Scholarly Works, School of Plant and Environmental Sciences
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Browsing Scholarly Works, School of Plant and Environmental Sciences by Content Type "Article - Refereed"
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- A Review of Bioactive Compound Effects from Primary Legume Protein Sources in Human and Animal HealthShea, Zachary; Ogando do Granja, Matheus; Fletcher, Elizabeth B.; Zheng, Yaojie; Bewick, Patrick; Wang, Zhibo; Singer, William M.; Zhang, Bo (MDPI, 2024-05-01)The global demand for sustainable and nutritious food sources has catalyzed interest in legumes, known for their rich repertoire of health-promoting compounds. This review delves into the diverse array of bioactive peptides, protein subunits, isoflavones, antinutritional factors, and saponins found in the primary legume protein sources—soybeans, peas, chickpeas, and mung beans. The current state of research on these compounds is critically evaluated, with an emphasis on the potential health benefits, ranging from antioxidant and anticancer properties to the management of chronic diseases such as diabetes and hypertension. The extensively studied soybean is highlighted and the relatively unexplored potential of other legumes is also included, pointing to a significant, underutilized resource for developing health-enhancing foods. The review advocates for future interdisciplinary research to further unravel the mechanisms of action of these bioactive compounds and to explore their synergistic effects. The ultimate goal is to leverage the full spectrum of benefits offered by legumes, not only to advance human health but also to contribute to the sustainability of food systems. By providing a comprehensive overview of the nutraceutical potential of legumes, this manuscript sets a foundation for future investigations aimed at optimizing the use of legumes in the global pursuit of health and nutritional security.
- Accelerated senescence and nitrogen remobilization in flag leaves enhance nitrogen use efficiency in soft red winter wheatAlpuerto, Jasper B.; Brasier, Kyle G.; Griffey, Carl A.; Thomason, Wade E.; Fukao, Takeshi (2021-01)Wheat (Triticum aestivum L.) production requires a large amount of nitrogen (N) supply because growers aim to achieve high grain yield and appropriate grain protein content simultaneously. A comprehensive understanding of the mechanisms that underpin efficient N usage at limited N in wheat can facilitate the development of new N-saving varieties in this major crop. Here, we performed comparative analysis of flag leaf responses to N availability in soft red winter wheat with contrasting N use efficiency (NUE); VA08MAS-369 (high NUE) and VA07W-415 (low NUE). This study demonstrated that accelerated senescence along with enhanced breakdown of protein and starch in flag leaves was correlated with higher grain yield, NUE for grain yield, and NUE for grain protein under N limitation. The more dramatic reductions in flag leaf N compounds and carbohydrate reserves in VA08MAS-369 were linked with significantly elevated expression of genes and enzymes associated with these metabolic pathways in this high NUE genotype. Consistent with the gene expression data, nitrate reductase, glutamine synthetase, and NAD-dependent glutamate dehydrogenase activities were highly induced under limited N in VA08MAS-369. It was previously reported that accelerated senescence contributes to increased grain protein content in wheat under regular N supply. This study provides molecular and physiological evidence that vigorous senescence and N remobilization also benefit grain yield under N deprivation.
- Accession-Level Differentiation of Urushiol Levels, and Identification of Cardanols in Nascent Emerged Poison Ivy SeedlingsLott, Aneirin A.; Baklajian, Emily R.; Dickinson, Christopher C.; Collakova, Eva; Jelesko, John G. (MDPI, 2019-11-20)Poison ivy (Toxicodendron radicans (L.) Kuntze) shows accession-level differentiation in a variety of morphometric traits, suggesting local adaptation. To investigate whether the presumed defense compound urushiol also demonstrates accession-level accumulation differences, in vitro nascent germinated poison ivy seedlings from geographically isolated populations were germinated in vitro and then assayed for known urushiol congener accumulation levels. Significant accession-level differences in the accumulation levels of total C15- and C17-, total C15-, total C17-, specific C15 congeners, and specific C17 congeners of urushiol were identified. In addition, hereto novel C15- and C17-urushiol isomers were identified as well. Cardanols are assumed to be the penultimate metabolites giving rise to urushiols, but this assumption was not previously empirically validated. C15-cardanol congeners and isomers corresponding to expected substrates needed to produce the observed C15-urushiol congeners and isomers were identified in the same poison ivy seedling extracts. Total C15-cardanol and C15-cardanol congeners also showed significant accession-level differences. Based on the observed C15-cardanol congeners in poison ivy, the penultimate step in urushiol biosynthesis was proposed to be a cardanol-specific hydroxylase activity.
