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152 records · Page 9Linked to original sources
PubMed2026

Graph-based pan-genome reveals structural and functional diversity across oil palm domestication gradients.

BACKGROUND: Oil palm (Elaeis guineensis Jacq.), the world's most land-efficient oil crop, underpins global vegetable oil supply yet faces mounting constraints from limited expansion, climate stress, and disease pressure. These challenges highlight the urgent need for genomic resources that capture species-wide diversity to support sustainable improvement. While recent reference assemblies have advanced trait discovery, single linear genomes fail to represent the full spectrum of structural and gene-content variation, limiting resolution of agronomic alleles. RESULTS: Here, we constructed a graph-based pan-genome from 30 diverse oil palm assemblies representing wild, semi-domesticated, and commercial accessions. We characterized structural variants, gene presence-absence variation, and copy-number gains, with focusing on functional stratification and resistance gene dynamics. The graph-based pan-genome revealed extensive structural and gene-content variation, including a large conserved core, complemented by shell and unique fractions enriched or biased toward regulatory, stress-responsive, and defense-related functions. Structural variation and duplication-derived copy-number gains contributed substantially to gene-content diversity, with semi-domesticated accessions exhibiting the greatest variability. Resistance gene repertoires showed contrasting patterns: receptor-like kinases remained comparatively stable, whereas the CNL subclass of NLR genes contributed disproportionately to shell-genome variation and duplication-associated turnover. CONCLUSIONS: This graph-based pan-genome provides a curated multi-assembly reference and comparative framework for oil palm genomics. By capturing structural variants, gene-content variations, copy-number gains, and resistance gene dynamics across domestication gradients, it establishes a foundation for future pan-GWAS analysis, functional genomics, and molecular breeding strategies aimed at improving resilience and productivity in this globally important crop.

Arecaceae↗
PubMed2006

Building resilience and adaptation to manage Arctic change.

Unprecedented global changes caused by human actions challenge society's ability to sustain the desirable features of our planet. This requires proactive management of change to foster both resilience (sustaining those attributes that are important to society in the face of change) and adaptation (developing new socioecological configurations that function effectively under new conditions). The Arctic may be one of the last remaining opportunities to plan for change in a spatially extensive region where many of the ancestral ecological and social processes and feedbacks are still intact. If the feasibility of this strategy can be demonstrated in the Arctic, our improved understanding of the dynamics of change can be applied to regions with greater human modification. Conditions may now be ideal to implement policies to manage Arctic change because recent studies provide the essential scientific understanding, appropriate international institutions are in place, and Arctic nations have the wealth to institute necessary changes, if they choose to do so.

Adaptation, Physiological↗
PubMed2025

Diversity of leaf- and root microbiomes among genotypes and market classes of desert-grown lettuce (Lactuca sativa L.).

Plant microbiomes are increasingly acknowledged both as extensions of plant characteristics and as biological factors that influence plant traits important for nutrition and resilience. In the context of global change, manipulation of microbiomes has the potential to complement genetic approaches to enhance crop health and productivity under rising heat and drought stress. Understanding the factors that influence microbial communities and their variation across plant genotypes is essential for developing such capabilities. We employed metabarcoding via the Illumina sequencing platform to investigate microbial communities that occur within healthy leaves and roots of 12 lettuce genotypes (Lactuca sativa L.) grown in a desert agriculture environment. We detected diverse foliar- and root-endophytic fungi and bacteria in field-grown lettuce at the Maricopa Agricultural Center (Arizona, USA). The composition of microbial community structure varied with foliar chemistry and root traits. Notably, levels of zinc and other beneficial nutrients in the leaves were strongly linked with specific endophytes. These results document the lettuce microbiome in desert farming and provide insights into endophytes in lettuce leaves, which are noteworthy because they remain after washing and are regularly ingested.

Lactuca↗
PubMed2026

Grafting and biodynamic nanosilica-induced physiological and transcriptomic modulation of chilli (Capsicum annuum L.) under drought stress.

