Plant Science Research Research Articles

A High-Throughput Phenotyping Pipeline for Image Processing and Functional Growth Curve Analysis.

High-throughput phenotyping system has become more and more popular in plant science research. The data analysis for such a system typically involves two steps: plant feature extraction through image processing and statistical analysis for the extracted features. The current approach is to perform those two steps on different platforms. We develop the package “implant” in R for both robust feature extraction and functional data analysis. For image processing, the “implant” package provides methods including thresholding, hidden Markov random field model, and morphological operations. For statistical analysis, this package can produce nonparametric curve fitting with its confidence region for plant growth. A functional ANOVA model to test for the treatment and genotype effects on the plant growth dynamics is also provided.

Impacts of Vaccinium arboreum Rootstocks on Vegetative Growth and Yield in Two Southern Highbush Blueberry Cultivars

Vaccinium arboreum Marsh is a small tree adapted to low-organic matter soils and is one of the few ericaceous species that tolerates soil pH greater than 6.0. It has a deep root system and is more drought tolerant than cultivated blueberry. The use of V. arboreum as a rootstock for commercial blueberry production has been studied previously in young blueberry plantings. The objective of the current study was to expand on earlier work and evaluate growth, productivity, and tolerance to bacterial leaf scorch (Xylella fastidiosa) in established plantings of own-rooted vs. grafted southern highbush blueberry (SHB). Two field plantings of grafted and own-rooted ‘Meadowlark’ and ‘Farthing’ SHB were established in May 2011: one at the University of Florida–Institute of Food and Agricultural Sciences (UF-IFAS) Plant Science Research and Education Unit in Citra, FL, and the other at a commercial blueberry farm in Archer, FL. At both sites, four rootstock–scion combinations were grown in either pine bark-amended or nonamended soil. Canopy volume was greater in grafted compared with own-rooted ‘Meadowlark’ at both locations throughout the 4 years of the study (2015–18), whereas canopy volume in ‘Farthing’ was not consistently different. For both cultivars and both locations, canopy volume was greater on amended compared with nonamended soil. Although canopy growth was not consistently increased in the grafted compared with own-rooted plants, yield was greater in grafted plants of both cultivars at both locations. Cumulative yield over the 4 years was similar between grafted plants grown on both amended and nonamended soil, and was significantly greater than yield of own-rooted plants on nonamended soil, suggesting the use of this rootstock may decrease the requirement for pine bark amendment. In general, grafted plants produced larger berries, with no negative impacts on fruit soluble solids, titratable acidity, or firmness. ‘Meadowlark’—an SHB cultivar that exhibits high sensitivity to bacterial leaf scorch—displayed decreased development of bacterial leaf scorch symptoms when grafted onto V. arboreum compared with own-rooted plants. These results indicate the potential benefits of grafting SHB onto V. arboreum rootstock, particularly under marginal soil conditions. However, a complete economic analysis that also takes into account any differences in longevity between the two systems must be done to determine whether the benefits of using grafting are feasible financially for the grower.

From phytochemistry to metabolomics: eight decades of research in plant and food science

From phytochemistry to metabolomics: eight decades of research in plant and food science

Mapping thermal conductivity across bamboo cell walls with scanning thermal microscopy

Scanning thermal microscopy is a powerful tool for investigating biological materials and structures like bamboo and its cell walls. Alongside nanoscale topographical information, the technique reveals local variations in thermal conductivity of this elegant natural material. We observe that at the tissue scale, fibre cells in the scattered vascular tissue would offer preferential pathways for heat transport due to their higher conductivities in both anatomical directions, in comparison to parenchymatic cells in ground tissue. In addition, the transverse orientation offers more resistance to heat flow. Furthermore, we observe each fibre cell to compose of up to ten layers, with alternating thick and thin lamellae in the secondary wall. Notably, we find the thin lamellae to have relatively lower conductivity than the thick lamellae in the fibre direction. This is due to the distinct orientation of cellulose microfibrils within the cell wall layers, and that cellulose microfibrils are highly anisotropic and have higher conductivity along their lengths. Microfibrils in the thick lamellae are oriented almost parallel to the fibre cell axis, while microfibrils in the thin lamellae are oriented almost perpendicular to the cell axis. Bamboo grasses have evolved to rapidly deposit this combination of thick and thin layers, like a polymer composite laminate or cross-laminated timber, for combination of axial and transverse stiffness and strength. However, this architecture is found to have interesting implications on thermal transport in bamboo, which is relevant for the application of engineered bamboo in buildings. We further conclude that scanning thermal microscopy may be a useful technique in plant science research, including for phenotyping studies.

