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Fulltext Modeling induced resistance to plant disease using a dynamical systems approach

Abdul Latif NS, Wake GC, Reglinski T, Elmer PA, Taylor JT

Front Plant Sci, 2013;4:19.
PMID: 23424585 DOI: 10.3389/fpls.2013.00019
Editorial: Advanced insights into environmental stress and tolerance mechanisms in forest trees

Abiri R, Abdul-Hamid H, Leung DW

Front Plant Sci, 2023;14:1273663.
PMID: 37771484 DOI: 10.3389/fpls.2023.1273663
Fulltext Jasmonates: Multifunctional Roles in Stress Tolerance

Ahmad P, Rasool S, Gul A, Sheikh SA, Akram NA, Ashraf M, et al.

Front Plant Sci, 2016;7:813.
PMID: 27379115 DOI: 10.3389/fpls.2016.00813

Jasmonates (JAs) [Jasmonic acid (JA) and methyl jasmonates (MeJAs)] are known to take part in various physiological processes. Exogenous application of JAs so far tested on different plants under abiotic stresses particularly salinity, drought, and temperature (low/high) conditions have proved effective in improving plant stress tolerance. However, its extent of effectiveness entirely depends on the type of plant species tested or its concentration. The effects of introgression or silencing of different JA- and Me-JA-related genes have been summarized in this review, which have shown a substantial role in improving crop yield and quality in different plants under stress or non-stress conditions. Regulation of JAs synthesis is impaired in stressed as well as unstressed plant cells/tissues, which is believed to be associated with a variety of metabolic events including signal transduction. Although, mitogen activated protein kinases (MAPKs) are important components of JA signaling and biosynthesis pathways, nitric oxide, ROS, calcium, ABA, ethylene, and salicylic acid are also important mediators of plant growth and development during JA signal transduction and synthesis. The exploration of other signaling molecules can be beneficial to examine the details of underlying molecular mechanisms of JA signal transduction. Much work is to be done in near future to find the proper answers of the questions like action of JA related metabolites, and identification of universal JA receptors etc. Complete signaling pathways involving MAPKs, CDPK, TGA, SIPK, WIPK, and WRKY transcription factors are yet to be investigated to understand the complete mechanism of action of JAs.
Fulltext A comprehensive phytochemical, biological, and toxicological studies of roots and aerial parts of Crotalaria burhia Buch.-Ham: An important medicinal plant

Anwar S, Faisal Nadeem M, Pervaiz I, Khurshid U, Akmal N, Aamir K, et al.

Front Plant Sci, 2022;13:988352.
PMID: 36212347 DOI: 10.3389/fpls.2022.988352

This study was designed to seek the phytochemical analysis, antioxidant, enzyme inhibition, and toxicity potentials of methanol and dichloromethane (DCM) extracts of aerial and root parts of Crotalaria burhia. Total bioactive content, high-performance liquid chromatography-photodiode array detector (HPLC-PDA) polyphenolic quantification, and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) analysis were utilized to evaluate the phytochemical composition. Antioxidant [including 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH)], 2,2'-azino-bis[3-ethylbenzothiazoline-6-sulfonic acid (ABTS), ferric reducing antioxidant power assay (FRAP), cupric reducing antioxidant capacity CUPRAC, phosphomolybdenum, and metal chelation assays] and enzyme inhibition [against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), α-glucosidase, α-amylase, and tyrosinase] assays were carried out for biological evaluation. The cytotoxicity was tested against MCF-7 and MDA-MB-231 breast cell lines. The root-methanol extract contained the highest levels of phenolics (37.69 mg gallic acid equivalent/g extract) and flavonoids (83.0 mg quercetin equivalent/g extract) contents, and was also the most active for DPPH (50.04 mg Trolox equivalent/g extract) and CUPRAC (139.96 mg Trolox equivalent /g extract) antioxidant assays. Likewise, the aerial-methanol extract exhibited maximum activity for ABTS (94.05 mg Trolox equivalent/g extract) and FRAP (64.23 mg Trolox equivalent/g extract) assays. The aerial-DCM extract was noted to be a convincing cholinesterase (AChE; 4.01 and BChE; 4.28 mg galantamine equivalent/g extract), and α-glucosidase inhibitor (1.92 mmol acarbose equivalent/g extract). All of the extracts exhibited weak to modest toxicity against the tested cell lines. A considerable quantities of gallic acid, catechin, 4-OH benzoic acid, syringic acid, vanillic acid, 3-OH-4-MeO benzaldehyde, epicatechin, p-coumaric acid, rutin, naringenin, and carvacrol were quantified via HPLC-PDA analysis. UHPLC-MS analysis of methanolic extracts from roots and aerial parts revealed the tentative identification of important phytoconstituents such as polyphenols, saponins, flavonoids, and glycoside derivatives. To conclude, this plant could be considered a promising source of origin for bioactive compounds with several therapeutic uses.
Fulltext Molecular Breeding Strategy and Challenges Towards Improvement of Blast Disease Resistance in Rice Crop

