Maximizing the research output from a limited investment is often the major challenge for minor and underutilized crops. However, such crops may be tolerant to biotic and abiotic stresses and are adapted to local, marginal, and low-input environments. Their development through breeding will provide an important resource for future agricultural system resilience and diversification in the context of changing climates and the need to achieve food security. The African Orphan Crops Consortium recognizes the values of genomic resources in facilitating the improvement of such crops. Prior to beginning genome sequencing there is a need for an assessment of line varietal purity and to estimate any residual heterozygosity. Here we present an example from bambara groundnut (Vigna subterranea (L.) Verdc.), an underutilized drought tolerant African legume. Two released varieties from Zimbabwe, identified as potential genotypes for whole genome sequencing (WGS), were genotyped with 20 species-specific SSR markers. The results indicate that the cultivars are actually a mix of related inbred genotypes, and the analysis allowed a strategy of single plant selection to be used to generate non-heterogeneous DNA for WGS. The markers also confirmed very low levels of heterozygosity within individual plants. The application of a pre-screen using co-dominant microsatellite markers is expected to substantially improve the genome assembly, compared to a cultivar bulking approach that could have been adopted.
Elucidating the physiological mechanisms of the irregular yet concerted flowering rhythm of mass flowering tree species in the tropics requires long-term monitoring of flowering phenology, exogenous and endogenous environmental factors, as well as identifying interactions and dependencies among these factors. To investigate the proximate factors for floral initiation of mast seeding trees in the tropics, we monitored the expression dynamics of two key flowering genes, meteorological conditions and endogenous resources over two flowering events of Shorea curtisii and Shorea leprosula in the Malay Peninsula. Comparisons of expression dynamics of genes studied indicated functional conservation of FLOWERING LOCUS T (FT) and LEAFY (LFY) in Shorea. The genes were highly expressed at least 1 month before anthesis for both species. A mathematical model considering the synergistic effect of cool temperature and drought on activation of the flowering gene was successful in predicting the observed gene expression patterns. Requirement of both cool temperature and drought for floral transition suggested by the model implies that flowering phenologies of these species are sensitive to climate change. Our molecular phenology approach in the tropics sheds light on the conserved role of flowering genes in plants inhabiting different climate zones and can be widely applied to dissect the flowering processes in other plant species.
Drought is a major abiotic stress that influences rice production. Although the transcriptomic data of rice against drought is widely available, the regulation of small open reading frames (sORFs) in response to drought stress in rice is yet to be investigated. Different levels of drought stress have different regulatory mechanisms in plants. In this study, drought stress was imposed on four-leaf stage rice, divided into two treatments, 40% and 30% soil moisture content (SMC). The RNAs of the samples were extracted, followed by the RNA sequencing analysis on their sORF expression changes under 40%_SMC and 30%_SMC, and lastly, the expression was validated through NanoString. A total of 122 and 143 sORFs were differentially expressed (DE) in 40%_SMC and 30%_SMC, respectively. In 40%_SMC, 69 sORFs out of 696 (9%) DEGs were found to be upregulated. On the other hand, 69 sORFs out of 449 DEGs (11%) were significantly downregulated. The trend seemed to be higher in 30%_SMC, where 112 (12%) sORFs were found to be upregulated from 928 significantly upregulated DEGs. However, only 8% (31 sORFs out of 385 DEGs) sORFs were downregulated in 30%_SMC. Among the identified sORFs, 110 sORFs with high similarity to rice proteome in the PsORF database were detected in 40%_SMC, while 126 were detected in 30%_SMC. The Gene Ontology (GO) enrichment analysis of DE sORFs revealed their involvement in defense-related biological processes, such as defense response, response to biotic stimulus, and cellular homeostasis, whereas enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that DE sORFs were associated with tryptophan and phenylalanine metabolisms. Several DE sORFs were identified, including the top five sORFs (OsisORF_3394, OsisORF_0050, OsisORF_3007, OsisORF_6407, and OsisORF_7805), which have yet to be characterised. Since these sORFs were responsive to drought stress, they might hold significant potential as targets for future climate-resilient rice development.
Haloxylon persicum is an endangered western Asiatic desert plant species, which survives under extreme environmental conditions. In this study, we focused on transcriptome analysis of H. persicum to understand the molecular mechanisms associated with drought tolerance. Two different periods of polyethylene glycol (PEG)-induced drought stress (48 h and 72 h) were imposed on H. persicum under in vitro conditions, which resulted in 18 million reads, subsequently assembled by de novo method with more than 8000 transcripts in each treatment. The N50 values were 1437, 1467, and 1524 for the control sample, 48 h samples, and 72 h samples, respectively. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis resulted in enrichment of mitogen-activated protein kinase (MAPK) and plant hormone signal transduction pathways under PEG-induced drought conditions. The differential gene expression analysis (DGEs) revealed significant changes in the expression pattern between the control and the treated samples. The KEGG analysis resulted in mapping transcripts with 138 different pathways reported in plants. The differential expression of drought-responsive transcription factors depicts the possible signaling cascades involved in drought tolerance. The present study provides greater insight into the fundamental transcriptome reprogramming of desert plants under drought.
