Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon

Abstract

Sweet-fleshed watermelon (Citrullus lanatus) is an important vegetable crop of the tropical origin. It is widely grown and consumed around the world for its hydration and nutritional quality values. Low-temperature stress can affect early planting, seedling establishment, and expansion of crop production to new areas. A collection of 122 citron watermelon (Citrullus amarus) accessions were obtained from the USDA's National Plant Germplasm Repository System gene bank in Griffin, GA. The accessions were genotyped using whole genome resequencing to generate single nucleotide polymorphisms (SNPs) molecular markers and screened under cold-stressed and non-stressed control conditions. Four low-temperature stress tolerance related traits including shoot biomass, vine length, maximum quantum efficiency of photosystem II, and chlorophyll content were measured under cold-stressed and non-stressed control treatment conditions. Correlation analysis revealed the presence of positive relationships among traits. Broad-sense heritability for all traits ranged from 0.35 to 0.73, implying the presence of genetic contributions to the observed phenotypic variation. Genomic regions underlying these traits across several citron watermelon chromosomes were identified. Four low-temperature stress tolerance related putative candidate genes co-located with the peak SNPs from genome-wide association study. These genomic regions and marker information could potentially be used in molecular breeding to accelerate genetic improvements for low-temperature stress tolerance in watermelon.

Cloning and functional analysis of Gb4CL1 and Gb4CL2 from Ginkgo biloba

Abstract

4-Coumarate-CoA ligase (4CL) gene plays vital roles in plant growth and development, especially the regulation of lignin metabolism and flavonoid synthesis. To investigate the potential function of 4CL in the lignin biosynthesis of Ginkgo biloba, this study identified two 4CL genes, Gb4CL1 and Gb4CL2, from G. biloba genome. Based on the phylogenetic tree analysis, Gb4CL1 and Gb4CL2 protein were classified into Class I, which has been confirmed to be involved in lignin biosynthesis. Therefore, it can be inferred that these two genes may also participate in lignin metabolism. The tissue-specific expression patterns of these two genes revealed that Gb4CL1 was highly expressed in microstrobilus, whereas Gb4CL2 was abundant in immature leaves. The onion transient expression assay indicated that Gb4CL1 was predominantly localized in the nucleus, indicating its potential involvement in nuclear functions, while Gb4CL2 was observed in the cell wall, suggesting its role in cell wall-related processes. Phytohormone response analysis revealed that the expression of both genes was upregulated in response to indole acetic acid, while methyl jasmonate suppressed it, gibberellin exhibited opposite effects on these genes. Furthermore, Gb4CL1 and Gb4CL2 expressed in all tissues containing lignin that showed a positive correlation with lignin content. Thus, these findings suggest that Gb4CL1 and Gb4CL2 are likely involved in lignin biosynthesis. Gb4CL1 and Gb4CL2 target proteins were successfully induced in Escherichia coli BL21 with molecular weights of 85.5 and 89.2 kDa, proving the integrity of target proteins. Our findings provided a basis for revealing that Gb4CL participated in lignin synthesis in G. biloba.

Structure, floristic composition, and distribution of swamp forests across a white‐water flood‐plain in the Colombian Amazon

Structure, floristic composition, and distribution of swamp forests across a white-water flood-plain in the Colombian Amazon

We identified three types of swamp forests across the flood-plains of the Caquetá River: permanent várzea, oxandrales and cananguchales. These forests showed successional patterns dissociated from their position relative to the main river channel. Still, they seemed more influenced by the interaction of floodings, sediment and nutrients input from white-water and/or black-water rivers, and peat accumulation.


Abstract

Questions

The fluvial dynamics of meandering white-water rivers of Amazonia drive vegetation primary succession. Directional successional processes have been recorded for the seasonal várzea forests that occupy well-drained soils on levees and point bars across the spatial gradient of the flood-plains. However, the types of forests occupying the swampy depressions interspersed between the point bars and their distribution along the flood-plain's spatial gradient are poorly understood. Here, we aimed to unravel the spatial patterns of swamp forests along the sequence defined by an axis perpendicular to the river and the relationship with edaphic and spatial factors.

Location

The flood-plains of the middle Caquetá River basin, Colombian Amazonia.

