Use of the growing environment as a source of variation to identify the quantitative trait transcripts and modules of co-expressed genes that determine chlorogenic acid accumulation

Developing Coffea arabica seeds accumulate large amounts of chlorogenic acids (CGAs) as a storage form of phenylpropanoid derivatives, making coffee a valuable model to investigate the metabolism of these widespread plant phenolics. However, developmental and environmental regulations of CGA metabolism are poorly understood. In the present work, the expression of selected phenylpropanoid genes, together with CGA isomer profiles, was monitored throughout seed development across a wide set of contrasted natural environments. Although CGA metabolism was controlled by major developmental factors, the mean temperature during seed development had a direct impact on the time-window of CGA biosynthesis, as well as on final CGA isomer composition through subtle transcriptional regulations. We provide evidence that the variability induced by the environment is a useful tool to test whether CGA accumulation is quantitatively modulated at the transcriptional level, hence enabling detection of rate-limiting transcriptional steps [quantitative trait transcripts (QTTs)] for CGA biosynthesis. Variations induced by the environment also enabled a better description of the phenylpropanoid gene transcriptional network throughout seed development, as well as the detection of three temporally distinct modules of quantitatively co-expressed genes. Finally, analysis of metabolite-to-metabolite relationships revealed new biochemical characteristics of the isomerization steps that remain uncharacterized at the gene level

The implications of nongenetic inheritance for evolution in changing environments

Nongenetic inheritance is a potentially important but poorly understood factor in population responses to rapid environmental change. Accumulating evidence indicates that nongenetic inheritance influences a diverse array of traits in all organisms and can allow for the transmission of environmentally induced phenotypic changes (‘acquired traits’), as well as spontaneously arising and highly mutable variants. We review models of adaptation to changing environments under the assumption of a broadened model of inheritance that incorporates nongenetic mechanisms of transmission, and survey relevant empirical examples. Theory suggests that nongenetic inheritance can increase the rate of both phenotypic and genetic change and, in some cases, alter the direction of change. Empirical evidence shows that a diversity of phenotypes – spanning a continuum from adaptive to pathological – can be transmitted nongenetically. The presence of nongenetic inheritance therefore complicates our understanding of evolutionary responses to environmental change. We outline a research program encompassing experimental studies that test for transgenerational effects of a range of environmental factors, followed by theoretical and empirical studies on the population-level consequences of such effects

Data from: Mediation of seed provisioning in the transmission of environmental maternal effects in Maritime pine (Pinus pinaster Aiton)

Although maternal environmental effects are increasingly recognized as an important source of phenotypic variation with relevant impacts in evolutionary processes, their relevance in long-lived plants such as pine trees is largely unknown. Here, we used a powerful sample size and a strong quantitative genetic approach to analyse the sources of variation of early seedling performance and to identify seed mass (SM)-dependent and -independent maternal environmental effects in Maritime pine. We measured SM of 8924 individual seeds collected from 10 genotypes clonally replicated in two environments of contrasting quality (favourable and stressful), and we measured seedling growth rate and biomass allocation to roots and shoots. SM was extremely variable (up to 14-fold) and strongly determined by the maternal environment and the genotype of the mother tree. The favourable maternal environment led to larger cones, larger seeds and reduced SM variability. The maternal environment also determined the offspring phenotype, with seedlings coming from the favourable environment being 35% larger and with greater root/shoot ratio. Transgenerational plasticity appears, thus, to be a relevant source of phenotypic variation in the early performance of this pine species. Seed provisioning explained most of the effect of the maternal environment on seedling total biomass. Environmental maternal effects on seedling biomass allocation were, however, determined through SM-independent mechanisms, suggesting that other epigenetic regulation channels may be involved