- The Accuracy of Genomic Prediction between Environments and Populations for Soft Wheat TraitsHuang, Mao; Ward, Brian P.; Griffey, Carl A.; Van Sanford, David A.; McKendry, Anne; Brown-Guedira, Gina L.; Tyagi, Priyanka; Sneller, Clay H. (2018-12)Genomic selection (GS) uses training population (TP) data to estimate the value of lines in a selection population. In breeding, the TP and selection population are often grown in different environments, which can cause low prediction accuracy when the correlation of genetic effects between the environments is low. Subsets of TP data may be more predictive than using all TP data. Our objectives were (i) to evaluate the effect of using subsets of TP data on GS accuracy between environments, and (ii) to assess the accuracy of models incorporating marker x environment interaction (MEI). Two wheat (Triticum aestivum L.) populations were phenotyped for 11 traits in independent environments and genotyped with single-nucleotide polymorphism markers. Within each population trait combination, environments were clustered. Data from one duster were used as the TP to predict the value of the same lines in the other cluster(s) of environments. Models were built using all TP data or subsets of markers selected for their effect and stability. The GS accuracy using all TP data was >0.25 for 9 of 11 traits. The between-environment accuracy was generally greatest using a subset of stable and significant markers; accuracy increased up to 48% relative to using all TP data. We also assessed accuracy using each population as the TP and the other as the selection population. Using subsets of TP data or the MEI models did not improve accuracy between populations. Using optimized subsets of markers within a population can improve GS accuracy by reducing noise in the prediction data set.
- Adaptive constraints at the range edge of a widespread and expanding invasive plantFletcher, Rebecca A.; Atwater, Daniel Z.; Haak, David C.; Bagavathiannan, Muthukumar; DiTommaso, Antonio; Lehnhoff, Erik; Paterson, Andrew H.; Auckland, Susan; Govindasamy, Prabhu; Lemke, Cornelia; Morris, Edward; Rainville, Lisa; Barney, Jacob N. (Oxford University Press, 2023-11-05)Identifying the factors that facilitate and limit invasive species' range expansion has both practical and theoretical importance, especially at the range edges. Here, we used reciprocal common garden experiments spanning the North/South and East/West range that include the North American core, intermediate and range edges of the globally invasive plant, Johnsongrass (Sorghum halepense) to investigate the interplay of climate, biotic interactions (i.e. competition) and patterns of adaptation. Our results suggest that the rapid range expansion of Johnsongrass into diverse environments across wide geographies occurred largely without local adaptation, but that further range expansion may be restricted by a fitness trade-off that limits population growth at the range edge. Interestingly, plant competition strongly dampened Johnsongrass growth but did not change the rank order performance of populations within a garden, though this varied among gardens (climates). Our findings highlight the importance of including the range edge when studying the range dynamics of invasive species, especially as we try to understand how invasive species will respond to accelerating global changes.
- Advances in Ecohydrology for Water Resources Optimization in Arid and Semi-Arid AreasCastellini, Mirko; Di Prima, Simone; Stewart, Ryan D.; Biddoccu, Marcella; Rahmati, Mehdi; Alagna, Vincenzo (MDPI, 2022-06-07)Conserving water resources is a current challenge that will become increasingly urgent in future due to climate change. The arid and semi-arid areas of the globe are expected to be particularly affected by changes in water availability. Consequently, advances in ecohydrology sciences, i.e., the interplay between ecological and hydrological processes, are necessary to enhance the understanding of the critical zone, optimize water resources’ usage in arid and semi-arid areas, and mitigate climate change. This Special Issue (SI) collected 10 original contributions on sustainable land management and the optimization of water resources in fragile environments that are at elevated risk due to climate change. In this context, the topics mainly concern transpiration, evapotranspiration, groundwater recharge, deep percolation, and related issues. The collection of manuscripts presented in this SI represents knowledge of ecohydrology. It is expected that ecohydrology will have increasing applications in the future. Therefore, it is realistic to assume that efforts to increase environmental sustainability and socio-economic development, with water as a central theme, will have a greater chance of success.