Super-Agrobacterium ver. 4: Improving the Transformation Frequencies and Genetic Engineering Possibilities for Crop Plants.

Agrobacterium tumefaciens has been utilized for both transient and stable transformations of plants. These transformation methods have been used in fields such as breeding GM crops, protein production in plant cells, and the functional analysis of genes. However, some plants have significantly lower transient gene transfer and stable transformation rates, creating a technical barrier that needs to be resolved. In this study, Super-Agrobacterium was updated to ver. 4 by introducing both the ACC deaminase (acdS) and GABA transaminase (gabT) genes, whose resultant enzymes degrade ACC, the ethylene precursor, and GABA, respectively. A. tumefaciens strain GV2260, which is similar to other major strains (EHA105, GV3101, LBA4404, and MP90), was used in this study. The abilities of the Super-Agrobacterium ver. 4 were evaluated in Erianthus ravennae, Solanum lycopersicum “Micro-Tom,” Nicotiana benthamiana, and S. torvum. Super-Agrobacterium ver. 4 showed the highest T-DNA transfer (transient transformation) frequencies in E. ravennae and S. lycopersicum, but not in N. benthamiana and S. torvum. In tomato, Super-Agrobacterium ver. 4 increased the stable transformation rate by 3.6-fold compared to the original GV2260 strain. Super-Agrobacterium ver. 4 enables reduction of the amount of time and labor required for transformations by approximately 72%, and is therefore a more effective and powerful tool for plant genetic engineering and functional analysis, than the previously developed strains. As our system has a plasmid containing the acdS and gabT genes, it could be used in combination with other major strains such as EHA105, EHA101, LBA4404, MP90, and AGL1. Super-Agrobacterium ver. 4, could thus possibly be a breakthrough application for improving basic plant science research methods.

Recent Advances in Radioisotope Imaging Technology for Plant Science Research in Japan

Soil provides most of the essential elements required for the growth of plants. These elements are absorbed by the roots and then transported to the leaves via the xylem. Photoassimilates and other nutrients are translocated from the leaves to the maturing organs via the phloem. Non-essential elements are also transported via the same route. Therefore, an accurate understanding of the movement of these elements across the plant body is of paramount importance in plant science research. Radioisotope imaging is often utilized to understand element kinetics in the plant body. Live plant imaging is one of the recent advancements in this field. In this article, we recapitulate the developments in radioisotope imaging technology for plant science research in Japanese research groups. This collation provides useful insights into the application of radioisotope imaging technology in wide domains including plant science.

Developing Heritable Mutations in Arabidopsis thaliana Using a Modified CRISPR/Cas9 Toolkit Comprising PAM-Altered Cas9 Variants and gRNAs.

Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9), comprising an RNA-guided DNA endonuclease and a programmable guide RNA (gRNA), is currently recognized to be a powerful genome-editing tool and is widely used in biological science. Despite the usefulness of the system, a protospacer-adjacent motif (PAM) immediately downstream of the target sequence needs to be taken into account in the design of the gRNA, a requirement which limits the flexibility of the CRISPR-based genome-editing system. To overcome this limitation, a Cas9 isolated from Streptococcus pyogenes, namely SpCas9, engineered to develop several variants of Cas9 nuclease, has been generated. SpCas9 recognizes the NGG sequence as the PAM, whereas its variants are capable of interacting with different PAMs. Despite the potential advantage of the Cas9 variants, their functionalities have not previously been tested in the widely used model plant, Arabidopsis thaliana. Here, we developed a plant-specific vector series harboring SpCas9-VQR (NGAN or NGNG) or SpCas9-EQR (NGAG) and evaluated their functionalities. These modified Cas9 nucleases efficiently introduced mutations into the CLV3 and AS1 target genes using gRNAs that were compatible with atypical PAMs. Furthermore, the generated mutations were passed on to their offspring. This study illustrated the usefulness of the SpCas9 variants because the ability to generate heritable mutations will be of great benefit in molecular genetic analyses. A greater number of potential SpCas9-variant-recognition sites in these genes are predicted, compared with those of conventional SpCas9. These results demonstrated the usefulness of the SpCas9 variants for genome editing in the field of plant science research.

