Plants

21 pages, 2568 KiB

Open AccessArticle

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

by Dong-Mei Li, Gen-Fa Zhu, Ye-Chun Xu, Yuan-Jun Ye and Jin-Mei Liu

Plants 2020, 9(2), 286; https://doi.org/10.3390/plants9020286 - 24 Feb 2020

Cited by 33 | Viewed by 4849

Abstract

Alpinia katsumadai (A. katsumadai), Alpinia oxyphylla (A. oxyphylla) and Alpinia pumila (A. pumila), which belong to the family Zingiberaceae, exhibit multiple medicinal properties. The chloroplast genome of a non-model plant provides valuable information for species identification and [...] Read more.

Alpinia katsumadai (A. katsumadai), Alpinia oxyphylla (A. oxyphylla) and Alpinia pumila (A. pumila), which belong to the family Zingiberaceae, exhibit multiple medicinal properties. The chloroplast genome of a non-model plant provides valuable information for species identification and phylogenetic analysis. Here, we sequenced three complete chloroplast genomes of A. katsumadai, A. oxyphylla sampled from Guangdong and A. pumila, and analyzed the published chloroplast genomes of Alpinia zerumbet (A. zerumbet) and A. oxyphylla sampled from Hainan to retrieve useful chloroplast molecular resources for Alpinia. The five Alpinia chloroplast genomes possessed typical quadripartite structures comprising of a large single copy (LSC, 87,248–87,667 bp), a small single copy (SSC, 15,306–18,295 bp) and a pair of inverted repeats (IR, 26,917–29,707 bp). They had similar gene contents, gene orders and GC contents, but were slightly different in the numbers of small sequence repeats (SSRs) and long repeats. Interestingly, fifteen highly divergent regions (rpl36, ycf1, rps15, rpl22, infA, psbT-psbN, accD-psaI, petD-rpoA, psaC-ndhE, ccsA-ndhD, ndhF-rpl32, rps11-rpl36, infA-rps8, psbC-psbZ, and rpl32-ccsA), which could be suitable for species identification and phylogenetic studies, were detected in the Alpinia chloroplast genomes. Comparative analyses among the five chloroplast genomes indicated that 1891 mutational events, including 304 single nucleotide polymorphisms (SNPs) and 118 insertion/deletions (indels) between A. pumila and A. katsumadai, 367 SNPs and 122 indels between A. pumila and A. oxyphylla sampled from Guangdong, 331 SNPs and 115 indels between A. pumila and A. zerumbet, 371 SNPs and 120 indels between A. pumila and A. oxyphylla sampled from Hainan, and 20 SNPs and 23 indels between the two accessions of A. oxyphylla, were accurately located. Additionally, phylogenetic relationships based on SNP matrix among 28 whole chloroplast genomes showed that Alpinia was a sister branch to Amomum in the family Zingiberaceae, and that the five Alpinia accessions were divided into three groups, one including A. pumila, another including A. zerumbet and A. katsumadai, and the other including two accessions of A. oxyphylla. In conclusion, the complete chloroplast genomes of the three medicinal Alpinia species in this study provided valuable genomic resources for further phylogeny and species identification in the family Zingiberaceae. Full article

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24 pages, 1290 KiB

Open AccessArticle

Use of Nitric Oxide and Hydrogen Peroxide for Better Yield of Wheat (Triticum aestivum L.) under Water Deficit Conditions: Growth, Osmoregulation, and Antioxidative Defense Mechanism

by Noman Habib, Qasim Ali, Shafaqat Ali, Muhammad Tariq Javed, Muhammad Zulqurnain Haider, Rashida Perveen, Muhammad Rizwan Shahid, Muhammad Rizwan, Mohamed M. Abdel-Daim, Amr Elkelish and May Bin-Jumah

Plants 2020, 9(2), 285; https://doi.org/10.3390/plants9020285 - 22 Feb 2020

Cited by 139 | Viewed by 8186

Abstract

The present experiment was carried out to study the influences of exogenously-applied nitric oxide (NO) donor sodium nitroprusside (SNP) and hydrogen peroxide (H₂O₂) as seed primers on growth and yield in relation with different physio-biochemical parameters, antioxidant activities, and [...] Read more.

The present experiment was carried out to study the influences of exogenously-applied nitric oxide (NO) donor sodium nitroprusside (SNP) and hydrogen peroxide (H₂O₂) as seed primers on growth and yield in relation with different physio-biochemical parameters, antioxidant activities, and osmolyte accumulation in wheat plants grown under control (100% field capacity) and water stress (60% field capacity) conditions. During soaking, the seeds were covered and kept in completely dark. Drought stress markedly reduced the plant growth, grain yield, leaf photosynthetic pigments, total phenolic content (TPC), total soluble proteins (TSP), leaf water potential (Ψ_w), leaf turgor potential (Ψ_p), osmotic potential (Ψ_s), and leaf relative water content (LRWC), while it increased the activities of enzymatic antioxidants and the accumulation of leaf ascorbic acid (AsA), proline (Pro), glycine betaine (GB), malondialdehyde (MDA), and H₂O₂. However, seed priming with SNP and H₂O₂ alone and in combination mitigated the deleterious effects of water stress on growth and yield by improving the Ψ_w, Ψ_s, Ψ_p, photosynthetic pigments, osmolytes accumulation (GB and Pro), TSP, and the antioxidative defense mechanism. Furthermore, the application of NO and H₂O₂ as seed primers also reduced the accumulation of H₂O₂ and MDA contents. The effectiveness was treatment-specific and the combined application was also found to be effective. The results revealed that exogenous application of NO and H₂O₂ was effective in increasing the tolerance of wheat plants under drought stress in terms of growth and grain yield by regulating plant–water relations, the antioxidative defense mechanism, and accumulation of osmolytes, and by reducing the membrane lipid peroxidation. Full article

(This article belongs to the Special Issue Plant Responses to Water-Deficit Stress)

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13 pages, 3599 KiB

Open AccessArticle

First Phylogeny of Bitterbush Family, Picramniaceae (Picramniales)

by Alexey Shipunov, Shyla Carr, Spencer Furniss, Kyle Pay and José Rubens Pirani

Plants 2020, 9(2), 284; https://doi.org/10.3390/plants9020284 - 21 Feb 2020

Cited by 4 | Viewed by 4237

Abstract

Picramniaceae is the only member of Picramniales which is sister to the clade (Sapindales (Huerteales (Malvales, Brassicales))) in the rosidsmalvids. Not much is known about most aspects of their ecology, geography, and morphology. The family is restricted to American tropics. Picramniaceae representatives are [...] Read more.

Picramniaceae is the only member of Picramniales which is sister to the clade (Sapindales (Huerteales (Malvales, Brassicales))) in the rosidsmalvids. Not much is known about most aspects of their ecology, geography, and morphology. The family is restricted to American tropics. Picramniaceae representatives are rich in secondary metabolites; some species are known to be important for pharmaceutical purposes. Traditionally, Picramniaceae was classified as a subfamily of Simaroubaceae, but from 1995 on, it has been segregated containing two genera, Picramnia and Alvaradoa, with the recent addition of a third genus, Nothotalisia, described in 2011. Only a few species of the family have been the subject of DNA-related research, and fewer than half of the species have been included in morphological phylogenetic analyses. It is clear that Picramniaceae remains a largely under-researched plant group. Here we present the first molecular phylogenetic tree of the group, based on both chloroplast and nuclear markers, widely adopted in the plant DNA barcoding. The main findings are: The family and its genera are monophyletic and Picramnia is sister to two other genera; some clades corroborate previous assumptions of relationships made on a morphological or geographical basis, while most parts of the molecular topology suggest high levels of homoplasy in the morphological evolution of Picramnia. Full article

(This article belongs to the Special Issue Plant DNA Barcode)

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15 pages, 2590 KiB

Open AccessArticle

Natural Variation in Volatile Emissions of the Invasive Weed Calluna vulgaris in New Zealand

by Evans Effah, D. Paul Barrett, Paul G. Peterson, A. Jonathan R. Godfrey, Murray A. Potter, Jarmo K. Holopainen and Andrea Clavijo McCormick

Plants 2020, 9(2), 283; https://doi.org/10.3390/plants9020283 - 21 Feb 2020

Cited by 26 | Viewed by 4927

Abstract

Invasive plants pose a threat to natural ecosystems, changing the community composition and ecological dynamics. One aspect that has received little attention is the production and emission of volatile organic compounds (VOCs) by invasive plants. Investigating VOCs is important because they are involved [...] Read more.

