Studying the genetic basis of masting

A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don

BACKGROUND

The Japanese cedar (Cryptomeria japonica D. Don) is one of the most important Japanese forest trees, occupying approximately 44% of artificial forests and planted in East Asia, the Azores Archipelago, and certain islands in the Indian Ocean. Although the huge genome of the species (ca. 9 Gbp) with abundant repeat elements may have represented an obstacle for genetic analysis, this species is easily propagated by cutting, flowered by gibberellic acid, transformed by Agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica recommend it as a model conifer species for which reference genome sequences are necessary.

RESULTS

Herein, we report the first chromosome-level assembly of C. japonica (2n = 22) using third-generation selfed progeny (estimated homozygosity rate = 0.96). Young leaf tissue was used to extract high molecular weight DNA (> 50 kb) for HiFi PacBio long-read sequencing and to construct an Hi-C/Omni-C library for Illumina short-read sequencing. The 29× and 26× genome coverage of HiFi and Illumina reads, respectively, for de novo assembly yielded 2,651 contigs (9.1 Gbp, N50 contig size 12.0 Mbp). Hi-C analysis mapped 97% of the nucleotides on 11 chromosomes. The assembly was verified through comparison with a consensus linkage map comprising 7,781 markers. BUSCO analysis identified ∼ 91% conserved genes.

CONCLUSIONS

Annotations of genes and comparisons of repeat elements with other Cupressaceae and Pinaceae species provide a fundamental resource for conifer research.

Evolutionary drivers of reproductive fitness in two endangered forest trees

Population genetics theory predicts a relationship between fitness, genetic diversity (H0) and effective population size (Ne), which is often tested through heterozygosity-fitness correlations (HFCs). We tested whether population and individual fertility and heterozygosity are correlated in two endangered Mexican spruces (Picea martinezii and Picea mexicana) by combining genomic, demographic and reproductive data (seed development and germination traits). For both species, there was a positive correlation between population size and seed development traits, but not germination rate. Individual genome-wide heterozygosity and seed traits were only correlated in P. martinezii (general-effects HFC), and none of the candidate single nucleotide polymorphisms (SNPs) associated with individual fertility showed heterozygote advantage in any species (no local-effects HFC). We observed a single and recent (c. 30 thousand years ago (ka)) population decline for P. martinezii; the collapse of P. mexicana occurred in two phases separated by a long period of stability (c. 800 ka). Recruitment always contributed more to total population census than adult trees in P. mexicana, while this was only the case in the largest populations of P. martinezii. Equating fitness to either H0 or Ne, as traditionally proposed in conservation biology, might not always be adequate, as species-specific evolutionary factors can decouple the expected correlation between these parameters.

Evolutionary ecology of masting: mechanisms, models, and climate change

Many perennial plants show mast seeding, characterized by synchronous and highly variable reproduction across years. We propose a general model of masting, integrating proximate factors (environmental variation, weather cues, and resource budgets) with ultimate drivers (predator satiation and pollination efficiency). This general model shows how the relationships between masting and weather shape the diverse responses of species to climate warming, ranging from no change to lower interannual variation or reproductive failure. The role of environmental prediction as a masting driver is being reassessed; future studies need to estimate prediction accuracy and the benefits acquired. Since reproduction is central to plant adaptation to climate change, understanding how masting adapts to shifting environmental conditions is now a central question.

Tail-dependence of masting synchrony results in continent-wide seed scarcity

Spatial synchrony may be tail-dependent, meaning it is stronger for peaks rather than troughs, or vice versa. High interannual variation in seed production in perennial plants, called masting, can be synchronized at subcontinental scales, triggering extensive resource pulses or famines. We used data from 99 populations of European beech (Fagus sylvatica) to examine whether masting synchrony differs between mast peaks and years of seed scarcity. Our results revealed that seed scarcity occurs simultaneously across the majority of the species range, extending to populations separated by distances up to 1800 km. Mast peaks were spatially synchronized at distances up to 1000 km and synchrony was geographically concentrated in northeastern Europe. Extensive synchrony in the masting lower tail means that famines caused by beech seed scarcity are amplified by their extensive spatial synchrony, with diverse consequences for food web functioning and climate change biology.

