The Effects of Gibberellic Acid and Auxin Hormones on Heliotropism in Sunflowers

Sunflowers are one of many different plant species that are able to track and face the sun in order to optimize the amount of sunlight they are exposed to. This process of orienting towards the sun is called Heliotropism. Sunflowers are able to effectively orient themselves towards the sun because the growth rate on the East and West side of the stem alternates depending on the time of day. At dawn, the East facing stem will grow at a faster rate than the West facing side, resulting in the flower orienting towards the West. This alternating and uneven growth is what allows the sunflower to track the sun during the day and reorient at night to face the East in preparation for sunrise. Not much is known about the biological processes that induce heliotropism. In our study, we focused on two known growth inducing hormones in plants that are present in sunflowers, Gibberellic Acid and Auxin, and their importance to heliotropism. Because of their prevalence in sunflowers and their known ability to induce growth in plants, we hypothesized that Gibberellic Acid (GA) and an Auxin hormone, Indole-3-Acetic Acid (IAA), play a significant role in sunflower’s ability to perform heliotropism

A Microbiome Engineering Framework to Evaluate Rhizobial Symbionts of Legumes

Background For well over a century, rhizobia have been recognized as effective biofertilizer options for legume crops. This has led to the widespread use of rhizobial inoculants in agricultural systems, but a recurring issue has emerged: applied rhizobia struggle to provide growth benefits to legume crops. This has largely been attributed to the presence of soil rhizobia and has been termed the ‘rhizobial competition problem.’ Scope Microbiome engineering has emerged as a methodology to circumvent the rhizobial competition problem by creating legume microbiomes that do not require exogenous rhizobia. However, we highlight an alternative implementation of microbiome engineering that focuses on untangling the complexities of the symbiosis that contribute to the rhizobial competition problem. We outline three approaches that use different starting inocula to test hypotheses to overcome the rhizobial competition problem. Conclusions The approaches we suggest are targeted at various stages of the legume-rhizobium symbiosis and will help us uncover underlying molecular mechanisms that contribute to the rhizobial competition problem. We conclude with an integrative perspective of these different approaches and suggest a path forward for future research on legumes and their complex microbiome

Virtual and In Vitro Screening of Natural Products Identifies Indole and Benzene Derivatives as Inhibitors of SARS-CoV-2 Main Protease (M\u3csup\u3epro\u3c/sup\u3e)

The rapid spread of the coronavirus disease 2019 (COVID-19) resulted in serious health, social, and economic consequences. While the development of effective vaccines substantially reduced the severity of symptoms and the associated deaths, we still urgently need effective drugs to further reduce the number of casualties associated with SARS-CoV-2 infections. Machine learning methods both improved and sped up all the different stages of the drug discovery processes by performing complex analyses with enormous datasets. Natural products (NPs) have been used for treating diseases and infections for thousands of years and represent a valuable resource for drug discovery when combined with the current computation advancements. Here, a dataset of 406,747 unique NPs was screened against the SARS-CoV-2 main protease (Mpro) crystal structure (6lu7) using a combination of ligand- and structural-based virtual screening. Based on 1) the predicted binding affinities of the NPs to the Mpro, 2) the types and number of interactions with the Mpro amino acids that are critical for its function, and 3) the desirable pharmacokinetic properties of the NPs, we identified the top 20 candidates that could potentially inhibit the Mpro protease function. A total of 7 of the 20 top candidates were subjected to in vitro protease inhibition assay and 4 of them (4/7; 57%), including two beta carbolines, one N-alkyl indole, and one Benzoic acid ester, had significant inhibitory activity against Mpro protease. These four NPs could be developed further for the treatment of COVID-19 symptoms

\u3cem\u3eDe novo\u3c/em\u3e Sequencing and Analysis of \u3cem\u3eSalvia hispanica\u3c/em\u3e Tissue-Specific Transcriptome and Identification of Genes Involved in Terpenoid Biosynthesis

Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which represented 92.8% transcriptome completeness and a diverse set of Gene Ontology terms. Dierential expression analysis identified 6151 and 8116 contigs significantly upregulated in the leaf and root tissues, respectively. In addition, we identified 30 contigs belonging to the Terpene synthase (TPS) family and demonstrated their evolutionary relationships to tomato TPS family members. Finally, we characterized the expression of S. hispanica TPS members in leaves subjected to abiotic stresses and hormone treatments. Abscisic acid had the most pronounced eect on the expression of the TPS genes tested in this study. Our work provides valuable community resources for future studies aimed at improving and utilizing the beneficial constituents of this emerging healthy food source