A novel rice grain size gene OsSNB was identified by genome-wide association study in natural population.

Increasing agricultural productivity is one of the most important goals of plant science research and imperative to meet the needs of a rapidly growing population. Rice (Oryza sativa L.) is one of the most important staple crops worldwide. Grain size is both a major determinant of grain yield in rice and a target trait for domestication and artificial breeding. Here, a genome-wide association study of grain length and grain width was performed using 996,722 SNP markers in 270 rice accessions. Five and four quantitative trait loci were identified for grain length and grain width, respectively. In particular, the novel grain size gene OsSNB was identified from qGW7, and further results showed that OsSNB negatively regulated grain size. Most notably, knockout mutant plants by CRISPR/Cas9 technology showed increased grain length, width, and weight, while overexpression of OsSNB yielded the opposite. Sequencing of this gene from the promoter to the 3’-untranslated region in 168 rice accessions from a wide geographic range identified eight haplotypes. Furthermore, Hap 3 has the highest grain width discovered in japonica subspecies. Compared to other haplotypes, Hap 3 has a 225 bp insertion in the promoter. Based on the difference between Hap 3 and other haplotypes, OsSNB_Indel2 was designed as a functional marker for the improvement of rice grain width. This could be directly used to assist selection toward an improvement of grain width. These findings suggest OsSNB as useful for further improvements in yield characteristics in most cultivars.

Nanotechnology in Plant Science: To Make a Long Story Short.

This mini-review aims at gaining knowledge on basic aspects of plant nanotechnology. While in recent years the enormous progress of nanotechnology in biomedical sciences has revolutionized therapeutic and diagnostic approaches, the comprehension of nanoparticle-plant interactions, including uptake, mobilization and accumulation, is still in its infancy. Deeper studies are needed to establish the impact of nanomaterials (NMs) on plant growth and agro-ecosystems and to develop smart nanotechnology applications in crop improvement. Herein we provide a short overview of NMs employed in plant science and concisely describe key NM-plant interactions in terms of uptake, mobilization mechanisms, and biological effects. The major current applications in plants are reviewed also discussing the potential use of polymeric soft NMs which may open new and safer opportunities for smart delivery of biomolecules and for new strategies in plant genetic engineering, with the final aim to enhance plant defense and/or stimulate plant growth and development and, ultimately, crop production. Finally, we envisage that multidisciplinary collaborative approaches will be central to fill the knowledge gap in plant nanotechnology and push toward the use of NMs in agriculture and, more in general, in plant science research.

Authentic Undergraduate Research in Plant Science: The Importance of Mentor-Student Relationships

Active learning can improve student engagement and learning outcomes by encouraging students to use higher order thinking skills. One strategy is involving students in research during their undergraduate studies where students are given the opportunity to design, implement, analyse and present a scientific research experiment under the guidance of an academic mentor. This study evaluates the role the student-mentor relationship played in the value of the research project for both students and mentors in a level II plant science course. Survey data collected between 2015 and 2017 showed that the majority (80% in 2017) of students agreed that the research project was a valuable part of the course. In addition, students found the interaction with their mentor was important. Communication between student and mentor was seen as very important with 90% of the student cohort indicating that they agreed or strongly agreed that communication was important to the research project. The vast majority of mentors (over 75%) were able to see the value to students of the research project. The majority of mentors felt it was easy to communicate with their student group and that students were responsive to their suggestions. This study has shown that preparing both students and mentors for participation in an authentic research project has positive impacts on student engagement.

