The time is ripe for functional genomics: Can epigenetic changes mediate reproductive timing?

Populations are under strong selection to match reproductive timing with favourable environmental conditions. This becomes particularly important and challenging with increasing interannual environmental variability. Adjusting reproductive timing requires the ability to sense and interpret relevant environmental cues, while responding flexibly to their interannual variation. For instance, in seasonal species, reproductive timing is often dependent on photoperiod and temperature. Although many genes influencing the timing of reproduction have been identified, far less attention has been paid to the gene-regulatory cascades orchestrating these complex gene-environment interactions. In a From the Cover article in this issue of Molecular Ecology, Lindner, Laine, et al. (2021) addressed this knowledge gap by investigating the role of DNA methylation in mediating reproductive timing in the seasonally breeding great tit (Parus major). Using a clever blood sampling design, they investigated genome-wide DNA methylation changes following individual female birds across multiple reproductive stages. This approach revealed 10 candidate genes with a strong correlation between promoter methylation and reproductive status. Some of these genes are known to be involved in reproductive timing (e.g., MYLK-like or NR5A1), yet for others this function was previously unknown (Figure 1). Interestingly, NR5A1 is a key transcription factor, which may affect other genes that are part of the same regulatory network. The findings of Lindner, Laine, et al. (2021) provide a strong case for studying DNA methylation to uncover how gene-environment interactions influence important life-history traits, such as reproductive timing

Two different epigenetic information channels in wild three-spined sticklebacks are involved in salinity adaptation

Epigenetic inheritance has been proposed to contribute to adaptation and acclimation via two information channels: (i) inducible epigenetic marks that enable transgenerational plasticity and (ii) noninducible epigenetic marks resulting from random epimutations shaped by selection. We studied both postulated channels by sequencing methylomes and genomes of Baltic three-spined sticklebacks ( Gasterosteus aculeatus ) along a salinity cline. Wild populations differing in salinity tolerance revealed differential methylation (pop-DMS) at genes enriched for osmoregulatory processes. A two-generation experiment demonstrated that 62% of these pop-DMS were noninducible by salinity manipulation, suggesting that they are the result of either direct selection or associated genomic divergence at cis- or trans-regulatory sites. Two-thirds of the remaining inducible pop-DMS increased in similarity to patterns detected in wild populations from corresponding salinities. The level of similarity accentuated over consecutive generations, indicating a mechanism of transgenerational plasticity. While we can attribute natural DNA methylation patterns to the two information channels, their interplay with genomic variation in salinity adaptation is still unresolved

Genome-wide association analysis of stalk biomass and anatomical traits in maize.

BackgroundMaize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk diameter and plant height) and stalk anatomy (rind thickness, vascular bundle density and area).ResultsUsing a panel of 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide polymorphism (SNP) markers were identified. Stalk traits were measured on 800 members of the panel in replicated field trials across years. GWAS revealed 16 candidate genes associated with four stalk traits. Most of the detected candidate genes were involved in fundamental cellular functions, such as regulation of gene expression and cell cycle progression. Two of the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated with plant height were previously shown to be involved in regulating the vegetative to floral transition. The association of Zmm22 with plant height was confirmed using a transgenic approach. Transgenic lines with increased expression of Zmm22 showed a significant decrease in plant height as well as tassel branch number, indicating a pleiotropic effect of Zmm22.ConclusionSubstantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs. Genome-wide association analyses detected several candidate genes associated with multiple traits, suggesting common regulatory elements underlie various stalk traits. Results of this study provide insights into the genetic control of maize stalk anatomy and biomass

From ecosystems to socio-economic benefits: A systematic review of coastal ecosystem services in the Baltic Sea

Highlights: • We summarized 20 ecosystem services provided by coastal Baltic ecosystems. • Information on how services translate into socio-economic benefits is lacking. • The deep knowledge gap impairs the sustainable management of the benefits. • We propose a framework with four key measures to close this knowledge gap. • Toxins and Nutrients are the most well-document pressures to these services. Abstract: Seagrass meadows, algal forests and mussel beds are widely regarded as foundation species that support communities providing valuable ecosystem services in many coastal regions; however, quantitative evidence of the relationship is scarce. Using the Baltic Sea as a case study, a region of significant socio-economic importance in the northern hemisphere, we systematically synthesized the primary literature and summarized the current knowledge on ecosystem services derived from seagrass, macroalgae, and mussels (see animated video summary of the manuscript: Video abstract). We found 1740 individual ecosystem service records (ESR), 61% of which were related to macroalgae, 26% to mussel beds and 13% to seagrass meadows. The most frequently reported ecosystem services were raw material (533 ESR), habitat provision (262 ESR) and regulation of pollutants (215 ESR). Toxins (356 ESR) and nutrients (302 ESR) were the most well-documented pressures to services provided by coastal ecosystems. Next, we assessed the current state of knowledge as well as knowledge transfer of ecosystem services to policies through natural, social, human and economic dimensions, using a systematic scoring tool, the Eco-GAME matrix. We found good quantitative information about how ecosystems generated the service but almost no knowledge of how they translate into socio-economic benefits (8 out of 657 papers, 1.2%). While we are aware that research on Baltic Sea socio-economic benefits does exist, the link with ecosystems providing the service is mostly missing. To close this knowledge gap, we need a better analytical framework that is capable of directly linking existing quantitative information about ecosystem service generation with human benefit