Invasive plants pose a threat to natural ecosystems, changing the community composition and ecological dynamics. One aspect that has received little attention is the production and emission of volatile organic compounds (VOCs) by invasive plants. Investigating VOCs is important because they are involved in vital ecological interactions such as pollination, herbivory and plant competition. Heather, Calluna vulgaris, is a major invasive weed in New Zealand, especially on the Central Plateau, where it has spread rapidly since its introduction in 1912, outcompeting native species. However, the chemical behaviour of heather in its invaded ranges is poorly understood. We aimed to explore the natural variation in volatile emissions of heather and the biotic and abiotic factors influencing them on the Central Plateau of New Zealand. To this end, foliar volatiles produced by heather at four different sites were collected and analysed using gas chromatography coupled to mass spectrometry. Soil properties, herbivory and other environmental data were also collected at each site to investigate their effects on VOC emissions using generalised linear models (GLMs). Our results reveal significant differences in VOC emissions between sites and suggest that soil nutrients are the main factor accounting for these differences. Herbivory and temperature had only a minor effect, while soil water content had no impact. Further studies are needed to investigate how these variations in the invasive plant’s foliar volatiles influence native species. Full article

(This article belongs to the Section Plant Ecology)

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19 pages, 1156 KiB

Open AccessArticle

Exploring Heterosis in Melon (Cucumis melo L.)

by Marco Napolitano, Niccolò Terzaroli, Subash Kashyap, Luigi Russi, Elen Jones-Evans and Emidio Albertini

Plants 2020, 9(2), 282; https://doi.org/10.3390/plants9020282 - 21 Feb 2020

Cited by 26 | Viewed by 5571

Abstract

Heterosis is the superiority of an F₁ hybrid over its parents. Since this phenomenon is still unclear in melon, a half diallel experiment based on eight genetically distant breeding lines was conducted in six environments of Central Italy, assessing commercially important traits: [...] Read more.

Heterosis is the superiority of an F₁ hybrid over its parents. Since this phenomenon is still unclear in melon, a half diallel experiment based on eight genetically distant breeding lines was conducted in six environments of Central Italy, assessing commercially important traits: yield, total soluble solids (TSS), and days to ripening (DTR). To estimate the additive (general combining ability; GCA) and the non-additive gene effects (specific combining ability; SCA), yield was analyzed by Griffing’s methods two and four, and the results were compared to the GGE (Genotype plus Genotype by Environment interaction) biplot methodology; TSS and earliness were evaluated only by Griffing’s method four. Overall, GCAs were significantly more relevant than SCAs for all examined traits. Least square means (LsM), mid-parent heterosis (MPH), best-parent heterosis (BPH), as well as Euclidean and Mahalanobis’ distances were calculated and compared with the genetic distance (GD). As a few correlations were found statistically significant (only for TSS), it was difficult to predict the value of a hybrid combination only by knowing the genetic distance of its parents. Despite this, heterosis was observed, indicating either the presence of epistatic effects (additive × additive interactions) and/or an underestimate of SCAs embedded within Griffing’s method. The significant Env × Entries source of variation suggests development of hybrids in specific environments. The results are discussed with a breeding perspective. Full article

(This article belongs to the Special Issue Plants Heterosis)

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20 pages, 1969 KiB

Open AccessArticle

Exogenous Kinetin Promotes the Nonenzymatic Antioxidant System and Photosynthetic Activity of Coffee (Coffea arabica L.) Plants Under Cold Stress Conditions

by Robert Acidri, Yumiko Sawai, Yuko Sugimoto, Takuo Handa, Daisuke Sasagawa, Tsugiyaki Masunaga, Sadahiro Yamamoto and Eiji Nishihara

Plants 2020, 9(2), 281; https://doi.org/10.3390/plants9020281 - 21 Feb 2020

Cited by 31 | Viewed by 4886

Abstract

Coffee plants are seasonally exposed to low chilling temperatures in many coffee-producing regions. In this study, we investigated the ameliorative effects of kinetin—a cytokinin elicitor compound on the nonenzymatic antioxidants and the photosynthetic physiology of young coffee plants subjected to cold stress conditions. [...] Read more.

Coffee plants are seasonally exposed to low chilling temperatures in many coffee-producing regions. In this study, we investigated the ameliorative effects of kinetin—a cytokinin elicitor compound on the nonenzymatic antioxidants and the photosynthetic physiology of young coffee plants subjected to cold stress conditions. Although net CO₂ assimilation rates were not significantly affected amongst the treatments, the subjection of coffee plants to cold stress conditions caused low gas exchanges and photosynthetic efficiency, which was accompanied by membrane disintegration and the breakdown of chlorophyll pigments. Kinetin treatment, on the other hand, maintained a higher intercellular-to-ambient CO₂ concentration ratio with concomitant improvement in stomatal conductance and mesophyll efficiency. Moreover, the leaves of kinetin-treated plants maintained slightly higher photochemical quenching (qP) and open photosystem II centers (qL), which was accompanied by higher electron transfer rates (ETRs) compared to their non-treated counterparts under cold stress conditions. The exogenous foliar application of kinetin also stimulated the metabolism of caffeine, trigonelline, 5-caffeoylquinic acid, mangiferin, anthocyanins and total phenolic content. The contents of these nonenzymatic antioxidants were highest under cold stress conditions in kinetin-treated plants than during optimal conditions. Our results further indicated that the exogenous application of kinetin increased the total radical scavenging capacity of coffee plants. Therefore, the exogenous application of kinetin has the potential to reinforce antioxidant capacity, as well as modulate the decline in photosynthetic productivity resulting in improved tolerance under cold stress conditions. Full article

(This article belongs to the Special Issue Roles of Cytokinins in Plants and Their Response to Environmental Stimuli)

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16 pages, 6613 KiB

Open AccessArticle

The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins

by Bastien Malbert, Matthias Burger, Mauricio Lopez-Obando, Kevin Baudry, Alexandra Launay-Avon, Barbara Härtel, Daniil Verbitskiy, Anja Jörg, Richard Berthomé, Claire Lurin, Mizuki Takenaka and Etienne Delannoy

Plants 2020, 9(2), 280; https://doi.org/10.3390/plants9020280 - 21 Feb 2020

Cited by 19 | Viewed by 4647

Abstract

C to U editing is one of the post-transcriptional steps which are required for the proper expression of chloroplast and mitochondrial genes in plants. It depends on several proteins acting together which include the PLS-class pentatricopeptide repeat proteins (PPR). DYW2 was recently shown [...] Read more.