Climate change is one of the major challenges societies round the world face at present. Apart from efforts to achieve a reduction of emissions of greenhouse gases so as to mitigate the problem, there is a perceived need for adaptation initiatives urgently. Ecosystems are known to play an important role in climate change adaptation processes, since some of the services they provide, may reduce the impacts of extreme events and disturbance, such as wildfires, floods, and droughts. This role is especially important in regions vulnerable to climate change such as the African continent, whose adaptation capacity is limited by many geographic and socio-economic constraints. In Africa, interventions aimed at enhancing ecosystem services may play a key role in supporting climate change adaptation efforts. In order to shed some light on this aspect, this paper reviews the role of ecosystems services and investigates how they are being influenced by climate change in Africa. It contains a set of case studies from a sample of African countries, which serve the purpose to demonstrate the damages incurred, and how such damages disrupt ecosystem services. Based on the data gathered, some measures which may assist in fostering the cause of ecosystems services are listed, so as to cater for a better protection of some of the endangered Africa ecosystems, and the services they provide.
Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.
Termites perform key ecological functions in tropical ecosystems, are strongly affected by variation in rainfall, and respond negatively to habitat disturbance. However, it is not known how the projected increase in frequency and severity of droughts in tropical rainforests will alter termite communities and the maintenance of ecosystem processes. Using a large-scale termite suppression experiment, we found that termite activity and abundance increased during drought in a Bornean forest. This increase resulted in accelerated litter decomposition, elevated soil moisture, greater soil nutrient heterogeneity, and higher seedling survival rates during the extreme El Niño drought of 2015-2016. Our work shows how an invertebrate group enhances ecosystem resistance to drought, providing evidence that the dual stressors of climate change and anthropogenic shifts in biotic communities will have various negative consequences for the maintenance of rainforest ecosystems.
Drought monitoring is crucial for assessing and mitigating the impacts of water scarcity on various sectors and ecosystems. Although traditional drought monitoring relies on soil moisture data, remote sensing technology has have significantly augmented the capabilities for drought monitoring. This study aims to evaluate the accuracy and applicability of two temperature vegetation drought indices (TVDI), TVDINDVI and TVDIEVI, constructed using the Normalized Difference Vegetation Index (NDVI) and the Enhanced Vegetation Index (EVI) vegetation indices for drought monitoring. Using Guangdong Province as a case, enhanced versions of these indices, developed through Savitzky-Golay filtering and terrain correction were employed. Additionally, Pearson correlation analysis and F-tests were utilized to determine the suitability of the Standardized Precipitation Index (SPI) and the Standardized Precipitation Evapotranspiration Index (SPEI) in correlation with TVDINDVI and TVDIEVI. The results show that TVDINDVI had more meteorological stations passing both significance test levels (P
Time-series data offer a way of investigating the causes driving ecological processes as phenomena. To test for possible differences in water relations between species of different forest structural guilds at Danum (Sabah, NE Borneo), daily stem girth increments (gthi), of 18 trees across six species were regressed individually on soil moisture potential (SMP) and temperature (TEMP), accounting for temporal autocorrelation (in GLS-arima models), and compared between a wet and a dry period. The best-fitting significant variables were SMP the day before and TEMP the same day. The first resulted in a mix of positive and negative coefficients, the second largely positive ones. An adjustment for dry-period showers was applied. Interactions were stronger in dry than wet period. Negative relationships for overstorey trees can be interpreted in a reversed causal sense: fast transporting stems depleted soil water and lowered SMP. Positive relationships for understorey trees meant they took up most water at high SMP. The unexpected negative relationships for these small trees may have been due to their roots accessing deeper water supplies (if SMP was inversely related to that of the surface layer), and this was influenced by competition with larger neighbour trees. A tree-soil flux dynamics manifold may have been operating. Patterns of mean diurnal girth variation were more consistent among species, and time-series coefficients were negatively related to their maxima. Expected differences in response to SMP in the wet and dry periods did not clearly support a previous hypothesis differentiating drought and non-drought tolerant understorey guilds. Trees within species showed highly individual responses when tree size was standardized. Data on individual root systems and SMP at several depths are needed to get closer to the mechanisms that underlie the tree-soil water phenomena in these tropical forests. Neighborhood stochasticity importantly creates varying local environments experienced by individual trees.
