carbohydrate-responsive gene expression might aid acclimation responses. Beyond basic knowledge of gene expression responses, a number of studies have demonstrated genotype-specific patterns of gene expression under different soil moisture and temperature conditions, providing insight into the molecular mechanisms of intraspecific variation in growth and performance . For example, in a comparison of two Arabidopsis ecotypes under progressive soil drying, minimal physiological changes were observed, but hundreds of transcripts showed differential expression between ecotypes . Such results could indicate that physiological homeostasis may be underlain by high molecular plasticity.

Similarly, Populus clones have shown contrasting patterns of gene expression responses with a drought-sensitive clone showing larger transcriptional responses in roots indicative of low C availability linked to low C fixation at the leaf level . A comparison of the molecular responses of two Eucalyptus genotypes under drought also found marked differences in gene expression, which corresponded with clone differences in productivity . A few studies have also examined transcript profiles of genotypes growing under ambient and eCO2. One particularly interesting study by Cseke et al.found that a CO2-responsive Populus clone showed transcript patterns associated with increased C partitioning to stress defence and growth, while a CO2- unresponsive clone partitioned more C towards chemical defence and cell wall thickening. Gene expression responses alone cannot explain patterns of G × E in growth and physiology, but examining gene expression patterns and physiological responses may provide a powerful way forward for understanding intraspecific variation in responsiveness to environmental change . It is particularly evident that intraspecific variation in molecular responses may have downstream impacts on carbon source – sink dynamics, which impact genotype function and productivity under stressful conditions and eCO2. Ultimately, understanding differential patterns of gene expression between individuals, and how these patterns are associated with the physiological traits, which influence yield and productivity will be crucial to harnessing the potential utility of G × E. Lastly, epigenetic effects, which change gene activity during development without altering DNA sequences may play important roles in regulating phenotypic responses to environmental factors and patterns of G × E. Epigenetic effects arise from signals from receptors and signalling cascades and have been linked to DNA methylation . Epigenetic effects are reversible, yet heritable in encoding antecedent environmental conditions that have carry-over effects on phenotypic responses of progeny. They can therefore constrain a genotype’s plastic response to future stress events or increased resource availability . For example, genotypic differences in Populus clone transcript abundance under drought have reflected similar patterns of DNA methylation, where individual ramets of clones with the most divergent transcriptomes and clone history showed the largest differences in DNA methylation . Clearly, epigenetic studies demonstrate huge potential in assessing the influence of environment on intraspecific variation in plastic responses to environmental change.Our assessment of previous studies illustrates that there is substantial intraspecific variation in phenotypic plasticity in response to drought, warming, heat stress and eCO2 within many agricultural and forest species.Our understanding of the physiological mechanisms and genetic factors,which influence intraspecific variation in responsiveness to these climate change factors, has also advanced tremendously. However, in our view, the following areas require further attention. Firstly, more explicit examinations of genotype plasticity–productivity relationships should be conducted in agriculture and forestry. Many of the studies we examined report differential growth and physiological responses to particular climate change factors, but to our knowledge, none have reported the degree to which genotype trait plasticity is associated with genotype performance across environments.

Where genotypic variation in agricultural and forest species responses to drought, temperature or eCO2 are substantial, and genotype plasticity has a beneficial effect on productivity, improving or sustaining productivity under climate change might require targeting not only individual traits under genetic control, but also genotypic variation in plasticity to environmental change . Secondly, despite important logistical and methodological challenges, more effort should go towards systematically assessing intraspecific variation in agricultural and forestry species responses to multiple climate change factors under field conditions . Numerous studies have investigated intraspecific variation in growth and function in response to one climate change factor under controlled environmental conditions , but studies conducted under field conditions with several genotypes and multiple climate change factors are rare . The lack of studies under field conditions creates uncertainty regarding the potential for genetic variation to buffer the combined effects of climate change. Independent of whether the mechanisms of intraspecific variation in growth and function in response to interacting climate change factors are known, screening large numbers of genotypes in the field and assessing the magnitude of G × E will be a key step forwardin identifying genotypes, which can persist under stressful conditions and maximize productivity under optimal conditions. Identifying such genotypes may be especially beneficial for forestry,plastic pots 30 liters where genotype productivity–stress tolerance trade-offs are common. Likewise, data collected from established agricultural and forestry field trials replicated across environmental gradients should be more fully utilized . By understanding variation in key local environmental conditions and genotype responses to those conditions, we may better understand thresholds for genotypes performance under climate change. In fact, re-examination of long-term data collected from established forestry provenance trials could partially address the lack of G × E studies under field conditions.

Analysis of long-term agricultural yield data might also provide insight into intraspecific variation in agricultural species yield responses to recent climate change. Nonetheless, newer, more extensive field trials should be established along key environmental gradients where climate change is likely to exert the strongest selective pressures. Provenance and field trials are a classical approach to assessing the degree of G × E, and they deserve continued focus. Thirdly, the growth and stress tolerance of ancestral or less domesticated genetic material in response to the main and interactive effects of drought, warming and eCO2 should be examined. For instance, there has been some speculation that plant breeding has inadvertently selected for genotypes which are more responsive to rising CO2, yet older genetic material has shown greater positive responses to eCO2 than newer genetic material . In support of this finding, undomesticated natural species generally demonstrate greater plasticity to environmental change than agricultural species , most likely reflecting the lack of a legacy of targeted artificial selection. Thus, surveying intraspecific variation in phenotypic plasticity to environmental change in ancestral or less domesticated genetic material conserved in gene banks or as land races could prove useful for adapting agriculture and forestry to climate change . Equally, concerted efforts to preserve agricultural and forest species genetic diversity should be made, as genotypes previously selected against may show desirable responses to novel climatic conditions . Fourthly, there remains an urgent need to develop high through put tools for screening phenotypic traits in many individual genotypes growing across a range of conditions . This is not a new recommendation , but one that requires continued focus if we are to utilize variation in genetically controlled traits and genetic variation in phenotypic plasticity. Lastly, plants are highly integrated organisms with traits often co-varying across hierarchical levels. Phenotypic changes occurring at any ‘level’ must coherently respond to changes occurring at another level, or risk reductions in plant growth, reproduction or survival under stress. For this reason, multivariate analyses which account for genetic covariation in trait values across scales may provide greater insight into the mechanisms and constraints on intraspecific variation in phenotypic plasticity. It may be particularly insightful to integrate responses occurring at the transcriptome, metabolome and physiological level . Carefully examining linear and non-linear relationships between gene expression and physiological traits may also provide insight into stress thresholds for individual genotypes .Agricultural easements are a compensatory and non-regulatory technique for protecting farmland from urbanization, through the purchase of development rights from landowners. Local conservation organizations, land trusts or public agencies acquire and hold the easements and manage them over time . Based on information provided by 34 identified programs with farmland protection objectives ,we estimate that California now has about 120,000 acres in agricultural easements. This projection updates an earlier estimate of about 84,000 acres statewide in mid-2000, based on individual reports from program managers at that time . The exact number is a moving target, since the most active programs have been picking up easements at a rapid pace. Even as program managers provided the data on easements completed in mid-2000, they also reported in-the-works transactions with landowners to acquire another 21,000 acres.