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1.	Abedi, Tayebeh (author) Arsenic Uptake and Accumulation Mechanisms in Rice Species 2020 In: Plants. - : MDPI AG. - 2223-7747. ; 9 Research review (peer-reviewed)abstract Rice consumption is a source of arsenic (As) exposure, which poses serious health risks. In this study, the accumulation of As in rice was studied. Research shows that As accumulation in rice in Taiwan and Bangladesh is higher than that in other countries. In addition, the critical factors influencing the uptake of As into rice crops are defined. Furthermore, determining the feasibility of using effective ways to reduce the accumulation of As in rice was studied. AsV and AsIII are transported to the root through phosphate transporters and nodulin 26-like intrinsic channels. The silicic acid transporter may have a vital role in the entry of methylated As, dimethylarsinic acid (DMA) and monomethylarsonic acid (MMA), into the root. Amongst As species, DMA(V) is particularly mobile in plants and can easily transfer from root to shoot. The OsPTR7 gene has a key role in moving DMA in the xylem or phloem. Soil properties can affect the uptake of As by plants. An increase in organic matter and in the concentrations of sulphur, iron, and manganese reduces the uptake of As by plants. Amongst the agronomic strategies in diminishing the uptake and accumulation of As in rice, using microalgae and bacteria is the most efficient.
2.	Abedi, Tayebeh (author) Cadmium Uptake by Wheat (Triticum aestivum L.): An Overview 2020 In: Plants. - : MDPI AG. - 2223-7747. ; 9 Research review (peer-reviewed)abstract Cadmium is a toxic heavy metal that may be detected in soils and plants. Wheat, as a food consumed by 60% of the world's population, may uptake a high quantity of Cd through its roots and translocate Cd to the shoots and grains thus posing risks to human health. Therefore, we tried to explore the journey of Cd in wheat via a review of several papers. Cadmium may reach the root cells by some transporters (such as zinc-regulated transporter/iron-regulated transporter-like protein, low-a ffinity calcium transporters, and natural resistance-associated macrophages), and some cation channels or Cd chelates via yellow stripe 1-like proteins. In addition, some of the effective factors regarding Cd uptake into wheat, such as pH, organic matter, cation exchange capacity (CEC), Fe and Mn oxide content, and soil texture (clay content), were investigated in this paper. Increasing Fe and Mn oxide content and clay minerals may decrease the Cd uptake by plants, whereas reducing pH and CEC may increase it. In addition, the feasibility of methods to diminish Cd accumulation in wheat was studied. Amongst agronomic approaches for decreasing the uptake of Cd by wheat, using organic amendments is most effective. Using biochar might reduce the Cd accumulation in wheat grains by up to 97.8%.
3.	Ahmed, Mukhtar (author) Agro-Morphological, Yield and Quality Traits and Interrelationship with Yield Stability in Quinoa (Chenopodium quinoa Willd.) Genotypes under Saline Marginal Environment 2020 In: Plants. - : MDPI AG. - 2223-7747. ; 9 Journal article (peer-reviewed)abstract Quinoa (Chenopodium quinoa Willd.) is a halophytic crop that shows resistance to multiple abiotic stresses, including salinity. In this study we investigated the salinity tolerance mechanisms of six contrasting quinoa cultivars belonging to the coastal region of Chile using agro-physiological parameters (plant height (PH), number of branches/plant (BN), number of panicles/plant (PN), panicle length (PL), biochemical traits (leaf C%, leaf N%, grain protein contents); harvest index and yield (seed yield and plant dry biomass (PDM) under three salinity levels (0, 10, and 20 d Sm-1 NaCl). The yield stability was evaluated through comparision of seed yield characteristics [(static environmental variance (S-2) and dynamic Wricke's ecovalence (W-2)]. Results showed that significant variations existed in agro-morphological and yield attributes. With increasing salinity levels, yield contributing parameters (number of panicles and panicle length) decreased. Salt stress reduced the leaf carbon and nitrogen contents. Genotypes Q21, and AMES13761 showed higher seed yield (2.30 t ha(-1)), more productivity and stability at various salinities as compared to the other genotypes. Salinity reduced seed yield to 44.48% and 60% at lower (10 dS m(-1)) and higher salinity (20 dS m(-1)), respectively. Grain protein content was highest in NSL106398 and lowest in Q29 when treated with saline water. Seed yield was positively correlated with PH, TB, HI, and C%. Significant and negative correlations were observed between N%, protein contents and seed yield. PH showed significant positive correlation with APL, HI, C% and C:N ratio. HI displayed positive correlations with C%, N% and protein content., All measured plant traits, except for C:N ratio, responded to salt in a genotype-specific way. Our results indicate that the genotypes (Q21 and AMES13761) proved their suitability under sandy desert soils of Dubai, UAE as they exhibited higher seed yield while NSL106398 showed an higher seed protein content. The present research highlights the need to preserve quinoa biodiversity for a better seedling establishment, survival and stable yield in the sandy desertic UAE environment.
4.	Ahmed, Mukhtar (author) Effect of Cadmium Toxicity on Growth, Oxidative Damage, Antioxidant Defense System and Cadmium Accumulation in Two Sorghum Cultivars 2020 In: Plants. - : MDPI AG. - 2223-7747. ; 9 Journal article (peer-reviewed)abstract Heavy metal stress is a leading environmental issue reducing crop growth and productivity, particularly in arid and semi-arid agro-ecological zones. Cadmium (Cd), a non-redox heavy metal, can indirectly increase the production of reactive oxygen species (ROS), inducing cell death. A pot experiment was conducted to investigate the effects of different concentrations of Cd (0, 5, 25, 50, 100 mu M) on physiological and biochemical parameters in two sorghum (Sorghum bicolor L.) cultivars: JS-2002 and Chakwal Sorghum. The results showed that various concentrations of Cd significantly increased the Cd uptake in both cultivars; however, the uptake was higher in JS-2002 compared to Chakwal Sorghum in leaf, stem and root. Regardless of the cultivars, there was a higher accumulation of the Cd in roots than in shoots. The Cd stress significantly reduced the growth and increased the electrolyte leakage (EL), hydrogen peroxide (H2O2) concentration and malondialdehyde (MDA) content in both cultivars, but the Chakwal Sorghum showed more pronounced oxidative damage than the JS-2002, as reflected by higher H2O2, MDA and EL. Moreover, Cd stress, particularly 50 mu M and 100 mu M, decreased the activity of different antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). However, the JS-2002 exhibited higher SOD, POD and CAT activities than the Chakwal Sorghum under different Cd-levels. These findings revealed that JS-2002 had a stronger Cd enrichment capacity and also exhibited a better tolerance to Cd stress due to its efficient antioxidant defense system than Chakwal Sorghum. The present study provides the available information about Cd enrichment and tolerance in S. bicolor, which is used as an important agricultural crop for livestock feed in arid and semi-arid regions.
5.	Ahmed, Mukhtar (author) Evaluation of Physiological and Morphological Traits for Improving Spring Wheat Adaptation to Terminal Heat Stress 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract Wheat crop experiences high temperature stress during flowering and grain-filling stages, which is termed as "terminal heat stress". Characterizing genotypes for adaptive traits could increase their selection for better performance under terminal heat stress. The present study evaluated the morpho-physiological traits of two spring wheat cultivars (Millet-11, Punjab-11) and two advanced lines (V-07096, V-10110) exposed to terminal heat stress under late sowing. Early maturing Millet-11 was used as heat-tolerant control. Late sowing reduced spike length (13%), number of grains per spike (10%), 1000-grain weight (13%) and biological yield (15-20%) compared to timely sowing. Nonetheless, higher number of productive tillers per plant (19-20%) and grain yield (9%) were recorded under late sowing. Advanced lines and genotype Punjab-11 had delayed maturity and better agronomic performance than early maturing heat-tolerant Millet-11. Advanced lines expressed reduced canopy temperature during grain filling and high leaf chlorophyll a (20%) and b (71-125%) contents during anthesis under late sowing. All wheat genotypes expressed improved stem water-soluble carbohydrates under terminal heat stress that were highest for heat-tolerant Millet-11 genotype during anthesis. Improved grain yield was associated with the highest chlorophyll contents showing stay green characteristics with maintenance of high photosynthetic rates and cooler canopies under late sowing. The results revealed that advanced lines and Punjab-11 with heat adaptive traits could be promising source for further use in the selection of heat-tolerant wheat genotypes.
