ACCESSORY COSTS OF SEED PRODUCTION AND THE EVOLUTION OF ANGIOSPERMS

Limits to reproduction and seed size-number trade-offs that shape forest dominance and future recovery

The relationships that control seed production in trees are fundamental to understanding the evolution of forest species and their capacity to recover from increasing losses to drought, fire, and harvest. A synthesis of fecundity data from 714 species worldwide allowed us to examine hypotheses that are central to quantifying reproduction, a foundation for assessing fitness in forest trees. Four major findings emerged. First, seed production is not constrained by a strict trade-off between seed size and numbers. Instead, seed numbers vary over ten orders of magnitude, with species that invest in large seeds producing more seeds than expected from the 1:1 trade-off. Second, gymnosperms have lower seed production than angiosperms, potentially due to their extra investments in protective woody cones. Third, nutrient-demanding species, indicated by high foliar phosphorus concentrations, have low seed production. Finally, sensitivity of individual species to soil fertility varies widely, limiting the response of community seed production to fertility gradients. In combination, these findings can inform models of forest response that need to incorporate reproductive potential.

The Patterns of Male and Female Flowers in Flowering Stage May Not Be Optimal Resource Allocation for Fruit and Seed Growth

Changes in the proportions of male and female flowers in monoecious plants in response to external environmental conditions are directly related to the reproductive fitness of plants. The monoecious cucumber (Cucumber sativus) plant was used in this study to assess the responses of sex differentiation and the breeding process to nutrient supply and the degree of artificial pollination using pollen solutions of different concentrations. We found that the nutrient supply significantly improved the number of female flowers, while pollination treatments did not obviously increase the number of male flowers. Continuous pollination changed the number of female flowers especially in the later stage of the pollination experiment. Therefore, pollination changed the ratio of male and female flowers in the flowering stage of cucumber. Pollination treatment affected the fruit growth, seed set, and fruit yield. The number of fruit, fruit set percentage, and total seeds per plant did not increase with the pollination level, but individual fruit weight and seed number in one fruit did increase. The differentiation of male and female flowers in the flowering stage of cucumber is a response to nutrient and pollination resources, but this response is not the optimal resource allocation for subsequent fruit development and seed maturity, which suggests that the response of plants to external environment resources is short-term and direct.

Ecological and phylogenetic constraints determine the stage of anthetic ovule development in orchids

PREMISE

Unlike most flowering plants, orchid flowers have under-developed ovules that complete development only after pollination. Classical studies reported variation in the stage in which ovule development is arrested, but the extent of this variation and its evolutionary and ecological significance are unclear.

METHODS

Here, we used light microscopy to observe ovule development at anthesis for 39 species not previously studied and surveyed the literature gaining information on 94 orchid species. Tropical and temperate members of all five orchid subfamilies as well as species with contrasting pollination strategies (rewarding versus deceptive) and life forms (epiphytic versus terrestrial) were represented. We analyzed the data using statistical comparisons and a phylogenetic generalized least square (PGLS) analysis.

RESULTS

Apostasioideae, the sister to the rest of the orchids, have mature ovules similar to other Asparagales, while under-differentiated ovules are present in the other subfamilies. Ovule developmental stages showed high variation even among closely related groups. Ovules were more developed in terrestrial than in epiphytic, in temperate than in tropical, and in rewarding than in deceptive pollination orchid species. This latter comparison was also significant in the PGLS analysis.

CONCLUSIONS

These results suggest that ovule developmental stage in orchids can be shaped by ecological factors, such as seasonality and pollination strategy, and can be selected for optimizing female reproductive investment.

Genetic Interaction of SEEDSTICK, GORDITA and AUXIN RESPONSE FACTOR 2 during Seed Development

Seed development is under the control of complex and coordinated molecular networks required for the formation of its different components. The seed coat development largely determines final seed size and shape, in addition to playing a crucial role in protecting the embryo and promoting germination. In this study, we investigated the role of three transcription factors known to be active during seed development in Arabidopsis thaliana: SEEDSTICK (STK) and GORDITA (GOA), two MADS-domain proteins, and AUXIN RESPONSE FACTOR 2 (ARF2), belonging to the ARF family. Through a reverse genetic approach, we characterized the seed phenotypes of all the single, double and triple loss-of-function mutants in relation to seed size/shape and the effects on metabolic pathways occurring in the seed coat. This approach revealed that dynamic networks involving these TFs are active throughout ovule and seed development, affecting the formation of the seed coat. Notably, while the genetic interaction among these genes results in synergies that control the promotion of cell expansion in the seed coat upon pollination and production of proanthocyanidins, functional antagonists arise in the control of cell proliferation and release of mucilage.