Methods

Forest types were identified by cluster analysis performed on 42 square plots (33 m × 33 m) set in poorly drained depressions of the flood-plain. Floristic composition and vegetation structure as response data, and edaphic and spatial variables as predictors, were analyzed through partial redundancy analysis (pRDA). The effect of geographic position was included by using the first two axes of a principal coordinates of neighbor matrix analysis as conditional factors in the pRDA.

Results

The three identified swamp forest types were not arranged along a directional spatial pattern. Permanent várzea forests, closest to the river, showed the greatest diversity and alluvial sediment input. Oxandrales, furthest from the river, dominated by Oxandra polyantha, showed the greatest tree density, basal area and soil sand content, and received additional flooding from black-water streams. Cananguchales, dominated by Mauritia flexuosa, exhibited the highest dominance and soil organic matter layer thickness. Distribution of the permanent várzea and oxandrales was relatively constrained by the distance to the river, whereas that of the cananguchales was not.

Conclusions

Flooding dynamics delay vegetation development of the swamp forests in permanent várzea and oxandrales. Cananguchales keep accumulating organic matter, becoming ombrotrophic peats after isolation from the river flooding influence. The swamp forests across these flood-plains are far from being arranged along a linear sequence.

Leaf trait variation in grassland plant species in response to soil phosphorus

Leaf trait variation in grassland plant species in response to soil phosphorus

This experimental study examines the changes in leaf functional traits in grassland species with different resource-use strategies along a soil phosphorus gradient. Findings indicate that within species there was a more acquisitive trait expression with increased phosphorus and more conservative with increased community biomass. Interestingly, the trait responses were generally consistent for species representing very different resource-use strategies and growth forms. The pictures show four species mixtures before trait measurements and harvest (May 2020).


Abstract

Questions

Increased soil phosphorus (P) availability in fertilized grasslands can drive both community degradation and delayed community recovery upon agricultural abandonment. Beyond describing grassland community patterns along gradients in P availability, it remains unclear how individual species with different strategies respond to increasing phosphorus. Here we studied intraspecific variability of leaf functional traits in response to soil phosphorus, for species with contrasting resource-use strategies.

Methods

We set up a pot experiment with communities containing four species, assembled from a pool of 20 mesotrophic grassland species growing along a soil P gradient. Species selection included various growth forms (grasses vs forbs) and resource-use strategies (acquisitive vs conservative resource use). We measured three variables characterizing the (a)biotic environmental context: bioavailable soil P concentration, total community biomass as a proxy for the intensity of competition, and the proportional biomass of a species in the community as a proxy for its competitive dominance. We investigated the effect of this environmental context on the expression of two leaf traits, specific leaf area (SLA) and leaf dry matter content (LDMC).

Results

We found an acquisitive trait expression within species (increase in SLA and decrease in LDMC) in response to increased soil P supply and a conservative trait expression (decrease in SLA and increase in LDMC) in response to an increase in total community biomass. Importantly, the trait responses to the environmental context were generally consistent for species representing very different resource-use strategies and growth forms.

Conclusions

Species responded with a shift from an acquisitive to a conservative trait expression in response to limited resources; i.e., driven by a decrease in soil phosphorus concentration or an increase in total community biomass. Unexpectedly, the intraspecific variability in response to the changing environmental conditions was not clearly mediated by the species’ strategy. These findings show that plant ecological strategies are probably not the main driver for intraspecific trait variability in an experimental grassland community.

Climbing aroids in a Panamanian lowland forest: We should reconsider our categories

Climbing aroids in a Panamanian lowland forest: We should reconsider our categories

Because of a lack of field data, ontogenetic patterns of herbaceous climbers like germination site and changes in root/shoot connection with the soil remain unclear. We provide rare quantitative data regarding this aspect and species richness and abundance in a tropical lowland forest. Few species fall neatly in the so far applied categories of vines, nomadic vines and hemiepiphytes.


Abstract

Background

In contrast to woody climbers, information on community composition or vertical extension within the forest is scarce for herbaceous climbers, even in well-studied field sites like Barro Colorado Island. Moreover, questions regarding ontogenetic patterns (site of germination, changes in root/shoot connection with the soil) are unresolved because of a lack of field data.