Characterization of Macrophomina phaseolina Infecting Chia Plants

Microbial organisms have caused detrimental effects to agricultural plants by significantly decreasing their plant growth yield and it’s nutritional qualities, leading to high levels of economic losses in society. Salvia Hispanica L., commonly known as chia, is becoming a rising agricultural crop because of its favorable nutritional qualities. Chia seeds have a high concentration of α-linolenic acid, commonly known as omega-3 fatty acids) which provide several different health benefits, in addition to being a rich source of protein and fiber. Chia field trial conducted by the Atamian lab during summer 2018, experienced high levels of disease incidence characterized by root rot, plant wilting, and eventual death of three-month-old chia plants. The fungus was isolated and identified as Macrophomina phaseolina based on its morphological analysis on potato dextrose agar plates. Macrophomina phaseolina is a widespread fungus that causes a high mortality rate in nursery plats as well as in agricultural crops such as soybean, maize, sorghum, and cotton. The fungus damages the root system of the plant host, resulting in the inability of the root to obtain the required nutrients and water for proper growth of the plant. The objective of this project was to use molecular techniques to confirm the accuracy of the morphological analysis and further characterize the fungus at the molecular level. The DNA of Macrophomina phaseolina was cloned through the process of A tailing, ligation, and transformation into E. coli cells, and then plasmids from the surviving cultured E coli. cells were sent to the lab for sequencing of the genes MPK-1, ITS 1 and 2, and SSU rRNA. Using the other strains of Macrophomina phaseolina in the NCBI database, the resulting gene sequences were compared to deduce that the fungus present was Macrophomina phaseolina, and if there was a presence of genetic variability between the strains infecting chia plants to previous cases in other plants

Prediction of Cultivation Areas for the Commercial and an Early Flowering Wild Accession of \u3cem\u3eSalvia hispanica\u3c/em\u3e L. in the United States

Salvia hispanica L., commonly known as chia, is a plant-based alternative to seafood and is rich in heart-healthy omega-3 fatty acid, protein, fiber, and antioxidants. In the Northern Hemisphere, chia flowering is triggered by the fall equinox (12-h light and dark, early October) and the seeds mature after approximately three months. Chia is sensitive to frost and end of season moisture which limits its cultivation to small areas in regions with temperate climate. The U.S. chia import has increased considerably over the years; however, chia is not widely cultivated in the United States. This study used the historical U.S. temperature and precipitation data as a first step to explore the potential of widescale chia cultivation. The 10th percentiles of 25 mm precipitation level as well as soft frost (32 °F: 0 °C) and hard frost (28 °F: −2.2 °C) were tabulated for the months of November and December. The results identified temperature as the main limiting factor for chia cultivation in the United States. The commercial chia variety (harvested in December) can be planted on approximately 10,000 km2 cropland (1,000,000 hectare) in the United States. The future development of early flowering variety (harvested in November) was demonstrated to open an additional 44,000 km2 (4,400,000 hectares) for chia cultivation in the United States. In conclusion, chia cultivation could provide economic benefits to U.S. farmers both by enriching the diversity within crop rotations aimed at reducing pest and pathogen populations and by its high economic value as an alternative specialty crop

Physiological and Transcriptomic Responses of Two \u3cem\u3eArtemisia californica\u3c/em\u3e Populations to Drought: Implications for Restoring Drought-Resilient Native Communities