- Aerial high-throughput phenotyping of peanut leaf area index and lateral growthSarkar, Sayantan; Cazenave, Alexandre-Brice; Oakes, Joseph C.; McCall, David S.; Thomason, Wade E.; Abbott, A. Lynn; Balota, Maria (Springer Nature, 2021-11-04)Leaf area index (LAI) is the ratio of the total one-sided leaf area to the ground area, whereas lateral growth (LG) is the measure of canopy expansion. They are indicators for light capture, plant growth, and yield. Although LAI and LG can be directly measured, this is time consuming. Healthy leaves absorb in the blue and red, and reflect in the green regions of the electromagnetic spectrum. Aerial high-throughput phenotyping (HTP) may enable rapid acquisition of LAI and LG from leaf reflectance in these regions. In this paper, we report novel models to estimate peanut (Arachis hypogaea L.) LAI and LG from vegetation indices (VIs) derived relatively fast and inexpensively from the red, green, and blue (RGB) leaf reflectance collected with an unmanned aerial vehicle (UAV). In addition, we evaluate the models’ suitability to identify phenotypic variation for LAI and LG and predict pod yield from early season estimated LAI and LG. The study included 18 peanut genotypes for model training in 2017, and 8 genotypes for model validation in 2019. The VIs included the blue green index (BGI), red-green ratio (RGR), normalized plant pigment ratio (NPPR), normalized green red difference index (NGRDI), normalized chlorophyll pigment index (NCPI), and plant pigment ratio (PPR). The models used multiple linear and artificial neural network (ANN) regression, and their predictive accuracy ranged from 84 to 97%, depending on the VIs combinations used in the models. The results concluded that the new models were time- and cost-effective for estimation of LAI and LG, and accessible for use in phenotypic selection of peanuts with desirable LAI, LG and pod yield.
- An aeroponic culture system for the study of root herbivory on Arabidopsis thalianaVaughan, Martha M.; Tholl, Dorothea; Tokuhisa, James G. (Biomed Central, 2011-03-10)Background Plant defense against herbivory has been studied primarily in aerial tissues. However, complex defense mechanisms have evolved in all parts of the plant to combat herbivore attack and these mechanisms are likely to differ in the aerial and subterranean environment. Research investigating defense responses belowground has been hindered by experimental difficulties associated with the accessibility and quality of root tissue and the lack of bioassays using model plants with altered defense profiles. Results We have developed an aeroponic culture system based on a calcined clay substrate that allows insect herbivores to feed on plant roots while providing easy recovery of the root tissue. The culture method was validated by a root-herbivore system developed for Arabidopsis thaliana and the herbivore Bradysia spp. (fungus gnat). Arabidopsis root mass obtained from aeroponically grown plants was comparable to that from other culture systems, and the plants were morphologically normal. Bradysia larvae caused considerable root damage resulting in reduced root biomass and water absorption. After feeding on the aeroponically grown root tissue, the larvae pupated and emerged as adults. Root damage of mature plants cultivated in aeroponic substrate was compared to that of Arabidopsis seedlings grown in potting mix. Seedlings were notably more susceptible to Bradysia feeding than mature plants and showed decreased overall growth and survival rates. Conclusions A root-herbivore system consisting of Arabidopsis thaliana and larvae of the opportunistic herbivore Bradysia spp. has been established that mimics herbivory in the rhizosphere. Bradysia infestation of Arabidopsis grown in this culture system significantly affects plant performance. The culture method will allow simple profiling and in vivo functional analysis of root defenses such as chemical defense metabolites that are released in response to belowground insect attack.
- AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadataLiang, Xiao; Akers, Kyle; Keenum, Ishi M.; Wind, Lauren L.; Gupta, Suraj; Chen, Chaoqi; Aldaihani, Reem; Pruden, Amy; Zhang, Liqing; Knowlton, Katharine F.; Xia, Kang; Heath, Lenwood S. (2021-03-10)Background Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
- Amino Acids Are an Ineffective Fertilizer for Dunaliella spp. GrowthMurphree, Colin A.; Dums, Jacob T.; Jain, Siddharth K.; Zhao, Chengsong; Young, Danielle Y.; Khoshnoodi, Nicole; Tikunov, Andrey; Macdonald, Jeffrey; Pilot, Guillaume; Sederoff, Heike (Frontiers, 2017-05-26)Autotrophic microalgae are a promising bioproducts platform. However, the fundamental requirements these organisms have for nitrogen fertilizer severely limit the impact and scale of their cultivation. As an alternative to inorganic fertilizers, we investigated the possibility of using amino acids from deconstructed biomass as a nitrogen source in the genus Dunaliella. We found that only four amino acids (glutamine, histidine, cysteine, and tryptophan) rescue Dunaliella spp. growth in nitrogen depleted media, and that supplementation of these amino acids altered the metabolic profile of Dunaliella cells. Our investigations revealed that histidine is transported across the cell membrane, and that glutamine and cysteine are not transported. Rather, glutamine, cysteine, and tryptophan are degraded in solution by a set of oxidative chemical reactions, releasing ammonium that in turn supports growth. Utilization of biomass-derived amino acids is therefore not a suitable option unless additional amino acid nitrogen uptake is enabled through genetic modifications of these algae.
- An Amphipathic Alpha-Helix Domain from Poliovirus 2C Protein Tubulate Lipid VesiclesVarkey, Jobin; Zhang, Jiantao; Kim, Junghyun; George, Gincy; He, Guijuan; Belov, George A.; Langen, Ralf; Wang, Xiaofeng (MDPI, 2020-12-18)Positive-strand RNA viruses universally remodel host intracellular membranes to form membrane-bound viral replication complexes, where viral offspring RNAs are synthesized. In the majority of cases, viral replication proteins are targeted to and play critical roles in the modulation of the designated organelle membranes. Many viral replication proteins do not have transmembrane domains, but contain single or multiple amphipathic alpha-helices. It has been conventionally recognized that these helices serve as an anchor for viral replication protein to be associated with membranes. We report here that a peptide representing the amphipathic α-helix at the N-terminus of the poliovirus 2C protein not only binds to liposomes, but also remodels spherical liposomes into tubules. The membrane remodeling ability of this amphipathic alpha-helix is similar to that recognized in other amphipathic alpha-helices from cellular proteins involved in membrane remodeling, such as BAR domain proteins. Mutations affecting the hydrophobic face of the amphipathic alpha-helix severely compromised membrane remodeling of vesicles with physiologically relevant phospholipid composition. These mutations also affected the ability of poliovirus to form plaques indicative of reduced viral replication, further underscoring the importance of membrane remodeling by the amphipathic alpha-helix in possible relation to the formation of viral replication complexes.
- Analysis of Shoot Architecture Traits in Edamame Reveals Potential Strategies to Improve Harvest EfficiencyDhakal, Kshitiz; Zhu, Qian; Zhang, Bo; Li, Mao; Li, Song (2021-03-03)Edamame is a type of green, vegetable soybean and improving shoot architecture traits for edamame is important for breeding of high-yield varieties by decreasing potential loss due to harvesting. In this study, we use digital imaging technology and computer vision algorithms to characterize major traits of shoot architecture for edamame. Using a population of edamame PIs, we seek to identify underlying genetic control of different shoot architecture traits. We found significant variations in the shoot architecture of the edamame lines including long-skinny and candle stick-like structures. To quantify the similarity and differences of branching patterns between these edamame varieties, we applied a topological measurement called persistent homology. Persistent homology uses algebraic geometry algorithms to measure the structural similarities between complex shapes. We found intriguing relationships between the topological features of branching networks and pod numbers in our plant population, suggesting combination of multiple topological features contribute to the overall pod numbers on a plant. We also identified potential candidate genes including a lateral organ boundary gene family protein and a MADS-box gene that are associated with the pod numbers. This research provides insight into the genetic regulation of shoot architecture traits and can be used to further develop edamame varieties that are better adapted to mechanical harvesting.
- Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype ColumbiaBowerman, Peter A.; Ramirez, Melissa V.; Price, Michelle B.; Helm, Richard F.; Winkel, Brenda S. J. (2012-09-04)BACKGROUND: The flavonoid pathway is a long-standing and important tool for plant genetics, biochemistry, and molecular biology. Numerous flavonoid mutants have been identified in Arabidopsis over the past several decades in a variety of ecotypes. Here we present an analysis of Arabidopsis lines of ecotype Columbia carrying T-DNA insertions in genes encoding enzymes of the central flavonoid pathway. We also provide a comprehensive summary of various mutant alleles for these structural genes that have been described in the literature to date in a wide variety of ecotypes. FINDINGS: The confirmed knockout lines present easily-scorable phenotypes due to altered pigmentation of the seed coat (or testa). Knockouts for seven alleles for six flavonoid biosynthetic genes were confirmed by PCR and characterized by UPLC for altered flavonol content. CONCLUSION: Seven mutant lines for six genes of the central flavonoid pathway were characterized in ecotype, Columbia. These lines represent a useful resource for integrating biochemical and physiological studies with genomic, transcriptomic, and proteomic data, much of which has been, and continues to be, generated in the Columbia background.
- Antibiotics ameliorate lupus-like symptoms in miceMu, Qinghui; Tavella, Vincent J.; Kirby, Jay L.; Cecere, Thomas E.; Chung, Matthias; Lee, Jiyoung; Li, Song; Ahmed, Sattar Ansar; Eden, Kristin; Allen, Irving C. (Nature, 2017-10-20)Gut microbiota and the immune system interact to maintain tissue homeostasis, but whether this interaction is involved in the pathogenesis of systemic lupus erythematosus (SLE) is unclear. Here we report that oral antibiotics given during active disease removed harmful bacteria from the gut microbiota and attenuated SLE-like disease in lupus-prone mice. Using MRL/lpr mice, we showed that antibiotics given after disease onset ameliorated systemic autoimmunity and kidney histopathology. They decreased IL-17-producing cells and increased the level of circulating IL-10. In addition, antibiotics removed Lachnospiraceae and increased the relative abundance of Lactobacillus spp., two groups of bacteria previously shown to be associated with deteriorated or improved symptoms in MRL/lpr mice, respectively. Moreover, we showed that the attenuated disease phenotype could be recapitulated with a single antibiotic vancomycin, which reshaped the gut microbiota and changed microbial functional pathways in a time-dependent manner. Furthermore, vancomycin treatment increased the barrier function of the intestinal epithelium, thus preventing the translocation of lipopolysaccharide, a cell wall component of Gram-negative Proteobacteria and known inducer of lupus in mice, into the circulation. These results suggest that mixed antibiotics or a single antibiotic vancomycin ameliorate SLE-like disease in MRL/lpr mice by changing the composition of gut microbiota.
- Antioxidant metabolism variation associated with alkali-salt tolerance in thirty switchgrass (Panicum virgatum) linesHu, Guofu; Liu, Yiming; Duo, Tianqi; Zhao, Bingyu Y.; Cui, Guowen; Ji, Jing; Kuang, Xiao; Ervin, Erik H.; Zhang, Xunzhong (PLOS, 2018-06-25)Soil salinization is a major factor limiting crop growth and development in many areas. Switchgrass (Panicum virgatum L.) is an important warm-season grass species used for biofuel production. The objective of this study was to investigate antioxidant metabolism, proline, and protein variation associated with alkali-salt tolerance among 30 switchgrass lines and identify metabolic markers for evaluating alkali-salt tolerance of switchgrass lines. The grass lines were transplanted into plastic pots containing fine sand. When the plants reached E5 developmental stage, they were subjected to either alkali-salt stress treatment (150 mM Na+ and pH of 9.5) or control (no alkali-salt stress) for 20 d. The 30 switchgrass lines differed in alkali-salt tolerance as determined by the level of leaf malondialdehyde (MDA), antioxidant enzyme activity [(superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX)], proline and protein. Alkali-salt stress increased MDA, proline, SOD, reduced CAT activity, but its effect on protein and APX varied depending on lines. Wide variations in the five parameters existed among the 30 lines. In general, the lines with higher CAT activity and lower proline content under alkali-salt stress had less MDA, exhibiting better alkali-salt tolerance. Among the five parameters, CAT can be considered as valuable metabolic markers for assessment of switchgrass tolerance to alkali-salt stress.