Ashkani S, Rafii MY, Shabanimofrad M, Miah G, Sahebi M, Azizi P, et al.

Front Plant Sci, 2015;6:886.
PMID: 26635817 DOI: 10.3389/fpls.2015.00886

Rice is a staple and most important security food crop consumed by almost half of the world's population. More rice production is needed due to the rapid population growth in the world. Rice blast caused by the fungus, Magnaporthe oryzae is one of the most destructive diseases of this crop in different part of the world. Breakdown of blast resistance is the major cause of yield instability in several rice growing areas. There is a need to develop strategies providing long-lasting disease resistance against a broad spectrum of pathogens, giving protection for a long time over a broad geographic area, promising for sustainable rice production in the future. So far, molecular breeding approaches involving DNA markers, such as QTL mapping, marker-aided selection, gene pyramiding, allele mining and genetic transformation have been used to develop new resistant rice cultivars. Such techniques now are used as a low-cost, high-throughput alternative to conventional methods allowing rapid introgression of disease resistance genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more durable blast resistance. The paper briefly reviewed the progress of studies on this aspect to provide the interest information for rice disease resistance breeding. This review includes examples of how advanced molecular method have been used in breeding programs for improving blast resistance. New information and knowledge gained from previous research on the recent strategy and challenges towards improvement of blast disease such as pyramiding disease resistance gene for creating new rice varieties with high resistance against multiple diseases will undoubtedly provide new insights into the rice disease control.
Fulltext Over-Expression of the Pikh Gene with a CaMV 35S Promoter Leads to Improved Blast Disease (Magnaporthe oryzae) Tolerance in Rice

Azizi P, Rafii MY, Abdullah SN, Hanafi MM, Maziah M, Sahebi M, et al.

Front Plant Sci, 2016;7:773.
PMID: 27379107 DOI: 10.3389/fpls.2016.00773

Magnaporthe oryzae is a rice blast fungus and plant pathogen that causes a serious rice disease and, therefore, poses a threat to the world's second most important food security crop. Plant transformation technology has become an adaptable system for cultivar improvement and to functionally analyze genes in plants. The objective of this study was to determine the effects (through over-expressing and using the CaMV 35S promoter) of Pikh on MR219 resistance because it is a rice variety that is susceptible to the blast fungus pathotype P7.2. Thus, a full DNA and coding DNA sequence (CDS) of the Pikh gene, 3172 bp, and 1206 bp in length, were obtained through amplifying the gDNA and cDNA template from a PH9-resistant rice variety using a specific primer. Agrobacterium-mediated transformation technology was also used to introduce the Pikh gene into the MR219 callus. Subsequently, transgenic plants were evaluated from the DNA to protein stages using polymerase chain reaction (PCR), semi-quantitative RT-PCR, real-time quantitative PCR and high performance liquid chromatography (HPLC). Transgenic plants were also compared with a control using a real-time quantification technique (to quantify the pathogen population), and transgenic and control plants were challenged with the local most virulent M. oryzae pathotype, P7.2. Based on the results, the Pikh gene encodes a hydrophilic protein with 18 sheets, 4 helixes, and 21 coils. This protein contains 401 amino acids, among which the amino acid sequence from 1 to 376 is a non-cytoplasmic region, that from 377 to 397 is a transmembrane region, and that from 398 to 401 is a cytoplasmic region with no identified disordered regions. The Pikh gene was up-regulated in the transgenic plants compared with the control plants. The quantity of the amino acid leucine in the transgenic rice plants increased significantly from 17.131 in the wild-type to 47.865 mg g(-1) in transgenic plants. The M. oryzae population was constant at 31, 48, and 72 h after inoculation in transgenic plants, while it was increased in the inoculated control plants. This study successfully clarified that over-expression of the Pikh gene in transgenic plants can improve their blast resistance against the M. oryzae pathotype P7.2.
Fulltext Interaction between zinc and selenium bio-fortification and toxic metals (loid) accumulation in food crops

