Common transcriptional regulation of ABA and ethylene

Plant hormones are versatile chemical regulators of plant growth. The concept of hormone ‘interaction’[1] has gained much importance and several key players of hormonal network are uncovered for major plant hormones. The fact that hormones are structurally unrelated and their interaction elicits different genomic and non-genomic responses suggest hormone interaction involve co-regulation at multiple levels [2]. Recent studies suggest that hormonal interaction involves control over biosynthesis genes [3-6], key components of signalling pathways [7, 8], hormone distribution [9, 10], and interaction at the level of gene expression [11-13]. The spatial and temporal changes in hormone sensitivity add further complexity as they are developmental stagedependent [14]. Understanding how these mechanisms are integrated would allow us to manipulate hormone interaction-regulated growth response under environmental changes. One such prominent emerging hormone interaction is ethylene and abscisic acid (ABA) in several growth processes. In this short review, I discuss some of the common transcriptional regulators of ethylene and ABA

Studies on water-soluble carbohydrates in wheat (Triticum aestivum L.): regulating traits, model analysis, early chilling effects, and future perspectives

Wheat is one of the major staple food crops of the world. Although a wealth of research has been made a significant progress in wheat productivity through genetic interventions in the last two decades, there remains an untapped potential for further yield gain. Water-soluble carbohydrates (WSCs) are excess carbohydrates stored in vegetative organs such as stem, sheaths, and tiller base during vegetative period. They are highly heritable agronomic trait that regulates plant growth and development as well as grain yields. In addition, WSCs also contribute to plant adaptation to abiotic stresses. Improving current understanding of the multi-faceted roles of WSCs is therefore essential for future crop improvement. The present thesis provides information on WSCs, its associated traits and future perspectives that derived from several experiments conducted under field and glasshouse conditions. Typically, the thesis has four objectives dealing with a specific set of questions. The first objective explains the traits regulating WSCs under three N levels (0, 100 and 200 kg ha-1). N concentration in the plant is negatively correlated with WSCs storage. The traits associated with total WSCs storage are also influenced by N levels. Three vegetative traits, viz., total biomass, flag-leaf width, root: shoot ratio and two physiological traits, viz., radiation use efficiency, and leaf N concentration were considered. Under high N level, lower biomass, flag-leaf width and root: shoot ratio is beneficial to increase total WSC storage. In contrast, increasing biomass and flag-leaf width is advantageous under lower N level. However, a specific set of traits, rather than a single trait, appeared to evolve under N-specific selection maximizing total WSC storage. The second objective describes the simulation model for WSC accumulation under three N levels. A simple phenological model for carbon accumulation, in the form of WSCs, during vegetative period in four wheat genotypes was developed. This model was integrated and evaluated under crop management factors such as low (0 kg ha-1), medium (100 kg ha-1), and high (200 kg ha-1) nitrogen supply. The proposed model predicted higher rate of WSC accumulation in the early stages of crop growth and lower rates in the later stages. Overall, the model predicted the rate of WSC accumulation with a RMSE of 6.58, suggesting that the proposed model simulated well. Nevertheless, the predicted rate of WSC accumulation was close to the observed data only in low and high N level. The model predicted total WSCs well with the observed data; however, it overestimated total WSCs at early stages and underestimated total WSCs at later stages, largely due to the respective rate of WSC accumulation. Overall, evaluation of the model with the predicted dataset indicated that the prediction errors for the rate of WSC accumulation were more with RMSE between 20-30% in all N levels. For total WSC accumulation, the prediction errors were less, and the RMSE, in most cases, was less than 20% in all N levels. The third objective reveals the plasticity of