- Apple miRNAs and tasiRNAs with novel regulatory networksXia, Rui; Zhu, Hong; An, Yong-qiang; Beers, Eric P.; Liu, Zongrang (2012-06-15)Background MicroRNAs (miRNAs) and their regulatory functions have been extensively characterized in model species but whether apple has evolved similar or unique regulatory features remains unknown. Results We performed deep small RNA-seq and identified 23 conserved, 10 less-conserved and 42 apple-specific miRNAs or families with distinct expression patterns. The identified miRNAs target 118 genes representing a wide range of enzymatic and regulatory activities. Apple also conserves two TAS gene families with similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profiles and target specificities. Importantly, we found that miR159, miR828 and miR858 can collectively target up to 81 MYB genes potentially involved in diverse aspects of plant growth and development. These miRNA target sites are differentially conserved among MYBs, which is largely influenced by the location and conservation of the encoded amino acid residues in MYB factors. Finally, we found that 10 of the 19 miR828-targeted MYBs undergo small interfering RNA (siRNA) biogenesis at the 3' cleaved, highly divergent transcript regions, generating over 100 sequence-distinct siRNAs that potentially target over 70 diverse genes as confirmed by degradome analysis. Conclusions Our work identified and characterized apple miRNAs, their expression patterns, targets and regulatory functions. We also discovered that three miRNAs and the ensuing siRNAs exploit both conserved and divergent sequence features of MYB genes to initiate distinct regulatory networks targeting a multitude of genes inside and outside the MYB family.
- Apple Pollen Tube Growth Rates Are Regulated by Parentage and EnvironmentDeLong, Candace N.; Yoder, Keith S.; Combs, Leon; Veilleux, Richard E.; Peck, Gregory M. (American Society For Horticultural Science, 2016)A greater understanding of apple (Malus domestica) pollen tube growth rates can improve crop load management in commercial orchards. Specifically, applications of caustic bloom-thinning chemicals need to occur when enough, but not too many, flowers have been fertilized to achieve crop load densities that balance yields with marketable fruit sizes. In this study, the pollen tube growth rates of five crabapple (Malus sp.) cultivars were measured in the styles of three maternal cultivars at 12, 18, 24, and 30 °C after 24 hours in a growth chamber. Pollen tube growth rates were greatest for ‘Selkirk’ and ‘Thunderchild’ at 12 °C, and greatest for ‘Indian Summer’, ‘Selkirk’, and ‘Thunderchild’ at 24 °C. Pollen tube growth increased with increasing temperatures until 24 °C. There were minimal pollen tube growth rate increases between 24 and 30 °C. Overall, ‘Snowdrift’ had the slowest pollen tube growth rate of the five evaluated crabapple genotypes. At 24 and 30 °C, ‘Indian Summer’ and ‘Thunderchild’ pollen tubes reached the base of the style most frequently, and ‘Snowdrift’ pollen tubes the least frequently. Pollen tube growth rate was also influenced by the maternal cultivar, with Golden Delicious having relatively faster pollen tube growth than Fuji at 24 and 30 °C. Interactions among paternal and maternal genotypes as well as temperature after pollination reveal complex biological and environmental relationships that can be used to develop more precise crop load management strategies for apple orchards.