Rice which belongs to the grass family is vulnerable to water stress. As water resources get limited, the productivity of rice is affected especially in granaries located at drought prone areas. It would be even worse in granaries located in drought prone areas such as KADA that receives the lowest rainfall in Malaysia. Spermine (SPM), a polyamine compound that is found ubiquitiosly in plants is involved in adaptation of biotic and abiotic stresses. The effect of SPM on growth,grain filling and yield of rice at three main granaries namely, IADA BLS, MADA and KADA representing unlimited water, limited water and water stress conditions respectively, were tested during the main season. Additinally, the growth enhancer was also tested during off season at KADA. Spermine increased plant height, number of tillers per hill and chlorophyll content in all three granaries. Application of SPM improved yield by 38, 29 and 20% in MADA, KADA and IADA BLS, respectively. Harvest index showed 2.6, 6 and 16% increases at IADA BLS, KADA and MADA, respectively in SPM treated plants as compared to untreated. Except for KADA which showed a reduction in yield at 2.54 tha-1, SPM improved yield at MADA, 7.21 tha-1 and IADA BLS, 9.13 tha-1 as compared to the average yield at these respective granaries. In the second trial, SPM increased the yield to 7.0 and 6.4 tha-1 during main and off seasons, respectively, indicating that it was significantly higher than control and the average yield reported by KADA. The yield of SPM treatments improved by 25 and 33% with an increment of farmer's income at main and off seasons, respectively. Stomatal width was significantly higher than control at 11.89 µm. In conclusion, irrespective of the tested granaries and rice variety, spermine mediated plots displayed increment in grain yield.
General flowering (GF) is a unique phenomenon wherein, at irregular intervals, taxonomically diverse trees in Southeast Asian dipterocarp forests synchronize their reproduction at the community level. Triggers of GF, including drought and low minimum temperatures a few months previously has been limitedly observed across large regional scales due to lack of meteorological stations. Here, we aim to identify the climatic conditions that trigger large-scale GF in Peninsular Malaysia using satellite sensors, Tropical Rainfall Measuring Mission (TRMM) and Moderate Resolution Imaging Spectroradiometer (MODIS), to evaluate the climatic conditions of focal forests. We observed antecedent drought, low temperature and high photosynthetic radiation conditions before large-scale GF events, suggesting that large-scale GF events could be triggered by these factors. In contrast, we found higher-magnitude GF in forests where lower precipitation preceded large-scale GF events. GF magnitude was also negatively influenced by land surface temperature (LST) for a large-scale GF event. Therefore, we suggest that spatial extent of drought may be related to that of GF forests, and that the spatial pattern of LST may be related to that of GF occurrence. With significant new findings and other results that were consistent with previous research we clarified complicated environmental correlates with the GF phenomenon.
Environmental or abiotic stresses are a common threat that remains a constant and common challenge to all plants. These threats whether singular or in combination can have devastating effects on plants. As a semiaquatic plant, rice succumbs to the same threats. Here we systematically look into the involvement of salicylic acid (SA) in the regulation of abiotic stress in rice. Studies have shown that the level of endogenous salicylic acid (SA) is high in rice compared to any other plant species. The reason behind this elevated level and the contribution of this molecule towards abiotic stress management and other underlying mechanisms remains poorly understood in rice. In this review we will address various abiotic stresses that affect the biochemistry and physiology of rice and the role played by SA in its regulation. Further, this review will elucidate the potential mechanisms that control SA-mediated stress tolerance in rice, leading to future prospects and direction for investigation.
Food and fuel prices have soared in recent years affecting most adversely the poor and those with fixed incomes. Since 2000, wheat price in the international market has more than tripled and maize prices have more than doubled. The price of rice, the staple of billions in Asia, has tripled in the past year. The surge of food prices has been blamed on multiple factors including higher energy and fertilizer costs, greater global demand, drought, the loss of arable land to biofuel crops and price speculation. In light of the spiraling rise in food prices, there is the prospect of increasing rates of under-nutrition worldwide. As it is, 800 million are estimated to be suffering from chronic malnourishment, with another 2.1 billion people living close to subsistence levels on less than US$2 a day. Some perspectives of the food production experience of Malaysia are shared here as a case of a country that has built up capabilities and resources through high level of foreign and domestic investment leading to a diversified economy. In response to the recent surge in the price of rice, the Malaysian government announced the setting up of a dedicated fund amounting to US$1.25 billion to increase production of food including fruits and vegetables, and targeting 100% self-sufficiency in rice, by growing rice on a massive scale in Sarawak. During the current five-year development plan for the period of 2006-2010, (Ninth Malaysia Plan), the role of the agriculture sector is considerably enhanced to be the third pillar of economic growth, after manufacturing and services. Among the measures taken, are those aimed at increasing incomes of smallholders and fishermen mainly through improving productivity. These measures include encouraging more rice farmers to participate in mini-estates and group farming, providing financial assistance to rehabilitate cocoa, pepper and sago smallholdings, enhancing the capabilities of coastal fishermen, and setting up of a special program to assist poor households in the agriculture sector to diversify their sources of income. The various socio-economic programs in Malaysia that have been put in place over the years may have cushioned to some extent so far the severity of the dramatic hikes in food prices.