Sensitivity of olive leaf turgor to air vapour pressure deficit correlates with diurnal maximum stomatal conductance

Effective study and management of crops and forests would benefit greatly from useful plant-based indicators of the biological controls on evapotranspiration, and particularly stomatal conductance (gs). Given the strong influence of gs on bulk leaf water potential and turgor pressure (P), in vivo measurement of P may provide useful information about diurnal or seasonal dynamics of gs. Moderate plant water stress affects the diurnal dynamics of P as leaf-to-air vapour pressure deficit (D) varies, and these dynamics correlate to gs. Here, we explored relative changes in P in response to changes in D under mild drought conditions, and how these changes are linked to stomatal behaviour, and specifically to diurnal maximum gs (gs,max), one of the best indicators of plant water stress. We monitored ecophysiological and environmental variables, as well as a relative proxy for P, during three consecutive seasons in a hedgerow olive orchard where trees were supplied with different irrigation treatments to create well-watered and moderately water-stressed conditions. Our results demonstrated that the sensitivity of P to D correlated well with gs,max reached by the trees within a range in which variations in gs are the main diffusional limitation to photosynthesis. We further showed that this correlation held under a wide range of meteorological conditions and soil water availability. This turgor proxy measurement, which is much easier to measure than gs, can facilitate the use of gs,max as an indicator of plant water stress and evapotranspiration in agriculture and plant science research.

Deciphering the nitric oxide, cyanide and iron-mediated actions of sodium nitroprusside in cotyledons of salt stressed sunflower seedlings

Nitric oxide (NO) is an endogenous signaling molecule in plants. Sodium nitroprusside (SNP), an established NO donor used in plant science research, simultaneously releases NO, cyanide (CN−) and iron (Fe) in solution. Since cyanide and iron mask NO effect of SNP, its use in NO research is debatable. Deciphering the action of SNP through NO, CN− or Fe has been undertaken in the present work. Cotyledons from salt stressed sunflower seedlings grown in the presence of NO donors were subjected to spectrofluorometric analysis of NO, CN− and Fe contents, and proteome and biochemical analyses. Diethylenetriamine NONOate (DETA) proved to be a better NO source since SNP enhanced ROS accumulation in the tissue. Abundance of 127 proteins is modulated by salt stress. SNP and exhausted SNP (exSNP) alter the abundance of 117 and 129 proteins, respectively. These proteins belong to primary metabolism, stress-response, transport, translation, proteolysis, chaperone, regulatory, and storage. Salt-responsive proteins, such as, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK) and isocitrate dehydrogenase are negatively modulated. DETA and SNP lower the activities of GAPDH and S-adenosylmethionine synthase (SAMS). Abundance of heat shock 70 kDa protein and actin are sensitive to both NaCl and NO. SNP affects plant growth by modulating proteome though iron, cyanide and NO. Its use only as an NO donor is thus debatable. exSNP control also releases substantial amount of cyanide and iron, thus questioning its use as control in NO research.

Mapping of plant science research productivity in Pakistan

Mapping of plant science research productivity in Pakistan

Opening the dialogue: Research networks between high- and low-income countries further understanding of global agro-climatic challenges.

Societal Impact Statement In the modern world it has become increasingly urgent to balance human food security needs with environmental needs. These needs are not necessarily mutually exclusive, and can be synergistic. The Cambridge‐India Network for Translational Research in Nitrogen (CINTRIN) seeks to reduce nitrogen fertilizer overapplication (and the resulting environmental pollution) in Indian agriculture: a situation with various scientific and sociopolitical drivers, which equally have various sociopolitical and scientific solutions. By listening to the needs of local farmers and applying the knowledge and resources of global plant science research, achieving higher crop yields with less nitrogen is an achievable prospect for India.

Jan J. Lyczakowski.

Jan J. Lyczakowski.

An entomocentric view of the Janzen–Connell hypothesis

In 1987, in the first issue of Conservation Biology, Edward O. Wilson wrote about the “little things that run the world” – the importance and conservation of insects (Wilson, 1987). Readers of Insect Conservation and Diversity will no doubt be very familiar with the concept. Sadly, however, this perception is not as widely shared among the rest of the scientific community as it should be, and insects are still comparatively neglected as a prime focus of scientific investigations.

Advances in Plant Sciences Research

Advances in Plant Sciences Research

Measuring ethylene in postharvest biology research using the laser-based ETD-300 ethylene detector