C to U editing is one of the post-transcriptional steps which are required for the proper expression of chloroplast and mitochondrial genes in plants. It depends on several proteins acting together which include the PLS-class pentatricopeptide repeat proteins (PPR). DYW2 was recently shown to be required for the editing of many sites in both organelles. In particular almost all the sites associated with the E+ subfamily of PPR proteins are depending on DYW2, suggesting that DYW2 is required for the function of E+-type PPR proteins. Here we strengthened this link by identifying 16 major editing sites controlled by 3 PPR proteins: OTP90, a DYW-type PPR and PGN and MEF37, 2 E+-type PPR proteins. A re-analysis of the DYW2 editotype showed that the 49 sites known to be associated with the 18 characterized E+-type PPR proteins all depend on DYW2. Considering only the 288 DYW2-dependent editing sites as potential E+-type PPR sites, instead of the 795 known editing sites, improves the performances of binding predictions systems based on the PPR code for E+-type PPR proteins. However, it does not compensate for poor binding predictions. Full article

(This article belongs to the Special Issue Chloroplast RNA Metabolism and Biology)

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16 pages, 862 KiB

Open AccessReview

Prospects of Arbuscular Mycorrhizal Fungi Utilization in Production of Allium Plants

by Nadezhda Golubkina, Leonid Krivenkov, Agnieszka Sekara, Viliana Vasileva, Alessio Tallarita and Gianluca Caruso

Plants 2020, 9(2), 279; https://doi.org/10.3390/plants9020279 - 21 Feb 2020

Cited by 38 | Viewed by 6507

Abstract

The need to improve crop yield and quality, decrease the level of mineral fertilizers and pesticides/herbicides supply, and increase plants’ immunity are important topics of agriculture in the 21st century. In this respect, arbuscular mycorrhizal fungi (AMF) may be considered as a crucial [...] Read more.

The need to improve crop yield and quality, decrease the level of mineral fertilizers and pesticides/herbicides supply, and increase plants’ immunity are important topics of agriculture in the 21st century. In this respect, arbuscular mycorrhizal fungi (AMF) may be considered as a crucial tool in the development of a modern environmentally friendly agriculture. The efficiency of AMF application is connected to genetic peculiarities of plant and AMF species, soil characteristics and environmental factors, including biotic and abiotic stresses, temperature, and precipitation. Among vegetable crops, Allium species are particularly reactive to soil mycorrhiza, due to their less expanded root apparatus surface compared to most other species. Moreover, Allium crops are economically important and able to synthesize powerful anti-carcinogen compounds, such as selenomethyl selenocysteine and gamma-glutamyl selenomethyl selenocysteine, which highlights the importance of the present detailed discussion about the AMF use prospects to enhance Allium plant growth and development. This review reports the available information describing the AMF effects on the seasonal, inter-, and intra-species variations of yield, biochemical characteristics, and mineral composition of Allium species, with a special focus on the selenium accumulation both in ordinary conditions and under selenium supply. Full article

(This article belongs to the Special Issue Factors Affecting Yield, Quality, Antioxidants, Mineral Composition and Residual Biomass Valorization of Vegetable Crops)

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12 pages, 2869 KiB

Open AccessArticle

Effects of Genotype and Culture Conditions on Microspore Embryogenesis and Plant Regeneration in Brassica Rapa ssp. Rapa L.

by Daria Shumilina, Dmitry Kornyukhin, Elena Domblides, Alexey Soldatenko and Anna Artemyeva

Plants 2020, 9(2), 278; https://doi.org/10.3390/plants9020278 - 21 Feb 2020

Cited by 24 | Viewed by 7189

Abstract

Turnip is a biennial crop and, consequently, the creation of pure lines for breeding is a time-consuming process. The production of pure turnip lines using doubled haploids produced in isolated microspore culture has not been sufficiently developed. The aim of the present work [...] Read more.

Turnip is a biennial crop and, consequently, the creation of pure lines for breeding is a time-consuming process. The production of pure turnip lines using doubled haploids produced in isolated microspore culture has not been sufficiently developed. The aim of the present work was to determine some key factors inducing embryogenesis in the isolated microspore culture of turnip, as well as investigating the manners of embryo development. It was shown that the acidity of the medium is an important factor in embryo production; different optimal pH levels ranging from 6.2 to 6.6 corresponded to individual genotypes. Such factors as the cold treatment of buds and the addition of activated charcoal to the nutrient medium increased the responsiveness of all genotypes studied. The turnip variety ‘Ronde witte roodkop herfst’ demonstrated a genetic disorder in the development of microspores; namely, non-separation of some microspores from tetrads. In the in vitro culture, each of the daughter microspores developed on its own. This indicates the dependence of the possibility of embryogenesis in the turnip microspore culture on the genotype. Results suggest that the initiation of secondary embryogenesis in primary embryos leads to an increase in the proportion of doubled haploid plants. Full article

(This article belongs to the Collection Doubled Haploid Technology in Plant Breeding)

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14 pages, 259 KiB

Open AccessArticle

A PCR, qPCR, and LAMP Toolkit for the Detection of the Wheat Blast Pathogen in Seeds

by Maud Thierry, Axel Chatet, Elisabeth Fournier, Didier Tharreau and Renaud Ioos

Plants 2020, 9(2), 277; https://doi.org/10.3390/plants9020277 - 21 Feb 2020

Cited by 20 | Viewed by 4933

Abstract

Wheat blast is a devastating disease caused by the pathogenic fungus Pyricularia oryzae. Wheat blast first emerged in South America before more recently reaching Bangladesh. Even though the pathogen can spread locally by air-dispersed spores, long-distance spread is likely to occur via infected [...] Read more.

Wheat blast is a devastating disease caused by the pathogenic fungus Pyricularia oryzae. Wheat blast first emerged in South America before more recently reaching Bangladesh. Even though the pathogen can spread locally by air-dispersed spores, long-distance spread is likely to occur via infected wheat seed or grain. Wheat blast epidemics are caused by a genetic lineage of the fungus, called the Triticum lineage, only differing from the other P. oryzae lineages by less than 1% genetic divergence. In order to prevent further spread of this pathogen to other wheat-growing areas in the world, sensitive and specific detection tools are needed to test for contamination of traded seed lots by the P. oryzae Triticum lineage. In this study, we adopted a comparative genomics approach to identify new loci specific to the P. oryzae Triticum lineage and used them to design a set of new markers that can be used in conventional polymerase chain reaction (PCR), real-time PCR, or loop-mediated isothermal amplification (LAMP) for the detection of the pathogen, with improved inclusivity and specificity compared to currently available tests. A preliminary biological enrichment step of the seeds was shown to improve the sensitivity of the tests, which enabled the detection of the target at an infection rate as low as 0.25%. Combined with others, this new toolkit may be particularly beneficial in preventing the trade of contaminated seeds and in limiting the spread of the disease. Full article

(This article belongs to the Special Issue Detection and Diagnostics of Fungal and Oomycete Plant Pathogens)

24 pages, 2332 KiB

Open AccessReview

Molecular Basis of Root Nodule Symbiosis between Bradyrhizobium and ‘Crack-Entry’ Legume Groundnut (Arachis hypogaea L.)

by Vinay Sharma, Samrat Bhattacharyya, Rakesh Kumar, Ashish Kumar, Fernando Ibañez, Jianping Wang, Baozhu Guo, Hari K. Sudini, Subramaniam Gopalakrishnan, Maitrayee DasGupta, Rajeev K. Varshney and Manish K. Pandey

Plants 2020, 9(2), 276; https://doi.org/10.3390/plants9020276 - 20 Feb 2020

Cited by 58 | Viewed by 15413

Abstract

Nitrogen is one of the essential plant nutrients and a major factor limiting crop productivity. To meet the requirements of sustainable agriculture, there is a need to maximize biological nitrogen fixation in different crop species. Legumes are able to establish root nodule symbiosis [...] Read more.