6.	Ahmed, Mukhtar (author) Rising Atmospheric Temperature Impact on Wheat and Thermotolerance Strategies 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Research review (peer-reviewed)abstract Temperature across the globe is increasing continuously at the rate of 0.15-0.17 degrees C per decade since the industrial revolution. It is influencing agricultural crop productivity. Therefore, thermotolerance strategies are needed to have sustainability in crop yield under higher temperature. However, improving thermotolerance in the crop is a challenging task for crop scientists. Therefore, this review work was conducted with the aim of providing information on the wheat response in three research areas, i.e., physiology, breeding, and advances in genetics, which could assist the researchers in improving thermotolerance. The optimum temperature for wheat growth at the heading, anthesis, and grain filling duration is 16 +/- 2.3 degrees C, 23 +/- 1.75 degrees C, and 26 +/- 1.53 degrees C, respectively. The high temperature adversely influences the crop phenology, growth, and development. The pre-anthesis high temperature retards the pollen viability, seed formation, and embryo development. The post-anthesis high temperature declines the starch granules accumulation, stem reserve carbohydrates, and translocation of photosynthates into grains. A high temperature above 40 degrees C inhibits the photosynthesis by damaging the photosystem-II, electron transport chain, and photosystem-I. Our review work highlighted that genotypes which can maintain a higher accumulation of proline, glycine betaine, expression of heat shock proteins, stay green and antioxidant enzymes activity viz., catalase, peroxidase, super oxide dismutase, and glutathione reductase can tolerate high temperature efficiently through sustaining cellular physiology. Similarly, the pre-anthesis acclimation with heat treatment, inorganic fertilizer such as nitrogen, potassium nitrate and potassium chloride, mulches with rice husk, early sowing, presoaking of a 6.6 mM solution of thiourea, foliar application of 50 ppm dithiothreitol, 10 mg per kg of silicon at heading and zinc ameliorate the crop against the high temperature. Finally, it has been suggested that modern genomics and omics techniques should be used to develop thermotolerance in wheat.
7.	Ahmed, Mukhtar (author) Selenium and Salt Interactions in Black Gram (Vigna mungo L.): Ion Uptake, Antioxidant Defense System, and Photochemistry Efficiency 2020 In: Plants. - : MDPI AG. - 2223-7747. ; 9 Journal article (peer-reviewed)abstract Salinity is a major abiotic stress which limits crop production, especially under rainfed conditions. Selenium (Se), as an important micronutrient, plays a vital role in mitigating detrimental effects of different abiotic stresses. The objective of this research was to examine the effect of Se fertilization on black gram (Vigna mungo) under salt stress. Our results showed that salt stress (100 mM NaCl) in leaves significantly induced oxidative damage and caused a decline in relative water content, chlorophyll (Chl), stomatal conductance (gs), photochemical efficiency (Fv/Fm), sucrose, and reducing sugars. A low dose of Se (1.5 ppm) significantly reduced hydrogen peroxide content, malondialdehyde formation, cell membrane damage, and also improved antioxidative enzyme activities, including superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase, and glutathione peroxidase under salt stress. Se-treated plants exhibited higher Chl, gs, Fv/Fm, sucrose, and reducing sugars than untreated plants in response to salt stress. In addition, Se application enhanced Se uptake and reduced Na+ uptake, but Cl remained unaffected. Our results indicated that a low dose of Se effectively alleviated salt damage via inhibition of Na+ uptake and enhanced antioxidant defense resulting in a significant decrease in oxidative damage, and maintained gaseous exchange and PS II function for sucrose and reducing sugars accumulation in black gram.
8.	Alhousari, Fadi, et al. (author) Silicon and Mechanisms of Plant Resistance to Insect Pests 2018 In: PLANTS. - : MDPI AG. - 2223-7747. ; 7:2 Research review (peer-reviewed)abstract This paper reviews the most recent progress in exploring silicon-mediated resistance to herbivorous insects and the mechanisms involved. The aim is to determine whether any mechanism seems more common than the others as well as whether the mechanisms are more pronounced in silicon-accumulating than non-silicon-accumulating species or in monocots than eudicots. Two types of mechanisms counter insect pest attacks: physical or mechanical barriers and biochemical/molecular mechanisms (in which Si can upregulate and prime plant defence pathways against insects). Although most studies have examined high Si accumulators, both accumulators and non-accumulators of silicon as well as monocots and eudicots display similar Si defence mechanisms against insects.
9.	Aubry, Emilie, et al. (author) Lateral Transport of Organic and Inorganic Solutes 2019 In: PLANTS. - : MDPI. - 2223-7747. ; 8:1 Research review (peer-reviewed)abstract Organic (e.g., sugars and amino acids) and inorganic (e.g., K+, Na+, PO42−, and SO42−) solutes are transported long-distance throughout plants. Lateral movement of these compounds between the xylem and the phloem, and vice versa, has also been reported in several plant species since the 1930s, and is believed to be important in the overall resource allocation. Studies of Arabidopsis thaliana have provided us with a better knowledge of the anatomical framework in which the lateral transport takes place, and have highlighted the role of specialized vascular and perivascular cells as an interface for solute exchanges. Important breakthroughs have also been made, mainly in Arabidopsis, in identifying some of the proteins involved in the cell-to-cell translocation of solutes, most notably a range of plasma membrane transporters that act in different cell types. Finally, in the future, state-of-art imaging techniques should help to better characterize the lateral transport of these compounds on a cellular level. This review brings the lateral transport of sugars and inorganic solutes back into focus and highlights its importance in terms of our overall understanding of plant resource allocation.
10.	Bag, Pushan, 1993- (author) Light harvesting in fluctuating environments : Evolution and function of antenna proteins across photosynthetic lineage 2021 In: PLANTS. - : MDPI. - 2223-7747. ; 10:6 Journal article (peer-reviewed)abstract Photosynthesis is the major natural process that can harvest and harness solar energy into chemical energy. Photosynthesis is performed by a vast number of organisms from single cellular bacteria to higher plants and to make the process efficient, all photosynthetic organisms possess a special type of pigment protein complex(es) that is (are) capable of trapping light energy, known as photosynthetic light-harvesting antennae. From an evolutionary point of view, simpler (unicellular) organisms typically have a simple antenna, whereas higher plants possess complex antenna systems. The higher complexity of the antenna systems provides efficient fine tuning of photosynthesis. This relationship between the complexity of the antenna and the increasing complexity of the organism is mainly related to the remarkable acclimation capability of complex organisms under fluctuating environmental conditions. These antenna complexes not only harvest light, but also provide photoprotection under fluctuating light conditions. In this review, the evolution, structure, and function of different antenna complexes, from single cellular organisms to higher plants, are discussed in the context of the ability to acclimate and adapt to cope under fluctuating environmental conditions.
11.	Banasiak, Alicja, et al. (author) Glycoside hydrolase activities in cell walls of sclerenchyma cells in the inflorescence stems of Arabidopsis thaliana visualized in situ 2014 In: PLANTS. - : MDPI AG. - 2223-7747. ; 3:4, s. 513-525 Journal article (peer-reviewed)abstract Techniques for in situ localization of gene products provide indispensable information for understanding biological function. In the case of enzymes, biological function is directly related to activity, and therefore, knowledge of activity patterns is central to understanding the molecular controls of plant development. We have previously developed a novel type of fluorogenic substrate for revealing glycoside hydrolase activity in planta, based on resorufin β-glycosides Here, we explore a wider range of such substrates to visualize glycoside hydrolase activities in Arabidopsis inflorescence stems in real time, especially highlighting distinct distribution patterns of these activities in the secondary cell walls of sclerenchyma cells. The results demonstrate that β-1,4-glucosidase, β-1,4-glucanase and β-1,4-galactosidase activities accompany secondary wall deposition. In contrast, xyloglucanase activity follows a different pattern, with the highest signal observed in mature cells, concentrated in the middle lamella. These data further the understanding of the process of cell wall deposition and function in sclerenchymatic tissues of plants.
12.	Belgacem, Imen, et al. (author) Transcriptomic Analysis of Orange Fruit Treated with Pomegranate Peel Extract (PGE) 2019 In: PLANTS. - : MDPI AG. - 2223-7747. ; 8:4 Journal article (peer-reviewed)abstract A Pomegranate Peel Extract (PGE) has been proposed as a natural antifungal substance with a wide range of activity against plant diseases. Previous studies showed that the extract has a direct antimicrobial activity and can elicit resistance responses in plant host tissues. In the present study, the transcriptomic response of orange fruit toward PGE treatments was evaluated. RNA-seq analyses, conducted on wounded fruits 0, 6, and 24 h after PGE applications, showed a significantly different transcriptome in treated oranges as compared to control samples. The majority (273) of the deferentially expressed genes (DEGs) were highly up-regulated compared to only 8 genes that were down-regulated. Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis showed the involvement of 1233 gene ontology (GO) terms and 35 KEGG metabolic pathways. Among these, important defense pathways were induced and antibiotic biosynthesis was the most enriched one. These findings may explain the underlying preventive and curative activity of PGE against plant diseases.
13.	Bohman, Björn (author) Three Chemically Distinct Floral Ecotypes in Drakaea livida, an Orchid Pollinated by Sexual Deception of Thynnine Wasps 2022 In: Plants. - : MDPI AG. - 2223-7747. ; 11 Journal article (peer-reviewed)abstract Sexually deceptive orchids are unusual among plants in that closely related species typically attract different pollinator species using contrasting blends of floral volatiles. Therefore, intraspecific variation in pollinator attraction may also be underpinned by differences in floral volatiles. Here, we tested for the presence of floral ecotypes in the sexually deceptive orchid Drakaea livida and investigated if the geographic range of floral ecotypes corresponded to variation in pollinator availability. Pollinator choice trials revealed the presence of three floral ecotypes within D. livida that each attracts a different species of thynnine wasp as a pollinator. Surveys of pollinator distribution revealed that the distribution of one of the ecotypes was strongly correlated with that of its pollinator, while another pollinator species was present throughout the range of all three ecotypes, demonstrating that pollinator availability does not always correlate with ecotype distribution. Floral ecotypes differed in chemical volatile composition, with a high degree of separation evident in principal coordinate analysis. Some compounds that differed between ecotypes, including pyrazines and (methylthio)phenols, are known to be electrophysiologically active in thynnine wasp antennae. Based on differences in pollinator response and floral volatile profile, the ecotypes represent distinct entities and should be treated as such in conservation management.
14.	Brouwer, Sophie, et al. (author) Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract Potato early blight is caused by the necrotrophic fungus Alternaria solani and can result in yield losses of up to 50% if left uncontrolled. At present, the disease is controlled by chemical fungicides, yet rapid development of fungicide resistance renders current control strategies unsustainable. On top of that, a lack of understanding of potato defences and the quantitative nature of resistance mechanisms against early blight hinders the development of more sustainable control methods. Necrotrophic pathogens, compared to biotrophs, pose an extra challenge to the plant, since common defence strategies to biotic stresses such as the hypersensitive response and programmed cell death are often beneficial for necrotrophs. With the aim of unravelling plant responses to both the early infection stages (i.e., before necrosis), such as appressorium formation and penetration, as well as to later responses to the onset of necrosis, we present here a transcriptome analysis of potato interactions with A. solani from 1 h after inoculation when the conidia have just commenced germination, to 48 h post inoculation when multiple cell necrosis has begun. Potato transcripts with putative functions related to biotic stress tolerance and defence against pathogens were upregulated, including a putative Nudix hydrolase that may play a role in defence against oxidative stress. A. solani transcripts encoding putative pathogenicity factors, such as cell wall degrading enzymes and metabolic processes that may be important for infection. We therefore identified the differential expression of several potato and A. solani transcripts that present a group of valuable candidates for further studies into their roles in immunity or disease development.
15.	Bru, Pierrick, et al. (author) A Genetic Screen to Identify New Molecular Players Involved in Photoprotection qH in Arabidopsis thaliana 2020 In: PLANTS. - : MDPI. - 2223-7747. ; 9:11 Journal article (peer-reviewed)abstract Photosynthesis is a biological process which converts light energy into chemical energy that is used in the Calvin–Benson cycle to produce organic compounds. An excess of light can induce damage to the photosynthetic machinery. Therefore, plants have evolved photoprotective mechanisms such as non-photochemical quenching (NPQ). To focus molecular insights on slowly relaxing NPQ processes in Arabidopsis thaliana, previously, a qE-deficient line—the PsbS mutant—was mutagenized and a mutant with high and slowly relaxing NPQ was isolated. The mutated gene was named suppressor of quenching 1, or SOQ1, to describe its function. Indeed, when present, SOQ1 negatively regulates or suppresses a form of antenna NPQ that is slow to relax and is photoprotective. We have now termed this component qH and identified the plastid lipocalin, LCNP, as the effector for this energy dissipation mode to occur. Recently, we found that the relaxation of qH1, ROQH1, protein is required to turn off qH. The aim of this study is to identify new molecular players involved in photoprotection qH by a whole genome sequencing approach of chemically mutagenized Arabidopsis thaliana. We conducted an EMS-mutagenesis on the soq1 npq4 double mutant and used chlorophyll fluorescence imaging to screen for suppressors and enhancers of qH. Out of 22,000 mutagenized plants screened, the molecular players cited above were found using a mapping-by-sequencing approach. Here, we describe the phenotypic characterization of the other mutants isolated from this genetic screen and an additional 8000 plants screened. We have classified them in several classes based on their fluorescence parameters, NPQ kinetics, and pigment content. A high-throughput whole genome sequencing approach on 65 mutants will identify the causal mutations thanks to allelic mutations from having reached saturation of the genetic screen. The candidate genes could be involved in the formation or maintenance of quenching sites for qH, in the regulation of qH at the transcriptional level, or be part of the quenching site itself.
16.	Cabianca, Alessandro, et al. (author) Changes in the Plant β-Sitosterol/Stigmasterol Ratio Caused by the Plant Parasitic Nematode Meloidogyne incognita 2021 In: PLANTS. - : MDPI AG. - 2223-7747. ; 10:2 Journal article (peer-reviewed)abstract Sterols play a key role in various physiological processes of plants. Commonly, stigmasterol, β-sitosterol and campesterol represent the main plant sterols, and cholesterol is often reported as a trace sterol. Changes in plant sterols, especially in β-sitosterol/stigmasterol levels, can be induced by different biotic and abiotic factors. Plant parasitic nematodes, such as the root-knot nematode Meloidogyne incognita, are devastating pathogens known to circumvent plant defense mechanisms. In this study, we investigated the changes in sterols of agricultural important crops, Brassica juncea (brown mustard), Cucumis sativus (cucumber), Glycine max (soybean), Solanum lycopersicum (tomato) and Zea mays (corn), 21 days post inoculation (dpi) with M. incognita. The main changes affected the β-sitosterol/stigmasterol ratio, with an increase of β-sitosterol and a decrease of stigmasterol in S. lycopersicum, G. max, C. sativus and Z. mays. Furthermore, cholesterol levels increased in tomato, cucumber and corn, while cholesterol levels often were below the detection limit in the respective uninfected plants. To better understand the changes in the β-sitosterol/stigmasterol ratio, gene expression analysis was conducted in tomato cv. Moneymaker for the sterol 22C-desaturase gene CYP710A11, responsible for the conversion of β-sitosterol to stigmasterol. Our results showed that the expression of CYP710A11 was in line with the sterol profile of tomato after M. incognita infection. Since sterols play a key role in plant-pathogen interactions, this finding opens novel insights in plant nematode interactions.
17.	Casanova, Ruben, et al. (author) Dynamics of Auxin and Cytokinin Metabolism during Early Root and Hypocotyl Growth in Theobroma cacao 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract The spatial location and timing of plant developmental events are largely regulated by the well balanced effects of auxin and cytokinin phytohormone interplay. Together with transport, localized metabolism regulates the concentration gradients of their bioactive forms, ultimately eliciting growth responses. In order to explore the dynamics of auxin and cytokinin metabolism during early seedling growth in Theobroma cacao (cacao), we have performed auxin and cytokinin metabolite profiling in hypocotyls and root developmental sections at different times by using ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC-MS/MS). Our work provides quantitative characterization of auxin and cytokinin metabolites throughout early root and hypocotyl development and identifies common and distinctive features of auxin and cytokinin metabolism during cacao seedling development.
