Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants

Abstract Crassulacean acid metabolism (CAM) photosynthesis is an important biological innovation enabling plant adaptation to hot and dry environments. CAM plants feature high water-use efficiency, with potential for sustainable crop production under water-limited conditions. A deep understanding of CAM-related gene function and molecular evolution of CAM plants is critical for exploiting the potential of engineering CAM into C3 crops to enhance crop production on semi-arid or marginal agricultural lands. With the newly emerging genomics resources for multiple CAM species, progress has been made in comparative genomics studies on the molecular basis and subsequently on the evolution of CAM. Here, recent advances in CAM comparative genomics research in constitutive and facultative CAM plants are reviewed, with a focus on the analyses of DNA/protein sequences and gene expression to provide new insights into the path and driving force of CAM evolution and to identify candidate genes involved in CAM-related biological processes. Potential applications of new computational and experimental technologies (e.g. CRISPR/Cas-mediated genome-editing technology) to the comparative and evolutionary genomics research on CAM plants are offered.

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Potential applications of biogenic selenium nanoparticles in alleviating biotic and abiotic stresses in plants: A comprehensive insight on the mechanistic approach and future perspectives

Green Processing and Synthesis ◽

10.1515/gps-2021-0047 ◽

2021 ◽

Vol 10 (1) ◽

pp. 456-475

Author(s):

Efat Zohra ◽

Muhammad Ikram ◽

Ahmad A. Omar ◽

Mujahid Hussain ◽

Seema Hassan Satti ◽

...

Keyword(s):

Abiotic Stresses ◽

Crop Production ◽

Plant Secondary Metabolites ◽

Selenium Nanoparticles ◽

Future Research ◽

Biotic And Abiotic Stresses ◽

Biotic Stresses ◽

Agriculture Sector ◽

Developmental Growth ◽

Potential Applications

Abstract In the present era, due to the increasing incidence of environmental stresses worldwide, the developmental growth and production of agriculture crops may be restrained. Selenium nanoparticles (SeNPs) have precedence over other nanoparticles because of the significant role of selenium in activating the defense system of plants. In addition to beneficial microorganisms, the use of biogenic SeNPs is known as an environmentally friendly and ecologically biocompatible approach to enhance crop production by alleviating biotic and abiotic stresses. This review provides the latest development in the green synthesis of SeNPs by using the results of plant secondary metabolites in the biogenesis of nanoparticles of different shapes and sizes with unique morphologies. Unfortunately, green synthesized SeNPs failed to achieve significant attention in the agriculture sector. However, research studies were performed to explore the application potential of plant-based SeNPs in alleviating drought, salinity, heavy metal, heat stresses, and bacterial and fungal diseases in plants. This review also explains the mechanistic actions that the biogenic SeNPs acquire to alleviate biotic and abiotic stresses in plants. In this review article, the future research that needs to use plant-mediated SeNPs under the conditions of abiotic and biotic stresses are also highlighted.

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Evolutionary Analyses of Protein Interaction Networks

Biological Data Mining in Protein Interaction Networks ◽

10.4018/978-1-60566-398-2.ch010 ◽

2009 ◽

pp. 169-181 ◽

Cited By ~ 2

Author(s):

Takashi Makino ◽

Aoife McLysaght

Keyword(s):

Molecular Evolution ◽

Comparative Genomics ◽

Protein Interaction ◽

Protein Interaction Networks ◽

Evolutionary Rates ◽

Interaction Networks ◽

Evolutionary Mechanisms ◽

Ancestral Gene ◽

Protein Protein Interaction ◽

A Genome

This chapter introduces evolutionary analyses of protein interaction networks and of proteins as components of the networks. The authors show relationships between proteins in the networks and their evolutionary rates. For understanding protein-protein interaction (PPI) divergence, duplicated genes are often compared because they are derived from a common ancestral gene. In order to reveal evolutionary mechanisms acting on the interactome it is necessary to compare PPIs across species. Investigation of co-localization of interacting genes in a genome shows that PPIs have an important role in the maintenance of a physical link between neighboring genes. The purpose of this chapter is to introduce methodologies for analyzing PPI data and to describe molecular evolution and comparative genomics insights gained from such studies.