As small bodied poikilothermic ectotherms, invertebrates, more so than any other animal group, are susceptible to extremes of temperature and low water availability. In few places is this more apparent than in the Arctic and Antarctic, where low temperatures predominate and water is unusable during winter and unavailable for parts of summer. Polar terrestrial invertebrates express a suite of physiological, biochemical and genomic features in response to these stressors. However, the situation is not as simple as responding to each stressor in isolation, as they are often faced in combination. We consider how polar terrestrial invertebrates manage this scenario in light of their physiology and ecology. Climate change is also leading to warmer summers in parts of the polar regions, concomitantly increasing the potential for drought. The interaction between high temperature and low water availability, and the invertebrates' response to them, are therefore also explored.
In 1877, the major towns of the Straits Settlements-Singapore, George Town, Penang Island and Malacca-suffered a drought of exceptional magnitude. The drought's natural instigator was the El Niño phase of the El Niño Southern Oscillation, a climatic phenomenon then not understood by contemporary observers. The 1877 event has been explored in some depth for countries including India, China and Australia. Its impact on Southeast Asia however is less well-known and the story of how the event unfolded in Singapore and Malaysia has not been told. This paper explores how the contemporary British government responded to the drought, arguing that its impact on hydraulic management was at best minimal yet, it did have impact on other areas, such as forest reservation with the hope of preserving future rainfall. It also highlights how, in contrast to studies on urban water plans in other British Asian colonies, the colonial authorities in the Straits Settlements had a far less coherent and meaningful relationship with water in their town planning schemes. As this paper is part of a special issue, Water History in the time of COVID-19, it has undergone modified peer review.
Occasional periods of drought are typical of most tropical forests, but climate change is increasing drought frequency and intensity in many areas across the globe, threatening the structure and function of these ecosystems. The effects of intermittent drought on tropical tree communities remain poorly understood and the potential impacts of intensified drought under future climatic conditions are even less well known. The response of forests to altered precipitation will be determined by the tolerances of different species to reduced water availability and the interactions among plants that alleviate or exacerbate the effects of drought. Here, we report the response of experimental monocultures and mixtures of tropical trees to simulated drought, which reveals a fundamental shift in the nature of interactions among species. Weaker competition for water in diverse communities allowed seedlings to maintain growth under drought while more intense competition among conspecifics inhibited growth under the same conditions. These results show that reduced competition for water among species in mixtures mediates community resistance to drought. The delayed onset of competition for water among species in more diverse neighbourhoods during drought has potential implications for the coexistence of species in tropical forests and the resilience of these systems to climate change.
The past 40 years in Southeast Asia have seen about 50% of lowland rainforests converted to oil palm and other plantations, and much of the remaining forest heavily logged. Little is known about how fragmentation influences recovery and whether climate change will hamper restoration. Here, we use repeat airborne LiDAR surveys spanning the hot and dry 2015-16 El Niño Southern Oscillation event to measure canopy height growth across 3,300 ha of regenerating tropical forests spanning a logging intensity gradient in Malaysian Borneo. We show that the drought led to increased leaf shedding and branch fall. Short forest, regenerating after heavy logging, continued to grow despite higher evaporative demand, except when it was located close to oil palm plantations. Edge effects from the plantations extended over 300 metres into the forests. Forest growth on hilltops and slopes was particularly impacted by the combination of fragmentation and drought, but even riparian forests located within 40 m of oil palm plantations lost canopy height during the drought. Our results suggest that small patches of logged forest within plantation landscapes will be slow to recover, particularly as ENSO events are becoming more frequent.
Aliphatic glucosinolate is an important secondary metabolite responsible in plant defense mechanism and carcinogenic
activity. It plays a crucial role in plant adaptation towards changes in the environment such as salinity and drought.