Location

Barro Colorado Island, Panama.

Methods

In 17 plots of 400 m2 each, which were distributed all over the island, we recorded all potential hosts (trees, palms, lianas) with a diameter at breast height larger than 1 cm, and all climbing aroids attached to them. For aroids, we recorded species identity, number of shoots, root connections to the ground, and vertical shoot extension. By distinguishing three size classes for each species in our analyses we deduced the site of germination and ontogenetic changes in the root/shoot connection with the soil.

Results

Only 16% of all potential hosts were occupied by climbing aroids. We recorded 1196 individuals of 17 species. Aroids preferred larger trees and old-growth forest. Species differed strongly in vertical distribution. Hemiepiphytic species germinate epiphytically, often high up in tree crowns and later establish root contact with the soil, while the majority of species establish on or close to the ground and reach moderate heights of 5–15 m (forest height ca. 35 m). In all of these species, we observed dieback of the proximal portion of the shoot to a varying extent but contact with the soil was invariably retained via adventitious roots.

Conclusions

We provide rare quantitative data on species richness and abundance of herbaceous climbers in a tropical lowland forest. Few species fall neatly into the categories of vines, nomadic vines and hemiepiphytes. This highlights the need for longitudinal observational and experimental studies to resolve the current debate on the appropriate grouping of these climbers.

Spatiotemporal patterns of microclimatic buffering in relict alpine communities

Spatiotemporal patterns of microclimatic buffering in relict alpine communities

We investigated the variation of soil microclimate in time and space in a relict alpine system of northern Spain. Spatial microclimatic variation in one year was higher than in 10 years of microclimate monitoring in permanent plots, supporting the buffer effect of topography in alpine landscapes. Protected sites with relatively longer snow cover are key microclimatic refugia for preventing local extinctions.


Abstract

Questions

In alpine landscapes, topography creates a mosaic of microclimatic niches that might prevent local extinctions, but the influence of this spatial heterogeneity on plant communities is largely unknown. Here we ask (1) how soil microclimatic variation is comparable at temporal and spatial scales, and (2) how such variation influences species composition and local extinctions in relict alpine communities.

Location

Picos de Europa National Park, northern Spain.

Methods

We resurveyed permanent plots in four alpine sites following the recording of soil temperatures (temporal survey) for 10 years. We then sampled the spatial variation in species composition and microclimatic temperatures in 80 plots around the permanent plots (spatial survey). We evaluated the variation of six microclimatic indices between the temporal and the spatial surveys, and calculated the temporal trends observed in species cover. We finally predicted local extinction rates under microclimatic scenarios based on the observed microclimate–community relations.

Results

Despite high interannual variation, we found a 10-year trend of temperature warming on (microridge) fellfields and (microvalley) snowbeds. Microclimatic variation was larger in space than in time, with little temperature variation in snowbeds and extreme low temperatures recorded in fellfields. Species composition was mainly influenced by growing degree days (GDD) and freezing degree days (FDD), which were both related to snow cover duration. Plant cover of 16 species (out of 36 frequent species) showed significant responses to microclimatic variation. Local extinctions were mainly predicted under relatively hotter and more freezing conditions.

Conclusions

Our results support the idea that microclimatic spatial heterogeneity can reduce the negative influence of climate change on alpine plant communities. However, a continuous reduction of snow cover will result in a tipping point beyond which the buffer effect of this spatial heterogeneity will not be effective in protected microsites, leading to community homogenization. This process may have started in relict alpine communities where species from snowy microclimates are being outcompeted by species adapted to below-zero winter temperatures.

Ecological indicator values of understorey plants perform poorly to infer forest microclimate temperature

Ecological indicator values of understorey plants perform poorly to infer forest microclimate temperature

For the first time, we test whether ecological indicator values (EIVs) of forest plant communities are solely able to capture macroclimate or also microclimate temperature. Vascular plant and bryophyte communities successfully inferred macroclimatic differences across forests but largely failed to do so for microclimate variation within forests. Refined temperature EIVs are needed to capture microclimates experienced by understorey species.