the phenotypic expression of two primitive wheat species (Triticum monococcum L. and T. dicoccum S.) in response to early chilling stress (4 oC). Early chilling stress resulted in lower total WSCs, in addition to lower flag leaf size, total biomass, specific leaf area and early flowering. While lower specific leaf area may reduce the early chilling stress effects at an individual leaf level, a higher leaf mass ratio and utilization of reserve carbohydrates indicated that the compensatory growth of chilled plants during the recovery period relied on the concerted action of altered resource allocations and reserve carbohydrate consumption. However, the lack of direct selection on sucrose indicates that sucrose has indirect effects on total WSCs. Thus, the total effects of reserve sucrose on relative fitness seem to be buffered via rapid growth rate in chilled plants. Nevertheless, a significant cost of plasticity was evident only for fructans. Further, a regression of daily cumulative plant biomass derived from a crop growth simulation model (CERES-Wheat) on crop growing period revealed a divergent developmental pathway for early chilled plants. These results showed that not only are the characteristic architectures in two Triticum species plastic, but the regulating mechanism of intrinsic developmental (ontogenetic) pathway is also sensitive to early chilling stress. Fourth objective provides future perspectives for WSCs, in particular fructans. Fructans can be involved in freezing tolerance by protecting cellular membranes. This opinion postulates that fructans can be transported from vacuole (site of synthesis) to apoplast (site of action) through vesicles derived from the vacuole. These results can improve the current understanding of WSCs in plant growth and development as well as grain yields. Traits can be used as WSCs markers to prescreen a large number of wheat germplasm for high total WSCs contents. However, a further understanding of different dimensions of WSCs in grain yield improvement and plant growth and development deserves more attention.Weizen ist eines der wichtigsten Grundnahrungsmittel in der Welt. Obwohl in den letzten zwei Jahrzehnten eine Fülle wissenschaftlicher Forschung zu einem signifikanten Fortschritt in der Weizenproduktion durch genetische Verbesserungen geführt hat, gibt es noch immer ein ungenutztes Potential für weitere Ertragssteigerungen. Wasserlösliche Kohlenhydrate (WLK, Saccharose, -Fruktane, Glukose und Fruktose) werden während des vegetativen Wachstums in Pflanzenteilen wie Stängelbasis oder Blattscheide gespeichert und sind hochgradig heritable agronomische Eigenschaften, die sowohl das Pflanzenwachstum und die Entwicklung als auch den Kornertrag beeinflussen. Weiterhin tragen sie zur zur Anpassung von Pflanzen an abiotischen Stress bei. Um die zukünftige Pflanzenproduktion zu verbessern, ist es notwendig, dass das derzeitige Verständnis für die Vielzahl von Steuerungsmechanismen von WLK verbessert wird. Die vorliegende Arbeit liefert Informationen über WLK und ihre Eigenschaften sowie daraus resultierende Perspektiven für die Zukunft anhand von Ergebnissen aus Feld- und Gewächshausversuchen Die Arbeit verfolgt vier Ziele mit unterschiedlichen, spezifischen Fragestellungen. Das erste Ziel der Arbeit erläutert die Merkmale, die WLK unter drei unterschiedlichen N-Versorgungsstufen (0, 100 und 200 kg ha-1) steuern. Die N-Konzentration in der Gesamtpflanze ist negativ mit der Einlagerung von WLK korreliert. Die Merkmale, die in die Gesamteinlagerung von WLK involviert sind, werden ebenso durch die N-Versorgungsstufen beeinflusst. In dieser Arbeit wurden drei vegetative Merkmale (Gesamtbiomasse, Fahnenblattbreite und Wurzel:Sproß-Verhältnis) und zwei physiologische Merkmale (Strahlungsnutzungseffizienz, Stickstoffkonzentration im Blatt) betrachtet. Bei hoher N-Versorgung scheint eine geringere Biomasse, eine geringe Breite des Fahnenblattes und ein geringeres Wurzel/Spross-Verhältnis die Einlagerung von WLK zu steigern. Dem gegenüber ist eine höhere Biomasse und eine größere Fahnenblattbreite von Vorteil unter geringer N-Versorgung. Vor allem die Kombination verschiedener Merkmale, und nicht einzelne Merkmale, schienen unter dem statistischen Ansatz einer N-spezifischer Selektion eine maximale Speicherung von WLK zur Folge zu haben. Das zweite Ziel der Arbeit umfasst die Ableitung eines Simulationsmodells für die Akkumulation von WLK unter