However, in many plant genomes, there are thousands of genes encoding proteins still with putative functions and
incomplete annotations. Therefore, the genome of Arabidopsis thaliana was selected to be investigated further to identify
any putative genes that are potentially involved in the aliphatic glucosinolate biosynthesis pathway, most of its gene are
with incomplete annotation. Known genes for aliphatic glucosinolates were retrieved from KEGG and AraCyc databases.
Three co-expression databases i.e., ATTED-II, GeneMANIA and STRING were used to perform the co-expression network
analysis. The integrated co-expression network was then being clustered, annotated and visualized using Cytoscape plugin,
MCODE and ClueGO. Then, the regulatory network of A. thaliana from AtRegNet was mapped onto the co-expression
network to build the transcriptional regulatory network. This study showed that a total of 506 genes were co-expressed
with the 61 aliphatic glucosinolate biosynthesis genes. Five transcription factors have been predicted to be involved
in the biosynthetic pathway of aliphatic glucosinolate, namely SEPALLATA 3 (SEP3), PHYTOCHROME INTERACTING FACTOR
3-like 5 (AtbHLH15/PIL5), ELONGATED HYPOCOTYL 5 (HY5), AGAMOUS-like 15 (AGL15) and GLABRA 3 (GL3). Meanwhile,
three other genes with high potential to be involved in the aliphatic glucosinolates biosynthetic pathway were identified,
i.e., methylthioalkylmalate-like synthase 4 (MAML-4) and aspartate aminotransferase (ASP1 and ASP4). These findings
can be used to complete the aliphatic glucosinolate biosynthetic pathway in A. thaliana and to update the information
on the glucosinolate-related pathways in public metabolic databases.
The purposes of this research were to study the characteristics chemistry of pH, anions and cations in rainwater, and to identify the possible sources that contributing to the acid precipitation during southwest monsoon season with occurrence of extreme drought event. During the southwest monsoon season, it normally occurs along with haze phenomenon that every year will hit Southeast Asia. This condition will aggravate with high acidic particles in the atmosphere due to the prolonged drought. The analysed parameters which involved pH, anions (NO3-, SO42- and Cl-) and cations (Ca2+, Mg2+, Na+ and K+) were analysed using pH meter, Hach DR 2800, argentometric method and ICP-OES. From the findings, it showed that acid rain occurred during the southwest monsoon season with the range of pH values from 4.95 ± 0.13 to 6.40 ± 0.03 and the total average of pH 5.71 ± 0.32. Anions NO3-, SO42- and Cl- were found to be the dominant compositions of the acid rain occurrences with higher concentrations detected. In overall, rural area recorded with higher acidity of precipitation at total average of pH 5.54 ± 0.39 compared to urban area at pH 5.77 ± 0.26. Rural area surprisingly recorded higher frequency occurrences of acid rain with pH lesser than 5.6 and below compared to urban area. As for public health and safety, all rainwater samples during the acid rain event were found exceeded the allowable limits of NWQS and WHO standards, that shown not suitable for skin contact, recreational purposes even for drinking purposes.
Drought and pests are primary abiotic and biotic factors proposed as selective filters acting on species distributions along rainfall gradients in tropical forests and may contribute importantly to species distributional limits, performance, and diversity gradients. Recent research demonstrates linkages between species distributions along rainfall gradients and physiological drought tolerance; corresponding experimental examinations of the contribution of pest pressure to distributional limits and potential interactions between drought and herbivory are limited. This study aims to quantitate differential performance and herbivory as a function of species range limits across a climatic and floristic transition in Southeast Asia. Khao Chong Botanical Garden, Thailand and Pasoh Forest Reserve, Malaysia straddle the Kangar-Pattani Line. A reciprocal transplantation across a seasonality gradient was established using two groups of species ("widespread" taxa whose distributions include seasonally dry forests and "aseasonal" taxa whose distributions are limited to aseasonal forests). Growth, biomass allocation, survival, and herbivory were monitored for 19 months. Systematic differences in performance were a function of species distribution in relation to rainfall seasonality. In aseasonal Pasoh, aseasonal species had both greater growth and survivorship than widespread species. These differences were not a function of differential herbivory as widespread and aseasonal species experienced similar damage in the aseasonal forest. In seasonally dry Khao Chong, widespread species showed higher survivorship than aseasonal species, but these differences were only apparent during drought. We link this differential performance to physiological mechanisms as well as differential tolerance of biotic pressure during drought stress. Systematic decreases in seedling survival in aseasonal taxa during drought corresponded with previously documented physiological differences and may be exacerbated by herbivore damage. These results have important implications for tropical diversity and community composition in light of predicted increases in the frequency and severity of drought in hyperdiverse tropical forests.