Requirements of 4G-Based Mobile Broadband on Future Transport Networks, Journal of Telecommunications and Information Technology, 2012, nr 2

Long term evolution technologies provide new standards in mobile communications regarding available bandwidth. It is expected that users of one radio cell will share more than 100 Mbit/s in future. To take advantage of the full feature set of next generation mobile networks, transport net- work design has to face new requirements, caused by the architectural changes of LTE technologies. Especially the newly defined X2 interface impacts on the transport network requirements. X2 enables direct communication between evolved base stations (eNBs) and thus, enforces local solutions. At the same time a tendency of locating network elements at fewer, central sites to reduce operational expenditure can be observed, in particular concerning the transport layer. This leads to the question of how the direct X2 connection of eNBs on the logical layer can be accommodated with a general centralization of transport networks. Our considerations show that for LTE, a centralized transport network is able to realize the local meshing between eNBs. However, for LTE Advanced, the standards currently discussed by the 3GPP initiative could lead to enhanced requirements on the X2 interface latency. Consequently, the implications for the network architecture have to be analyzed in more detail

The Mediterranean evergreen Quercus ilex and the semi-deciduous Cistus albidus differ in their leaf gas exchange regulation and acclimation to repeated drought and re-watering cycles

Plants may exhibit some degree of acclimation after experiencing drought, but physiological adjustments to consecutive cycles of drought and re-watering (recovery) have scarcely been studied. The Mediterranean evergreen holm oak (Q. ilex) and the semi-deciduous rockrose (C. albidus) showed some degree of acclimation after the first of three drought cycles (S1, S2, and S3). For instance, during S2 and S3 both species retained higher relative leaf water contents than during S1, despite reaching similar leaf water potentials. However, both species showed remarkable differences in their photosynthetic acclimation to repeated drought cycles. Both species decreased photosynthesis to a similar extent during the three cycles (20–40% of control values). However, after S1 and S2, photosynthesis recovered only to 80% of control values in holm oak, due to persistently low stomatal (gs) and mesophyll (gm) conductances to CO2. Moreover, leaf intrinsic water use efficiency (WUE) was kept almost constant in this species during the entire experiment. By contrast, photosynthesis of rockrose recovered almost completely after each drought cycle (90–100% of control values), while the WUE was largely and permanently increased (by 50–150%, depending on the day) after S1. This was due to a regulation which consisted in keeping gs low (recovering to 50–60% of control values after re-watering) while maintaining a high gm (even exceeding control values during re-watering). While the mechanisms to achieve such particular regulation of water and CO2 diffusion in leaves are unknown, it clearly represents a unique acclimation feature of this species after a drought cycle, which allows it a much better performance during successive drought events. Thus, differences in the photosynthetic acclimation to repeated drought cycles can have important consequences on the relative fitness of different Mediterranean species or growth forms within the frame of climate change scenarios

Understanding 'non-genetic' inheritance : insights from molecular-evolutionary crosstalk

The idea for this paper was initially proposed by I.A.-K. and was further developed by all authors in a workshop generously funded by grant No 789240 from the European Research Council (ERC) to F.J.W. S.E.S. acknowledges support from Wesleyan University and The John Templeton Foundation.Understanding the evolutionary and ecological roles of 'non-genetic' inheritance (NGI) is daunting due to the complexity and diversity of epigenetic mechanisms. We draw on insights from molecular and evolutionary biology perspectives to identify three general features of 'non-genetic' inheritance systems: (i) they are functionally interdependent with, rather than separate from, DNA sequence; (ii) precise mechanisms vary phylogenetically and operationally; and (iii) epigenetic elements are probabilistic, interactive regulatory factors and not deterministic 'epialleles' with defined genomic locations and effects. We discuss each of these features and offer recommendations for future empirical and theoretical research that implements a unifying inherited gene regulation (IGR) approach to studies of 'non-genetic' inheritance.Publisher PDFPeer reviewe