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Current Land Use in the Poplar Box (Eucalyptus Populnea) Lands.

The Rangeland Journal ◽

10.1071/rj9800031 ◽

1980 ◽

Vol 2 (1) ◽

pp. 31 ◽

Cited By ~ 2

Author(s):

EJ Weston ◽

DF Thompson ◽

BJ Scott

Keyword(s):

Land Use ◽

Native Species ◽

Crop Production ◽

New South ◽

New South Wales ◽

High Water ◽

Grazing Pressure ◽

Small Areas ◽

South Wales ◽

Domestic Livestock

Poplar box (Eucalyptus populnee) woodlands mainly occuron duplex, clay and red earth soils between the 300 mm and 750 mm rainfall isohyets. The poplar box lands have been occupied for from 100 to 150 years and have been modified extensively through tree felling, ringbarking, clearing, cultivation, burning and grazing by domestic livestock. The current land use is described for six vegetation groups which together comprise the poplar box lands. The eastern areas of the poplar box lands are mainly used for intensive agriculture based on wheat. barley and grain sorghum, with small areas sown to c~ops of high water demand. Mixed farming involves dairying (in Queensland) and fat lambs (in New South Wales) and broad-acre cereal and fodder cropping. Sheep and cattle grazing replace intensive crop production as the rainfall decreases. In all areas used for cropping the stability and fertility of the soil are of paramount importance in maintainihg production. The use of woodlands in areas of lower rainfall can lead to deterioration of the resource and to the encroachment of woody native species into the grazing lands. Because cropping is unreliable the opportunity to use cultivation to control woody regrowth is reduced. In central areas much of the land can be sown to improved pastures, but in western areas diversification is limited by the low rainfall and land use is restricted to grazing, initially only by sheep but now by sheep and cattle. Particularly in western New South Wales the increase in unpalatable shrubs and the decrease in available forage has resulted in low stocking rates, and high grazing pressure, making reclamation and pasture improvement difficult. In consequence many enterprises are becoming uneconomic.

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Editorial for the Special Issue “Estimation of Crop Phenotyping Traits using Unmanned Ground Vehicle and Unmanned Aerial Vehicle Imagery”

Remote Sensing ◽

10.3390/rs12060940 ◽

2020 ◽

Vol 12 (6) ◽

pp. 940 ◽

Cited By ~ 1

Author(s):

Xiuliang Jin ◽

Zhenhai Li ◽

Clement Atzberger

Keyword(s):

Unmanned Aerial Vehicle ◽

Crop Production ◽

Unmanned Ground Vehicle ◽

Special Issue ◽

Climate Conditions ◽

Ground Vehicle ◽

Global Food Security ◽

3D Data ◽

Potential Applications ◽

Aerial Vehicle

High-throughput crop phenotyping is harnessing the potential of genomic resources for the genetic improvement of crop production under changing climate conditions. As global food security is not yet assured, crop phenotyping has received increased attention during the past decade. This spectral issue (SI) collects 30 papers reporting research on estimation of crop phenotyping traits using unmanned ground vehicle (UGV) and unmanned aerial vehicle (UAV) imagery. Such platforms were previously not widely available. The special issue includes papers presenting recent advances in the field, with 22 UAV-based papers and 12 UGV-based articles. The special issue covers 16 RGB sensor papers, 11 papers on multi-spectral imagery, and further 4 papers on hyperspectral and 3D data acquisition systems. A total of 13 plants’ phenotyping traits, including morphological, structural, and biochemical traits are covered. Twenty different data processing and machine learning methods are presented. In this way, the special issue provides a good overview regarding potential applications of the platforms and sensors, to timely provide crop phenotyping traits in a cost-efficient and objective manner. With the fast development of sensors technology and image processing algorithms, we expect that the estimation of crop phenotyping traits supporting crop breeding scientists will gain even more attention in the future.

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Vertically Aligned Carbon Nanotube Membranes: Water Purification and Beyond

Membranes ◽

10.3390/membranes10100273 ◽

2020 ◽

Vol 10 (10) ◽

pp. 273

Author(s):

Jeong Hoon Lee ◽

Han-Shin Kim ◽

Eun-Tae Yun ◽

So-Young Ham ◽

Jeong-Hoon Park ◽

...