Summer solstice orchestrates the subcontinental-scale synchrony of mast seeding

High interannual variation in seed production in perennial plants can be synchronized at subcontinental scales with wide consequences for ecosystem functioning, but how such synchrony is generated is unclear1-3. We investigated the factors contributing to masting synchrony in European beech (Fagus sylvatica), which extends to a geographic range of 2,000 km. Maximizing masting synchrony via spatial weather coordination, known as the Moran effect, requires a simultaneous response to weather conditions across distant populations. A celestial cue that occurs simultaneously across the entire hemisphere is the longest day (the summer solstice). We show that European beech abruptly opens its temperature-sensing window on the solstice, and hence widely separated populations all start responding to weather signals in the same week. This celestial 'starting gun' generates ecological events with high spatial synchrony across the continent.

Relatives reproduce in synchrony: kinship and individual condition shape intraspecific variation in masting phenotype

Masting (synchronous and interannually variable seed production) is frequently called a reproductive strategy; yet it is unclear whether the reproductive behaviour of individuals has a heritable component. To address this, we used 22 years of annual fruit production data from 110 Sorbus aucuparia L. trees to examine the contributions of genetic factors to the reproductive phenotype of individuals, while controlling for environmental variation. Trees sharing close genetic relationships and experiencing similar habitat conditions exhibited similar levels of reproductive synchrony. Trees of comparable sizes displayed similar levels of year-to-year variation in fruiting, with relatedness contributing to this variation. External factors, such as shading, influenced the time intervals between years with abundant fruit production. The effects of genetic relatedness on the synchrony of reproduction among trees and on interannual variation provide long-awaited evidence that the masting phenotype is heritable, and can respond to natural selection.

An overview of floral regulatory genes in annual and perennial plants

The floral initiation in angiosperms is a complex process influenced by endogenous and exogenous signals. With this approach, we aim to provide a comprehensive review to integrate this complex floral regulatory process and summarize the regulatory genes and their functions in annuals and perennials. Seven primary paths leading to flowering have been discovered in Arabidopsis under several growth condition that include; photoperiod, ambient temperature, vernalization, gibberellins, autonomous, aging and carbohydrates. These pathways involve a series of interlinked signaling pathways that respond to both internal and external signals, such as light, temperature, hormones, and developmental cues, to coordinate the expression of genes that are involved in flower development. Among them, the photoperiodic pathway was the most important and conserved as some of the fundamental loci and mechanisms are shared even by closely related plant species. The activation of floral regulatory genes such as FLC, FT, LFY, and SOC1 that determine floral meristem identity and the transition to the flowering stage result from the merging of these pathways. Recent studies confirmed that alternative splicing, antisense RNA and epigenetic modification play crucial roles by regulating the expression of genes related to blooming. In this review, we documented recent progress in the floral transition time in annuals and perennials, with emphasis on the specific regulatory mechanisms along with the application of various molecular approaches including overexpression studies, RNA interference and Virus-induced flowering. Furthermore, the similarities and differences between annual and perennial flowering will aid significant contributions to the field by elucidating the mechanisms of perennial plant development and floral initiation regulation.

Masting is uncommon in trees that depend on mutualist dispersers in the context of global climate and fertility gradients

The benefits of masting (volatile, quasi-synchronous seed production at lagged intervals) include satiation of seed predators, but these benefits come with a cost to mutualist pollen and seed dispersers. If the evolution of masting represents a balance between these benefits and costs, we expect mast avoidance in species that are heavily reliant on mutualist dispersers. These effects play out in the context of variable climate and site fertility among species that vary widely in nutrient demand. Meta-analyses of published data have focused on variation at the population scale, thus omitting periodicity within trees and synchronicity between trees. From raw data on 12 million tree-years worldwide, we quantified three components of masting that have not previously been analysed together: (i) volatility, defined as the frequency-weighted year-to-year variation; (ii) periodicity, representing the lag between high-seed years; and (iii) synchronicity, indicating the tree-to-tree correlation. Results show that mast avoidance (low volatility and low synchronicity) by species dependent on mutualist dispersers explains more variation than any other effect. Nutrient-demanding species have low volatility, and species that are most common on nutrient-rich and warm/wet sites exhibit short periods. The prevalence of masting in cold/dry sites coincides with climatic conditions where dependence on vertebrate dispersers is less common than in the wet tropics. Mutualist dispersers neutralize the benefits of masting for predator satiation, further balancing the effects of climate, site fertility and nutrient demands.