drei unterschiedlichen N-Versorgungs-stufen. In diesem Zusammenhang wurde ein simples (phänologisches) Modell für die Anreicherung von Kohlenhydraten in Form von WLK in der Pflanze während der vegetativen Periode von vier unterschiedlichen Weizen-Genotypen entwickelt. Das Modell wurde hinsichtlich des Managementfaktors N (geringe Versorgung (0 kg ha-1), mittlere Versorgung (100 kg ha-1) und hohe Versorgung (200 kg ha-1)) integriert und evaluiert. Das aufgestellte Modell überschätzte die WLK-Akkumulation in frühen Stadien des Pflanzenwachstums und unterschätzte die WLK-Akkumulation in späten Stadien. Zusammenfassend lässt sich sagen, dass das Modell die Rate der WLK Akkumulation mit einem root mean square error (RMSE) von 6.58 gut abbildete. Dennoch lag die über das Modell geschätzte Akkumulationsrate für WLK im Bereich l der geringen und der hohen N Versorgung nahe an den gemessenen Werten, wobei die größeren Abweichungen im mittleren N-Versorgungsbereich zu finden waren. Das Modell lieferte gute Vorhersagen für die Gesamtgehalte an WLK für die gemessenen Daten, doch überschätzte es die Gesamtgehalte an WLK in frühen und späten Entwicklungsstadien deutlich aufgrund der jeweiligen Rate für die Akkumulation von WLK. Unter verschiedenen N-Versorgungsstufen war der Gesamtgehalt an WLK 11 % bzw. 17 % höher als die gemessenen Werte bei geringer und mittlerer N Versorgungsstufe. Demgegenüber wurde bei der hohen N-Versorgungsstufe vom Modell ein 12 % geringerer Gehalt an WLK geschätzt. Die Gesamtbewertung des Modells für den genutzten Datensatz zeigte, dass die Schätzfehler für die Rate der WLK-Akkumulation größer waren, und dass der RMSE für alle N-Versorgungsstufen bei 20?30 % lag. Die Schätzfehler für die Gesamtakkukumulation der WLK war dagegen geringer und der RMSE lag für alle N-Versorgungsstufen bei etwa 20 %. Das dritte Ziel der Arbeit war die Anpassung zweier ursprünglicher Weizenarten (Triticum monococcum L. und T. dicoccum S.) hinsichtlich der phänotypischen Erscheinung in Abhängigkeit von frühem Kältestress (4 °C). Ein früher Kältestress resultierte in geringeren Gehalten an WLK, und zusätzlich in einem kleineren Fahnenblatt, einer geringerer Gesamtbiomasse, geringerer spezifischer Blattfläche und einer früheren Blüte der Pflanzen. Während die reduzierte Spezifische Blattfläche die Effekte eines frühen Kältestresses auf dem Level einzelner Blätter reduzieren könnte, zeigten das höhereBlatt/Biomasse-Verhältnis und die Ausnutzung von Reservekohlenhydraten, dass das Kompensationswachstum von kältegestressten Pflanzen in der Erholungsphase auf die gezielte Veränderung der Ressourcenallokation und des Verbrauchs von Reservekohlenhydraten zurückzuführen war. In Ermangelung einer direkten Selektion auf Saccharose wird jedoch deutlich, dass die Saccharose einen indirekten Effekt auf den Gesamtgehalt an WLK hat. Demnach scheint der Gesamteffekt der Reservesaccharosen auf die relative Fitness durch eine schnellere Wachstumsrate der kältegestressten Pflanzen gepuffert zu werden. Dennoch war ein signifikanter Aufwand an Anpassungsfähigkeit nur für Fruktane nachweisbar. Ein Rückgang der täglich aufsummierten Pflanzenbiomasse, abgeleitet vom Pflanzenwachstumsmodell CERES-Wheat, auf die Wachstumsperiode ergaben einen abweichenden Entwicklungspfad für kältegestresste Pflanzen. Diese Ergebnisse zeigen, dass nicht nur die charakteristische Architektur der beiden Triticum Spezies anpassungsfähig ist, sondern dass auch Regulationsmechanismen der spezifisch Entwicklungspfade auf Kältestress in frühen Entwicklungsstadien reagieren. Das vierte Ziel der Arbeit zeigt die Zukunftsperspektiven für WLK, im Speziellen für Fruktane. Fruktane können in die Ausbildung von Kältetoleranz durch den Schutz der zellulären Membranen einbezogen sein. Der Autor kommt zu dem Schluss, dass die Fruktane von der Vakuole (Syntheseort) zum Apoplasten (Aktionsort) durch Bläschen aus der Vakuole transportiert werden. Die Ergebnisse dieser Arbeit können das Verständnis von WLK im Pflanzenwachstum und der Entwicklung verbessern und genutzt werden, den Kornertrag zu steigern. Die untersuchten Merkmale können als WLK-Marker genutzt werden, um eine große Anzahl von Weizengenotypen auf hohen Gehalt an WLK zu screenen. Insgesamt sollte einem vertieften Verständnis der unterschiedlichen Dimensionen von WLK hinsichtlich der Ertragssteigerung und des Pflanzenwachstums und der Entwicklung mehr Aufmerksamkeit geschenkt werden