Nitrogen is one of the essential plant nutrients and a major factor limiting crop productivity. To meet the requirements of sustainable agriculture, there is a need to maximize biological nitrogen fixation in different crop species. Legumes are able to establish root nodule symbiosis (RNS) with nitrogen-fixing soil bacteria which are collectively called rhizobia. This mutualistic association is highly specific, and each rhizobia species/strain interacts with only a specific group of legumes, and vice versa. Nodulation involves multiple phases of interactions ranging from initial bacterial attachment and infection establishment to late nodule development, characterized by a complex molecular signalling between plants and rhizobia. Characteristically, legumes like groundnut display a bacterial invasion strategy popularly known as “crack-entry’’ mechanism, which is reported approximately in 25% of all legumes. This article accommodates critical discussions on the bacterial infection mode, dynamics of nodulation, components of symbiotic signalling pathway, and also the effects of abiotic stresses and phytohormone homeostasis related to the root nodule symbiosis of groundnut and Bradyrhizobium. These parameters can help to understand how groundnut RNS is programmed to recognize and establish symbiotic relationships with rhizobia, adjusting gene expression in response to various regulations. This review further attempts to emphasize the current understanding of advancements regarding RNS research in the groundnut and speculates on prospective improvement possibilities in addition to ways for expanding it to other crops towards achieving sustainable agriculture and overcoming environmental challenges. Full article

(This article belongs to the Special Issue Nitrogen-Fixing Plants )

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18 pages, 2122 KiB

Open AccessArticle

Seed Weight as a Covariate in Association and Prediction Studies for Biomass Traits in Maize Seedlings

by Vlatko Galic, Maja Mazur, Andrija Brkic, Josip Brkic, Antun Jambrovic, Zvonimir Zdunic and Domagoj Simic

Plants 2020, 9(2), 275; https://doi.org/10.3390/plants9020275 - 20 Feb 2020

Cited by 3 | Viewed by 3650

Abstract

Background: The seedling stage has received little attention in maize breeding to identify genotypes tolerant to water deficit. The aim of this study is to evaluate incorporation of seed weight (expressed as hundred kernel weight, HKW) as a covariate into genomic association and [...] Read more.

Background: The seedling stage has received little attention in maize breeding to identify genotypes tolerant to water deficit. The aim of this study is to evaluate incorporation of seed weight (expressed as hundred kernel weight, HKW) as a covariate into genomic association and prediction studies for three biomass traits in a panel of elite inbred lines challenged by water withholding at seedling stage. Methods: 109 genotyped-by-sequencing (GBS) elite maize inbreds were phenotyped for HKW and planted in controlled conditions (16/8 day/night, 25 °C, 50% RH, 200 µMol/m²/s) in trays filled with soil. Plants in control (C) were watered every two days, while watering was stopped for 10 days in water withholding (WW). Fresh weight (FW), dry weight (DW), and dry matter content (DMC) were measured. Results: Adding HKW as a covariate increased the power of detection of associations in FW and DW by 44% and increased genomic prediction accuracy in C and decreased in WW. Conclusions: Seed weight was effectively incorporated into association studies for biomass traits in maize seedlings, whereas the incorporation into genomic predictions, particularly in water-stressed plants, was not worthwhile. Full article

(This article belongs to the Special Issue The Impacts of Abiotic Stresses on Plant Development)

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15 pages, 3057 KiB

Open AccessArticle

Water Deficit Affects the Growth and Leaf Metabolite Composition of Young Loquat Plants

by Giovanni Gugliuzza, Giuseppe Talluto, Federico Martinelli, Vittorio Farina and Riccardo Lo Bianco

Plants 2020, 9(2), 274; https://doi.org/10.3390/plants9020274 - 19 Feb 2020

Cited by 19 | Viewed by 4623

Abstract

Water scarcity in the Mediterranean area is very common and understanding responses to drought is important for loquat management and production. The objective of this study was to evaluate the effect of drought on the growth and metabolism of loquat. Ninety two-year-old plants [...] Read more.

Water scarcity in the Mediterranean area is very common and understanding responses to drought is important for loquat management and production. The objective of this study was to evaluate the effect of drought on the growth and metabolism of loquat. Ninety two-year-old plants of ‘Marchetto’ loquat grafted on quince were grown in the greenhouse in 12-liter pots and three irrigation regimes were imposed starting on 11 May and lasting until 27 July, 2013. One-third of the plants was irrigated with 100% of the water consumed (well watered, WW), a second group of plants was irrigated with 66% of the water supplied to the WW plants (mild drought, MD), and a third group was irrigated with 33% of the water supplied to the WW plants (severe drought, SD). Minimum water potential levels of −2.0 MPa were recorded in SD plants at the end of May. Photosynthetic rates were reduced according to water supply (WW > MD > SD), especially during the morning hours. By the end of the trial, severe drought reduced all growth parameters and particularly leaf growth. Drought induced early accumulation of sorbitol in leaves, whereas other carbohydrates were not affected. Of over 100 leaf metabolites investigated, 9 (squalene, pelargonic acid, glucose-1-phosphate, palatinol, capric acid, aconitic acid, xylitol, lauric acid, and alanine) were found to be useful to discriminate between the three irrigation groups, suggesting their involvement in loquat metabolism under drought conditions. Loquat behaved as a moderately drought-tolerant species (limited stem water potential and growth reductions) and the accumulation of sorbitol in favor of sucrose in mildly-stressed plants may be considered an early protective mechanism against leaf dehydration and a potential biochemical marker for precise irrigation management. Full article

(This article belongs to the Special Issue Physiological Responses of Tree Fruits to Environmental and Management Factors)

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13 pages, 377 KiB

Open AccessEditor’s ChoiceArticle

Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting Prunus spp.

by Alfredo Diaz-Lara, Kristian Stevens, Vicki Klaassen, Deborah Golino and Maher Al Rwahnih

Plants 2020, 9(2), 273; https://doi.org/10.3390/plants9020273 - 19 Feb 2020

Cited by 22 | Viewed by 5357

Abstract

Viruses can cause economic losses in fruit trees, including Prunus spp., by reducing yield and marketable fruit. Given the genetic diversity of viruses, reliable diagnostic methods relying on PCR are critical in determining viral infection in fruit trees. This study evaluated the broad-range [...] Read more.

Viruses can cause economic losses in fruit trees, including Prunus spp., by reducing yield and marketable fruit. Given the genetic diversity of viruses, reliable diagnostic methods relying on PCR are critical in determining viral infection in fruit trees. This study evaluated the broad-range detection capacity of currently available real-time RT-PCR assays for Prunus-infecting viruses and developed new assays when current tests were inadequate or absent. Available assays for 15 different viruses were exhaustively evaluated in silico to determine their capacity to detect virus isolates deposited in GenBank. During this evaluation, several isolates deposited since the assay was designed exhibited nucleotide mismatches in relation to the existing assay’s primer sequences. In cases where updating an existing assay was impractical, we performed a redesign with the dual goals of assay compactness and comprehensive inclusion of genetic diversity. The efficiency of each developed assay was determined by a standard curve. To validate the assay designs, we tested them against a comprehensive set of 87 positive and negative Prunus samples independently analyzed by high throughput sequencing. As a result, all the real-time RT-PCR assays described herein successfully detected the different viruses and their corresponding isolates. To further validate the new and updated assays a Prunus germplasm collection was surveyed. The sensitive and reliable detection methods described here will be used for the large-scale pathogen testing required to maintain the highest quality nursery stock. Full article

(This article belongs to the Special Issue Diagnosis and Control of Plant Viral Diseases)

14 pages, 2908 KiB

Open AccessCommunication

AUXIN RESPONSE FACTOR 1 Acts as a Positive Regulator in the Response of Poplar to Trichoderma asperellum Inoculation in Overexpressing Plants

by Yue-Feng Wang, Xue-Yue Hou, Jun-Jie Deng, Zhi-Hong Yao, Man-Man Lyu and Rong-Shu Zhang

Plants 2020, 9(2), 272; https://doi.org/10.3390/plants9020272 - 19 Feb 2020

Cited by 20 | Viewed by 3425

Abstract

Numerous Trichoderma strains have been reported to be optimal biofertilizers and biocontrol agents with low production costs and environmentally friendly properties. Trichoderma spp. promote the growth and immunity of plants by multiple means. Interfering with the hormonal homeostasis in plants is the most [...] Read more.

Numerous Trichoderma strains have been reported to be optimal biofertilizers and biocontrol agents with low production costs and environmentally friendly properties. Trichoderma spp. promote the growth and immunity of plants by multiple means. Interfering with the hormonal homeostasis in plants is the most critical strategy. However, the mechanisms underlying plants’ responses to Trichoderma remain to be further elucidated. Auxin is the most important phytohormone that regulates almost every aspect of a plant’s life, especially the trade-off between growth and defense. The AUXIN RESPONSE FACTOR (ARF) family proteins are key players in auxin signaling. We studied the responses and functions of the PdPapARF1 gene in a hybrid poplar during its interaction with beneficial T. asperellum strains using transformed poplar plants with PdPapARF1 overexpression (on transcription level in this study). We report that PdPapARF1 is a positive regulator for promoting poplar growth and defense responses, as does T. asperellum inoculation. PdPapARF1 also turned out to be a positive stimulator of adventitious root formation. Particularly, the overexpression of PdPapARF1 induced a 32.3% increase in the height of 40-day-old poplar plants and a 258% increase in the amount of adventitious root of 3-week-old subcultured plant clones. Overexpressed PdPapARF1 exerted its beneficial functions through modulating the hormone levels of indole acetic acid (IAA), jasmonic acid (JA), and salicylic acid (SA) in plants and activating their signaling pathways, creating similar results as inoculated with T. asperellum. Particularly, in the overexpressing poplar plants, the IAA level increased by approximately twice of the wild-type plants; and the signaling pathways of IAA, JA, and SA were drastically activated than the wild-type plants under pathogen attacks. Our report presents the potential of ARFs as the crucial and positive responders in plants to Trichoderma inducing. Full article

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14 pages, 1844 KiB

Open AccessArticle

Leaf Age and Position Effects on Quantum Yield and Photosynthetic Capacity in Hemp Crowns

by William L. Bauerle, Cole McCullough, Megan Iversen and Michael Hazlett

Plants 2020, 9(2), 271; https://doi.org/10.3390/plants9020271 - 19 Feb 2020

Cited by 30 | Viewed by 7283

Abstract

We examined the aging of leaves prior to abscission and the consequences for estimating whole-crown primary production in Cannabis sativa L. (hemp). Leaves at three vertical positions in hemp crowns were examined from initial full leaf expansion until 42 days later. Photosynthetic capacity [...] Read more.

We examined the aging of leaves prior to abscission and the consequences for estimating whole-crown primary production in Cannabis sativa L. (hemp). Leaves at three vertical positions in hemp crowns were examined from initial full leaf expansion until 42 days later. Photosynthetic capacity decreased as leaves aged regardless of crown position, light intensity, or photoperiod. Although leaves remained green, the photosynthetic capacity declined logarithmically to values of 50% and 25% of the maximum 9 and 25 days later, respectively. Plants grown under +450 μmol m⁻² s⁻¹ supplemental photosynthetically active radiation or enriched diffuse light responded similarly; there was no evidence that photoperiod or enriched diffuse light modified the gas exchange pattern. At approximately 14 days after full leaf expansion, leaf light levels >500 μmol m⁻² s⁻¹ decreased photosynthesis, which resulted in ≥10% lower maximum electron transport rate at ≥ 20 days of growth period. Furthermore, leaves were saturated at lower light levels as leaf age progressed (≤500 μmol m⁻² s⁻¹). Incorporating leaf age corrections of photosynthetic physiology is needed when estimating hemp primary production. Full article

(This article belongs to the Special Issue Plant Stress Physiology Modelling)

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15 pages, 906 KiB

Open AccessArticle

Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses

by Yamkela Mgwatyu, Allison Anne Stander, Stephan Ferreira, Wesley Williams and Uljana Hesse

Plants 2020, 9(2), 270; https://doi.org/10.3390/plants9020270 - 18 Feb 2020

Cited by 14 | Viewed by 5778

Abstract

Plant genomes provide information on biosynthetic pathways involved in the production of industrially relevant compounds. Genome size estimates are essential for the initiation of genome projects. The genome size of rooibos (Aspalathus linearis species complex) was estimated using DAPI flow cytometry and [...] Read more.

Plant genomes provide information on biosynthetic pathways involved in the production of industrially relevant compounds. Genome size estimates are essential for the initiation of genome projects. The genome size of rooibos (Aspalathus linearis species complex) was estimated using DAPI flow cytometry and k-mer analyses. For flow cytometry, a suitable nuclei isolation buffer, plant tissue and a transport medium for rooibos ecotype samples collected from distant locations were identified. When using radicles from commercial rooibos seedlings, Woody Plant Buffer and Vicia faba as an internal standard, the flow cytometry-estimated genome size of rooibos was 1.24 ± 0.01 Gbp. The estimates for eight wild rooibos growth types did not deviate significantly from this value. K-mer analysis was performed using Illumina paired-end sequencing data from one commercial rooibos genotype. For biocomputational estimation of the genome size, four k-mer analysis methods were investigated: A standard formula and three popular programs (BBNorm, GenomeScope, and FindGSE). GenomeScope estimates were strongly affected by parameter settings, specifically CovMax. When using the complete k-mer frequency histogram (up to 9 × 10⁵), the programs did not deviate significantly, estimating an average rooibos genome size of 1.03 ± 0.04 Gbp. Differences between the flow cytometry and biocomputational estimates are discussed. Full article

(This article belongs to the Section Plant Molecular Biology)

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20 pages, 3543 KiB

Open AccessArticle

Combined Effects of UV-B and Drought on Native and Exotic Populations of Verbascum thapsus L.

by Maria Hock, Carolin Plos, Maria Sporbert and Alexandra Erfmeier

Plants 2020, 9(2), 269; https://doi.org/10.3390/plants9020269 - 18 Feb 2020

Cited by 5 | Viewed by 4446

Abstract

During plant invasions, exotic species have to face new environmental challenges and are affected by interacting components of global change, which may include more stressful environmental conditions. We investigated an invasive species of New Zealand grasslands, commonly exposed to two concomitant and limiting [...] Read more.