Bayanati M, Al-Tawaha AR, Al-Taey D, Al-Ghzawi AL, Abu-Zaitoon YM, Shawaqfeh S, et al.

Front Plant Sci, 2022;13:1001992.
PMID: 36388536 DOI: 10.3389/fpls.2022.1001992

Biofortification is the supply of micronutrients required for humans and livestock by various methods in the field, which include both farming and breeding methods and are referred to as short-term and long-term solutions, respectively. The presence of essential and non-essential elements in the atmosphere, soil, and water in large quantities can cause serious problems for living organisms. Knowledge about plant interactions with toxic metals such as cadmium (Cd), mercury (Hg), nickel (Ni), and lead (Pb), is not only important for a healthy environment, but also for reducing the risks of metals entering the food chain. Biofortification of zinc (Zn) and selenium (Se) is very significant in reducing the effects of toxic metals, especially on major food chain products such as wheat and rice. The findings show that Zn- biofortification by transgenic technique has reduced the accumulation of Cd in shoots and grains of rice, and also increased Se levels lead to the formation of insoluble complexes with Hg and Cd. We have highlighted the role of Se and Zn in the reaction to toxic metals and the importance of modifying their levels in improving dietary micronutrients. In addition, cultivar selection is an essential step that should be considered not only to maintain but also to improve the efficiency of Zn and Se use, which should be considered more climate, soil type, organic matter content, and inherent soil fertility. Also, in this review, the role of medicinal plants in the accumulation of heavy metals has been mentioned, and these plants can be considered in line with programs to improve biological enrichment, on the other hand, metallothioneins genes can be used in the program biofortification as grantors of resistance to heavy metals.
The 4-Dimensional Plant: Effects of Wind-Induced Canopy Movement on Light Fluctuations and Photosynthesis

Burgess AJ, Retkute R, Preston SP, Jensen OE, Pound MP, Pridmore TP, et al.

Front Plant Sci, 2016;7:1392.
PMID: 27708654

Physical perturbation of a plant canopy brought about by wind is a ubiquitous phenomenon and yet its biological importance has often been overlooked. This is partly due to the complexity of the issue at hand: wind-induced movement (or mechanical excitation) is a stochastic process which is difficult to measure and quantify; plant motion is dependent upon canopy architectural features which, until recently, were difficult to accurately represent and model in 3-dimensions; light patterning throughout a canopy is difficult to compute at high-resolutions, especially when confounded by other environmental variables. Recent studies have reinforced the expectation that canopy architecture is a strong determinant of productivity and yield; however, links between the architectural properties of the plant and its mechanical properties, particularly its response to wind, are relatively unknown. As a result, biologically relevant data relating canopy architecture, light- dynamics, and short-scale photosynthetic responses in the canopy setting are scarce. Here, we hypothesize that wind-induced movement will have large consequences for the photosynthetic productivity of our crops due to its influence on light patterning. To address this issue, in this study we combined high resolution 3D reconstructions of a plant canopy with a simple representation of canopy perturbation as a result of wind using solid body rotation in order to explore the potential effects on light patterning, interception, and photosynthetic productivity. We looked at two different scenarios: firstly a constant distortion where a rice canopy was subject to a permanent distortion throughout the whole day; and secondly, a dynamic distortion, where the canopy was distorted in incremental steps between two extremes at set time points in the day. We find that mechanical canopy excitation substantially alters light dynamics; light distribution and modeled canopy carbon gain. We then discuss methods required for accurate modeling of mechanical canopy excitation (here coined the 4-dimensional plant) and some associated biological and applied implications of such techniques. We hypothesize that biomechanical plant properties are a specific adaptation to achieve wind-induced photosynthetic enhancement and we outline how traits facilitating canopy excitation could be used as a route for improving crop yield.
Fulltext Exploring Relationships between Canopy Architecture, Light Distribution, and Photosynthesis in Contrasting Rice Genotypes Using 3D Canopy Reconstruction