Current advances in genomics and gene editing tools for crop improvement in a changing climate scenario

The unprecedented global climate change has severely impacted our environment and engendered severe threats to agricultural productivity (Shahzad et al., 2021; Cinner et al., 2022; Ozdemir, 2022). This has led to the emergence of new races of plant pathogens and insect pests, accentuated abiotic stresses, depleted water resources and shrunken arable land, posing grave challenges to the food security of an ever-increasing global population (IPCC Sixth Assessment Report, 2022). The advantages offered by the Green Revolution of the mid-1960s are also fading away, resulting in a fragile food system (Davis et al., 2019; John and Babu 2021). Agriculture today faces newer challenges exacerbated by genetic erosion, the narrow genetic base of commercial crops and environmental degradation. There is an urgent need to make agriculture more resilient and sustainable while still continuing to develop high-yielding, stress-resistant and climate-smart crop varieties

Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence

Deep learning methodologies have revolutionized prediction in many fields and show potential to do the same in molecular biology and genetics. However, applying these methods in their current forms ignores evolutionary dependencies within biological systems and can result in false positives and spurious conclusions. We developed two approaches that account for evolutionary relatedness in machine learning models: (i) gene-family–guided splitting and (ii) ortholog contrasts. The first approach accounts for evolution by constraining model training and testing sets to include different gene families. The second approach uses evolutionarily informed comparisons between orthologous genes to both control for and leverage evolutionary divergence during the training process. The two approaches were explored and validated within the context of mRNA expression level prediction and have the area under the ROC curve (auROC) values ranging from 0.75 to 0.94. Model weight inspections showed biologically interpretable patterns, resulting in the hypothesis that the 3′ UTR is more important for fine-tuning mRNA abundance levels while the 5′ UTR is more important for large-scale changes

Sustainable and Intelligent Phytoprotection in Photovoltaic Agriculture: New Challenges and Opportunities

Photovoltaic Agriculture (PA) is a new management system combining industry with modern agriculture that can effectively reduce the competition for limited land resource usage between electric power production and agricultural production. However, PA has been facing the challenge of managing plant protection measures because it is difficult to monitor plants grown under the photovoltaic panels by remote sensing satellites and pesticide applications using drones. To overcome this challenge, Solar Insecticidal Lamps (SILs) can be used for phytoprotection in PA. However, to effectively use SILs in PA, it is important to identify a suitable field location to maintain strong wireless communication signals. In this paper, two testbeds were designed and a series of experiments in PA was performed. The results indicate that there is considerable interference exists around the confluence box. A higher interference seriously reduces the Packet Reception Rate (PRR) of the nearby node, which is an important constraint for deploying wireless sensors in PA. Finally, new challenges and future research opportunities are proposed

Robotics and autonomous systems for net-zero agriculture

Purpose of ReviewThe paper discusses how robotics and autonomous systems (RAS) are being deployed to decarbonise agricultural production. The climate emergency cannot be ameliorated without dramatic reductions in greenhouse gas emis-sions across the agri-food sector. This review outlines the transformational role for robotics in the agri-food system and considers where research and focus might be prioritised.Recent FindingsAgri-robotic systems provide multiple emerging opportunities that facilitate the transition towards net zero agriculture. Five focus themes were identified where robotics could impact sustainable food production systems to (1) increase nitrogen use efficiency, (2) accelerate plant breeding, (3) deliver regenerative agriculture, (4) electrify robotic vehicles, (5) reduce food waste.SummaryRAS technologies create opportunities to (i) optimise the use of inputs such as fertiliser, seeds, and fuel/energy; (ii) reduce the environmental impact on soil and other natural resources; (iii) improve the efficiency and precision of agri-cultural processes and equipment; (iv) enhance farmers’ decisions to improve crop care and reduce farm waste. Further and scaled research and technology development are needed to exploit these opportunities

Image dataset of tea chrysanthemums in complex outdoor scenes

There is currently no publicly available tea chrysanthemum dataset to the authors’ knowledge. Consequently, we provide an image dataset for six varieties of tea chrysanthemums in three camera view angles obtained under complex outdoor scenes, and this open-source image dataset can greatly promote the development of tea chrysanthemums detection methodology

Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor)

Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how deleterious variants impact phenotypes, we identified putative deleterious mutations among ∼5.5 M segregating variants of 229 diverse biomass sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that ∼33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups. Across racial groups, the mutation burden correlated negatively with biomass, plant height, specific leaf area (SLA), and tissue starch content (TSC), suggesting that deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly one-half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (average of 3.1% across all stages). There is no advantage in total heritable variance for SLA and TSC. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, these results suggest that incorporating putatively deleterious variants into genomic models slightly improves prediction accuracy because of extensive linkage. Knowledge of deleterious variants could be leveraged for sorghum breeding through either genome editing and/or conventional breeding that focuses on the selection of progeny with fewer deleterious alleles

Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions

Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE