bluuebunny/crossref_metadata_2025 huggingface dataset:
Artocarpus lakoocha Roxb. and Artocarpus heterophyllus Lam. Flowers: New Sources of Bioactive Compounds
Authors: Gupta Arun Kumar , Rather Muzamil Ahmad , Kumar Jha Avinash , Shashank Abhinay , Singhal Somya , Sharma Maanas , Pathak Urbi , Sharma Dipti , Mastinu Andrea
Published: October 2020

Artocarpus heterophyllus Lam. (AH) and Artocarpus lakoocha Roxb. (AL) are two endemic plants that grow on the Asian continent. To date, their applications have been aimed at using their fruit as a food source or for some of their therapeutic virtues. In this study, attention was given to the flowers of AH and AL. Initially, the cytotoxicity of the phytoextracts was assessed, and the content of minerals, phenols, and flavonoids was determined. Furthermore, some antioxidant components were identified by HPLC. Furthermore, the ability of AH and AL extracts to modulate the gene expression of some targets involved in the antioxidant response was studied. The results obtained highlighted the nutritional and antioxidant value of the AH and AL flower extracts. This study will contribute to enhancing the use of AH and AL flowers as potential supplements in human nutrition.
Computational Identification and Comparative Analysis of Conserved miRNAs and Their Putative Target Genes in the Juglans regia and J. microcarpa Genomes
Authors: Wang Le , Zhu Tingting , Deal Karin R. , Dvorak Jan , Luo Ming-Cheng
Published: October 2020

MicroRNAs (miRNAs) are important factors for the post-transcriptional regulation of protein-coding genes in plants and animals. They are discovered either by sequencing small RNAs or computationally. We employed a sequence-homology-based computational approach to identify conserved miRNAs and their target genes in Persian (English) walnut, Juglans regia, and its North American wild relative, J. microcarpa. A total of 119 miRNA precursors (pre-miRNAs) were detected in the J. regia genome and 121 in the J. microcarpa genome and miRNA target genes were predicted and their functional annotations were performed in both genomes. In the J. regia genome, 325 different genes were targets; 87.08% were regulated by transcript cleavage and 12.92% by translation repression. In the J. microcarpa genome, 316 different genes were targets; 88.92% were regulated by transcript cleavage and 11.08% were regulated by translation repression. Totals of 1.3% and 2.0% of all resistance gene analogues (RGA) and 2.7% and 2.6% of all transcription factors (TFs) were regulated by miRNAs in the J. regia and J. microcarpa genomes, respectively. Juglans genomes evolved by a whole genome duplication (WGD) and consist of eight pairs of fractionated homoeologous chromosomes. Within each pair, the chromosome that has more genes with greater average transcription also harbors more pre-miRNAs and more target genes than its homoeologue. While only minor differences were detected in pre-miRNAs between the J. regia and J. microcarpa genomes, about one-third of the pre-miRNA loci were not conserved between homoeologous chromosome within each genome. Pre-miRNA and their corresponding target genes showed a tendency to be collocated within a subgenome.
Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification
Authors: Jiang Kai , Miao Li-Yuan , Wang Zheng-Wei , Ni Zi-Yi , Hu Chao , Zeng Xin-Hua , Huang Wei-Chang
Published: October 2020

Although the medicinal properties of Coelogyne spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of Coelogyne fimbriata and Coelogyne ovalis. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two Coelogyne species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes’ medium variable regions and evaluated the transferability to another 16 Coelogyne species. We constructed phylogenetic trees including 18 Coelogyne species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of C. fimbriata and C. ovalis contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in C. fimbriata and 26,715 bp C. ovalis, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera Coelogyne and Pleione. The newly developed primers revealed good transferability among the Coelogyne taxa and provided enough variable sites to distinguish C. fimbriata and C. ovalis. The two complete cp genomes and the eight new primers of Coelogyne provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Coelogyne taxa.
Natural Variations and Dynamic Changes of Nitrogen Indices throughout Growing Seasons for Twenty Tea Plant (Camellia sinensis) Varieties
Authors: Zhang Yange , Ye Xiangsheng , Zhang Xinwan , Huang Wei , Zhao Hua
Published: October 2020

Tea (Camellia sinensis (L.) O. Kuntze) leaves are harvested multiple times annually accompanied by a large amount of nitrogen (N) removed. Therefore, tea plantations are characterized by high requirements of N. This study aimed to assess the variations of N-level, apparent N remobilization efficiency (ANRE), and N utilization efficiency (NUtE) and their dynamic changes during growing seasons for twenty tea varieties. The N-level was highest in the one bud with two leaves as the youngest category, followed by mature leaves attached to green-red stems, and then by aging leaves attached to grey stems. The dynamic N-level presented different profiles of “S”-, “U”-, and “S-like”-shape in the three categories of leaves during the growing seasons. Here, specifically defined ANRE indicated N fluxes in a specific category of leaves, showing that sources and sinks alternate during the period of two consecutive rounds of growth. The dynamic of averaged NUtE followed an “S”-shape. The results revealed annual rhythms and physiological characters related with N indices, which were variety dependent and closely related with the amount of N requirements at proper time. An optimized NUtE is a complex character determined by the combination of tea plantation management and breeding practices to achieve sustainable development with economic benefit.
Identification of Candidate Genes Involved in Fruit Ripening and Crispness Retention Through Transcriptome Analyses of a ‘Honeycrisp’ Population
Authors: Chang Hsueh-Yuan , Tong Cindy B. S.
Published: October 2020