Burgess AJ, Retkute R, Herman T, Murchie EH

Front Plant Sci, 2017;8:734.
PMID: 28567045 DOI: 10.3389/fpls.2017.00734

The arrangement of leaf material is critical in determining the light environment, and subsequently the photosynthetic productivity of complex crop canopies. However, links between specific canopy architectural traits and photosynthetic productivity across a wide genetic background are poorly understood for field grown crops. The architecture of five genetically diverse rice varieties-four parental founders of a multi-parent advanced generation intercross (MAGIC) population plus a high yielding Philippine variety (IR64)-was captured at two different growth stages using a method for digital plant reconstruction based on stereocameras. Ray tracing was employed to explore the effects of canopy architecture on the resulting light environment in high-resolution, whilst gas exchange measurements were combined with an empirical model of photosynthesis to calculate an estimated carbon gain and total light interception. To further test the impact of different dynamic light patterns on photosynthetic properties, an empirical model of photosynthetic acclimation was employed to predict the optimal light-saturated photosynthesis rate (Pmax ) throughout canopy depth, hypothesizing that light is the sole determinant of productivity in these conditions. First, we show that a plant type with steeper leaf angles allows more efficient penetration of light into lower canopy layers and this, in turn, leads to a greater photosynthetic potential. Second the predicted optimal Pmax responds in a manner that is consistent with fractional interception and leaf area index across this germplasm. However, measured Pmax , especially in lower layers, was consistently higher than the optimal Pmax indicating factors other than light determine photosynthesis profiles. Lastly, varieties with more upright architecture exhibit higher maximum quantum yield of photosynthesis indicating a canopy-level impact on photosynthetic efficiency.
Fulltext Phylogenomic analyses reveal reticulate evolution between Neomicrocalamus and Temochloa (Poaceae: Bambusoideae)

Cai ZY, Niu ZY, Zhang YY, Tong YH, Vu TC, Goh WL, et al.

Front Plant Sci, 2023;14:1274337.
PMID: 38111884 DOI: 10.3389/fpls.2023.1274337

Neomicrocalamus and Temochloa are closely related to bamboo genera. However, when considered with newly discovered and morphologically similar material from China and Vietnam, the phylogenetic relationship among these three groups was ambiguous in the analyses based on DNA regions. Here, as a means of investigating the relationships among the three bamboo groups and exploring potential sources of genomic conflicts, we present a phylogenomic examination based on the whole plastome, single-nucleotide polymorphism (SNP), and single-copy nuclear (SCN) gene datasets. Three different phylogenetic hypotheses were found. The inconsistency is attributed to the combination of incomplete lineage sorting and introgression. The origin of newly discovered bamboos is from introgressive hybridization between Temochloa liliana (which contributed 80.7% of the genome) and Neomicrocalamus prainii (19.3%), indicating that the newly discovered bamboos are closer to T. liliana in genetics. The more similar morphology and closer distribution elevation also imply a closer relationship between Temochloa and newly discovered bamboos.
Fulltext Genetic Loci Governing Grain Yield and Root Development under Variable Rice Cultivation Conditions

Catolos M, Sandhu N, Dixit S, Shamsudin NAA, Naredo MEB, McNally KL, et al.