BackgroundAbility to measure ethylene is an important aspect of postharvest management, as knowledge of endogenous ethylene production is used in assessing physiological status, while response of crops to exogenous ethylene informs efforts needed to control unwanted ripening. An ethylene monitoring device with a laser-based photoacoustic detector, ETD-300, was recently developed by Sensor Sense B.V., Nijmegen, The Netherlands. In terms of performance, the ETD-300 is superior to all other current ethylene measurement devices, with a sensitivity of 0.3 nL L−1, a response time of 5 s, and an ability to monitor ethylene in real time. Although the ETD-300 is relatively easy to operate, the performance and correctness of the data obtained depends on the choice of settings, which depends on the application.ResultsThis article provides a description of different ways in which the ETD-300 can be used in postharvest research for monitoring ethylene production and ethylene presence in an environment. We provided guidelines on selecting the appropriate method (Continuous Flow, Stop and Flow, and Sample methods), and operational curves for deciding on suitable combination of free volume, flow rates, and period for the different measurement methods.ConclusionsUsing these guidelines and operational curves, ETD-300 users can considerably reduce the measurement effort by limiting trial and error in establishing appropriate methodologies for their application. The guidelines also comment on accurate use of the ETD-300, as using the inappropriate settings could lead to erroneous measurements. Although these methodologies were developed primarily for postharvest application, they can be applied in other plant science research.

Forward and reverse genetics approaches for combined stress tolerance in rice

Climate change impact on global agricultural food production has been evident in the past few decades. Abiotic factors such as heat, drought, and salinity share a major proportion of crop yield losses and posing a serious threat to global food security. Developing climate resilient crops has become a frontier area of basic plant science and agricultural research. Persistent efforts by scientists to understand crop responses under natural environment and progress in the field of genomics and phenomics has provided unprecedented pace to crop development programs. Rice is the most important cereal crop and staple food for more than 3 billion people worldwide. Heat, drought and salinity stress are the major constraints for global rice production. Hence, efforts are warranted to develop climate-resilient rice cultivars that can produce substantially under different abiotic stresses. Crop plants seldom face single stress in the natural environment. Indeed, heat and drought or drought and salinity are documented as very obvious combinations suggesting multiple stress tolerance as an important breeding target. Forward and reverse genetic tools could effectively contribute towards achieving the target food production to feed the future population despite limiting resources and unfavorable climatic conditions. Genetic approaches adopted for crop improvement programs categorized as forward and reverse genetics are discussed highlighting their potential benefits for tailoring stress tolerant cultivars.

Reinventing postgraduate training in the plant sciences: T-training defined through modularity, customization, and distributed mentorship.

The Plant Science Research Network (PSRN) comprises scientific societies and organizations with a mission to build and communicate a consensus vision of the future of plant science research, education, and training. This report enumerates a set of far‐reaching recommendations for postgraduate training that emerged from workshops held in October 2016 and September 2017. These recommendations broaden and deepen the T‐training concept presented in the Decadal Vision for Plant Science, which emphasizes experiential learning beyond the traditional disciplinary focus. Both workshops used the scenarios developed in Imagining Science in 2035 as a mechanism to encourage out‐of‐the‐box thinking, an approach that led to the innovative recommendations and solutions described here. At the heart of our recommendations is the empowerment of trainees, who should be enabled to customize and take ownership of their training experiences. This fundamental concept is embodied in five principles: (a) Trainees should be provided guidance and resources needed to define and pursue career objectives within and beyond academia, conferring to them greater independence and responsibility in shaping their own future. (b) Learning should be flexible, adaptable, and distributed. Training should combine traditional and modular coursework to encompass both technical and professional skills. Guidance from diverse mentoring teams will support and tailor training toward diverse, personalized career paths. (c) Scientific research experiences should be broad and question‐driven, whether motivated by basic discovery or seeking solutions to societal challenges. Trainees should continue to gain mastery of one or a few core scientific disciplines and their key tools and approaches. (d) Trainees should be skilled in science communication and incentivized to engage with and learn from the broader public community, helping to maintain an active dialogue among public, private, and academic sectors. (e) Training programs should foster and facilitate the inclusion of individuals with a diverse range of life experiences and should prioritize trainee well‐being. The report recommendations call for a profound cultural shift, one that embraces and extends educational delivery trends toward self‐learning and distance learning, considers trainee well‐being as an essential requirement for success, and acknowledges the importance of effective two‐way communication with the public. This shift is intended to broaden participation in the plant science workforce, both in terms of diversity and numbers, while maintaining excellence in core scientific training. Cultural change takes time, but among academic institutions the need for significant change and innovation in postgraduate training is increasingly pressing. As such, the immediate intent is for these recommendations to catalyze pilot programs and also build on emergent prototypes that exist globally while creating momentum for larger scale changes over longer time periods.