Crispness retention is a postharvest trait that fruit of the ’Honeycrisp’ apple and some of its progeny possess. To investigate the molecular mechanisms of crispness retention, progeny individuals derived from a ’Honeycrisp’ × MN1764 population with fruit that either retain crispness (named “Retain”), lose crispness (named “Lose”), or that are not crisp at harvest (named “Non-crisp”) were selected for transcriptomic comparisons. Differentially expressed genes (DEGs) were identified using RNA-Seq, and the expression levels of the DEGs were validated using nCounter®. Functional annotation of the DEGs revealed distinct ripening behaviors between fruit of the “Retain” and “Non-crisp” individuals, characterized by opposing expression patterns of auxin- and ethylene-related genes. However, both types of genes were highly expressed in the fruit of “Lose” individuals and ’Honeycrisp’, which led to the potential involvements of genes encoding auxin-conjugating enzyme (GH3), ubiquitin ligase (ETO), and jasmonate O-methyltransferase (JMT) in regulating fruit ripening. Cell wall-related genes also differentiated the phenotypic groups; greater numbers of cell wall synthesis genes were highly expressed in fruit of the “Retain” individuals and ’Honeycrisp’ when compared with “Non-crisp” individuals and MN1764. On the other hand, the phenotypic differences between fruit of the “Retain” and “Lose” individuals could be attributed to the functioning of fewer cell wall-modifying genes. A cell wall-modifying gene, MdXTH, was consistently identified as differentially expressed in those fruit over two years in this study, so is a major candidate for crispness retention.
Understanding Host–Pathogen Interactions in Brassica napus in the Omics Era
Authors: Neik Ting Xiang , Amas Junrey , Barbetti Martin , Edwards David , Batley Jacqueline
Published: October 2020

Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host–pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.
OsmiR535, a Potential Genetic Editing Target for Drought and Salinity Stress Tolerance in Oryza sativa
Authors: Yue Erkui , Cao Huan , Liu Bohan
Published: October 2020

OsmiR535 belongs to the miR156/miR529/miR535 superfamily, a highly conserved miRNA family in plants. OsmiR535 is involved in regulating the cold-stress response, modulating plant development, and determining panicle architecture and grain length. However, the role that OsmiR535 plays in plant responses to drought and salinity are elusive. In the current study, molecular and genetic engineering techniques were used to elucidate the possible role of OsmiR535 in response to NaCl, PEG(Poly ethylene glycol), ABA(Abscisic acid), and dehydration stresses. Our results showed that OsmiR535 is induced under stressed conditions as compared to control. With transgenic and CRISPR/Cas9 knockout system techniques, our results verified that either inhibition or knockout of OsmiR535 in rice could enhance the tolerance of plants to NaCl, ABA, dehydration and PEG stresses. In addition, the overexpression of OsmiR535 significantly reduced the survival rate of rice seedlings during PEG and dehydration post-stress recovery. Our results demonstrated that OsmiR535 negatively regulates the stress response in rice. Moreover, our practical application of CRISPR/Cas9 mediated genome editing created a homozygous 5 bp deletion in the coding sequence of OsmiR535, demonstrating that OsmiR535 could be a useful genetic editing target for drought and salinity tolerance and a new marker for molecular breeding of Oryza sativa.
Structural and Functional Organization of the Root System: A Comparative Study on Five Plant Species
Authors: Sofo Adriano , Elshafie Hazem S. , Camele Ippolito
Published: October 2020

Plants are affected by soil environments to the same extent that they affect soil functioning through interactions between environmental and genetic factors. Here, five plant species (broad bean, pea, cabbage, fennel, and olive) grown under controlled pot conditions were tested for their ability to differently stimulate the degradation of standard litter. Litter, soil C and N contents were measured for evaluating chemical changes due to plant presence, while soil microbial abundance was evaluated to assess if it had a positive or negative catalyzing influence on litter decomposition. The architecture and morphological traits of roots systems were also evaluated by using specific open-source software (SmartRoot). Soil chemical and microbiological characteristics were significantly influenced by the plant species. Variations in soil C/N dynamics were correlated with the diversity of root traits among species. Early stage decomposition of the standard litter changed on the basis of the plant species. The results indicated that key soil processes are governed by interactions between plant roots, soil C and N, and the microbial metabolism that stimulate decomposition reactions. This, in turn, can have marked effects on soil chemical and microbiological fertility, both fundamental for sustaining crops, and can promote the development of new approaches for optimizing soil C and N cycling, managing nutrient transport, and sustaining and improving net primary production.
Development of a Full-Length Infectious cDNA Clone of the Grapevine Berry Inner Necrosis Virus
Authors: Fan Xudong , Zhang Zunping , Ren Fang , Hu Guojun , Li Chen , Zhang Baodong , Dong Yafeng
Published: October 2020

