Aspects Of Plant Science Research Articles

A primer on artificial intelligence in plant digital phenomics: embarking on the data to insights journey.

Artificial intelligence (AI) has emerged as a fundamental component of global agricultural research that is poised to impact on many aspects of plant science. In digital phenomics, AI is capable of learning intricate structure and patterns in large datasets. We provide a perspective and primer on AI applications to phenome research. We propose a novel human-centric explainable AI (X-AI) system architecture consisting of data architecture, technology infrastructure, and AI architecture design. We clarify the difference between post hoc models and 'interpretable by design' models. We include guidance for effectively using an interpretable by design model in phenomic analysis. We also provide directions to sources of tools and resources for making data analytics increasingly accessible. This primer is accompanied by an interactive online tutorial.

Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics.

RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.

Forensic botany: time to embrace natural history collections, large scale environmental data and environmental DNA

Forensic botany is a diverse discipline that spans many aspects of plant sciences, particularly taxonomy, field botany, anatomy, and ecology. Internationally, there is a significant opportunity to expand the application of forensic botany in criminal investigations, especially war crimes, genocide, homicide, sexual violence, serious physical assault, illegal trade in endangered species and wildlife crime. In civil proceedings, forensic botany may, for example, be called upon in trade disputes such as accidental contamination of commodities. Despite the potential, there are barriers to the wider application of forensic botany in criminal cases; there is a widespread need to improve the efficiency of botanical trace evidence identification. This could partly be addressed by embracing innovations in image recognition and by accessing the huge quantity of specimens and images housed in natural history collections worldwide. Additionally, the recent advances in DNA sequencing technologies and the expansion of environmental DNA (eDNA) and forensic ecogenomics, offers opportunities to more rapidly provide species-level identifications. The impact of taphonomic processes upon vegetation, and vice versa, remains poorly understood; improved understanding of these interactions and their ecological impacts may be invaluable in improving clandestine burial search protocols.

Real-time detection of wound-induced H2O2 signalling waves in plants with optical nanosensors.

Decoding wound signalling in plants is critical for understanding various aspects of plant sciences, from pest resistance to secondary metabolite and phytohormone biosynthesis. The plant defence responses are known to primarily involve NADPH-oxidase-mediated H2O2 and Ca2+ signalling pathways, which propagate across long distances through the plant vasculature and tissues. Using non-destructive optical nanosensors, we find that the H2O2 concentration profile post-wounding follows a logistic waveform for six plant species: lettuce (Lactuca sativa), arugula (Eruca sativa), spinach (Spinacia oleracea), strawberry blite (Blitum capitatum), sorrel (Rumex acetosa) and Arabidopsis thaliana, ranked in order of wave speed from 0.44 to 3.10 cm min-1. The H2O2 wave tracks the concomitant surface potential wave measured electrochemically. We show that the plant RbohD glutamate-receptor-like channels (GLR3.3 and GLR3.6) are all critical to the propagation of the wound-induced H2O2 wave. Our findings highlight the utility of a new type of nanosensor probe that is species-independent and capable of real-time, spatial and temporal biochemical measurements in plants.

Light Gradient-Based Screening of Arabidopsis thaliana on a 384-Well Type Plant Array Chip.

Arabidopsis thaliana (Arabidopsis), as a model for plant research, is widely used for various aspects of plant science. To provide a more sophisticated and microscopic environment for the germination and growth of Arabidopsis, we report a 384-well type plant array chip in which each Arabidopsis seed is independently seeded in a solid medium. The plant array chip is made of a poly(methyl methacrylate) (PMMA) acrylic material and is assembled with a home-made light gradient module to investigate the light effects that significantly affect the germination and growth of Arabidopsis. The light gradient module was used to observe the growth pattern of seedlings according to the intensity of the white light and to efficiently screen for the influence of the white light. To investigate the response to red light (600 nm), which stimulates seed germination, the light gradient module was also applied to the germination test. As a result, the germination results showed that the plant array chip can be used to simultaneously screen wild type seeds and phytochrome B mutant seeds on a single array chip according to the eight red light intensities.

Mechanical properties of Polygonatum multiflorum leaves after treatment with growth stimulants

The mechanical properties of leaves are important in many aspects of plant science. Because of their delicate structure, leaves are sensitive to different, potentially harmful, environmental factors. The mechanical properties of leaves are important factors affecting leaf quality, longevity, susceptibility to damage, and decomposition. Two growth stimulants were applied to investigate selected mechanical properties of Solomon’s seal Variegatum [Polygonatum multiflorum (L.) All.] leaves grown under field cultivation and in an unheated polytunnel. The mechanical properties of leaves were assessed by measuring Young’s modulus. The agents used in the treatment were Actisil Hydro Plus at a concentration of 0.4% in the first series and Pentakeep V at a concentration of 0.04% in the second series. Foliar treatment with the stimulants was conducted six times at weekly intervals. The control plots were sprayed with distilled water. The research was carried out between 2012 and 2014. In comparison to the test series, the respective effects of Actisil Hydro Plus and Pentakeep V on the change in Young’s modulus was more notable in plant leaves obtained from the tunnel than those from field cultivation. Specifically, growth stimulants had more impact on the stiffness of leaves obtained from plants grown in the tunnel. Generally, plant leaves from field cultivation were stiffer than those from the tunnel.

Evaluation of Using Eicosapentaenoic Acid in Plant Tissue Culture Media

Biotechnology is name given to the methods and techniques that involve the use of living organisms like bacteria, yeast, plant cells or their parts or products as tools. Plant tissue culture techniques are essential to many types of academic inquiry, as well as to many applied aspects of plant science. Plant tissue culture techniques are also central to innovative areas of applied plant science, including plant biotechnology and agriculture. The omega-3 fatty acids are "essential" fatty acids because they are vital for normal metabolism and cannot be synthesized by the human body. Eicosapentaenoic acid is an omega-3 fatty acid. With this research we obtain the strong plants with benefits of Omega-3 fatty acids.

A New Year in plant science

The New Year is an interesting watershed in any aspect of life, offering the opportunity to revisit the achievements of the previous year and to consider plans for the year ahead. For New Phytologist, 2007 was our busiest year ever in terms of manuscript submissions, with a 20% increase being recorded compared with the previous year. However, our service to the authors remains undiminished, with an average time-period of only 28 d from receipt of a manuscript to the first decision from the Editor. The combination of speed, efficiency and accuracy in dealing with submissions is the result of a large team, all of whom are thanked profusely. The team consists of an Editorial Board of 21 Editors, the Central Office with five staff, 69 Advisors to the board and more than 1200 Referees who reviewed manuscripts in 2007 – a total of 1295 devoted to publishing quality plant science research. What might come the way of New Phytologist in this New Year? We have relied on the opinions of the Editorial Board for a glimpse of a future with new and emerging opportunities in plant science research. Although the interests and expertise of the board are very broad, there was a rather widespread view that very large data sets of biological information will increasingly underpin new synthetic and systems understanding. The most obvious area is in molecular plant science, where high-throughput technologies and reducing costs for DNA sequencing, for a wide range of plant and fungal species, provide the underpinning for insight into how plants work, from the cell to the whole organism. Genomic data are increasingly complemented by other ‘omic’ approaches, such as transcriptomics, proteomics and metabolomics. These data sets also create a problem in terms of accumulating, managing and interpreting them. However, they also provide completely new opportunities for understanding how interacting networks work and respond, not only to environmental challenges but in major processes that are poorly understood, such as developmental epigenetics and plant signalling. The level of genetic and molecular detail varies considerably, with some model species, such as Arabidopsis thaliana, particularly well quantified. However, association genetic approaches offer a means for identification of the genes that cause adaptive variation, even in virtually wild taxa such as Pinus. Although it is clear that the large majority of genes are common in their basic functions between widely different species, it may not be the case that the same phenotypic functions emerge. Interactions between plants and other organisms, such as in mycorrhizal associations, but also with fungal endophytes and insects, are important but difficult to study; here again the data provided by mass-sequencing technologies will provide novel catalogues of processes occurring within and between organisms and in response to the environment. This rapidly growing field of ecosystem-level, multi-organism genomics has been termed ‘metagenomics’. Progressing from sequence collections to whole-system understanding uses new tools of bioinformatics, mathematical statistics and simulation modelling. This development is a feature of many aspects of plant science, not just genomics. In ecosystem studies the increased resolution and measurement of organismal activity, in both time and space, indicates a complex array of responses. Just like the equivalent in accumulating molecular sequences, this new proliferation of data results from new technologies, and just like the molecular area it still remains to be determined how this complexity of responses determines the response of the ecosystem, as a whole, to environmental changes. It is notable that new understanding in plant physiology, in particular the controls of photosynthetic carbon dioxide exchange, is now quite central to parallel fields of research such as hydrology, meteorology and atmospheric chemistry, yet this was very rare, even over a decade ago. So we see another exciting year ahead with a whole suite of emerging opportunities providing a new raft of papers to further the development of plant science. We look forward to seeing them in New Phytologist.