Keyword(s):

Carbon Nanotube ◽

Water Purification ◽

Water Permeability ◽

Proton Exchange Membrane ◽

Antibacterial Properties ◽

High Water ◽

Proton Exchange ◽

Conductive Membranes ◽

Potential Applications ◽

Vertically Aligned

Vertically aligned carbon nanotube (VACNT) membranes have attracted significant attention for water purification owing to their ultra-high water permeability and antibacterial properties. In this paper, we critically review the recent progresses in the synthesis of VACNT arrays and fabrication of VACNT membrane methods, with particular emphasis on improving water permeability and anti-biofouling properties. Furthermore, potential applications of VACNT membranes other than water purification (e.g., conductive membranes, electrodes in proton exchange membrane fuel cells, and solar electricity–water generators) have been introduced. Finally, future outlooks are provided to overcome the limitations of commercialization and desalination currently faced by VACNT membranes. This review will be useful to researchers in the broader scientific community as it discusses current and new trends regarding the development of VACNT membranes as well as their potential applications.

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Agricultural infrastructure: the forgotten key driving force on crop-related water footprints and virtual water flows in developing countries: a case for China

10.5194/egusphere-egu2020-3366 ◽

2020 ◽

Author(s):

Hongrong Huang ◽

La Zhuo ◽

Pute Wu

Keyword(s):

Developing Countries ◽

Water Consumption ◽

Environmental Sustainability ◽

Crop Production ◽

Water Footprint ◽

Water Productivity ◽

Virtual Water ◽

High Water ◽

North Coast ◽

Water Flows

<p>Agricultural infrastructure plays important roles in boosting food production and trade system in developing countries, while as being a &#8216;grey solutions&#8217;, generates increasingly risks on the environmental sustainability. There is little information on impacts of agricultural infrastructure developments on water consumption and flows, (i.e. water footprint and virtual water flows) related to crop production, consumption and trade especially in developing countries with high water risk. Here we, taking mainland China over 2000-2017 as the study case, identified and evaluated the strengths and spatial heterogeneities in main socio-economic driving factors of provincial water footprints and inter-provincial virtual water flows related to three staple crops (rice, wheat and maize). For the first time, we consider irrigation (II), electricity (EI) and road infrastructures (RI) in the driving factor analysis through the extended STIRPAT (stochastic impacts by regression on population, affluence and technology) model. Results show that the II, EI and RI in China were expanded by 33.8 times, 4.5 times and 2.4 times, respectively by year 2017 compared to 2000. Although the II was the most critical driver to effectively reduce the per unit water footprint, especially the blue water footprint in crop production (i.e., increasing water efficiency), the developments of II led to the bigger total water consumption. Such phenomenon was observed in Jing-Jin region, North Coast and Northwest China with water resource shortage. The EI and RI had increasing effects on provincial virtual water export, and the corresponding driving strengths varied across spaces. Obviously, the visible effects from the agricultural infrastructures on regional water consumption, water productivity and virtual water patterns cannot be neglected.&#160;</p>

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DRAINAGE OF AN IRRIGATED SALINE SOIL IN ALBERTA

Canadian Journal of Soil Science ◽

10.4141/cjss82-042 ◽

1982 ◽

Vol 62 (2) ◽

pp. 387-396

Author(s):

D. R. BENNETT ◽

G. R. WEBSTER ◽

B. A. PATERSON ◽

D. B. HARKER

Keyword(s):

Water Table ◽

Crop Production ◽

Saline Soil ◽

Soil Depth ◽

Drainage System ◽

High Water ◽

Coarse Sand ◽

Irrigation Period ◽

Dilution Effects ◽

Sand And Gravel

A shallow subsurface drainage system effectively controlled a high water table and reduced salinity in an irrigated soil near Magrath, Alberta. Plastic corrugated tubing was installed in 1976 at depths of 1.1–1.5 m and spacings of 15 and 30 m in a moderately saline soil. During the irrigation period, the water table rose to within 0.3 m of the surface but was lowered to pre-irrigation levels within 48 h. The water table was maintained at, or below, the depth of the drains between irrigations. The 15- and 30-m spacings of the drain lines were equally effective in providing water table control in this lacustrine soil which was underlain by a coarse sand and gravel layer. Salinity levels were decreased substantially only within the surface 0.3-m soil depth. Quality of the drainage effluent remained constant throughout the growing season with only small dilution effects detected during irrigations. Barley yields increased to 3900 kg/ha in 1978, 2 yr following drainage of this saline soil which had been out of crop production for 20 yr.