Front Plant Sci, 2017;8:1763.
PMID: 29085383 DOI: 10.3389/fpls.2017.01763

Drought is the major abiotic stress to rice grain yield under unpredictable changing climatic scenarios. The widely grown, high yielding but drought susceptible rice varieties need to be improved by unraveling the genomic regions controlling traits enhancing drought tolerance. The present study was conducted with the aim to identify quantitative trait loci (QTLs) for grain yield and root development traits under irrigated non-stress and reproductive-stage drought stress in both lowland and upland situations. A mapping population consisting of 480 lines derived from a cross between Dular (drought-tolerant) and IR64-21 (drought susceptible) was used. QTL analysis revealed three major consistent-effect QTLs for grain yield (qDTY1.1, qDTY1.3 , and qDTY8.1 ) under non-stress and reproductive-stage drought stress conditions, and 2 QTLs for root traits (qRT9.1 for root-growth angle and qRT5.1 for multiple root traits, i.e., seedling-stage root length, root dry weight and crown root number). The genetic locus qDTY1.1 was identified as hotspot for grain yield and yield-related agronomic and root traits. The study identified significant positive correlations among numbers of crown roots and mesocotyl length at the seedling stage and root length and root dry weight at depth at later stages with grain yield and yield-related traits. Under reproductive stage drought stress, the grain yield advantage of the lines with QTLs ranged from 24.1 to 108.9% under upland and 3.0-22.7% under lowland conditions over the lines without QTLs. The lines with QTL combinations qDTY1.3 +qDTY8.1 showed the highest mean grain yield advantage followed by lines having qDTY1.1 +qDTY8.1 and qDTY1.1 +qDTY8.1 +qDTY1.3 , across upland/lowland reproductive-stage drought stress. The identified QTLs for root traits, mesocotyl length, grain yield and yield-related traits can be immediately deployed in marker-assisted breeding to develop drought tolerant high yielding rice varieties.
Editorial: Soil biota and climate smart crops

Cheng A, Gajic G, Doni F

Front Plant Sci, 2023;14:1250831.
PMID: 37538065 DOI: 10.3389/fpls.2023.1250831
Fulltext Integrated Assessment of Nickel Electroplating Industrial Wastewater Effluent as a Renewable Resource of Irrigation Water Using a Hydroponic Cultivation System

Chow YN, Lee LK, Zakaria NA, Foo KY

Front Plant Sci, 2021;12:609396.
PMID: 33746995 DOI: 10.3389/fpls.2021.609396

Nickel, a micronutrient essential for plant growth and development, has been recognized as a metallic pollutant in wastewater. The concentration of nickel ions in the water course, exceeding the maximum tolerable limit, has called for an alarming attention, due to the bioaccumulative entry in the water-plant-human food chain, leaving a burden of deteriorative effects on visible characteristics, physiological processes, and oxidative stress response in plants. In this work, the renewable utilization of nickel electroplating industrial wastewater effluent (0, 5, 10, 25, 50, and 100%) as a viable source of irrigation water was evaluated using a hydroponic cultivation system, by adopting Lablab purpureus and Brassica chinensis as the plant models, in relation to the physical growth, physiological and morphological characteristics, photosynthetic pigments, proline, and oxidative responses. The elongation of roots and shoots in L. purpureus and B. chinensis was significantly inhibited beyond 25 and 5% of industrial wastewater. The chlorophyll-a, chlorophyll-b, total chlorophyll, and carotenoid contents, accompanied by alterations in the morphologies of xylem, phloem, and distortion of stomata, were recorded in the industrial wastewater-irrigated groups, with pronounced toxicity effects detected in B. chinensis. Excessive proline accumulation was recorded in the treated plant models. Ascorbate peroxidase (APX), guaiacol peroxidase (POD), and catalase (CAT) scavenging activities were drastically altered, with a profound upregulation effect in the POD activity in L. purpureus and both POD and APX in B. chinensis, predicting the nickel-induced oxidative stress. Conclusively, the diluted industrial wastewater effluent up to the optimum concentrations of 5 and 25%, respectively, could be feasibly reused as a renewable resource for B. chinensis and L. purpureus irrigation, verified by the minimal or negligible phytotoxic implications in the plant models. The current findings have shed light on the interruption of nickel-contaminated industrial wastewater effluent irrigation practice on the physical and biochemical features of food crops and highlighted the possibility of nutrient recycling via wastewater reuse in a sustainable soilless cultivation.
Fulltext Enhancing drought tolerance in cauliflower (Brassica oleracea var. botrytis) by targeting LFY transcription factor modulation via the ethylene precursor, ACCA: an innovative computational approach