Chilli (Capsicum annuum L.) is an economically important vegetable crop cultivated worldwide. Increasing drought stress associated with climate change has severely reduced chilli productivity. Although grafting and silicon-based nanomaterials have each been investigated independently as drought mitigation strategies in Solanaceae crops, this study represents, to our knowledge, the first investigation of their combined physiological, yield, and genome-wide transcriptomic effects in chilli under experimentally validated drought stress. Biodynamic nanosilica (BNS) is an &#x3b1;-quartz nanoparticle preparation (20-200 nm) derived from the biodynamic agricultural preparation BD501 through a vortex-triturating process, and distinct from chemically synthesised nanosilica in preparation method and surface bioavailability, applied as a foliar spray at 50 mg L-1. Five treatments were established: well-watered (WW), drought (D), grafting + BNS + drought (G+B+D), grafting + drought (G+D), and BNS + drought (B+D), each with three independent biological replicates. Under moderate-to-severe drought conditions (DSI 62-64%; VWC ~12% v/v at 14 days), the combined G+B+D treatment significantly improved plant height (3.05-fold over D), leaf relative water content (83% vs 49% in D), net photosynthetic rate (2.0-fold over D), water-use efficiency (+40%), and antioxidant enzyme activities (SOD: 3.1-fold; CAT: 2.8-fold over D), while reducing lipid peroxidation by 76%. Root architecture was also substantially enhanced, with a 4.1-fold increase in root length and a 3.1-fold increase in root surface area relative to D. Fruit yield increased by 79% relative to drought-stressed non-grafted plants. Transcriptomic analysis using Illumina NovaSeq 6000 identified 1,051 DEGs (431 upregulated, 620 downregulated; FDR < 0.05, |log2FC| > 1). Integrated transcriptomic-phenotypic concordance analysis revealed enrichment of MAPK signalling, ABA-mediated regulation (including ABA binding and (+)-ABA 8'-hydroxylase activity), and phenylpropanoid biosynthesis as the enriched pathways. Protein-protein interaction network analysis further revealed coordinated regulation of redox homeostasis, drought-responsive hormone signalling, and water transport gene modules in the combined treatment. These findings demonstrate that integrating grafting with biodynamic nanosilica is a promising strategy to enhance drought resilience and productivity in chilli, offering a sustainable approach for vegetable production under drought.

Capsicum↗
PubMed2006

The functional value of Caribbean coral reef, seagrass and mangrove habitats to ecosystem processes.

Caribbean coral reef habitats, seagrass beds and mangroves provide important goods and services both individually and through functional linkages. A range of anthropogenic factors are threatening the ecological and economic importance of these habitats and it is vital to understand how ecosystem processes vary across seascapes. A greater understanding of processes will facilitate further insight into the effects of disturbances and assist with assessing management options. Despite the need to study processes across whole seascapes, few spatially explicit ecosystem-scale assessments exist. We review the empirical literature to examine the role of different habitat types for a range of processes. The importance of each of 10 generic habitats to each process is defined as its "functional value" (none, low, medium or high), quantitatively derived from published data wherever possible and summarised in a single figure. This summary represents the first time the importance of habitats across an entire Caribbean seascape has been assessed for a range of processes. Furthermore, we review the susceptibility of each habitat to disturbances to investigate spatial patterns that might affect functional values. Habitat types are considered at the scale discriminated by remotely-sensed imagery and we envisage that functional values can be combined with habitat maps to provide spatially explicit information on processes across ecosystems. We provide examples of mapping the functional values of habitats for populations of three commercially important species. The resulting data layers were then used to generate seascape-scale assessments of "hot spots" of functional value that might be considered priorities for conservation. We also provide an example of how the literature reviewed here can be used to parameterise a habitat-specific model investigating reef resilience under different scenarios of herbivory. Finally, we use multidimensional scaling to provide a basic analysis of the overall functional roles of different habitats. The resulting ordination suggests that each habitat has a unique suite of functional values and, potentially, a distinct role within the ecosystem. This review shows that further data are required for many habitat types and processes, particularly forereef and escarpment habitats on reefs and for seagrass beds and mangroves. Furthermore, many data were collected prior to the regional mass mortality of Diadema and Acropora, and subsequent changes to benthic communities have, in many cases, altered a habitat's functional value, hindering the use of these data for parameterising maps and models. Similarly, few data exist on how functional values change when environmental parameters, such as water clarity, are altered by natural or anthropogenic influences or the effects of a habitat's spatial context within the seascape. Despite these limitations, sufficient data are available to construct maps and models to better understand tropical marine ecosystem processes and assist more effective mitigation of threats that alter habitats and their functional values.

Algorithms↗
PubMed2006

Resilience of southwestern Amazon forests to anthropogenic edge effects.

Anthropogenic edge effects can compromise the conservation value of mature tropical forests. To date most edge-effect research in Amazonia has concentrated on forests in relatively seasonal locations or with poor soils in the east of the basin. We present the first evaluation from the relatively richer soils of far western Amazonia on the extent to which mature forest biomass, diversity, and composition are affected by edges. In a southwestern Amazonian landscape we surveyed woody plant diversity, species composition, and biomass in 88x0.1 ha samples of unflooded forest that spanned a wide range in soil properties and included samples as close as 50 m and as distant as >10 km from anthropogenic edges. We applied Mantel tests, multiple regression on distance matrices, and other multivariate techniques to identify anthropogenic effects before and after accounting for soil factors and spatial autocorrelation. The distance to the nearest edge, access point, and the geographical center of the nearest community ("anthropogenic-distance effects") all had no detectable effect on tree biomass or species diversity. Anthropogenic-distance effects on tree species composition were also below the limits of detection and were negligible in comparison with natural environmental and spatial factors. Analysis of the data set's capacity to detect anthropogenic effects confirmed that the forests were not severely affected by edges, although because our study had few plots within 100 m of forest edges, our confidence in patterns in the immediate vicinity of edges is limited. It therefore appears that the conservation value of most "edge" forests in this region has not yet been compromised substantially. We caution that because this is one case study it should not be overinterpreted, but one explanation for our findings may be that western Amazonian tree species are naturally faster growing and more disturbance adapted than those farther east.