Grapevine berry inner necrosis virus (GINV) belongs to the genus Trichovirus in the family Betaflexiviridae. The GINV isolate LN_BETA_RS was obtained from a “Beta” grapevine (Vitis riparia × Vitis labrusca) exhibiting chlorotic mottling and ring spot in Xingcheng, Liaoning Province, China. To verify the correlation between GINV and grapevine chlorotic mottling and ring spot disease, we constructed an infectious cDNA clone of GINV isolate LN_BETA_RS using the seamless assembly approach. Applied treatments of agroinfiltration infectious cDNA confirmed systemic GINV infection of the Nicotianaoccidentalis 37B by reverse transcription polymerase chain reaction (RT-PCR) and transmission electron microscopy, exhibiting chlorotic mottling symptoms on leaves. Infectious cDNA was also transmitted to new healthy N. occidentalis plants through rub-inoculation. Moreover, the cDNA clone was agroinfiltrated into “Beta” and “Thompson Seedless” grapevine plantlets, and the inoculated grapevines exhibited leaf chlorotic mottling and ringspot during the two years of observation. GINV-inoculated “Beta” grapevines had serious leaf chlorotic mottling and ringspot symptoms on the whole plant, while relatively few symptoms were observed on the leaves of agroinoculated “Thompson Seedless” grapevines in early spring and only weak ring spot gradually appeared later in the top young leaves. Our experiments fulfilled Koch’s postulates and revealed the causative role of GINV in grapevine chlorotic mottling and ring spot disease.
Drought-Induced Responses of Nitrogen Metabolism in Ipomoea batatas
Authors: Xia Houqiang , Xu Tao , Zhang Jing , Shen Ke , Li Zongyun , Liu Jingran
Published: October 2020

This study investigated the effect of water stress, simulated by the polyethylene glycol (PEG-6000) method, on nitrogen (N) metabolism in leaves and roots of hydroponically grown sweet potato seedlings, Xushu 32 (X32) and Ningzishu 1 (N1). The concentrations of PEG-6000 treatments were 0%, 5% and 10% (m/v). The results showed that the drought-treated plants showed a decline leaf relative water content, and revealed severe growth inhibition, compared with the 0% treatment. Under drought stress, the decline in biomass of the leaf and stem was more noticeable than in root biomass for X32, leading to a higher root to shoot ratio. Drought stress increased the nitrate nitrogen (NO3−-N) and protein in leaves, but reduced all the activities of N-metabolism enzymes and the transcriptional levels of nitrate reductase (NR), glutamine synthetase (GS) and glutamate synthase (GOGAT); in roots, NO3−-N and NR had opposite trends. The leaf ammonium nitrogen (NH4+-N), GS and amino acid had different trends between X32 and N1 under drought stress. Furthermore, the transcriptional level of nitrate transporter genes NRT1.1 in leaves and roots were upregulated under drought stress, except in N1 roots. In conclusion, NR determined the different response to drought in leaves for X32 and N1, and GS and GOGAT determined the response to drought in roots, respectively.
Zebrafish as a Successful Animal Model for Screening Toxicity of Medicinal Plants
Authors: Modarresi Chahardehi Amir , Arsad Hasni , Lim Vuanghao
Published: October 2020

The zebrafish (Danio rerio) is used as an embryonic and larval model to perform in vitro experiments and developmental toxicity studies. Zebrafish may be used to determine the toxicity of samples in early screening assays, often in a high-throughput manner. The zebrafish embryotoxicity model is at the leading edge of toxicology research due to the short time required for analyses, transparency of embryos, short life cycle, high fertility, and genetic data similarity. Zebrafish toxicity studies range from assessing the toxicity of bioactive compounds or crude extracts from plants to determining the optimal process. Most of the studied extracts were polar, such as ethanol, methanol, and aqueous solutions, which were used to detect the toxicity and bioactivity. This review examines the latest research using zebrafish as a study model and highlights its power as a tool for detecting toxicity of medicinal plants and its effectiveness at enhancing the understanding of new drug generation. The goal of this review was to develop a link to ethnopharmacological zebrafish studies that can be used by other researchers to conduct future research.
Phytotoxicity, Morphological, and Metabolic Effects of the Sesquiterpenoid Nerolidol on Arabidopsis thaliana Seedling Roots
Authors: Landi Marco , Misra Biswapriya Biswavas , Muto Antonella , Bruno Leonardo , Araniti Fabrizio
Published: October 2020

Natural herbicides that are based on allelopathy of compounds, can offer effective alternatives to chemical herbicides towards sustainable agricultural practices. Nerolidol, a sesquiterpenoid alcohol synthesized by many plant families, was shown to be the most effective allelopathic compound in a preliminary screening performed with several other sesquiterpenoids. In the present study, Arabidopsis thaliana seedlings were treated for 14 d with various cis-nerolidol concentrations (0, 50, 100, 200, 400, and 800 µM) to investigate its effects on root growth and morphology. To probe the underlying changes in root metabolome, we conducted untargeted gas chromatography mass spectrometry (GC-MS) based metabolomics to find out the specificity or multi-target action of this sesquiterpenoid alcohol. Oxidative stress (measured as levels of H2O2 and malondialdehyde (MDA) by-product) and antioxidant enzyme activities, i.e., superoxide dismutase (SOD) and catalase (CAT) were also evaluated in the roots. Nerolidol showed an IC50 (120 µM), which can be considered low for natural products. Nerolidol caused alterations in root morphology, brought changes in auxin balance, induced changes in sugar, amino acid, and carboxylic acid profiles, and increased the levels of H2O2 and MDA in root tissues in a dose-dependent manner. Several metabolomic-scale changes induced by nerolidol support the multi-target action of nerolidol, which is a positive feature for a botanical herbicide. Though it warrants further mechanistic investigation, nerolidol is a promising compound for developing a new natural herbicide.
Evaluation of the Antidiabetic and Insulin Releasing Effects of A. squamosa, Including Isolation and Characterization of Active Phytochemicals
Authors: Ansari Prawej , Flatt Peter R. , Harriott Patrick , Abdel-Wahab Yasser H.A.
Published: October 2020

Annona squamosa is generally referred to as a ‘custard apple’. Antidiabetic actions of hot water extract of Annona squamosa (HWAS) leaves together with isolation of active insulinotropic compounds were studied. Insulin release, membrane potential and intracellular Ca2+ were determined using BRIN-BD11 cells and isolated mouse islets. 3T3L1 adipocytes and in vitro models were used to determine cellular glucose uptake, insulin action, starch digestion, glucose diffusion, DPP-IV activity and glycation. Glucose intolerant high-fat fed rats were used for in vivo studies. Active compounds were isolated and characterized by HPLC, LCMS and NMR. HWAS stimulated insulin release from clonal β-cells and mouse islets. Using fluorescent indicator dyes and modulators of insulin secretion, effects could be attributed to depolarization of β-cells and influx of Ca2+. Secretion was stimulated by isobutylmethylxanthine (IBMX), tolbutamide or 30 mM KCl, indicating additional non-KATP dependent pathways. Extract stimulated cellular glucose uptake and insulin action and inhibited starch digestion, protein glycation, DPP-IV enzyme activity and glucose diffusion. Oral HWAS improved glucose tolerance and plasma insulin in high-fat fed obese rats. Treatment for 9 days with HWAS (250 mg/5 mL/kg), partially normalised energy intake, body weight, pancreatic insulin content, and both islet size and beta cell mass. This was associated with improved oral glucose tolerance, increased plasma insulin and inhibition of plasma DPP-IV activity. Isolated insulinotropic compounds, including rutin (C27H30O16), recapitulated the positive actions of HWAS on beta cells and in vivo glucose tolerance and plasma insulin responses. Annona squamosa is attractive as a dietary adjunct in treatment of T2DM and as a source of potential antidiabetic agents including rutin.
Novel Bioformulations Developed from Pseudomonas putida BSP9 and Its Biosurfactant for Growth Promotion of Brassica juncea (L.)
Authors: Mishra Isha , Fatima Tahmish , Egamberdieva Dilfuza , Arora Naveen Kumar
Published: October 2020

In this study, Pseudomonas putida BSP9 isolated from rhizosphere of Brassica juncea was investigated for its plant growth promoting and biosurfactant producing activities. The isolate showed the ability to produce indole acetic acid, siderophore, phosphate solubilization activity and was an efficient producer of biosurfactant. Purification (of the biosurfactant) by thin layer chromatography (TLC) and further characterization by Fourier transform infrared spectroscopy (FTIR) revealed that biosurfactant produced by the isolate belonged to the glycolipid category, which is largely produced by Pseudomonas sp. In addition, liquid chromatography-mass spectroscopy (LC-MS) analysis showed the presence of a mixture of six mono-rhamnolipidic and a di-rhamnolipidic congeners, confirming it as a rhamnolipid biosurfactant. Bioformulations were developed using BSP9 and its biosurfactant to check their impact on promoting plant growth in B. juncea. It was noted from the study that bioformulations amended with biosurfactant (singly or in combination with BSP9) resulted in enhancement in the growth parameters of B. juncea as compared to untreated control. Maximum increment was achieved by plants inoculated with bioformulation that had BSP9 plus biosurfactant. The study also suggested that growth promotion was significant up to a threshold level of biosurfactant and that further increasing the concentration did not further enhance the growth parameter values of the plant. The study proves that novel bioformulations can be developed by integrating plant growth promoting rhizobacteria (PGPR) and their biosurfactant, and they can be effectively used for increasing agricultural productivity while minimizing our dependence on agrochemicals.
In Vitro Plant Evaluation Trial: Reliability Test of Salinity Assays in Citrus Plants
Authors: Pérez-Jiménez Margarita , Pérez-Tornero Olaya
Published: October 2020

Salinity is one of the major abiotic stresses affecting crops worldwide, and breeders are urged to evaluate new genotypes to know their degree of tolerance to this selective agent. However, obtaining a number of plants high enough to make the evaluation can prove to be a long and laborious process which could be overcome by using tissue culture techniques. In the present study, the reliability of tissue culture evaluations is called into question through two parallel experiments, in vitro and ex vitro, using Citrus macrophylla and four mutants thereof, previously selected by their different behavior to salinity, as a plant material. Plants were subjected to salinity for 8 weeks in both in vitro (80 mM NaCl) and ex vitro (100 mM NaCl) experiments, and differences with plants grown in control conditions without salt were analyzed. After the experiments, length, leaf damage, shoot dry weight, chlorophylls and ions were measured in both conditions and experiments. As a result, it was demonstrated that tissue culture is a reliable tool to determine whether a genotype is tolerant to salinity or not, since plants of the same genotype responded in a similar way to salinity in both experiments. Henceforth, in vitro evaluations can be employed to test genotypes in a very early stage and using very little time and space. However, genotypes that showed the biggest or lowest changes when cultured in salinity were not always the same in both experiments. Thus, only ex vitro experiments can be performed if the goal is to compare genotypes and see which genotype is the most or least resistant to salinity.
Variable Fall Climate Conditions on Carbon Assimilation and Spring Phenology of Young Peach Trees
Authors: Lawrence Brian T. , Melgar Juan Carlos
Published: October 2020

Variable fall temperature and moisture conditions may alter leaf senescence of deciduous fruit trees, influencing carbon assimilation before dormancy and phenology the following spring. This study explored gas exchange of young peach trees (Prunus persica (L.) Batsch) when senescence proceeded normally or was delayed during the fall under two soil moisture treatments: Well-irrigated trees or water deficit. Results showed leaf carbon assimilation was similar between the senescence treatments, but whole tree assimilation was estimated to be greater in delayed senescence trees compared to normal senescence trees based on timing of defoliation and total leaf area. The effect of soil moisture on carbon assimilation was not consistent between years. Delayed sap flow and bloom time resulted as a consequence of delayed senescence the previous fall, but soil moisture did not affect spring phenology.
Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review
Authors: Sahu Parmeshwar K. , Sao Richa , Mondal Suvendu , Vishwakarma Gautam , Gupta Sudhir Kumar , Kumar Vinay , Singh Sudhir , Sharma Deepak , Das Bikram K.
Published: October 2020

The recent advancements in forward genetics have expanded the applications of mutation techniques in advanced genetics and genomics, ahead of direct use in breeding programs. The advent of next-generation sequencing (NGS) has enabled easy identification and mapping of causal mutations within a short period and at relatively low cost. Identifying the genetic mutations and genes that underlie phenotypic changes is essential for understanding a wide variety of biological functions. To accelerate the mutation mapping for crop improvement, several high-throughput and novel NGS based forward genetic approaches have been developed and applied in various crops. These techniques are highly efficient in crop plants, as it is relatively easy to grow and screen thousands of individuals. These approaches have improved the resolution in quantitative trait loci (QTL) position/point mutations and assisted in determining the functional causative variations in genes. To be successful in the interpretation of NGS data, bioinformatics computational methods are critical elements in delivering accurate assembly, alignment, and variant detection. Numerous bioinformatics tools/pipelines have been developed for such analysis. This article intends to review the recent advances in NGS based forward genetic approaches to identify and map the causal mutations in the crop genomes. The article also highlights the available bioinformatics tools/pipelines for reducing the complexity of NGS data and delivering the concluding outcomes.
Ecosystem Services, Physiology, and Biofuels Recalcitrance of Poplars Grown for Landfill Phytoremediation
Authors: Jr. Ronald S. Zalesny , Zhu J. Y. , Headlee William L. , Gleisner Roland , Pilipović Andrej , Acker Joris Van , Bauer Edmund O. , Birr Bruce A. , Wiese Adam H.
Published: October 2020

Long-term poplar phytoremediation data are lacking, especially for ecosystem services throughout rotations. We tested for rotation-age differences in biomass productivity and carbon storage of clones Populus deltoides Bartr. ex Marsh × P. nigra L. ‘DN34′ and P. nigra × P. maximowiczii A. Henry ‘NM6′ grown for landfill phytoremediation in Rhinelander, WI, USA (45.6° N, 89.4° W). We evaluated tree height and diameter, carbon isotope discrimination (Δ), and phytoaccumulation and phytoextraction of carbon, nitrogen, and inorganic pollutants in leaves, boles, and branches. We measured specific gravity and fiber composition, and determined biofuels recalcitrance of the Rhinelander landfill trees versus these genotypes that were grown for biomass production on an agricultural site in Escanaba, MI, USA (45.8° N, 87.2° W). ‘NM6′ exhibited 3.4 times greater biomass productivity and carbon storage than ‘DN34′, yet both of the clones had similar Δ, which differed for tree age rather than genotype. Phytoaccumulation and phytoextraction were clone- and tissue-specific. ‘DN34′ generally had higher pollutant concentrations. Across contaminants, stand-level mean annual uptake was 28 to 657% greater for ‘NM6′, which indicated its phytoremediation superiority. Site-related factors (not genotypic effects) governed bioconversion potential. Rhinelander phytoremediation trees exhibited 15% greater lignin than Escanaba biomass trees, contributing to 46% lower glucose yield for Rhinelander trees.
Chia, Quinoa, and Their Coproducts as Potential Antioxidants for the Meat Industry
Authors: Fernández-López Juana , Viuda-Martos Manuel , Sayas-Barberá María Estrella , Navarro-Rodríguez de Vera Casilda , Lucas-González Raquel , Roldán-Verdú Alba , Botella-Martínez Carmen , Pérez-Alvarez Jose Angel
Published: October 2020

Chia and quinoa have gained popularity among consumers worldwide due to the wide variety of nutrients but also to the bioactive compounds that they contain. Lately, their processing has generated different coproducts (non-commercial grains, flour, partially deoiled flour, rich-fiber fraction, and oil, among others), which could be reincorporated to the food chain with important technological properties, antioxidant activity included. Both sets of ingredients have been revealed a great technological potential for meat product development and innovation, taking into account that oxidation is one of the main reactions responsible for their deterioration and shelf life reduction. This review focuses on the antioxidant compounds of chia and quinoa coproducts and on the strategies used to add them to meat products highlighting their effect on the lipid oxidation control. Apart from the different ways in which quinoa and chia can be incorporated into meat products and their antioxidant properties, innovative approaches for increasing this antioxidant effect and counteracting any negative alterations they may cause will be discussed.
Improving Horticultural Crops via CRISPR/Cas9: Current Successes and Prospects
Authors: Bhatta Bed Prakash , Malla Subas
Published: October 2020

Horticultural crops include a diverse array of crops comprising fruits, vegetables, nuts, flowers, aromatic and medicinal plants. They provide nutritional, medicinal, and aesthetic benefits to mankind. However, these crops undergo many biotic (e.g., diseases, pests) and abiotic stresses (e.g., drought, salinity). Conventional breeding strategies to improve traits in crops involve the use of a series of backcrossing and selection for introgression of a beneficial trait into elite germplasm, which is time and resource consuming. Recent new plant breeding tools such as clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein-9 (Cas9) technique have the potential to be rapid, cost-effective, and precise tools for crop improvement. In this review article, we explore the CRISPR/Cas9 technology, its history, classification, general applications, specific uses in horticultural crops, challenges, existing resources, associated regulatory aspects, and the way forward.
Spatial Differentiation of Physical and Chemical Soil Parameters under Integrated, Organic, and Biodynamic Viticulture
Authors: Hendgen Maximilian , Döring Johanna , Stöhrer Verena , Schulze Fabian , Lehnart Ruth , Kauer Randolf
Published: October 2020

Vineyard soils show an increased risk of degradation due to being intensively cultivated. The preservation of soil integrity and fertility is a key concept of organic and biodynamic farming. However, both systems are also subject to criticism due to their higher amount of plant protection products used and their increased traffic intensity compared to integrated viticulture, both detrimental to soil quality. The aim of this study was therefore to assess long-term effects of these three management systems on chemical and physical soil quality parameters. For this purpose, topsoil samples were taken in a long-term field trial vineyard at different positions and examined for bulk density, available water capacity (AWC), soil organic carbon (SOC), N, pH, and for total and bioavailable copper (Cu) concentrations. Biodynamic plots had a lower bulk density and higher SOC concentration than the integrated ones, which is probably due to the species-rich cover crop mixture used in the inter-row. However, organic and biodynamic farming showed an accumulation of copper in the under-vine area and in the tractor track, which is problematic for soil fertility in the long-term. Therefore, alternatives for copper in plant protection are necessary to ensure sustainable soil quality through organic and biodynamic viticulture.
Profiling Volatile Terpenoids from Calabrian Pine Stands Infested by the Pine Processionary Moth
Authors: Foti Vincenza , Araniti Fabrizio , Manti Francesco , Alicandri Enrica , Giuffrè Angelo Maria , Bonsignore Carmelo Peter , Castiglione Elvira , Sorgonà Agostino , Covino Stefano , Paolacci Anna Rita , Ciaffi Mario , Badiani Maurizio
Published: October 2020

Terpenoids make up the biggest and most diversified class of chemical substances discovered in plants, encompassing over 40,000 individual compounds. In conifers, the production of terpenoids, either as oleoresin or emitted as volatile compounds, play an important role in the physical and chemical defence responses against pathogens and herbivores. In the present work, we examined, for the first time to the best of our knowledge, the terpenic defensive relations of Calabrian pine (Pinus nigra subsp. laricio (Poiret) Maire), facing the attack of the pine processionary moth (Thaumetopoea pityocampa (Denis and Schiffermüller, 1775)), brought about in the open on adult plant individuals growing at two distinct forest sites. Among the volatile terpenoids emitted from pine needles, bornyl acetate [(4,7,7-trimethyl-3-bicyclo[2.2.1]heptanyl) acetate] was the most frequently and selectively associated with the infestation, increasing during the period of most intense trophic activity of the caterpillars (defoliation), and decreasing thereafter. Although further work is needed to clarify whether the observed response reflects defence reactions and/or they are involved in communication among the infested plants and their biotic environment, the present results boost the currently growing interest in the isolation and characterization of plant secondary metabolites that can be used to control pests, pathogens, and weeds.
Spatial and Temporal Dynamics of Electrical and Photosynthetic Activity and the Content of Phytohormones Induced by Local Stimulation of Pea Plants
Authors: Ladeynova Maria , Mudrilov Maxim , Berezina Ekaterina , Kior Dmitry , Grinberg Marina , Brilkina Anna , Sukhov Vladimir , Vodeneev Vladimir
Published: October 2020

A local leaf burning causes variation potential (VP) propagation, a decrease in photosynthesis activity, and changes in the content of phytohormones in unstimulated leaves in pea plants. The VP-induced photosynthesis response develops in two phases: fast inactivation and long-term inactivation. Along with a decrease in photosynthetic activity, there is a transpiration suppression in unstimulated pea leaves, which corresponds to the long-term phase of photosynthesis response. Phytohormone level analysis showed an increase in the concentration of jasmonic acid (JA) preceding a transpiration suppression and a long-term phase of the photosynthesis response. Analysis of the spatial and temporal dynamics of electrical signals, phytohormone levels, photosynthesis, and transpiration activity showed the most pronounced changes in the more distant leaf from the area of local stimulation. The established features are related to the architecture of the vascular bundles in the pea stem.
The Challenge for Rapid Detection of High-Structured Circular RNA: Assay of Potato Spindle Tuber Viroid Based on Recombinase Polymerase Amplification and Lateral Flow Tests
Authors: Ivanov Aleksandr V. , Shmyglya Irina V. , Zherdev Anatoly V. , Dzantiev Boris B. , Safenkova Irina V.
Published: October 2020

An assay was developed to detect the potato spindle tuber viroid (PSTVd), a dangerous plant pathogen that causes crop damage resulting in economic losses in the potato agriculture sector. The assay was based on the reverse transcription and recombinase polymerase amplification (RT-RPA) of PSTVd RNA coupled with amplicon detection via lateral flow assay (LFA). Primers labeled with fluorescein and biotin were designed for RT-RPA for effective recognition of the loop regions in the high-structured circular RNA of PSTVd. The labeled DNA amplicon was detected using lateral flow test strips consisting of a conjugate of gold nanoparticles with antibodies specific to fluorescein and streptavidin in the test zone. The RT-RPA-LFA detected 106 copies of in vitro transcribed PSTVd RNA in reaction or up to 1:107 diluted extracts of infected plant leaves. The assay took 30 min, including the RT-RPA stage and the LFA stage. The testing of healthy and infected potato samples showed full concordance between the developed RT-RPA-LFA and quantitative reverse transcription polymerase chain reaction (RT-qPCR) and the commercial kit. The obtained results proved the feasibility of using the developed assay to detect PSTVd from a natural source.
Comparative Physiological and Proteomic Analysis Reveals Different Involvement of Proteins during Artificial Aging of Siberian Wildrye Seeds
Authors: Lei Xiong , Liu Wenhui , Zhao Junming , You Minghong , Xiong Chaohui , Xiong Yi , Xiong Yanli , Yu Qingqing , Bai Shiqie , Ma Xiao
Published: October 2020

Seed aging has an important effect on the germplasm preservation and industrialized production of Siberian wildrye (Elymus sibiricus) in the Qinghai-Tibet Plateau. However, so far its underlying molecular mechanisms still largely remain unknown. To shed light on this topic, one-year stored seeds of E. sibiricus were exposed to artificial aging treatments (AAT), followed by seed vigor characteristics and physiological status monitoring. Then global proteomics analysis was undertaken by the tandem mass tags (TMT) technique, and the proteins were quantified with liquid chromatography-tandem mass spectrometry on three aging time points (0 h, 36 h and 72 h). Finally, we verified the expression of related proteins by parallel reaction monitoring (PRM). Our results demonstrated that the seed vigor decreased remarkably in response to artificial aging, but the relative ion-leakage and malondialdehyde content, superoxide anion and hydrogen peroxide showed the opposite situation. Proteomic results showed that a total of 4169 proteins were identified and quantified. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that a series of key pathways including carbohydrate metabolism, lipid metabolism, and antioxidant activity were severely damaged by aging treatments. Numerous key proteins such as glyceraldehyde triphosphate glyceraldehyde dehydrogenase, succinate dehydrogenase, lipoxygenase, peroxidase, glutathione-s-transferase and late embryogenesis abundant proteins were significantly down-regulated. However, the up-regulation of the heat shock protein family has made a positive contribution to oxidative stress resistance in seeds. This study provides a useful catalog of the E. sibiricus proteomes with insights into the future genetic improvement of seed storability.
Development of EST-SSR Markers Linked to Flowering Candidate Genes in Elymus sibiricus L. Based on RNA Sequencing
Authors: Zheng Yuying , Zhang Zongyu , Wan Yiyang , Tian Jiaoyang , Xie Wengang
Published: October 2020

Elymus sibiricus L. is an important cold-season grass with excellent cold and drought tolerance, good palatability, and nutrition. Flowering time is a key trait that affects forage and seed yield. Development of EST-SSR (expressed sequence tag simple sequence repeat) markers based on flowering genes contributes to the improvement of flowering traits. In the study, we detected 155 candidate genes related to flowering traits from 10,591 unigenes via transcriptome sequencing in early- and late-flowering genotypes. These candidate genes were mainly involved in the photoperiodic pathway, vernalization pathway, central integrator, and gibberellin pathway. A total of 125 candidate gene-based EST-SSRs were developed. Further, 15 polymorphic EST-SSRs closely associated to 13 candidate genes were used for genetic diversity and population structure analysis among 20 E. sibiricus accessions, including two contrasting panels (early-flowering and late-flowering). Among them, primer 28366, designed from heading date 3a (HD3a), effectively distinguished early- and late-flowering genotypes using a specifically amplified band of 175 bp. The polymorphic information content (PIC) value ranged from 0.12 to 0.48, with an average of 0.25. The unweighted pair group method analysis (UPGMA) cluster and structure analysis showed that the 20 E. sibiricus genotypes with similar flowering times tended to group together. These newly developed EST-SSR markers have the potential to be used for molecular markers assisted selection and germplasm evaluation of flowering traits in E. sibiricus.
Metabolic Responses to Waterlogging Differ between Roots and Shoots and Reflect Phloem Transport Alteration in Medicago truncatula
Authors: Lothier Jérémy , Diab Houssein , Cukier Caroline , Limami Anis M. , Tcherkez Guillaume
Published: October 2020

Root oxygen deficiency that is induced by flooding (waterlogging) is a common situation in many agricultural areas, causing considerable loss in yield and productivity. Physiological and metabolic acclimation to hypoxia has mostly been studied on roots or whole seedlings under full submergence. The metabolic difference between shoots and roots during waterlogging, and how roots and shoots communicate in such a situation is much less known. In particular, the metabolic acclimation in shoots and how this, in turn, impacts on roots metabolism is not well documented. Here, we monitored changes in the metabolome of roots and shoots of barrel clover (Medicago truncatula), growth, and gas-exchange, and analyzed phloem sap exudate composition. Roots exhibited a typical response to hypoxia, such as γ-aminobutyrate and alanine accumulation, as well as a strong decline in raffinose, sucrose, hexoses, and pentoses. Leaves exhibited a strong increase in starch, sugars, sugar derivatives, and phenolics (tyrosine, tryptophan, phenylalanine, benzoate, ferulate), suggesting an inhibition of sugar export and their alternative utilization by aromatic compounds production via pentose phosphates and phosphoenolpyruvate. Accordingly, there was an enrichment in sugars and a decline in organic acids in phloem sap exudates under waterlogging. Mass-balance calculations further suggest an increased imbalance between loading by shoots and unloading by roots under waterlogging. Taken as a whole, our results are consistent with the inhibition of sugar import by waterlogged roots, leading to an increase in phloem sugar pool, which, in turn, exert negative feedback on sugar metabolism and utilization in shoots.
Molecular Markers Improve Abiotic Stress Tolerance in Crops: A Review
Authors: Younis Adnan , Ramzan Fahad , Ramzan Yasir , Zulfiqar Faisal , Ahsan Muhammad , Lim Ki Byung
Published: October 2020

Plants endure many abiotic stresses, such as temperature (heat or frost), drought, and salt. Such factors are primary and frequent stressors that reduce agriculture crop yields. Often alterations in nutrient management and constituents, along with variations in biosynthetic capacity, ultimately reduce or halt plant growth. Genetically, stress is an environmental condition that interferes with complete genetic expression. A vast range of molecular genomic markers is available for the analysis of agricultural crops. These markers are classified into various groups based on how the markers are used: RAPD (Random amplified polymorphic DNA) markers serve to identify and screen hybrids based on salinity and drought stress tolerance, while simple sequence repeat (SSR) markers are excellent for the assessment of stress tolerance. Such markers also play an important role in the QTL (Quantitative trait loci) mapping of stress-related genes. Dehydrins for drought and saltol for salinity stresses are primitive genes which regulate responses to these conditions. Further, a focus on traits using single-gene single nucleotide polymorphisms (SNP) markers supports genetic mapping and the sequencing of stress-related traits in inbred lines. DNA markers facilitate marker-assisted breeding to enhance abiotic stress tolerance using advanced techniques and marker modification.