Not all 'pine cones' flex: functional trade-offs and the evolution of seed release mechanisms

Seed dispersal is critical for plants, but the evolution of mechanisms that actually release seeds from their parents is not well understood. We use the reproductive cones of conifers, specifically the Pinaceae clade, to explore the factors driving the evolution of different release mechanisms in plants. We combine comparative anatomical and phylogenetic analyses to test whether fundamental trade-offs in the mechanical and hydraulic properties of vasculature underlie the evolution of two seed release mechanisms: cone scale flexion and cone scale shedding. We then test whether these mechanisms are linked with differences in seed size, dispersal syndrome and reproductive allocation. Cone scale xylem in flexing species is tough, but poorly conductive. Xylem in shedding species is less extensive, fragile and highly conductive; its thin-walled tracheids allow scales to easily fracture at maturity. Shedding is also consistently associated with large, densely packed seeds. Pinaceae cones exploit a well-known trade-off in xylem mechanical strength vs hydraulic efficiency to generate release mechanisms that allow seeds of various sizes to leave the protecting cone. The linkage among release mechanisms, vascular anatomy and seed traits illustrates how a wide variety of selective pressures may influence the function and physiology of reproductive structures.

Twelve fundamental life histories evolving through allocation-dependent fecundity and survival

An organism's life history is closely interlinked with its allocation of energy between growth and reproduction at different life stages. Theoretical models have established that diminishing returns from reproductive investment promote strategies with simultaneous investment into growth and reproduction (indeterminate growth) over strategies with distinct phases of growth and reproduction (determinate growth). We extend this traditional, binary classification by showing that allocation‐dependent fecundity and mortality rates allow for a large diversity of optimal allocation schedules. By analyzing a model of organisms that allocate energy between growth and reproduction, we find twelve types of optimal allocation schedules, differing qualitatively in how reproductive allocation increases with body mass. These twelve optimal allocation schedules include types with different combinations of continuous and discontinuous increase in reproduction allocation, in which phases of continuous increase can be decelerating or accelerating. We furthermore investigate how this variation influences growth curves and the expected maximum life span and body size. Our study thus reveals new links between eco‐physiological constraints and life‐history evolution and underscores how allocation‐dependent fitness components may underlie biological diversity.

Shoot and Root Traits Contribute to Drought Resistance in Recombinant Inbred Lines of MD 23-24 × SEA 5 of Common Bean

Drought is the major abiotic stress factor limiting yield of common bean (Phaseolus vulgaris L.) in smallholder systems in Latin America and eastern and southern Africa; where it is a main source of protein in the daily diet. Identification of shoot and root traits associated with drought resistance contributes to improving the process of designing bean genotypes adapted to drought. Field and greenhouse studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia to determine the relationship between grain yield and different shoot and root traits using a recombinant inbred lines (RILs) population (MD23-24 × SEA 5) of common bean. The main objectives of this study were to identify: (i) specific shoot and root morpho-physiological traits that contribute to improved resistance to drought and that could be useful as selection criteria in breeding beans for drought resistance; and (ii) superior genotypes with desirable shoot and root traits that could serve as parents in breeding programs that are aimed at improving drought resistance. A set of 121 bean genotypes (111 RILs, 2 parents, 8 checks) belonging to the Mesoamerican gene pool and one cowpea variety were evaluated under field conditions with two levels of water supply (irrigated and rainfed) over three seasons. To complement field studies, a greenhouse study was conducted using plastic cylinders with soil inserted into PVC pipes, to determine the relationship between grain yield obtained under field conditions with different root traits measured under greenhouse conditions. Resistance to drought stress was positively associated with a deeper and vigorous root system, better shoot growth, and superior mobilization of photosynthates to pod and seed production. The drought resistant lines differed in their root characteristics, some of them with a vigorous and deeper root system while others with a moderate to shallow root system. Among the shoot traits measured, pod harvest index, and seed number per area could serve as useful selection criteria for assessing sink strength and for genetic improvement of drought resistance in common bean.

The global spectrum of plant form and function

Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have proved evolutionarily viable in today's terrestrial biosphere. By analysing worldwide variation in six major traits critical to growth, survival and reproduction within the largest sample of vascular plant species ever compiled, we found that occupancy of six-dimensional trait space is strongly concentrated, indicating coordination and trade-offs. Three-quarters of trait variation is captured in a two-dimensional global spectrum of plant form and function. One major dimension within this plane reflects the size of whole plants and their parts; the other represents the leaf economics spectrum, which balances leaf construction costs against growth potential. The global plant trait spectrum provides a backdrop for elucidating constraints on evolution, for functionally qualifying species and ecosystems, and for improving models that predict future vegetation based on continuous variation in plant form and function.