Debnath S, Elgorban AM, Bahkali AH, Eswaramoorthy R, Verma M, Syed A, et al.

Front Plant Sci, 2024;15:1255979.
PMID: 38481405 DOI: 10.3389/fpls.2024.1255979

BACKGROUND: Brassica oleracea var. botrytis is an annual or biennial herbaceous vegetable plant in the Brassicaceae family notable for its edible blossom head. A lot of effort has gone into finding defense-associated proteins in order to better understand how cauliflower and pathogens interact. Endophytes are organisms that live within the host plant and reproduce. Endophytes are bacteria and fungi that reside in plant tissues and can either help or harm the plant. Several species have aided molecular biologists and plant biotechnologists in various ways. Water is essential for a healthy cauliflower bloom. When the weather is hot, this plant dries up, and nitrogen scarcity can be detrimental to cauliflower growth.
OBJECTIVE: The study sought to discern plant growth promoting (PGP) compounds that can amplify drought resilience and boost productivity in cauliflower.
METHODS: Investigations were centered on endophytes, microorganisms existing within plant tissues. The dual role of beneficial and detrimental Agrobacterium was scrutinized, particularly emphasizing the ethylene precursor compound, 1-amino-cyclopropane-1-carboxylic acid (ACCA).
RESULTS: ACCA possessed salient PGP traits, particularly demonstrating a pronounced enhancement of drought resistance in cauliflower plants. Specifically, during the pivotal marketable curd maturity phase, which necessitates defense against various threats, ACCA showcased a binding energy of -8.74 kcal/mol.
CONCLUSION: ACCA holds a significant promise in agricultural productivity, with its potential to boost drought resistance and cauliflower yield. This could be particularly impactful for regions grappling with high temperatures and possible nitrogen shortages. Future research should explore ACCA's performance under diverse environmental settings and its applicability in other crops.
Editorial: Global excellence in plant science: Southeast Asia

Doni F, Mispan MS

Front Plant Sci, 2023;14:1285250.
PMID: 37746022 DOI: 10.3389/fpls.2023.1285250
Evaluating the underlying physiological and molecular mechanisms in the system of rice intensification performance with Trichoderma-rice plant symbiosis as a model system

Doni F, Safitri R, Suhaimi NSM, Miranti M, Rossiana N, Mispan MS, et al.

Front Plant Sci, 2023;14:1214213.
PMID: 37692429 DOI: 10.3389/fpls.2023.1214213

The system of rice intensification (SRI) is an extensively-researched and increasingly widely-utilized methodology for alleviating current constraints on rice production. Many studies have shown physiological and morphological improvements in rice plants induced by SRI management practices to be very similar to those that are associated with the presence of beneficial microbial endophytes in or around rice plants, especially their roots. With SRI methods, grain yields are increased by 25-100% compared to conventional methods, and the resulting plant phenotypes are better able to cope with biotic and abiotic stresses. SRI management practices have been shown to be associated with significant increases in the populations of certain microorganisms known to enhance soil health and plant growth, e.g., Azospirillum, Trichoderma, Glomus, and Pseudomonas. This article evaluates the effects of applying Trichoderma as a model microbe for assessing microbial growth-promotion, biological control activity, and modulation of gene expression under the conditions created by SRI practices. Information about the molecular changes and interactions associated with certain effects of SRI management suggests that these practices are enhancing rice plants' expression of their genetic potentials. More systematic studies that assess the effects of SRI methods respectively and collectively, compared with standard rice production methods, are needed to develop a more encompassing understanding of how SRI modifications of crops' growing environment elicit and contribute to more robust and more productive phenotypes of rice.
Fulltext Image-based phenotyping of seed architectural traits and prediction of seed weight using machine learning models in soybean

Duc NT, Ramlal A, Rajendran A, Raju D, Lal SK, Kumar S, et al.