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PlantRep: a resource of plant repeats

10.21203/rs.3.rs-498874/v1 ◽

2021 ◽

Author(s):

Yu Zhang ◽

Xizhi Luo ◽

Shiyu Chen

Keyword(s):

Comparative Genomics ◽

Taxonomic Group ◽

Repeat Elements ◽

Plant Genomes ◽

Repeat Sequences ◽

Free Resource ◽

Genomics Research

Abstract We re-annotated repeats sequence of 459 plant genomes and release a new resource of plant repeats: PlantRep (http://www.plantrep.cn/). We compared the structural and evolutionary characteristics of repeat sequences in different plant taxonomic group. The contribution of repeat sequences to the genes was examined systematically. PlantRep sheds lights of evolution of plant repeats and provides a free-resource for deep annotation of genome and comparative genomics research of repeat elements in plants.

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A roadmap for gene functional characterisation in wheat

10.7287/peerj.preprints.26877v2 ◽

2019 ◽

Author(s):

Nikolai M Adamski ◽

Philippa Borrill ◽

Jemima Brinton ◽

Sophie Harrington ◽

Clemence Marchal ◽

...

Keyword(s):

Gene Function ◽

Gene Networks ◽

Crop Production ◽

Crop Improvement ◽

Basic Research ◽

Reference Sequence ◽

Background Information ◽

World Population ◽

Putative Gene ◽

Functional Characterisation

To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind, a lack of genomic information and resources has hindered the functional characterisation of genes in this species. The recent release of a high-quality reference sequence for wheat underpins a suite of genetic and genomic resources that support basic research and breeding. These include accurate gene model annotations, gene expression atlases and gene networks that provide background information about putative gene function. In parallel, sequenced mutation populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources to study gene function in wheat and thereby accelerate improvement in this important crop. We hope that this review provides a helpful guide for plant scientists, especially those expanding into wheat research for the first time, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of wheat, a complex polyploid crop, of vital importance for food and nutrition security.

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Evaluation of Water Scarcity in Selected Countries of the Middle East

Water ◽

10.3390/w10101482 ◽

2018 ◽

Vol 10 (10) ◽

pp. 1482 ◽

Cited By ~ 5

Author(s):

Petr Procházka ◽

Vladimír Hönig ◽

Mansoor Maitah ◽

Ivana Pljučarská ◽

Jakub Kleindienst

Keyword(s):

Saudi Arabia ◽

Middle East ◽

Water Scarcity ◽

Agricultural Production ◽

Crop Production ◽

Agricultural Sector ◽

Supply And Demand ◽

High Water ◽

Economic Effects ◽

The Impact

The primary goal of this article is to evaluate water scarcity in selected countries of the Middle-East and assess the impact on agricultural production. To begin with, the Weighted Anomaly Standardized Precipitation (WASP) Index from 1979 to 2017 was spatially computed for Iran, Iraq and Saudi Arabia. In order to demonstrate the effect of reduced levels of water, the water shortage situation in cities with the population higher than one million was examined. This was accomplished by utilizing the Composite Index approach to make water related statistics more intelligible. A projection for the years of 2020 to 2030 was created in order to demonstrate possible changes in the supply and demand for water in selected countries of the Middle-East. In regards to evaluating the economic effects of water shortages on agricultural sector, effects of lower precipitation on agricultural production in Iran, Iraq and Saudi Arabia were estimated. With ever-increasing urbanization, all countries are currently experiencing a moderate to high water risk. Our research points to excessively high water stress for most analyzed cities through the year 2030. Also, it is demonstrated how much precipitation decreases influence agricultural production in Iran, Iraq and Saudi Arabia. From the analyzed countries, some evidence is found that precipitation negatively influences crop production, primarily for Iran.

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