Diversification of the duplicated Rab1a genes in a hypoxia-tolerant fish, common carp (Cyprinus carpio)

Common carp is a widely cultivated fish with longer than 2,000 years domestication history, due to its strong environmental adaptabilities, especially hypoxia tolerance. The common carp genome has experienced a very recent whole genome duplication (WGD) event. Among a large number of highly similar duplicated genes, a pair of Ras-associated binding-GTPase 1a (Rab1a) genes were found fast diverging. Four analogous Rab1a genes were identified in the common carp genome. Comparisons of gene structures and sequences indicated Rab1a-1 and Rab1a-2 was a pair of fast diverging duplicates, while Rab1a-3 and Rab1a-4 was a pair of less diverged duplicates. All putative Rab1a proteins shared conserved GTPase domain, which enabled the proteins serve as molecular switches for vesicular trafficking. Rab1a-1 and Rab1a-2 proteins varied in their C-terminal sequences, which were generally considered to encode the membrane localization signals. Differential expression patterns were observed between Rab1a-1 and Rab1a-2 genes. In blood, muscle, spleen, and heart, the mRNA level of Rab1a-1 was higher than that of Rab1a-2. In liver and intestine, the mRNA level of Rab1a-2 was higher. Expression of Rab1a-1 and Rab1a-2 showed distinct hypoxia responses. Under severe hypoxia, Rab1a-1 expression was down-regulated in blood, while Rab1a-2 expression was up-regulated in liver. Compared with the less diverged Rab1a-3/4 gene pair, common carp Rab1a-1/2 gene pair exhibited strong characteristics of sub-functionalization, which might contribute to a sophisticated and efficient Ras-dependent regulating network for the hypoxia-tolerant fish.

Crop yield components - photoassimilate supply- or utilisation limited-organ development?

Yield potential is the genome-encoded capacity of a crop species to generate yield in an optimal growth environment. Ninety per cent of plant biomass is derived from the photosynthetic reduction of carbon dioxide to organic carbon (photoassimilates - primarily sucrose). Thus, development of yield components (organ numbers and individual organ masses) can be limited by photoassimilate supply (photosynthesis arranged in series with phloem transport) or by their inherent capacity to utilise imported photoassimilates for growth or storage. To this end, photoassimilate supply/utilisation of crop yield has been quantitatively re-evaluated using published responses of yield components to elevated carbon dioxide concentrations across a selection of key crop species including cereal and pulse grains, fleshy fruits, tubers and sugar storing stems and tap roots. The analysis demonstrates that development of harvested organ numbers is strongly limited by photoassimilate supply. Vegetative branching and, to a lesser extent, flower/pod/fleshy fruit abortion, are the major yield components contributing to sensitivity of organ numbers to photoassimilate supply. In contrast, harvested organ size is partially dependent (eudicots), or completely independent (cereals), of photoassimilate supply. Processes limiting photoassimilate utilisation by harvested organs include membrane transport of soluble sugars and their allocation into polymeric storage products.

Transcriptional circuitry underlying seed coat development in Arabidopsis

We analyzed two sub-regions of the maternal seed coat, chalazal (CZSC) and distal (SC), using transcriptomic and histological analyses in the model plant Arabidopsis thaliana. Hierarchical clustering analysis showed that the CZSC and SC are transcriptionally distinct, though the two sub-regions are more similar during early stages of seed development. Robust statistical and network analysis revealed novel roles for both sub-regions during the course of the seed lifecycle and provides insight into the regulatory circuitry underlying these poorly studied sub-regions of the seed. Data show many of the processes that characterize the SC including starch deposition during the morphogenesis phase, and mucilage deposition and cell wall thickening during the maturation phase, are either absent or expressed to a much lesser extent in the CZSC. We further analyzed the CZSC in detail and show that this sub-region is likely involved in the control of information into the seed from the maternal plant and that some of these processes are predicted to operate through the activity of bZIP transcription factors through the G-box DNA sequence motif.

The fate of duplicated genes in a polyploid plant genome

Polyploidy is generally not tolerated in animals, but is widespread in plant genomes and may result in extensive genetic redundancy. The fate of duplicated genes is poorly understood, both functionally and evolutionarily. Soybean (Glycine max L.) has undergone two separate polyploidy events (13 and 59 million years ago) that have resulted in 75% of its genes being present in multiple copies. It therefore constitutes a good model to study the impact of whole-genome duplication on gene expression. Using RNA-seq, we tested the functional fate of a set of approximately 18 000 duplicated genes. Across seven tissues tested, approximately 50% of paralogs were differentially expressed and thus had undergone expression sub-functionalization. Based on gene ontology and expression data, our analysis also revealed that only a small proportion of the duplicated genes have been neo-functionalized or non-functionalized. In addition, duplicated genes were often found in collinear blocks, and several blocks of duplicated genes were co-regulated, suggesting some type of epigenetic or positional regulation. We also found that transcription factors and ribosomal protein genes were differentially expressed in many tissues, suggesting that the main consequence of polyploidy in soybean may be at the regulatory level.