Adaptation, Physiological↗
PubMed1998

Kangaroo mother care and the bonding hypothesis.

BACKGROUND: Based on the general bonding hypothesis, it is suggested that kangaroo mother care (KMC) creates a climate in the family whereby parents become prone to sensitive caregiving. The general hypothesis is that skin-to-skin contact in the KMC group will build up a positive perception in the mothers and a state of readiness to detect and respond to infant's cues. METHOD: The randomized controlled trial was conducted on a set of 488 infants weighing <2001 g, with 246 in the KMC group and 242 in the traditional care (TC) group. The design allows precise observation of the timing and duration of mother-infant contact, and takes into account the infant's health status at birth and the socioeconomic status of the parents. BONDING ASSESSMENT: Two series of outcomes are assessed as manifestations of a mother's attachment behavior. The first is the mother's feelings and perceptions of her premature birth experience, including her sense of competence, feelings of worry and stress, and perception of social support. The second outcome is derived from observations of the mother and child's responsivity to each other during breastfeeding at 41 weeks of gestational age. INTERVENTIONS: KMC has three components. The first is the kangaroo position. Once the premature infant has adapted to extrauterine life and is able to breastfeed, he is positioned on the mother's chest, in a upright position, with direct skin-to-skin contact. The second component is kangaroo nutrition. Although breastfeeding is the prime source of nutrition, infants also may receive preterm formula whenever necessary and vitamin supplements. The third component is the clinical control; infants are monitored on a regular basis, daily until they are gaining at least 20 g per day. Afterward, weekly clinic visits are scheduled until term, which constitutes the ambulatory minimal neonatal care. In the TC group, infants are kept in incubators until they are able to self-regulate their temperature and are thriving (ie, have an appropriate weight gain). Infants are discharged according to current hospital practice, usually not before their weight is approximately 1700 g. Afterward, as with the KMC group, weekly clinic visits are scheduled until term. RESULTS: We observed a change in the mothers' perception of her child, attributable to the skin-to-skin contact in the kangaroo-carrying position. This effect is related to a subjective "bonding effect" that may be understood readily by the empowering nature of the KMC intervention. Moreover, in stressful situations when the infant has to remain in the hospital longer, mothers practicing KMC feel more competent than do mothers in the TC group. This is what we call a resilience effect. In these stressful situations we also found a negative effect on the feelings of received support of mothers practicing KMC. We interpret this as an isolation effect. To thwart this deleterious effect, we would suggest adding social support as an integral component of KMC. The observations of the mothers' sensitive behavior did not show a definite bonding effect, but rather a resilience effect. This is attributable to the KMC intervention; mothers practicing KMC were more responsive to an at-risk infant whose development has been threatened by a longer hospital stay. Otherwise, we observed that the mothers (in both the KMC group and the TC group) had behavioral patterns that were adapted to the child's at-risk health status and to the precarious condition of some premature infants requiring intensive care. We conclude that the infant's health status may be a more prominent factor in explaining a mother's more sensitive behavior, which overshadows the kangaroo-carrying effect. CONCLUSION: These results suggest that KMC should be promoted actively and that mothers should be encouraged to use it as soon as possible during the intensive care period up to the 40 weeks of gestational age. Thus, KMC should be viewed as a means of humanizing the process of g

Analysis of Variance↗
PubMed2003

Improving pig husbandry in tropical resource-poor communities and its potential to reduce risk of porcine cysticercosis.

To minimise the risk of cysticercosis in pigs it is necessary to raise pigs in confinement. The prevailing production system using free-range pigs is apparently very resilient although economic studies have shown that these traditional production systems are wasteful and unprofitable due to poor feed conversion, high mortality rates, low reproductive rates and poor final products. However, experiences from Africa show that intensive pig farming is stagnant and the sustainability of the traditional sector is better than that of the intensive sector. Examples from various African countries are given on the failure of intensive pig farming. This apparent paradox has various explanations. The lower fixed cost of traditional pig production compared with intensive production is one. Another explanation is that many households have some kind of kitchen waste, which can be exploited by a pig, but there is only enough for the partial feeding of a single pig. A third explanation of the paradox is that the pig has functions that are not reflected in a simple economic balance. The pig is a source of capital income, which can be realised at times of major expenses, and it can also be used as a way to put aside small amounts of money, which alternatively might evaporate. The pig's scavenging behaviour has clear nutritional benefits. Thus, a diet consisting of e.g. maize or sorghum, which are some of the feeds available on the small farms, will only provide approximately 30% of the pigs requirements of lysine and methionine, which are the most limiting amino-acids in pig feeds. Simulations with data available for green feeds and material of animal origin show that a 20% "supplement" from the fields may increase the amino-acid provision to about 80% of the optimum. If pigs are kept enclosed this supplement has to be fed to the pig which involves purchase and labour costs. The paper discusses the various options in terms of feeding, housing and use of genetic resources for the improvement of pig husbandry in tropical resource-poor countries.

Animal Feed↗