18.	Chawade, Aakash (author) New Genotypes and Genomic Regions for Resistance to Wheat Blast in South Asian Germplasm 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract Wheat blast (WB) disease, since its first identification in Bangladesh in 2016, is now an established serious threat to wheat production in South Asia. There is a need for sound knowledge about resistance sources and associated genomic regions to assist breeding programs. Hence, a panel of genotypes from India and Bangladesh was evaluated for wheat blast resistance and a genome-wide association study (GWAS) was performed. Disease evaluation was done during five crop seasons-at precision phenotyping platform (PPPs) for wheat blast disease at Jashore (2018-19), Quirusillas (2018-19 and 2019-20) and Okinawa (2019 and 2020). Single nucleotide polymorphisms (SNP) across the genome were obtained using DArTseq genotyping-by-sequencing platform, and in total 5713 filtered markers were used. GWAS revealed 40 significant markers associated with WB resistance, of which 33 (82.5%) were in the 2NS/2AS chromosome segment and one each on seven chromosomes (3B, 3D, 4A, 5A, 5D, 6A and 6B). The 2NS markers contributed significantly in most of the environments, explaining an average of 33.4% of the phenotypic variation. Overall, 22.4% of the germplasm carried 2NS/2AS segment. So far, 2NS translocation is the only effective WB resistance source being used in the breeding programs of South Asia. Nevertheless, the identification of non-2NS/2AS genomic regions for WB resistance provides a hope to broaden and diversify resistance for this disease in years to come.
19.	Chawade, Aakash, et al. (author) RNA Interference and CRISPR/Cas Gene Editing for Crop Improvement: Paradigm Shift towards Sustainable Agriculture 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Research review (peer-reviewed)abstract With the rapid population growth, there is an urgent need for innovative crop improvement approaches to meet the increasing demand for food. Classical crop improvement approaches involve, however, a backbreaking process that cannot equipoise with increasing crop demand. RNA-based approaches i.e., RNAi-mediated gene regulation and the site-specific nuclease-based CRISPR/Cas9 system for gene editing has made advances in the efficient targeted modification in many crops for the higher yield and resistance to diseases and different stresses. In functional genomics, RNA interference (RNAi) is a propitious gene regulatory approach that plays a significant role in crop improvement by permitting the downregulation of gene expression by small molecules of interfering RNA without affecting the expression of other genes. Gene editing technologies viz. the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) have appeared prominently as a powerful tool for precise targeted modification of nearly all crops’ genome sequences to generate variation and accelerate breeding efforts. In this regard, the review highlights the diverse roles and applications of RNAi and CRISPR/Cas9 system as powerful technologies to improve agronomically important plants to enhance crop yields and increase tolerance to environmental stress (biotic or abiotic). Ultimately, these technologies can prove to be important in view of global food security and sustainable agriculture.
20.	Dubreuil, Carole, et al. (author) The PIP Peptide of INFLORESCENCE DEFICIENT IN ABSCISSION Enhances Populus Leaf and Elaeis guineensis Fruit Abscission 2019 In: Plants. - : MDPI AG. - 2223-7747. ; 8 Journal article (peer-reviewed)abstract The programmed loss of a plant organ is called abscission, which is an important cell separation process that occurs with different organs throughout the life of a plant. The use of floral organ abscission in Arabidopsis thaliana as a model has allowed greater understanding of the complexities of organ abscission, but whether the regulatory pathways are conserved throughout the plant kingdom and for all organ abscission types is unknown. One important pathway that has attracted much attention involves a peptide ligand-receptor signalling system that consists of the secreted peptide IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) and at least two leucine-rich repeat (LRR) receptor-like kinases (RLK), HAESA (HAE) and HAESA-LIKE2 (HSL2). In the current study we examine the bioactive potential of IDA peptides in two different abscission processes, leaf abscission in Populus and ripe fruit abscission in oil palm, and find in both cases treatment with IDA peptides enhances cell separation and abscission of both organ types. Our results provide evidence to suggest that the IDA-HAE-HSL2 pathway is conserved and functions in these phylogenetically divergent dicot and monocot species during both leaf and fruit abscission, respectively.
21.	Gonzalez-Mendoza, V. M., et al. (author) Phospholipases C and D and Their Role in Biotic and Abiotic Stresses 2021 In: Plants-Basel. - : MDPI AG. - 2223-7747. ; 10:5 Journal article (peer-reviewed)abstract Plants, as sessile organisms, have adapted a fine sensing system to monitor environmental changes, therefore allowing the regulation of their responses. As the interaction between plants and environmental changes begins at the surface, these changes are detected by components in the plasma membrane, where a molecule receptor generates a lipid signaling cascade via enzymes, such as phospholipases (PLs). Phospholipids are the key structural components of plasma membranes and signaling cascades. They exist in a wide range of species and in different proportions, with conversion processes that involve hydrophilic enzymes, such as phospholipase-C (PLC), phospholipase-D (PLD), and phospholipase-A (PLA). Hence, it is suggested that PLC and PLD are highly conserved, compared to their homologous genes, and have formed clusters during their adaptive history. Additionally, they generate responses to different functions in accordance with their protein structure, which should be reflected in specific signal transduction responses to environmental stress conditions, including innate immune responses. This review summarizes the phospholipid systems associated with signaling pathways and the innate immune response.
22.	Helmstetter, A. J., et al. (author) Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae) 2020 In: Plants-Basel. - : MDPI AG. - 2223-7747. ; 9:4 Journal article (peer-reviewed)abstract Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling, and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution, and other eco-evolutionary aspects of this charismatic, socially, and economically important palm genus.
23.	Hennigs, Lars (author) FLOWERING LOCUS T Triggers Early and Fertile Flowering in Glasshouse Cassava (Manihot esculenta Crantz) 2017 In: Plants. - : MDPI AG. - 2223-7747. ; 6 Journal article (peer-reviewed)abstract Accelerated breeding of plant species has the potential to help challenge environmental and biochemical cues to support global crop security. We demonstrate the over-expression of Arabidopsis FLOWERING LOCUS T in Agrobacterium-mediated transformed cassava (Manihot esculenta Crantz; cultivar 60444) to trigger early flowering in glasshouse-grown plants. An event seldom seen in a glasshouse environment, precocious flowering and mature inflorescence were obtained within 4–5 months from planting of stem cuttings. Manual pollination using pistillate and staminate flowers from clonal propagants gave rise to viable seeds that germinated into morphologically typical progeny. This strategy comes at a time when accelerated crop breeding is of increasing importance to complement progressive genome editing techniques.
24.	Jägerbrand, Annika, 1972-, et al. (author) Short-term responses in maximum quantum yield of PSII (Fv/Fm) to ex situ temperature treatment of populations of bryophytes originating from different sites in Hokkaido, Northern Japan 2016 In: Plants. - : MDPI. - 2223-7747. ; 5:2, s. 455-465 Journal article (peer-reviewed)abstract There is limited knowledge available on the thermal acclimation processes for bryophytes, especially when considering variation between populations or sites. This study investigated whether short-term ex situ thermal acclimation of different populations showed patterns of site dependency and whether the maximum quantum yield of PSII (Fv/Fm) could be used as an indicator of adaptation or temperature stress in two bryophyte species: Pleurozium schreberi (Willd. ex Brid.) Mitt. and Racomitrium lanuginosum (Hedw.) Brid.We sought to test the hypothesis that differences in the ability to acclimate to short-term temperature treatment would be revealed as differences in photosystem II maximum yield (Fv/Fm). Thermal treatments were applied to samples from 12 and 11 populations during 12 or 13 days in growth chambers and comprised: (1) 10/5 °C; (2) 20/10 °C; (3) 25/15 °C; (4) 30/20 °C (12 hours day/night temperature).In Pleurozium schreberi, there were no significant site-dependent differences before or after the experiment, while site dependencies were clearly shown in Racomitrium lanuginosum throughout the study. Fv/Fm in Pleurozium schreberi decreased at the highest and lowest temperature treatments, which can be interpreted as a stress response, but no similar trends were shown by Racomitrium lanuginosum.
25.	Kalle, Raivo, et al. (author) Early Citizen Science Action in Ethnobotany : The Case of the Folk Medicine Collection of Dr. Mihkel Ostrov in the Territory of Present-Day Estonia, 1891-1893 2022 In: PLANTS. - : MDPI. - 2223-7747. ; 11:3 Journal article (peer-reviewed)abstract Presently, collecting data through citizen science (CS) is increasingly being used in botanical, zoological and other studies. However, until now, ethnobotanical studies have underused CS data collection methods. This study analyses the results of the appeal organized by the physician Dr. Mihkel Ostrov (1863-1940), which can be considered the first-ever internationally known systematic example of ethnopharmacological data collection involving citizens. We aim to understand what factors enhanced or diminished the success of the collaboration between Ostrov and the citizens of that time. The reliability of Ostrov's collection was enhanced by the herbarium specimens (now missing) used in the identification of vernacular names. The collection describes the use of 65 species from 27 genera. The timing of its collection coincided with not only a national awakening and recently obtained high level of literacy but also the activation of civil society, people's awareness of the need to collect folklore, the voluntary willingness of newspapers to provide publishing space and later to collect data, and the use of a survey method focusing on a narrow topic. While Ostrov's only means of communication with the public was through newspapers, today, with electronic options, social media can also be used.
26.	Kaur, Harmanjit, et al. (author) A Review on Si Uptake and Transport System 2019 In: PLANTS. - : MDPI AG. - 2223-7747. ; 8:4 Research review (peer-reviewed)abstract Silicon (Si) was long listed as a non-essential component for plant growth and development because of its universal availability. However, there has been a resurgence of interest in studying the underlying uptake and transport mechanism of silicon in plants because of the reported dynamic role of silicon in plants under stressed environmental conditions. This uptake and transport mechanism is greatly dependent upon the uptake ability of the plant's roots. Plant roots absorb Si in the form of silicic acid from the soil solution, and it is moved through different parts of the plant using various influx and efflux transporters. Both these influx and efflux transporters are mostly found in the plasma membrane; however, their location and pattern of expression varies among different plants. The assessment of these features provides a new understanding of different species-dependent Si accumulations, which have been studied in monocots but are poorly understood in other plant groups. Therefore, the present review provides insight into the most recent research exploring the use of Si transporters in angiosperms and cryptogams. This paper presents an extensive representation of data from different families of angiosperms, including monocots and eudicots. Eudicots (previously referred to as dicots) have often been neglected in the literature, because they are categorized as low/intermediate Si accumulators. However, in this review, we attempt to highlight the accumulating species of different plant groups in which Si uptake is mediated through transporters.
27.	Kiryushkin, Alexey S., et al. (author) Hairy CRISPR : Genome Editing in Plants Using Hairy Root Transformation 2022 In: PLANTS. - : MDPI AG. - 2223-7747. ; 11:1 Journal article (peer-reviewed)abstract CRISPR/Cas-mediated genome editing is a powerful tool of plant functional genomics. Hairy root transformation is a rapid and convenient approach for obtaining transgenic roots. When combined, these techniques represent a fast and effective means of studying gene function. In this review, we outline the current state of the art reached by the combination of these approaches over seven years. Additionally, we discuss the origins of different Agrobacterium rhizogenes strains that are widely used for hairy root transformation; the components of CRISPR/Cas vectors, such as the promoters that drive Cas or gRNA expression, the types of Cas nuclease, and selectable and screenable markers; and the application of CRISPR/Cas genome editing in hairy roots. The modification of the already known vector pKSE401 with the addition of the rice translational enhancer OsMac3 and the gene encoding the fluorescent protein DsRed1 is also described.
28.	Kumar, Uttam, et al. (author) Comparative Analysis of Phenology Algorithms of the Spring Barley Model in APSIM 7.9 and APSIM Next Generation: A Case Study for High Latitudes 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract Phenology algorithms in crop growth models have inevitable systematic errors and uncertainties. In this study, the phenology simulation algorithms in APSIM classical (APSIM 7.9) and APSIM next generation (APSIM-NG) were compared for spring barley models at high latitudes. Phenological data of twelve spring barley varieties were used for the 2014-2018 cropping seasons from northern Sweden and Finland. A factorial-based calibration approach provided within APSIM-NG was performed to calibrate both models. The models have different mechanisms to simulate days to anthesis. The calibration was performed separately for days to anthesis and physiological maturity, and evaluations for the calibrations were done with independent datasets. The calibration performance for both growth stages of APSIM-NG was better compared to APSIM 7.9. However, in the evaluation, APSIM-NG showed an inclination to overestimate days to physiological maturity. The differences between the models are possibly due to slower thermal time accumulation mechanism, with higher cardinal temperatures in APSIM-NG. For a robust phenology prediction at high latitudes with APSIM-NG, more research on the conception of thermal time computation and implementation is suggested.
29.	Leiva, Fernanda, et al. (author) Phenocave: An Automated, Standalone, and Affordable Phenotyping System for Controlled Growth Conditions 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract Controlled plant growth facilities provide the possibility to alter climate conditions affecting plant growth, such as humidity, temperature, and light, allowing a better understanding of plant responses to abiotic and biotic stresses. A bottleneck, however, is measuring various aspects of plant growth regularly and non-destructively. Although several high-throughput phenotyping facilities have been built worldwide, further development is required for smaller custom-made affordable systems for specific needs. Hence, the main objective of this study was to develop an affordable, standalone and automated phenotyping system called "Phenocave" for controlled growth facilities. The system can be equipped with consumer-grade digital cameras and multispectral cameras for imaging from the top view. The cameras are mounted on a gantry with two linear actuators enabling XY motion, thereby enabling imaging of the entire area of Phenocave. A blueprint for constructing such a system is presented and is evaluated with two case studies using wheat and sugar beet as model plants. The wheat plants were treated with different irrigation regimes or high nitrogen application at different developmental stages affecting their biomass accumulation and growth rate. A significant correlation was observed between conventional measurements and digital biomass at different time points. Post-harvest analysis of grain protein content and composition corresponded well with those of previous studies. The results from the sugar beet study revealed that seed treatment(s) before germination influences germination rates. Phenocave enables automated phenotyping of plants under controlled conditions, and the protocols and results from this study will allow others to build similar systems with dimensions suitable for their custom needs.
30.	Lin, SC, et al. (author) A Natural Botanical Product, Resveratrol, Effectively Suppresses Vesicular Stomatitis Virus Infection In Vitro 2021 In: Plants (Basel, Switzerland). - : MDPI AG. - 2223-7747. ; 10:6 Journal article (peer-reviewed)abstract Numerous natural phytochemicals such as resveratrol are acknowledged as potent botanical agents in regulating immune responses. However, it is less understood whether such immunomodulatory phytochemicals are appropriate for use as direct treatments in veterinary viral diseases. In the present study, we investigated the efficacy of resveratrol in suppressing vesicular stomatitis virus (VSV) infection. Outbreaks of VSV can cause massive economic loss in poultry and livestock husbandry farming, and VSV treatment is in need of therapeutic development. We utilized a recombinant VSV that expresses green fluorescent protein (GFP) to measure viral replication in cells treated with resveratrol. Our findings revealed that resveratrol treatment affords a protective effect, shown by increased viability and reduced viral replication, as indicated by a reduction in fluorescent signals. Additionally, we found that resveratrol inhibition of VSV infection occurs via suppression of the caspase cascade. Structural analysis also indicated that resveratrol potentially interacts with the active sites of caspase-3 and -7, facilitating antiviral activity. The potential effect of resveratrol on reducing VSV infection in vitro suggests that resveratrol should be further investigated as a potential veterinary therapeutic or prophylactic agent.
31.	Liu, Hui, et al. (author) Shoot and Root Traits Underlying Genotypic Variation in Early Vigor and Nutrient Accumulation in Spring Wheat Grown in High-Latitude Light Conditions 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract Plants with improved nutrient use efficiency are needed to maintain and enhance future crop plant production. The aim of this study was to explore candidate traits for pre-breeding to improve nutrient accumulation and early vigor of spring wheat grown at high latitudes. We quantified shoot and root traits together with nutrient accumulation in nine contrasting spring wheat genotypes grown in rhizoboxes for 20 days in a greenhouse. Whole-plant relative growth rate was here correlated with leaf area productivity and plant nitrogen productivity, but not leaf area ratio. Furthermore, the total leaf area was correlated with the accumulation of six macronutrients, and could be suggested as a candidate trait for the pre-breeding towards improved nutrient accumulation and early vigor in wheat to be grown in high-latitude environments. Depending on the nutrient of interest, different root system traits were identified as relevant for their accumulation. Accumulation of nitrogen, potassium, sulfur and calcium was correlated with lateral root length, whilst accumulation of phosphorus and magnesium was correlated with main root length. Therefore, special attention needs to be paid to specific root system traits in the breeding of wheat towards improved nutrient accumulation to counteract the suboptimal uptake of some nutrient elements.
32.	Ljung, Karin (author) Natural Variation in Adventitious Rooting in the Alpine Perennial Arabis alpina 2020 In: Plants. - : MDPI AG. - 2223-7747. ; 9 Journal article (peer-reviewed)abstract Arctic alpine species follow a mixed clonal-sexual reproductive strategy based on the environmental conditions at flowering. Here, we explored the natural variation for adventitious root formation among genotypes of the alpine perennial Arabis alpina that show differences in flowering habit. We scored the presence of adventitious roots on the hypocotyl, main stem and axillary branches on plants growing in a long-day greenhouse. We also assessed natural variation for adventitious rooting in response to foliar auxin spray. In both experimental approaches, we did not detect a correlation between adventitious rooting and flowering habit. In the greenhouse, and without the application of synthetic auxin, the accession Wca showed higher propensity to produce adventitious roots on the main stem compared to the other accessions. The transcript accumulation of the A. alpina homologue of the auxin inducible GH3.3 gene (AaGH3.3) on stems correlated with the adventitious rooting phenotype of Wca. Synthetic auxin, 1-Naphthaleneacetic acid (1-NAA), enhanced the number of plants with adventitious roots on the main stem and axillary branches. A. alpina plants showed an age-, dosage- and genotype-dependent response to 1-NAA. Among the genotypes tested, the accession Dor was insensitive to auxin and Wca responded to auxin on axillary branches.
33.	Mohammed Saifur, Rahman, et al. (author) Estimation of Yield, Photosynthetic Rate, Biochemical, and Nutritional Content of Red Leaf Lettuce (Lactuca sativa L.) Grown in Organic Substrates 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract This study aimed to evaluate the effect of organic substrates on the growth yield, photosynthetic response, and nutritional profile of red leaf lettuce grown in different compositions of cocopeat (CP), sawdust (SD), and rice husk (RH). The result showed that the properties of substrates were influenced variably by their mixing ratios. The highest water holding capacity and moisture content were found in CP, and it provided the preferable pH, electrical conductivity, bulk density, and air-filled porosity in association with other categories of the substrate. Cocopeat-based media provides ample microclimate conditions in the root region of plants and increased their height, number of leaves, and fresh biomass components. The utmost dry biomass of plant parts also remarkably increased in CP; L, a, and b* chromaticity of leaves remained unchanged. The maximum chlorophyll content was attained in CP substrate, except for chlorophyll a/b, which was higher in RH. The net photosynthetic rate (PN), transpiration rate (E), and nitrate in leaves were enhanced substantially in CP, while it was lower in SD. Biochemical compositions and nutrients in leaves were likewise stimulated under the culture of cocopeat-based media. Results indicate that cocopeat, sawdust, and rice husk are a possible substrates mixture in a volume ratio of 3:1:1, which would be a better choice in the cultivation of red leaf lettuce.
34.	Moran-Velizquez, Dalia C., et al. (author) Unravelling Chemical Composition of Agave Spines : News from Agave fourcroydes Lem. 2020 In: PLANTS. - : MDPI. - 2223-7747. ; 9:12 Journal article (peer-reviewed)abstract Spines are key plant modifications developed to deal against herbivores; however, its physical structure and chemical composition have been little explored in plant species. Here, we took advantage of high-throughput chromatography to characterize chemical composition of Agave fourcroydes Lem. spines, a species traditionally used for fiber extraction. Analyses of structural carbohydrate showed that spines have lower cellulose content than leaf fibers (52 and 72%, respectively) but contain more than 2-fold the hemicellulose and 1.5-fold pectin. Xylose and galacturonic acid were enriched in spines compared to fibers. The total lignin content in spines was 1.5-fold higher than those found in fibers, with elevated levels of syringyl (S) and guaiacyl (G) subunits but similar S/G ratios within tissues. Metabolomic profiling based on accurate mass spectrometry revealed the presence of phenolic compounds including quercetin, kaempferol, (+)-catechin, and (-)-epicatechin in A. fourcroydes spines, which were also detected in situ in spines tissues and could be implicated in the color of these plants' structures. Abundance of (+)-catechins could also explain proanthocyanidins found in spines. Agave spines may become a plant model to obtain more insights about cellulose and lignin interactions and condensed tannin deposition, which is valuable knowledge for the bioenergy industry and development of naturally dyed fibers, respectively.
35.	Naznin, Most Tahera (author) Blue Light added with Red LEDs Enhance Growth Characteristics, Pigments Content, and Antioxidant Capacity in Lettuce, Spinach, Kale, Basil, and Sweet Pepper in a Controlled Environment 2019 In: Plants. - : MDPI AG. - 2223-7747. ; 8 Journal article (peer-reviewed)abstract The aim of this study was to investigate the different combinations of red (R) and blue (B) light emitting diode (LEDs') lighting effects on growth, pigment content, and antioxidant capacity in lettuce, spinach, kale, basil, and pepper in a growth chamber. The growth chamber was equipped with R and B light percentages based on total light intensity: 83% R + 17% B; 91% R + 9% B; 95% R + 5% B; and control was 100% R. The photosynthetic photon flux density (PPFD), photoperiod, temperature, and relative humidity of the growth chamber were maintained at 200 +/- 5 mol m(-2) s(-1), 16 h, 25/21 +/- 2.5 degrees C, and 65 +/- 5%, respectively. It is observed that the plant height of lettuce, kale, and pepper was significantly increased under 100% R light, whereas the plant height of spinach and basil did not show any significant difference. The total leaf number of basil and pepper was significantly increased under the treatment of 95% R + 5% B light, while no significant difference was observed for other plant species in the same treatment. Overall, the fresh and dry mass of the studied plants was increased under 91% R + 9% B and 95% R + 5% B light treatment. The significantly higher flower and fruit numbers of pepper were observed under the 95% R + 5% B treatment. The chlorophyll a, chlorophyll b, and total chlorophyll content of lettuce, spinach, basil, and pepper was significantly increased under the 91% R + 9% B treatment while the chlorophyll content of kale was increased under the 95% R + 5% B light treatment. The total carotenoid content of lettuce and spinach was higher in the 91% R + 9% B treatment whereas the carotenoid content of kale, basil, and pepper was increased under the 83% R + 17% B treatment. The antioxidant capacity of the lettuce, spinach, and kale was increased under the 83% R + 17% B treatment while basil and pepper were increased under the 91% R + 9% B treatment. This result indicates that the addition of B light is essential with R light to enhance growth, pigment content, and antioxidant capacity of the vegetable plant in a controlled environment. Moreover, the percentage of B with R light is plant species dependent.
36.	Norbäck, Dan, et al. (author) A Review on Epidemiological and Clinical Studies on Buckwheat Allergy 2021 In: PLANTS. - : MDPI. - 2223-7747. ; 10:3 Research review (peer-reviewed)abstract Background: Cultivated buckwheat include two species originating from China: common buckwheat (Fagopyrum esculentum) and tartary buckwheat (Fagopyrum tartaricum). Buckwheat can cause IgE-mediated allergy, including severe allergic reactions and anaphylaxis. Exposure can occure when eating buckwheat food (food allergen), when producing or handling buckwheat food (occupational exposure) or when sleeping on buckwheat husk pillows (houeshold environmental exposure).Methods: A search on buckwheat allergy in the medical database PubMed from 1970-2020.Result: A number of allergenic proteins have been identified in common buckwheat (e.g., Fag e 1, Fag e 2 and Fag e 3) and in tartary buckwheat (e.g., Fag t 1, Fag t 2, Fag t 3). Clinically relevant cross-reactivity has been described between buckwheat and peanut, latex, coconut, quinoa, and poppy seed. The prevalence of buckwheat allergy in the population can be estimated as 0.1-0.4% in Japan, Korea and buckwheat consuming areas of China. Among patients in allergy clinics in different countries, 2-7% has confirmed buckwheat allergy. School studies from Japan and Korea found 4-60 cases of buckwheat-related anaphylaxis per 100,000 school children. The incidence of severe allergic reactions to buckwheat, including anaphylaxis, can be estimated as 0.1-0.01 cases per 100,000 person-years.Conclusions: Buckwheat allergy is a neglected allegy deserving further attention but severe allergic reactions are rare.