Front Plant Sci, 2023;14:1206357.
PMID: 37771485 DOI: 10.3389/fpls.2023.1206357

Among seed attributes, weight is one of the main factors determining the soybean harvest index. Recently, the focus of soybean breeding has shifted to improving seed size and weight for crop optimization in terms of seed and oil yield. With recent technological advancements, there is an increasing application of imaging sensors that provide simple, real-time, non-destructive, and inexpensive image data for rapid image-based prediction of seed traits in plant breeding programs. The present work is related to digital image analysis of seed traits for the prediction of hundred-seed weight (HSW) in soybean. The image-based seed architectural traits (i-traits) measured were area size (AS), perimeter length (PL), length (L), width (W), length-to-width ratio (LWR), intersection of length and width (IS), seed circularity (CS), and distance between IS and CG (DS). The phenotypic investigation revealed significant genetic variability among 164 soybean genotypes for both i-traits and manually measured seed weight. Seven popular machine learning (ML) algorithms, namely Simple Linear Regression (SLR), Multiple Linear Regression (MLR), Random Forest (RF), Support Vector Regression (SVR), LASSO Regression (LR), Ridge Regression (RR), and Elastic Net Regression (EN), were used to create models that can predict the weight of soybean seeds based on the image-based novel features derived from the Red-Green-Blue (RGB)/visual image. Among the models, random forest and multiple linear regression models that use multiple explanatory variables related to seed size traits (AS, L, W, and DS) were identified as the best models for predicting seed weight with the highest prediction accuracy (coefficient of determination, R2=0.98 and 0.94, respectively) and the lowest prediction error, i.e., root mean square error (RMSE) and mean absolute error (MAE). Finally, principal components analysis (PCA) and a hierarchical clustering approach were used to identify IC538070 as a superior genotype with a larger seed size and weight. The identified donors/traits can potentially be used in soybean improvement programs.
Fulltext Genome Size, Molecular Phylogeny, and Evolutionary History of the Tribe Aquilarieae (Thymelaeaceae), the Natural Source of Agarwood

Farah AH, Lee SY, Gao Z, Yao TL, Madon M, Mohamed R

Front Plant Sci, 2018;9:712.
PMID: 29896211 DOI: 10.3389/fpls.2018.00712

The tribe Aquilarieae of the family Thymelaeaceae consists of two genera, Aquilaria and Gyrinops, with a total of 30 species, distributed from northeast India, through southeast Asia and the south of China, to Papua New Guinea. They are an important botanical resource for fragrant agarwood, a prized product derived from injured or infected stems of these species. The aim of this study was to estimate the genome size of selected Aquilaria species and comprehend the evolutionary history of Aquilarieae speciation through molecular phylogeny. Five non-coding chloroplast DNA regions and a nuclear region were sequenced from 12 Aquilaria and three Gyrinops species. Phylogenetic trees constructed using combined chloroplast DNA sequences revealed relationships of the studied 15 members in Aquilarieae, while nuclear ribosomal DNA internal transcribed spacer (ITS) sequences showed a paraphyletic relationship between Aquilaria species from Indochina and Malesian. We exposed, for the first time, the estimated divergence time for Aquilarieae speciation, which was speculated to happen during the Miocene Epoch. The ancestral split and biogeographic pattern of studied species were discussed. Results showed no large variation in the 2C-values for the five Aquilaria species (1.35-2.23 pg). Further investigation into the genome size may provide additional information regarding ancestral traits and its evolution history.
Fulltext Increasing Leaf Vein Density via Mutagenesis in Rice Results in an Enhanced Rate of Photosynthesis, Smaller Cell Sizes and Can Reduce Interveinal Mesophyll Cell Number

Feldman AB, Leung H, Baraoidan M, Elmido-Mabilangan A, Canicosa I, Quick WP, et al.

Front Plant Sci, 2017;8:1883.
PMID: 29163607 DOI: 10.3389/fpls.2017.01883

Improvements to leaf photosynthetic rates of crops can be achieved by targeted manipulation of individual component processes, such as the activity and properties of RuBisCO or photoprotection. This study shows that simple forward genetic screens of mutant populations can also be used to rapidly generate photosynthesis variants that are useful for breeding. Increasing leaf vein density (concentration of vascular tissue per unit leaf area) has important implications for plant hydraulic properties and assimilate transport. It was an important step to improving photosynthetic rates in the evolution of both C3 and C4 species and is a foundation or prerequisite trait for C4 engineering in crops like rice (Oryza sativa). A previous high throughput screen identified five mutant rice lines (cv. IR64) with increased vein densities and associated narrower leaf widths (Feldman et al., 2014). Here, these high vein density rice variants were analyzed for properties related to photosynthesis. Two lines were identified as having significantly reduced mesophyll to bundle sheath cell number ratios. All five lines had 20% higher light saturated photosynthetic capacity per unit leaf area, higher maximum carboxylation rates, dark respiration rates and electron transport capacities. This was associated with no significant differences in leaf thickness, stomatal conductance or CO2 compensation point between mutants and the wild-type. The enhanced photosynthetic rate in these lines may be a result of increased RuBisCO and electron transport component amount and/or activity and/or enhanced transport of photoassimilates. We conclude that high vein density (associated with altered mesophyll cell length and number) is a trait that may confer increased photosynthetic efficiency without increased transpiration.
Fulltext The Phenylpropanoid Pathway and Lignin in Defense against Ganoderma boninense Colonized Root Tissues in Oil Palm (Elaeis guineensis Jacq.)

Govender NT, Mahmood M, Seman IA, Wong MY

Front Plant Sci, 2017;8:1395.
PMID: 28861093 DOI: 10.3389/fpls.2017.01395

Basal stem rot, caused by the basidiomycete fungus, Ganoderma boninense, is an economically devastating disease in Malaysia. Our study investigated the changes in lignin content and composition along with activity and expression of the phenylpropanoid pathway enzymes and genes in oil palm root tissues during G. boninense infection. We sampled control (non-inoculated) and infected (inoculated) seedlings at seven time points [1, 2, 3, 4, 8, and 12 weeks post-inoculation (wpi)] in a randomized design. The expression profiles of phenylalanine ammonia lyase (PAL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD) genes were monitored at 1, 2, and 3 wpi using real-time quantitative polymerase chain reaction. Seedlings at 4, 8, and 12 wpi were screened for lignin content, lignin composition, enzyme activities (PAL, CAD, and POD), growth (weight and height), and disease severity (DS). Gene expression analysis demonstrated up-regulation of PAL, CAD, and POD genes in the infected seedlings, relative to the control seedlings at 1, 2, and 3 wpi. At 2 and 3 wpi, CAD showed highest transcript levels compared to PAL and POD. DS increased progressively throughout sampling, with 5, 34, and 69% at 4, 8, and 12 wpi, respectively. Fresh weight and height of the infected seedlings were significantly lower compared to the control seedlings at 8 and 12 wpi. Lignin content of the infected seedlings at 4 wpi was significantly higher than the control seedlings, remained elicited with no change at 8 wpi, and then collapsed with a significant reduction at 12 wpi. The nitrobenzene oxidation products of oil palm root lignin yielded both syringyl and guaiacyl monomers. Accumulation of lignin in the infected seedlings was in parallel to increased syringyl monomers, at 4 and 8 wpi. The activities of PAL and CAD enzymes in the infected seedlings at DS = 5-34% were significantly higher than the control seedlings and thereafter collapsed at DS = 69%.

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