During plant invasions, exotic species have to face new environmental challenges and are affected by interacting components of global change, which may include more stressful environmental conditions. We investigated an invasive species of New Zealand grasslands, commonly exposed to two concomitant and limiting abiotic factors—high levels of ultraviolet-B radiation and drought. The extent to which Verbascum thapsus may respond to these interacting stress factors via adaptive responses was assessed in a greenhouse experiment comprising native German plants and plants of exotic New Zealand origins. Plants from both origins were grown within four treatments resulting from the crossed combinations of two levels of UV-B and drought. Over twelve weeks, we recorded growth, morphological characteristics, physiological responses and productivity. The results showed that drought stress had the strongest effect on biomass, morphology and physiology. Significant effects of UV-B radiation were restricted to variables of leaf morphology and physiology. We found neither evidence for additive effects of UV-B and drought nor origin-dependent stress responses that would indicate local adaptation of native or exotic populations. We conclude that drought-resistant plant species might be predisposed to handle high UV-B levels, but emphasize the importance of setting comparable magnitudes in stress levels when testing experimentally for antagonistic interaction effects between two manipulated factors. Full article

(This article belongs to the Special Issue Invasive Plants)

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8 pages, 1620 KiB

Open AccessTechnical Note

CRISPR/Cas9-Mediated Mutagenesis of RCO in Cardamine hirsuta

by Claire Lessa Alvim Kamei, Bjorn Pieper, Stefan Laurent, Miltos Tsiantis and Peter Huijser

Plants 2020, 9(2), 268; https://doi.org/10.3390/plants9020268 - 18 Feb 2020

Cited by 4 | Viewed by 4821

Abstract

The small crucifer Cardamine hirsuta bears complex leaves divided into leaflets. This is in contrast to its relative, the reference plant Arabidopsis thaliana, which has simple leaves. Comparative studies between these species provide attractive opportunities to study the diversification of form. Here, [...] Read more.

The small crucifer Cardamine hirsuta bears complex leaves divided into leaflets. This is in contrast to its relative, the reference plant Arabidopsis thaliana, which has simple leaves. Comparative studies between these species provide attractive opportunities to study the diversification of form. Here, we report on the implementation of the CRISPR/Cas9 genome editing methodology in C. hirsuta and with it the generation of novel alleles in the RCO gene, which was previously shown to play a major role in the diversification of form between the two species. Thus, genome editing can now be deployed in C. hirsuta, thereby increasing its versatility as a model system to study gene function and evolution. Full article

(This article belongs to the Special Issue From Genes to Shape and Function: Leaf Morphogenesis at Play)

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11 pages, 1852 KiB

Open AccessEditor’s ChoiceArticle

In Vitro Anti-HSV-1 Activity of Polyphenol-Rich Extracts and Pure Polyphenol Compounds Derived from Pistachios Kernels (Pistacia vera L.)

by Maria Musarra-Pizzo, Rosamaria Pennisi, Ichrak Ben-Amor, Antonella Smeriglio, Giuseppina Mandalari and Maria Teresa Sciortino

Plants 2020, 9(2), 267; https://doi.org/10.3390/plants9020267 - 18 Feb 2020

Cited by 44 | Viewed by 6174

Abstract

Natural compounds are a prominent source of novel antiviral drugs. Several reports have previously shown the antimicrobial activity of pistachio polyphenol extracts. Therefore, the aim of our research was to investigate the activity of polyphenol-rich extracts of natural shelled (NPRE) pistachios kernels ( [...] Read more.

Natural compounds are a prominent source of novel antiviral drugs. Several reports have previously shown the antimicrobial activity of pistachio polyphenol extracts. Therefore, the aim of our research was to investigate the activity of polyphenol-rich extracts of natural shelled (NPRE) pistachios kernels (Pistacia vera L.) on herpes simplex virus type 1 (HSV-1) replication. The Vero cell line was used to assess the cytotoxicity and antiviral activity. The cell viability was calculated by detection of cellular ATP after treatment with various concentrations of NPRE. For antiviral studies, five nontoxic-concentrations (0.1, 0.2, 0.4, 0.6, 0.8 mg/mL) were tested. Our study demonstrated that treatment with NPRE (0.4, 0.6, 0.8 mg/mL) reduced the expression of the viral proteins ICP8 (infected cell polypeptide 8), UL42 (unique long UL42 DNA polymerase processivity factor), and US11 (unique short US11 protein), and resulted in a decrease of viral DNA synthesis. The 50% cytotoxic concentration (CC₅₀), 50% inhibitory concentration (EC₅₀), and the selectivity index (SI) values for NPRE were 1.2 mg/mL, 0.4mg/mL, and 3, respectively. Furthermore, we assessed the anti-herpetic effect of a mix of pure polyphenol compounds (NS MIX) present in NPRE. In conclusion, our findings indicate that natural shelled pistachio kernels have remarkable inhibitory activity against HSV-1. Full article

(This article belongs to the Special Issue Mechanisms of Plant Antioxidants Action)

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12 pages, 1564 KiB

Open AccessArticle

Endophytic Bacterial Microbiome Diversity in Early Developmental Stage Plant Tissues of Wheat Varieties

by Jana Žiarovská, Juraj Medo, Matúš Kyseľ, Lucia Zamiešková and Miroslava Kačániová

Plants 2020, 9(2), 266; https://doi.org/10.3390/plants9020266 - 18 Feb 2020

Cited by 25 | Viewed by 5489

Abstract

Endophytic bacteria are an important part of different functions in plants that lead to plants’ production characteristics as well as their stress response mechanisms. Endophytic bacterial diversity was analyzed in this study to describe 16S rRNA variability and changes in the leaves of [...] Read more.

Endophytic bacteria are an important part of different functions in plants that lead to plants’ production characteristics as well as their stress response mechanisms. Endophytic bacterial diversity was analyzed in this study to describe 16S rRNA variability and changes in the leaves of drought-tolerant and drought-susceptible wheat when growth under in vitro conditions. A metagenomic analysis was applied and a pilot exploratory study was performed to prove this type of analysis as applicable to tracking endophytic bacterial diversity changes when a drought stress is applied to an in vitro culture of wheat. The study showed that the changes in the bacterial endophytes’ variabilities associated preferentially with the drought stress varietal characteristics of the analyzed wheat instead of the applied stress conditions. Full article

(This article belongs to the Section Plant Response to Abiotic Stress and Climate Change)

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14 pages, 1112 KiB

Open AccessArticle

Chemical Composition of Aerial Parts Essential Oils from Six Endemic Malagasy Helichrysum Species

by Delphin J. R. Rabehaja, Guillaume Bezert, Stéphan R. Rakotonandrasana, Panja A. R. Ramanoelina, Charles Andrianjara, Ange Bighelli, Félix Tomi and Mathieu Paoli

Plants 2020, 9(2), 265; https://doi.org/10.3390/plants9020265 - 18 Feb 2020

Cited by 3 | Viewed by 3573

Abstract

The essential oils of six endemic Malagasy Helichrysum species were investigated by GC (RI), GC–MS and ¹³C NMR spectrometry. In total, 153 compounds were identified accounting for 90.8% to 99.9% of the total composition. The main constituents were α-pinene for H. benthamii, [...] Read more.

The essential oils of six endemic Malagasy Helichrysum species were investigated by GC (RI), GC–MS and ¹³C NMR spectrometry. In total, 153 compounds were identified accounting for 90.8% to 99.9% of the total composition. The main constituents were α-pinene for H. benthamii, 1,8-cineole for H. dubardii, (E)-β-caryophyllene for H. indutum, and H. bojerianum. H. diotoides essential oil was characterized by the presence of two lilac alcohols and four lilac acetates whereas H. hirtum essential oil exhibited an atypical composition with 7β-H-silphiperfol-5-ene, 7-epi-subergorgiol, and 7-epi-silphiperfol-5-en-13-oic acid as major components. Full article

(This article belongs to the Section Phytochemistry)

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Graphical abstract

13 pages, 487 KiB

Open AccessArticle

Plant Growth Inhibitory Activities and Volatile Active Compounds of 53 Spices and Herbs

by Takayuki Sekine, Kwame Sarpong Appiah, Majid Azizi and Yoshiharu Fujii

Plants 2020, 9(2), 264; https://doi.org/10.3390/plants9020264 - 18 Feb 2020

Cited by 14 | Viewed by 4974

Abstract

The inhibitory activities of the leachates and volatiles from 53 plant species (spices and herbs) were evaluated against lettuce (Lactuca sativa “Great Lakes 366”) seedling growth using the sandwich and dish pack methods, respectively. With the sandwich method, parsley (Petroselinum sativum [...] Read more.