37.	Nybom, Hilde, et al. (author) Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Research review (peer-reviewed)abstract Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
38.	Nybom, Hilde, et al. (author) Review of the Impact of Apple Fruit Ripening, Texture and Chemical Contents on Genetically Determined Susceptibility to Storage Rots 2020 In: Plants. - : MDPI AG. - 2223-7747. ; 9 Research review (peer-reviewed)abstract Fungal storage rots like blue mould, grey mould, bull's eye rot, bitter rot and brown rot destroy large amounts of the harvested apple crop around the world. Application of fungicides is nowadays severely restricted in many countries and production systems, and these problems are therefore likely to increase. Considerable variation among apple cultivars in resistance/susceptibility has been reported, suggesting that efficient defence mechanisms can be selected for and used in plant breeding. These are, however, likely to vary between pathogens, since some fungi are mainly wound-mediated while others attack through lenticels or by infecting blossoms. Since mature fruits are considerably more susceptible than immature fruits, mechanisms involving fruit-ripening processes are likely to play an important role. Significant associations have been detected between the susceptibility to rots in harvested fruit and various fruit maturation-related traits like ripening time, fruit firmness at harvest and rate of fruit softening during storage, as well as fruit biochemical contents like acidity, sugars and polyphenols. Some sources of resistance to blue mould have been described, but more research is needed on the development of spore inoculation methods that produce reproducible data and can be used for large screenings, especially for lenticel-infecting fungi.
39.	Nybom, Hilde (author) SSR-Based Analysis of Genetic Diversity and Structure of Sweet Cherry (Prunus avium L.) from 19 Countries in Europe 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract Sweet cherry (Prunus avium L.) is a temperate fruit species whose production might be highly impacted by climate change in the near future. Diversity of plant material could be an option to mitigate these climate risks by enabling producers to have new cultivars well adapted to new environmental conditions. In this study, subsets of sweet cherry collections of 19 European countries were genotyped using 14 SSR. The objectives of this study were (i) to assess genetic diversity parameters, (ii) to estimate the levels of population structure, and (iii) to identify germplasm redundancies. A total of 314 accessions, including landraces, early selections, and modern cultivars, were monitored, and 220 unique SSR genotypes were identified. All 14 loci were confirmed to be polymorphic, and a total of 137 alleles were detected with a mean of 9.8 alleles per locus. The average number of alleles (N = 9.8), PIC value (0.658), observed heterozygosity (H-o = 0.71), and expected heterozygosity (H-e = 0.70) were higher in this study compared to values reported so far. Four ancestral populations were detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA), and two of them (K1 and K4) could be attributed to the geographical origin of the accessions. A N-J tree grouped the 220 sweet cherry accessions within three main clusters and six subgroups. Accessions belonging to the four STRUCTURE populations roughly clustered together. Clustering confirmed known genealogical data for several accessions. The large genetic diversity of the collection was demonstrated, in particular within the landrace pool, justifying the efforts made over decades for their conservation. New sources of diversity will allow producers to face challenges, such as climate change and the need to develop more sustainable production systems.
40.	Nybom, Hilde (author) Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.
41.	Pandey, Shashank (author) Understanding the Modus Operandi of Class II KNOX Transcription Factors in Secondary Cell Wall Biosynthesis 2022 In: Plants. - : MDPI AG. - 2223-7747. ; 11 Journal article (peer-reviewed)abstract Lignocellulosic biomass from the secondary cell walls of plants has a veritable potential to provide some of the most appropriate raw materials for producing second-generation biofuels. Therefore, we must first understand how plants synthesize these complex secondary cell walls that consist of cellulose, hemicellulose, and lignin in order to deconstruct them later on into simple sugars to produce bioethanol via fermentation. Knotted-like homeobox (KNOX) genes encode homeodomain-containing transcription factors (TFs) that modulate various important developmental processes in plants. While Class I KNOX TF genes are mainly expressed in the shoot apical meristems of both monocot and eudicot plants and are involved in meristem maintenance and/or formation, Class II KNOX TF genes exhibit diverse expression patterns and their precise functions have mostly remained unknown, until recently. The expression patterns of Class II KNOX TF genes in Arabidopsis, namely KNAT3, KNAT4, KNAT5, and KNAT7, suggest that TFs encoded by at least some of these genes, such as KNAT7 and KNAT3, may play a significant role in secondary cell wall formation. Specifically, the expression of the KNAT7 gene is regulated by upstream TFs, such as SND1 and MYB46, while KNAT7 interacts with other cell wall proteins, such as KNAT3, MYB75, OFPs, and BLHs, to regulate secondary cell wall formation. Moreover, KNAT7 directly regulates the expression of some xylan synthesis genes. In this review, we summarize the current mechanistic understanding of the roles of Class II KNOX TFs in secondary cell wall formation. Recent success with the genetic manipulation of Class II KNOX TFs suggests that this may be one of the biotechnological strategies to improve plant feedstocks for bioethanol production.
42.	Pironon, S., et al. (author) Toward Unifying Global Hotspots of Wild and Domesticated Biodiversity 2020 In: Plants. - : MDPI AG. - 2223-7747. ; 9:9 Journal article (peer-reviewed)abstract Global biodiversity hotspots are areas containing high levels of species richness, endemism and threat. Similarly, regions of agriculturally relevant diversity have been identified where many domesticated plants and animals originated, and co-occurred with their wild ancestors and relatives. The agro-biodiversity in these regions has, likewise, often been considered threatened. Biodiversity and agro-biodiversity hotspots partly overlap, but their geographic intricacies have rarely been investigated together. Here we review the history of these two concepts and explore their geographic relationship by analysing global distribution and human use data for all plants, and for major crops and associated wild relatives. We highlight a geographic continuum between agro-biodiversity hotspots that contain high richness in species that are intensively used and well known by humanity (i.e., major crops and most viewed species on Wikipedia) and biodiversity hotspots encompassing species that are less heavily used and documented (i.e., crop wild relatives and species lacking information on Wikipedia). Our contribution highlights the key considerations needed for further developing a unifying concept of agro-biodiversity hotspots that encompasses multiple facets of diversity (including genetic and phylogenetic) and the linkage with overall biodiversity. This integration will ultimately enhance our understanding of the geography of human-plant interactions and help guide the preservation of nature and its contributions to people.
43.	Ragazzola, Federica, et al. (author) Structural and elemental analysis of the freshwater, low-Mg calcite coralline alga Pneophyllum cetinaensis 2020 In: PLANTS. - : MDPI. - 2223-7747. ; 9:9 Journal article (peer-reviewed)abstract Coralline algae are one of the most diversified groups of red algae and represent a major component of marine benthic habitats from the poles to the tropics. This group was believed to be exclusively marine until 2016, when the first freshwater coralline algae Pneophyllum cetinaensis was discovered in the Cetina River, southern Croatia. While several studies investigated the element compositions of marine coralline algal thalli, no information is yet available for the freshwater species. Using XRD, LA-ICP-MS and nano indentation, this study presents the first living low-Mg calcite coralline algae with Mg concentrations ten times lower than is common for the average marine species. Despite the lower Mg concentrations, hardness and elastic modulus (1.71 ± 1.58 GPa and 29.7 ± 18.0 GPa, respectively) are in the same range as other marine coralline algae, possibly due to other biogenic impurities. When compared to marine species, Ba/Ca values were unusually low, even though Ba concentrations are generally higher in rivers than in seawater. These low values might be linked to different physical and chemical characteristics of the Cetina River.
44.	Salminen, Tiina A, et al. (author) Deciphering the Evolution and Development of the Cuticle by Studying Lipid Transfer Proteins in Mosses and Liverworts. 2018 In: Plants (Basel, Switzerland). - : MDPI AG. - 2223-7747. ; 7:1 Journal article (peer-reviewed)abstract When plants conquered land, they developed specialized organs, tissues, and cells in order to survive in this new and harsh terrestrial environment. New cell polymers such as the hydrophobic lipid-based polyesters cutin, suberin, and sporopollenin were also developed for protection against water loss, radiation, and other potentially harmful abiotic factors. Cutin and waxes are the main components of the cuticle, which is the waterproof layer covering the epidermis of many aerial organs of land plants. Although the in vivo functions of the group of lipid binding proteins known as lipid transfer proteins (LTPs) are still rather unclear, there is accumulating evidence suggesting a role for LTPs in the transfer and deposition of monomers required for cuticle assembly. In this review, we first present an overview of the data connecting LTPs with cuticle synthesis. Furthermore, we propose liverworts and mosses as attractive model systems for revealing the specific function and activity of LTPs in the biosynthesis and evolution of the plant cuticle.