Abstract

Question

Ecological indicator values (EIVs) reflect species‘ optimal conditions on an environmental gradient, such as temperature. Averaged over a community, they are used to quantify thermophilization stemming from climate change, i.e. the reshuffling of communities toward more warm-adapted species. In forests, understorey plant communities do not keep up with global warming and accumulate a climatic debt. Although the causes are still debated, this thermal lag may be partly explained by forest microclimate buffering. For the first time, we test whether community means of EIVs are able to capture microclimate (here, under forest canopies) temperature across, or also within forests.

Location

157 forest plots across three French deciduous forests covering a large macroclimatic gradient.

Methods

To assess whether EIVs can be used to infer the mean and range of microclimate temperature in forests, we measured understorey air temperature for ca. 1 year (10 months) with sensors located 1 m above the ground. We surveyed bryophytes and vascular plants within 400-m2 plots, and computed floristic temperature from ordinal-scale EIVs (Ellenberg, Julve) and degree-scale EIVs (ClimPlant, Bryophytes of Europe Traits) for both temperature and continentality, i.e. temperature annual range. Finally, we fitted linear models to assess whether EIVs could explain the mean and range of microclimate temperature in forests.

Results

Vascular plant and bryophyte communities successfully reflected differences in mean annual temperatures across forests but largely failed to do so for microclimate variation within forests. Bryophytes did not perform better than vascular plants to infer microclimate conditions. The annual range of microclimate temperatures was poorly associated with ordinal-scale EIVs for continentality but was positively correlated with degree-scale EIVs for annual range within lowland forests, especially for vascular plant communities.

Conclusion

Overall, the capabilities of EIVs to infer microclimate was inconsistent. Refined EIVs for temperature are needed to capture forest microclimates experienced by understorey species.

Mining exotic germplasm for genetic improvement of protein quantity and quality in soybean (Glycine max)

Abstract

Soybean meal is the main protein source for animal feed, but it has low content of the essential amino acids cysteine (Cys) and methionine (Met). In this research, an exotic germplasm (PI 399000) was crossed with ‘Woodruff’ to develop an F5-derived recombinant inbred line (RIL) population for mapping quantitative trait loci for seed composition. The population was grown in six environments, and protein, oil, Cys, and Met were determined with near-infrared spectroscopy. RILs were genotyped with the SoySNP6K BeadChip, and 1865 SNPs were used for analysis. QTL analysis identified three loci on chromosomes (Chrs) 6, 15 and 17 in at least five environments for protein; two QTLs on Chrs 14 and 17 in all environments for oil; three QTLs on Chrs 3, 6 and 10 for Cys and Met in at least three environments; and two QTLs for seed size on Chrs 17 and 20 in all environments. Stacking of protein and Cys + Met QTLs can increase both traits simultaneously, and 13 breeding lines were identified with improved seed composition. The markers linked to the QTLs can be used to assist the development of cultivars with improved meal quality.

Selective autophagy receptor‐encoding sequences in shallot transcriptome: In silico identification and expression patterns in response to asymptomatic shallot virus X infection

Selective autophagy receptor-encoding sequences in shallot transcriptome: In silico identification and expression patterns in response to asymptomatic shallot virus X infection

Shallot homologues of Nicotiana benthamiana and Oryza sativa P3IP selective autophagy receptors (SARs) have the ability to bind the shallot virus X p11 movement protein and initiate its autophagic degradation, thus carrying dual function as SAR and negative regulators of programmed cell death.


Abstract

Plant host tolerance is a key plant defence response to parasites, including viruses. This complex genetic trait involves multiple molecular mechanisms and, in particular, selective autophagy. Experimental data on the role of various selective autophagy factors and, in particular, cargo receptors in plant tolerance to viral infection are extremely limited. In this communication, I present the results of in silico identification of sequences in the shallot transcriptome encoding homologues of several selective autophagy receptors (SARs) related to the immune response and their expression patterns in response to asymptomatic infection of shallot virus X, a member of the genus Allexivirus, subgenus Acarallexivirus, within the family Alphaflexiviridae. The results obtained, together with the relevant literature data, suggest that some SARs likely to be involved in the regulation of the unfolded protein response and programmed cell death may play an active role in the formation of the state of tolerance of the host plant to allexivirus infection.