The inhibitory activities of the leachates and volatiles from 53 plant species (spices and herbs) were evaluated against lettuce (Lactuca sativa “Great Lakes 366”) seedling growth using the sandwich and dish pack methods, respectively. With the sandwich method, parsley (Petroselinum sativum) showed the strongest inhibitory effect on lettuce radicle growth (77%), followed by tarragon (Artemisia dracunculus) (72%). However, caraway (Carum carvi), dill (Anethum graveolens) (seed), laurel (Laurus nobilis), rosemary (Rosmarinus officinalis), and sage (Salvia officinalis) were the most inhibitory species (100% inhibition of lettuce radicle and hypocotyl growth inhibition at all distance wells) in the dish pack method. Cardamom (Elettaria cardamomum) and thyme (Thymus vulgaris) also showed strong inhibitory activity (100% for radicle and hypocotyl growth inhibition at all 41 and 58 mm distance wells). The headspace sampling and gas chromatography-mass spectrometry (GC-MS) analysis identified the main inhibitory active compounds as carvone in caraway and dill (seeds), 1,8-cineole in laurel and cardamom, and borneol in thyme. Both camphor and 1,8-cineole were detected in rosemary and sage, and the total activity evaluation showed that camphor was the major inhibitory compound in rosemary, although both compounds played equal roles in sage. Full article

(This article belongs to the Section Phytochemistry)

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18 pages, 2279 KiB

Open AccessArticle

Metagenomic Insights of the Root Colonizing Microbiome Associated with Symptomatic and Non-Symptomatic Bananas in Fusarium Wilt Infected Fields

by Manoj Kaushal, George Mahuku and Rony Swennen

Plants 2020, 9(2), 263; https://doi.org/10.3390/plants9020263 - 18 Feb 2020

Cited by 47 | Viewed by 7645

Abstract

Plants tissues are colonized by diverse communities of microorganisms called endophytes. They are key determinants of plant production and health, for example by facilitating nutrient exchanges or limiting disease development. Endophytic communities of banana plants have not been studied until very recently, and [...] Read more.

Plants tissues are colonized by diverse communities of microorganisms called endophytes. They are key determinants of plant production and health, for example by facilitating nutrient exchanges or limiting disease development. Endophytic communities of banana plants have not been studied until very recently, and their potential role in disease development has not been explored so far. Roots from symptomatic and non-symptomatic banana plants were sampled from fields infected by Fusarium oxysporum f.sp. cubense race 1. The goal was to compare the endophytic microbiota between symptomatic and non-symptomatic plants through high throughput sequencing of 16s rDNA and shotgun metagenome sequencing. The results revealed that the endophytic root microbiome in bananas is dominated by Proteobacteria and Bacteroidetes followed to a lesser extent by Actinobacteria. The development of disease greatly impacted the endophytic microbial communities. For example, Flavobacteriales abundance was correlated with symptom development. Full article

(This article belongs to the Special Issue Fusarium spp. and Plants)

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13 pages, 2173 KiB

Open AccessArticle

Long-Chain acyl-CoA Synthetase LACS2 Contributes to Submergence Tolerance by Modulating Cuticle Permeability in Arabidopsis

by Li-Juan Xie, Wei-Juan Tan, Yi-Cong Yang, Yi-Fang Tan, Ying Zhou, De-Mian Zhou, Shi Xiao and Qin-Fang Chen

Plants 2020, 9(2), 262; https://doi.org/10.3390/plants9020262 - 18 Feb 2020

Cited by 26 | Viewed by 5121

Abstract

In Arabidopsis thaliana, LONG-CHAIN ACYL-COA SYNTHETASEs (LACSs) catalyze the synthesis of long-chain acyl-CoAs and function in diverse biological processes. We have recently revealed that LACS2 is primarily involved in the production of polyunsaturated linolenoyl-CoA, essential for the activation of ethylene response transcription [...] Read more.

In Arabidopsis thaliana, LONG-CHAIN ACYL-COA SYNTHETASEs (LACSs) catalyze the synthesis of long-chain acyl-CoAs and function in diverse biological processes. We have recently revealed that LACS2 is primarily involved in the production of polyunsaturated linolenoyl-CoA, essential for the activation of ethylene response transcription factors-mediated hypoxia signaling. Here, we further reported the dual role of LACS2 in the regulation of submergence tolerance by modulating cuticle permeability in Arabidopsis cells. LACS2-overexpressors (LACS2-OEs) showed improved tolerance to submergence, with higher accumulation of cuticular wax and cutin in their rosettes. In contrast, knockout of LACS2 in the lacs2-3 mutant resulted in hypersensitivity to submergence with reduced wax crystals and thinner cutin layer. By analyses of plant surface permeability, we observed that the hypoxic sensitivities in the LACS2-OEs and lacs2-3 mutant were physiologically correlated with chlorophyll leaching, water loss rates, ionic leakage, and gas exchange. Thus, our findings suggest the role of LACS2 in plant response to submergence by modulating cuticle permeability in plant cells. Full article

(This article belongs to the Special Issue Function of Lipids in Plant Stress)

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18 pages, 1158 KiB

Open AccessFeature PaperArticle

Mitochondrial DNA Repair in an Arabidopsis thaliana Uracil N-Glycosylase Mutant

by Emily Wynn, Emma Purfeerst and Alan Christensen

Plants 2020, 9(2), 261; https://doi.org/10.3390/plants9020261 - 18 Feb 2020

Cited by 10 | Viewed by 3999

Abstract

Substitution rates in plant mitochondrial genes are extremely low, indicating strong selective pressure as well as efficient repair. Plant mitochondria possess base excision repair pathways; however, many repair pathways such as nucleotide excision repair and mismatch repair appear to be absent. In the [...] Read more.

Substitution rates in plant mitochondrial genes are extremely low, indicating strong selective pressure as well as efficient repair. Plant mitochondria possess base excision repair pathways; however, many repair pathways such as nucleotide excision repair and mismatch repair appear to be absent. In the absence of these pathways, many DNA lesions must be repaired by a different mechanism. To test the hypothesis that double-strand break repair (DSBR) is that mechanism, we maintained independent self-crossing lineages of plants deficient in uracil-N-glycosylase (UNG) for 11 generations to determine the repair outcomes when that pathway is missing. Surprisingly, no single nucleotide polymorphisms (SNPs) were fixed in any line in generation 11. The pattern of heteroplasmic SNPs was also unaltered through 11 generations. When the rate of cytosine deamination was increased by mitochondrial expression of the cytosine deaminase APOBEC3G, there was an increase in heteroplasmic SNPs but only in mature leaves. Clearly, DNA maintenance in reproductive meristem mitochondria is very effective in the absence of UNG while mitochondrial genomes in differentiated tissue are maintained through a different mechanism or not at all. Several genes involved in DSBR are upregulated in the absence of UNG, indicating that double-strand break repair is a general system of repair in plant mitochondria. It is important to note that the developmental stage of tissues is critically important for these types of experiments. Full article

(This article belongs to the Special Issue Plant Organelle DNA Maintenance)

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13 pages, 1383 KiB

Open AccessArticle

Assessment of Genetic Diversity of the “Acquaviva Red Onion” (Allium cepa L.) Apulian Landrace

by Luigi Ricciardi, Rosa Mazzeo, Angelo Raffaele Marcotrigiano, Guglielmo Rainaldi, Paolo Iovieno, Vito Zonno, Stefano Pavan and Concetta Lotti

Plants 2020, 9(2), 260; https://doi.org/10.3390/plants9020260 - 18 Feb 2020

Cited by 20 | Viewed by 7346

Abstract

Onion (Allium cepa L.) is the second most important vegetable crop worldwide and is widely appreciated for its health benefits. Despite its significant economic importance and its value as functional food, onion has been poorly investigated with respect to its genetic diversity. [...] Read more.