45.	Sayed, Mohammed A., et al. (author) Analyses of mads‐box genes suggest hvmads56 to regulate lateral spikelet development in barley 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10:12 Journal article (peer-reviewed)abstract MADS‐box transcription factors are crucial regulators of inflorescence and flower development in plants. Therefore, the recent interest in this family has received much attention in plant breeding programs due to their impact on plant development and inflorescence architecture. The aim of this study was to investigate the role of HvMADS‐box genes in lateral spikelet development in barley (Hordeum vulgare L.). A set of 30 spike‐contrasting barley lines were phenotypically and genotypically investigated under controlled conditions. We detected clear variations in the spike and spikelet development during the developmental stages among the tested lines. The lateral flo-rets in the deficiens and semi‐deficiens lines were more reduced than in two‐rowed cultivars except cv. Kristina. Interestingly, cv. Kristina, int‐h.43 and int‐i.39 exhibited the same behavior as def.5, def.6, semi‐def.1, semi‐def.8 regarding development and showed reduced lateral florets size. In HOR1555, HOR7191 and HOR7041, the lateral florets continued their development, eventually setting seeds. In contrast, lateral florets in two‐rowed barley stopped differentiating after the awn primordia stage giving rise to lateral floret sterility. At harvest, the lines tested showed large variation for all central and lateral spikelet‐related traits. Phylogenetic analysis showed that more than half of the 108 MADS‐box genes identified are highly conserved and are expressed in different barley tissues. Re-sequence analysis of a subset of these genes showed clear polymorphism in either SNPs or in/del. Variation in HvMADS56 correlated with altered lateral spikelet morphology. This suggests that HvMADS56 plays an important role in lateral spikelet development in barley.
46.	Schmidt, John, et al. (author) Substrate and plant genotype strongly influence the growth and gene expression response to trichoderma afroharzianum T22 in sugar beet 2020 In: Plants. - : MDPI AG. - 2223-7747. ; 9:8, s. 1-14 Journal article (peer-reviewed)abstract Many strains of Trichoderma fungi have beneficial effects on plant growth and pathogen control, but little is known about the importance of plant genotype, nor the underlying mechanisms. We aimed to determine the effect of sugar beet genotypic variation on Trichoderma biostimulation. The effect of Trichoderma afroharzianum T22 on sugar beet inbred genotypes were investigated in soil and on sterile agar medium regarding plant growth, and by quantitative reverse transcriptase-linked polymerase chain reaction (qRT-PCR) analysis for gene expression. In soil, T22 application induced up to 30% increase or decrease in biomass, depending on plant genotype. In contrast, T22 treatment of sterile-grown seedlings resulted in a general decrease in fresh weight and root length across all sugar beet genotypes. Root colonization of T22 did not vary between the sugar beet genotypes. Sand-and sterile-grown roots were investigated by qRT-PCR for expression of marker genes for pathogen response pathways. Genotype-dependent effects of T22 on, especially, the jasmonic acid/ethylene expression marker PR3 were observed, and the effects were further dependent on the growth system used. Thus, both growth substrate and sugar beet genotype strongly affect the outcome of inoculation with T. afroharzianum T22.
47.	Selga, Catja, et al. (author) A Bioinformatics Pipeline to Identify a Subset of SNPs for Genomics-Assisted Potato Breeding 2021 In: Plants. - : MDPI AG. - 2223-7747. ; 10 Journal article (peer-reviewed)abstract Modern potato breeding methods following a genomic-led approach provide means for shortening breeding cycles and increasing breeding efficiency across selection cycles. Acquiring genetic data for large breeding populations remains expensive. We present a pipeline to reduce the number of single nucleotide polymorphisms (SNPs) to lower the cost of genotyping. First, we reduced the number of individuals to be genotyped with a high-throughput method according to the multi-trait variation as defined by principal component analysis of phenotypic characteristics. Next, we reduced the number of SNPs by pruning for linkage disequilibrium. By adjusting the square of the correlation coefficient between two adjacent loci, we obtained reduced subsets of SNPs. We subsequently tested these SNP subsets by two methods; (1) a genome-wide association study (GWAS) for marker identification, and (2) genomic selection (GS) to predict genomic estimated breeding values. The results indicate that both GWAS and GS can be done without loss of information after SNP reduction. The pipeline allows for creating custom SNP subsets to cover all variation found in any particular breeding population. Low-throughput genotyping will reduce the genotyping cost associated with large populations, thereby making genomic breeding methods applicable to large potato breeding populations by reducing genotyping costs.
48.	Souguir, Dalila, et al. (author) Vicia—Micronucleus Test Application for Saline Irrigation Water Risk Assessment 2022 In: Plants. - : MDPI AG. - 2223-7747. ; 11:3 Journal article (peer-reviewed)abstract In view of climate change, increasing soil salinity is expected worldwide. It is therefore important to improve prediction ability of plant salinity effects. For this purpose, brackish/saline irrigation water from two areas in central and coastal Tunisia was sampled. The water samples were classified as C3 (EC: 2.01–2.24 dS m−1) and C4 (EC: 3.46–7.00 dS m−1), indicating that the water was questionable and not suitable for irrigation, respectively. The water samples were tested for their genotoxic potential and growth effects on Vicia faba seedlings. Results showed a decrease in mitotic index (MI) and, consequently, growth parameters concomitant to the appearance of micronucleus (MCN) and chromosome aberrations when the water salinity increased. Salt ion concentration had striking influence on genome stability and growth parameters. Pearson correlation underlined the negative connection between most ions in the water inappropriate for irrigation (C4) and MI as well as growth parameters. MI was strongly influenced by Mg2+, Na+, Cl−, and to a less degree Ca2+, K+, and SO42−. Growth parameters were moderately to weakly affected by K+ and Ca2+, respectively. Regarding MCN, a very strong positive correlation was found for MCN and K+. Despite its short-term application, the Vicia-MCN Test showed a real ability to predict toxicity induced by salt ions con-firming that is has a relevant role in hazard identification and risk assessment of salinity effects.
49.	Stuart, David, et al. (author) Aerobic barley mg-protoporphyrin ix monomethyl ester cyclase is powered by electrons from ferredoxin 2020 In: Plants. - : MDPI AG. - 2041-2851 .- 2223-7747. ; 9:9 Journal article (peer-reviewed)abstract Chlorophyll is the light-harvesting molecule central to the process of photosynthesis. Chlorophyll is synthesized through 15 enzymatic steps. Most of the reactions have been characterized using recombinant proteins. One exception is the formation of the isocyclic E-ring characteristic of chlorophylls. This reaction is catalyzed by the Mg-protoporphyrin IX monomethyl ester cyclase encoded by Xantha-l in barley (Hordeum vulgare L.). The Xantha-l gene product (XanL) is a membrane-bound diiron monooxygenase, which requires additional soluble and membrane-bound components for its activity. XanL has so far been impossible to produce as an active recombinant protein for in vitro assays, which is required for deeper biochemical and structural analyses. In the present work, we performed cyclase assays with soluble and membrane-bound fractions of barley etioplasts. Addition of antibodies raised against ferredoxin or ferredoxin-NADPH oxidoreductase (FNR) inhibited assays, strongly suggesting that reducing electrons for the cyclase reaction involves ferredoxin and FNR. We further developed a completely recombinant cyclase assay. Expression of active XanL required co-expression with an additional protein, Ycf54. In vitro cyclase activity was obtained with recombinant XanL in combination with ferredoxin and FNR. Our experiment demonstrates that the cyclase is a ferredoxin-dependent enzyme. Ferredoxin is part of the photosynthetic electron-transport chain, which suggests that the cyclase reaction might be connected to photosynthesis under light conditions.
50.	Svenberg, Linus, et al. (author) Chemical Diversity between Three Graminoid Plants Found in Western Kenya Analyzed by Headspace Solid-Phase Microextraction Gas Chromatography-Mass Spectrometry (HS-SPME-GC-MS) 2021 In: PLANTS. - : MDPI AG. - 2223-7747. ; 10:11, s. 2423- Journal article (peer-reviewed)abstract In recent work, it was shown that the graminoid plants Cynodon dactylon (Poaceae), Cyperus exaltatus (Cyperaceae), and Panicum repens (Poaceae) have an ovipositional effect on the malaria vector Anopheles gambiae in olfactometric bioassays. In order to get a view of the diversity of semiochemicals present in the environment of the vector during olfactometric trials, in the present work, the volatile profiles of these graminoid plants were analyzed using headspace solid-phase microextraction (HS-SPME) together with gas chromatography-mass spectrometry (GC-MS). In addition, one-way ANOVA comparison of compounds detected in two or more headspace samples are presented in order to provide a basis for comparison of compounds that could constitute a starting point for novel blends of volatile organic compounds to be tested as oviposition attractants.

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