Mechanisms driving interspecific variation in regional synchrony of trees reproduction

Seed production in many plants is characterized by large interannual variation, which is synchronized at subcontinental scales in some species but local in others. The reproductive synchrony affects animal migrations, trophic responses to resource pulses and the planning of management and conservation. Spatial synchrony of reproduction is typically attributed to the Moran effect, but this alone is unable to explain interspecific differences in synchrony. We show that interspecific differences in the conservation of seed production-weather relationships combine with the Moran effect to explain variation in reproductive synchrony. Conservative timing of weather cues that trigger masting allows populations to be synchronized at distances >1000 km. Conversely, if populations respond to variable weather signals, synchrony cannot be achieved. Our study shows that species vary in the extent to which their weather cueing is spatiotemporally conserved, with important consequences, including an interspecific variation of masting vulnerability to climate change.

Oak masting drivers vary between populations depending on their climatic environments

Large interannual variation in seed production, called masting, is very common in wind-pollinated tree populations and has profound implications for the dynamics of forest ecosystems and the epidemiology of certain human diseases.^1,2,3,4,5 Comparing the reproductive characteristics of populations established in climatically contrasting environments would provide powerful insight into masting mechanisms, but the required data are extremely scarce. We built a database from an unprecedented fine-scale 8-year survey of 150 sessile oak trees (Quercus petraea) from 15 populations distributed over a broad climatic gradient, including individual recordings of annual flowering effort, fruiting rate, and fruit production. Although oak masting was previously considered to depend mainly on fruiting rate variations,^6,7 we show that the female flowering effort is highly variable from year to year and explains most of the fruiting dynamics in two-thirds of the populations. What drives masting was found to differ among populations living under various climates. In soft-climate populations, the fruiting rate increases initially strongly with the flowering effort, and the intensity of masting results mainly from the flowering synchrony level between individuals. By contrast, the fruiting rate of harsh-climate populations depends mainly on spring weather, which ensures intense masting regardless of the flowering synchronization level. Our work highlights the need for jointly measuring flowering effort and fruit production to decipher the diversity of masting mechanisms among populations. Accounting for such diversity will be decisive in proposing accurate, and possibly contrasted, scenarios about future reproductive patterns of perennial plants with ongoing climate change and their numerous cascading effects.

A cross-scale approach to unravel the molecular basis of plant phenology in temperate and tropical climates

Plants have evolved to time their leafing, flowering and fruiting in appropriate seasons for growth, reproduction and resting. As a consequence of their adaptation to geographically different environments, there is a rich diversity in plant phenology from temperate and tropical climates. Recent progress in genetic and molecular studies will provide numerous opportunities to study the genetic basis of phenological traits and the history of adaptation of phenological traits to seasonal and aseasonal environments. Integrating molecular data with long-term phenology and climate data into predictive models will be a powerful tool to forecast future phenological changes in the face of global environmental change. Here, we review the cross-scale approach from genes to plant communities from three aspects: the latitudinal gradient of plant phenology at the community level, the environmental and genetic factors underlying the diversity of plant phenology, and an integrated approach to forecast future plant phenology based on genetically informed knowledge. Synthesizing the latest knowledge about plant phenology from molecular, ecological and mathematical perspectives will help us understand how natural selection can lead to the further evolution of the gene regulatory mechanisms in phenological traits in future forest ecosystems.

The effects of ENSO and the North American monsoon on mast seeding in two Rocky Mountain conifer species

We aimed to disentangle the patterns of synchronous and variable cone production (i.e. masting) and its relationship to climate in two conifer species native to dry forests of western North America. We used cone abscission scars to reconstruct ca 15 years of recent cone production in Pinus edulis and Pinus ponderosa, and used redundancy analysis to relate time series of annual cone production to climate indices describing the North American monsoon and the El Niño Southern Oscillation (ENSO). We show that the sensitivity to climate and resulting synchrony in cone production varies substantially between species. Cone production among populations of P. edulis was much more spatially synchronous and more closely related to large-scale modes of climate variability than among populations of P. ponderosa. Large-scale synchrony in P. edulis cone production was associated with the North American monsoon and we identified a dipole pattern of regional cone production associated with ENSO phase. In P. ponderosa, these climate indices were not strongly associated with cone production, resulting in asynchronous masting patterns among populations. This study helps frame our understanding of mast seeding as a life-history strategy and has implications for our ability to forecast mast years in these species. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