As climate change brings drier and more variable rainfall patterns to many arid and semi-arid regions, land managers must re-assemble appropriate plant communities for these conditions. Transcriptome sequencing can elucidate the molecular mechanisms underlying plant responses to changing environmental conditions, potentially enhancing our ability to screen suitable genotypes and species for restoration. We examined physiological and morphological traits and transcriptome sequences of coastal and inland populations of California sagebrush (Artemisia californica), a critical shrub used to restore coastal sage scrub vegetation communities, grown under low and high rainfall environments. The populations are located approximately 36 km apart but differ in mean annual precipitation, with the coastal population experiencing approximately 42% more rainfall. We found subtle phenotypic differences between populations, with plants from the coastal population showing higher rates of carbon assimilation and growth, and a more considerable decrease in function in response to drought compared to the inland population. We observed more extensive transcriptome responses in A. californica root compared to leaf tissues. While the two populations shared several responses to drought, such as upregulated protein folding and stabilization, coastal populations demonstrated more extensive responses to stress than inland populations. Furthermore, transcriptomic results from inland populations showed reduced aboveground growth and early flowering which may reduce evaporative loss and maximize reproductive output, respectively, under low rainfall conditions. These patterns are consistent with a trade-off between growth and stress tolerance, where the coastal population has a strategy more aligned with growth compared to the inland population, which may be better able to tolerate stress. Identifying drought-tolerant populations can ultimately lead to cost savings in maintaining restored areas under future climate conditions

Multiple Light Signaling Pathways Control Solar Tracking in Sunflowers

Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We found the expected transcriptome signatures of phototropin-mediated phototropism in sunflower stems bending towards monochromatic blue light. Surprisingly, the expression patterns of these phototropism-regulated genes are quite different in heliotropic plants. Most genes rapidly induced during phototropism display only minor differences in expression across solar tracking stems. However, some genes that are both rapidly induced during phototropism and are implicated in growth responses to foliar shade are rapidly induced on the west sides of stems at the onset of heliotropism, suggesting a possible role for red light photoreceptors in solar tracking. To test the involvement of different photoreceptor signaling pathways in heliotropism, we modulated the light environment of plants initiating solar tracking. We found that depletion of either red and far-red light or blue light did not hinder the initiation or maintenance of heliotropism in the field. Together, our results suggest that the transcriptional regulation of heliotropism is distinct from phototropin-mediated phototropism and likely involves inputs from multiple light signaling pathways

Reporting Charcoal Rot in Chia and Developing a Susceptibility Assay

Chia (Salvia Hispanica) cross breeds were planted in the summer of 2018 with the intent of selective breeding for agricultural benefit. Preexisting pathogens in the soil caused 40-50% fatality of adult plants. This was surprising due to the precursory knowledge that chia has antibiotic and antifungal oils (Elshafie et. al. 2018); chia was only recently documented to be susceptible to Fusarium wilt (Fusarium oxysporum). The primary pathogen responsible was identified as Macrophomina phaseolina (aka charcoal rot); a widespread soilborne pathogen which has multiple commercial hosts (Su et. al. 2001). M. phaesolina on wheat seed vector where used as inoculums (Brandari 2017) for chia to evaluate disease progression and symptoms in chia. Samples of this trial produced M. phaseolina from diseased chia tissues confirming susceptibility to M. phaseolina; in addition carefully sampled root and stem fractions identified the pathology of fungus from root to stem. The two parental varieties of the cross, chia-Pinta and chia-Tropic continue to be compared for their disease resistance to M. phaseolina. Identifying disease resistant genes allows for breeding of resistant cultivars, improving the marketability of chia

Evaluation of qPCR to Detect Shifts in Population Composition of the Rhizobial Symbiont \u3cem\u3eMesorhizobium japonicum\u3c/em\u3e during Serial in Planta Transfers

Microbial symbionts range from mutualistic to commensal to antagonistic. While these roles are distinct in their outcome, they are also fluid in a changing environment. Here, we used the Lotus japonicus–Mesorhizobium japonicum symbiosis to investigate short-term and long-term shifts in population abundance using an effective, fast, and low-cost tracking methodology for M. japonicum. We use quantitative polymerase chain reaction (qPCR) to track previously generated signature-tagged M. japonicum mutants targeting the Tn5 transposon insertion and the flanking gene. We used a highly beneficial wild type and moderately beneficial and non-beneficial mutants of M. japonicum sp. nov. to demonstrate the specificity of these primers to estimate the relative abundance of each genotype within individual nodules and after serial transfers to new hosts. For the moderate and non-beneficial genotypes, qPCR allowed us to differentiate genotypes that are phenotypically indistinguishable and investigate host control with suboptimal symbionts. We consistently found the wild type increasing in the proportion of the population, but our data suggest a potential reproductive trade-off between the moderate and non-beneficial genotypes. The multi-generation framework we used, coupled with qPCR, can easily be scaled up to track dozens of M. japonicum mutants simultaneously. Moreover, these mutants can be used to explore M. japonicum genotype abundance in the presence of a complex soil community