Commentary on Pereira's review

Transgenic crops are very much in the news due to the increasing public debate on their acceptance. In the scientific community though, transgenic plants are proving to be powerful tools to study various aspects of plant sciences. The emerging scientific revolution sparked by genomics based technologies is producing enormous amounts of DNA sequence information that, together with plant transformation methodology, is opening up new experimental opportunities for functional genomics analysis. An overview is provided here on the use of transgenic technology for the functional analysis of plant genes in model plants and a link made to their utilization in transgenic crops. In transgenic plants, insertional mutagenesis using heterologous maize transposons or Agrobacterium mediated T-DNA insertions, have been valuable tools for the identification and isolation of genes that display a mutant phenotype. To discover functions of genes that do not display phenotypes when mutated, insertion sequences have been engineered to monitor or change the expression pattern of adjacent genes. These gene detector insertions can detect adjacent promoters, enhancers or gene exons and precisely reflect the expression pattern of the tagged gene. Activation tag insertions can mis-express the adjacent gene and confer dominant phenotypes that help bridge the phenotype gap. Employment of various forms of gene silencing technology broadens the scope of recovering knockout phenotypes for genes with redundant function. All these transgenic strategies describing gene-phenotype relationships can be addressed by high throughput reverse genetics methods that will help provide functions to the genes discovered by genome sequencing. The gene functions discovered by insertional mutagenesis and silencing strategies along with expression pattern analysis will provide an integrated functional genomics perspective and offer unique applications in transgenic crops.

A transgenic perspective on plant functional genomics.

Transgenic crops are very much in the news due to the increasing public debate on their acceptance. In the scientific community though, transgenic plants are proving to be powerful tools to study various aspects of plant sciences. The emerging scientific revolution sparked by genomics based technologies is producing enormous amounts of DNA sequence information that, together with plant transformation methodology, is opening up new experimental opportunities for functional genomics analysis. An overview is provided here on the use of transgenic technology for the functional analysis of plant genes in model plants and a link made to their utilization in transgenic crops. In transgenic plants, insertional mutagenesis using heterologous maize transposons or Agrobacterium mediated T-DNA insertions, have been valuable tools for the identification and isolation of genes that display a mutant phenotype. To discover functions of genes that do not display phenotypes when mutated, insertion sequences have been engineered to monitor or change the expression pattern of adjacent genes. These gene detector insertions can detect adjacent promoters, enhancers or gene exons and precisely reflect the expression pattern of the tagged gene. Activation tag insertions can mis-express the adjacent gene and confer dominant phenotypes that help bridge the phenotype gap. Employment of various forms of gene silencing technology broadens the scope of recovering knockout phenotypes for genes with redundant function. All these transgenic strategies describing gene-phenotype relationships can be addressed by high throughput reverse genetics methods that will help provide functions to the genes discovered by genome sequencing. The gene functions discovered by insertional mutagenesis and silencing strategies along with expression pattern analysis will provide an integrated functional genomics perspective and offer unique applications in transgenic crops.

Plant Molecular Biology in Mexico

OverviewPlant molecular biology researchin Mexico is concentratedin two insti-tutions: CINVESTAV (Center for Research and Advanced Studies) andUNAM (Mexico’s National University). Plant biology research at CIN-VESTAV is carried out at its Irapuato Unit. The primary UNAM groupsare located at Cuernavaca (Biotechnology Institute, Nitrogen FixationResearchCenter) andMexicoCity (Facultadde Qu´imica). Other institu-tions that carry outplant biologyresearchincludetheCenter of Scientif-ic Research of Yucatan (CICY), University of Michoacan, Postgraduate´College, and CIMMYT. The state universities of Aguascalientes andPuebla are currently establishing research groups in plant biology. Sim-ilarly, the National Institute for Research in Agronomy, Forestry andLivestock (INIFAP) is creating a biotechnology group. With the excep-tion ofCIMMYT andINIFAP, allinstitutions offergraduateprogramsinthe different aspects of plant sciences. A brief description of represent-ative research lines in the two main centers of plant molecular biologyis as follows:CINVESTAVIrapuato UnitThe Irapuato Unit of CINVESTAV was created in 1981 to carry outresearch in plant biotechnology. However, the work actually started

Aspects of Plant Sciences, Volume 3. Pteridophytes

Aspects of Plant Sciences, Volume 3. Pteridophytes