Delayed fertilization facilitates flowering time diversity in Fagaceae

Fagaceae includes typical masting species that exhibit highly synchronized and fluctuating acorn production. Fagaceae shows an interesting feature in that fertilization is delayed by several weeks to more than 1 year after pollination. Although delayed fertilization was recorded over a century ago, the evolutionary advantage of delayed fertilization is still poorly understood. Here, we present a new hypothesis that delayed fertilization facilitates temporal niche differentiation via non-overlapping flowering times among species. Comparing flowering and fruiting times in 228 species from five genera in Fagaceae, we first show that there is a close association between a wider spread of flowering times and the likelihood of a 2-year fruiting habit in which there is a long delay from pollination to fertilization. To study the coevolution of flowering time and delayed fertilization, we developed a mathematical model that incorporates the effects of competition for pollinators, seed predator satiation and unfavourable season for reproduction on fitness. The model shows that delayed fertilization facilitates the diversification of flowering time in a population, which is advantageous for animal-pollinated trees that compete over pollinators. Our new hypothesis about the coevolution of delayed fertilization and flowering time will provide new insight into the evolution of masting. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

The ecology and evolution of synchronized reproduction in long-lived plants

Populations of many long-lived plants exhibit spatially synchronized seed production that varies extensively over time, so that seed production in some years is much higher than on average, while in others, it is much lower or absent. This phenomenon termed masting or mast seeding has important consequences for plant reproductive success, ecosystem dynamics and plant-human interactions. Inspired by recent advances in the field, this special issue presents a series of articles that advance the current understanding of the ecology and evolution of masting. To provide a broad overview, we reflect on the state-of-the-art of masting research in terms of underlying proximate mechanisms, ontogeny, adaptations, phylogeny and applications to conservation. While the mechanistic drivers and fitness consequences of masting have received most attention, the evolutionary history, ontogenetic trajectory and applications to plant-human interactions are poorly understood. With increased availability of long-term datasets across broader geographical and taxonomic scales, as well as advances in molecular approaches, we expect that many mysteries of masting will be solved soon. The increased understanding of this global phenomenon will provide the foundation for predictive modelling of seed crops, which will improve our ability to manage forests and agricultural fruit and nut crops in the Anthropocene. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

By wind or wing: pollination syndromes and alternate bearing in horticultural systems

Cyclical fluctuations in reproductive output are widespread among perennial plants, from multi-year masting cycles in forest trees to alternate bearing in horticultural crops. In natural systems, ecological drivers such as climate and pollen limitation can result in synchrony among plants. Agricultural practices are generally assumed to outweigh ecological drivers that might synchronize alternate-bearing individuals, but this assumption has not been rigorously assessed and little is known about the role of pollen limitation as a driver of synchrony in alternate-bearing crops. We tested whether alternate-bearing perennial crops show signs of alternate bearing at a national scale and whether the magnitude of national-scale alternate bearing differs across pollination syndromes. We analysed the Food and Agriculture Organization of the United Nations time series (1961-2018) of national crop yields across the top-producing countries of 27 alternate-bearing taxa, 6 wind-pollinated and 21 insect-pollinated. Alternate bearing was common in these national data and more pronounced in wind-pollinated taxa, which exhibited a more negative lag-1 autocorrelation and a higher coefficient of variation (CV). We highlight the mutual benefits of integrating ecological theory and agricultural data for (i) advancing our understanding of perennial plant reproduction across time, space and taxa, and (ii) promoting stable farmer livelihoods and global food supply. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

Climate change and plant reproduction: trends and drivers of mast seeding change

Climate change is reshaping global vegetation through its impacts on plant mortality, but recruitment creates the next generation of plants and will determine the structure and composition of future communities. Recruitment depends on mean seed production, but also on the interannual variability and among-plant synchrony in seed production, the phenomenon known as mast seeding. Thus, predicting the long-term response of global vegetation dynamics to climate change requires understanding the response of masting to changing climate. Recently, data and methods have become available allowing the first assessments of long-term changes in masting. Reviewing the literature, we evaluate evidence for a fingerprint of climate change on mast seeding and discuss the drivers and impacts of these changes. We divide our discussion into the main characteristics of mast seeding: interannual variation, synchrony, temporal autocorrelation and mast frequency. Data indicate that masting patterns are changing but the direction of that change varies, likely reflecting the diversity of proximate factors underlying masting across taxa. Experiments to understand the proximate mechanisms underlying masting, in combination with the analysis of long-term datasets, will enable us to understand this observed variability in the response of masting. This will allow us to predict future shifts in masting patterns, and consequently ecosystem impacts of climate change via its impacts on masting. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.