Onion (Allium cepa L.) is the second most important vegetable crop worldwide and is widely appreciated for its health benefits. Despite its significant economic importance and its value as functional food, onion has been poorly investigated with respect to its genetic diversity. Herein, we surveyed the genetic variation in the “Acquaviva red onion” (ARO), a landrace with a century-old history of cultivation in a small town in the province of Bari (Apulia, Southern of Italy). A set of 11 microsatellite markers were used to explore the genetic variation in a germplasm collection consisting of 13 ARO populations and three common commercial types. Analyses of genetic structure with parametric and non-parametric methods highlighted that the ARO represents a well-defined gene pool, clearly distinct from the Tropea and Montoro landraces with which it is often mistaken. In order to provide a description of bulbs, usually used for fresh consumption, soluble solid content and pungency were evaluated, showing higher sweetness in the ARO with respect to the two above mentioned landraces. Overall, the present study is useful for the future valorization of the ARO, which could be promoted through quality labels which could contribute to limit commercial frauds and improve the income of smallholders. Full article

(This article belongs to the Special Issue Germplasm Diversity for Sustainability and Crop Improvement)

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14 pages, 1958 KiB

Open AccessArticle

Co-Suppression of NbClpC1 and NbClpC2, Encoding Clp Protease Chaperons, Elicits Significant Changes in the Metabolic Profile of Nicotiana benthamiana

by Md. Sarafat Ali and Kwang-Hyun Baek

Plants 2020, 9(2), 259; https://doi.org/10.3390/plants9020259 - 18 Feb 2020

Cited by 5 | Viewed by 3350

Abstract

Metabolites in plants are the products of cellular metabolic processes, and their differential amount can be regarded as the final responses of plants to genetic, epigenetic, or environmental stresses. The Clp protease complex, composed of the chaperonic parts and degradation proteases, is the [...] Read more.

Metabolites in plants are the products of cellular metabolic processes, and their differential amount can be regarded as the final responses of plants to genetic, epigenetic, or environmental stresses. The Clp protease complex, composed of the chaperonic parts and degradation proteases, is the major degradation system for proteins in plastids. ClpC1 and ClpC2 are the two chaperonic proteins for the Clp protease complex and share more than 90% nucleotide and amino acid sequence similarities. In this study, we employed virus-induced gene silencing to simultaneously suppress the expression of ClpC1 and ClpC2 in Nicotiana benthamiana (NbClpC1/C2). The co-suppression of NbClpC1/C2 in N. benthamiana resulted in aberrant development, with severely chlorotic leaves and stunted growth. A comparison of the control and NbClpC1/C2 co-suppressed N. benthamiana metabolomes revealed a total of 152 metabolites identified by capillary electrophoresis time-of-flight mass spectrometry. The co-suppression of NbClpC1/C2 significantly altered the levels of metabolites in glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway, and the purine biosynthetic pathway, as well as polyamine and antioxidant metabolites. Our results show that the simultaneous suppression of ClpC1 and ClpC2 leads to aberrant morphological changes in chloroplasts and that these changes are related to changes in the contents of major metabolites acting in cellular metabolism and biosynthetic pathways. Full article

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14 pages, 918 KiB

Open AccessReview

Jute: A Potential Candidate for Phytoremediation of Metals—A Review

by Muhammad Hamzah Saleem, Shafaqat Ali, Muzammal Rehman, Mirza Hasanuzzaman, Muhammad Rizwan, Sana Irshad, Fahad Shafiq, Muhammad Iqbal, Basmah M. Alharbi, Taghreed S. Alnusaire and Sameer H. Qari

Plants 2020, 9(2), 258; https://doi.org/10.3390/plants9020258 - 17 Feb 2020

Cited by 148 | Viewed by 11086

Abstract

Jute (Corchorus capsularis) is a widely cultivated fibrous species with important physiological characteristics including biomass, a deep rooting system, and tolerance to metal stress. Furthermore, Corchorus species are indigenous leafy vegetables and show phytoremediation potential for different heavy metals. This species [...] Read more.

Jute (Corchorus capsularis) is a widely cultivated fibrous species with important physiological characteristics including biomass, a deep rooting system, and tolerance to metal stress. Furthermore, Corchorus species are indigenous leafy vegetables and show phytoremediation potential for different heavy metals. This species has been used for the phytoremediation of different toxic pollutants such as copper (Cu), cadmium (Cd), zinc (Zn), mercury (Hg) and lead (Pb). The current literature highlights the physiological and morphological characteristics of jute that are useful to achieve successful phytoremediation of different pollutants. The accumulation of these toxic heavy metals in agricultural regions initiates concerns regarding food safety and reductions in plant productivity and crop yield. We discuss some innovative approaches to increase jute phytoremediation using different chelating agents. There is a need to remediate soils contaminated with toxic substances, and phytoremediation is a cheap, effective, and in situ alternative, and jute can be used for this purpose. Full article

(This article belongs to the Special Issue Plant Responses and Tolerance to Metal/Metalloid Toxicity)

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14 pages, 2993 KiB

Open AccessArticle

Regulation of Ammonium Cellular Levels is An Important Adaptive Trait for the Euhalophytic Behavior of Salicornia europaea

by Jinbiao Ma, Valerio Cirillo, Dayong Zhang, Albino Maggio, Lei Wang, Xinlong Xiao and Yinan Yao

Plants 2020, 9(2), 257; https://doi.org/10.3390/plants9020257 - 17 Feb 2020

Cited by 12 | Viewed by 3650

Abstract

Salinization of agricultural land is a devastating phenomenon which will affect future food security. Understanding how plants survive and thrive in response to salinity is therefore critical to potentiate tolerance traits in crop species. The halophyte Salicornia europaea has been used as model [...] Read more.

Salinization of agricultural land is a devastating phenomenon which will affect future food security. Understanding how plants survive and thrive in response to salinity is therefore critical to potentiate tolerance traits in crop species. The halophyte Salicornia europaea has been used as model system for this purpose. High salinity causes NH₄⁺ accumulation in plant tissues and consequent toxicity symptoms that may further exacerbate those caused by NaCl. In this experiment we exposed Salicornia plants to five concentrations of NaCl (0, 1, 10, 50 and 200 mM) in combination with two concentrations of NH₄Cl (1 and 50 mM). We confirmed the euhalophytic behavior of Salicornia that grew better at 200 vs. 0 mM NaCl in terms of both fresh (+34%) and dry (+46%) weights. Addition of 50 mM NH₄Cl to the growth medium caused a general growth reduction, which was likely caused by NH₄⁺ accumulation and toxicity in roots and shoots. When plants were exposed to high NH₄Cl, high salinity reduced roots NH₄⁺ concentration (−50%) compared to 0 mM NaCl. This correlates with the activation of the NH₄⁺ assimilation enzymes, glutamine synthetase and glutamate dehydrogenase, and the growth inhibition was partially recovered. We argue that NH₄⁺ detoxification is an important trait under high salinity that may differentiate halophytes from glycophytes and we present a possible model for NH₄⁺ detoxification in response to salinity. Full article

(This article belongs to the Special Issue Mechanism of Salinity Tolerance in Plants)

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