- Application of alignment-free bioinformatics methods to identify an oomycete protein with structural and functional similarity to the bacterial AvrE effector proteinDeb, Devdutta; Mackey, David; Opiyo, Stephen O.; McDowell, John M. (PLOS, 2018-04-11)Diverse plant pathogens export effector proteins to reprogram host cells. One of the most challenging goals in the molecular plant-microbe field is to functionally characterize the complex repertoires of effectors secreted by these pathogens. For bacterial pathogens, the predominant class of effectors is delivered to host cells by Type III secretion. For oomycetes, the predominant class of effectors is defined by a signal peptide that mediates secretion from the oomycete and a conserved RxLR motif. Downy mildew pathogens and Phytophthora species maintain hundreds of candidate RxLR effector genes in their genomes. Although no primary sequence similarity is evident between bacterial Type III effectors (T3Es) and oomycete RXLR effectors, some bacterial and oomycete effectors have convergently evolved to target the same host proteins. Such effectors might have evolved domains that are functionally similar but sequence-unrelated. We reasoned that alignment-free bioinformatics approaches could be useful to identify structural similarities between bacterial and oomycete effectors. To test this approach, we used partial least squares regression, alignment-free bioinformatics methods to identify effector proteins from the genome of the oomycete Hyaloperonospora arabidopsidis that are similar to the well-studied AvrE1 effector from Pseudomonas syringae. This approach identified five RxLR proteins with putative structural similarity to AvrE1. We focused on one, HaRxL23, because it is an experimentally validated effector and it is conserved between distantly related oomycetes. Several experiments indicate that HaRxL23 is functionally similar to AvrE1, including the ability to partially rescue an AvrE1 loss-of-function mutant. This study provides an example of how an alignment-free bioinformatics approach can identify functionally similar effector proteins in the absence of primary sequence similarity. This approach could be useful to identify effectors that have convergently evolved regardless of whether the shared host target is known.
- Application of biochar to soils may result in plant contamination and human cancer risk due to exposure of polycyclic aromatic hydrocarbonsWang, Jian; Xia, Kang; Waigi, Michael Gatheru; Gao, Yanzheng; Odinga, Emmanuel Stephen; Ling, Wanting; Liu, Juan (2018-12)Biochars are added to soil to improve agronomic yield. This greenhouse- and field-scale study evaluated poly cyclic aromatic hydrocarbon (PAH) contamination in 35 commercial and laboratory-produced biochars, and assessed the effects of biochar amendment of soils on PAH accumulation in vegetables and the risk for cancer. The total and bioavailable PAH concentrations in biochars varied from 638 to 12,347 mu g/kg and from below the detection limit (BDL) to 2792 mu g/kg, respectively. PAH formation in biochars decreased with increasing production temperature (350-650 degrees C). Root exudates enhanced PAH release from biochars. The total PAH concentrations in eight edible vegetables growing in biochar-amended soil varied according to biochar and vegetables type from BDL to 565 mu g/kg. A health risk assessment framework was integrated with the benzo [a] pyrene toxic equivalency quotient and the incremental lifetime cancer risk (ILCR) to estimate the exposure risk for human beings via ingestion of PAH-contaminated vegetables. The total ILCR for adults was above 10(-6), which suggests a risk to human health from direct exposure to PAHs in vegetables grown in biochar-amended soil. These results demonstrate that biochar application may lead to contamination of plants with PAHs, which represents a risk to human health. The PAH levels in biochars produced using different conditions and/or feed-stocks need to be evaluated and biochars should be pretreated to remove PAHs before their large-scale agronomic application.
- Applications of High-Resolution Imaging for Open Field Container Nursery CountingShe, Ying; Ehsani, Reza; Robbins, James; Nahún Leiva, Josué; Owen, James S. Jr. (MDPI, 2018-12-12)Frequent inventory data of container nurseries is needed by growers to ensure proper management and marketing strategies. In this paper, inventory data are estimated from aerial images. Since there are thousands of nursery species, it is difficult to find a generic classification algorithm for all cases. In this paper, the development of classification methods was confined to three representative categories: green foliage, yellow foliage, and flowering plants. Vegetation index thresholding and the support vector machine (SVM) were used for classification. Classification accuracies greater than 97% were obtained for each case. Based on the classification results, an algorithm based on canopy area mapping was built for counting. The effects of flight altitude, container spacing, and ground cover type were evaluated. Results showed that container spacing and interaction of container spacing with ground cover type have a significant effect on counting accuracy. To mimic the practical shipping and moving process, incomplete blocks with different voids were created. Results showed that the more plants removed from the block, the higher the accuracy. The developed algorithm was tested on irregular- or regular-shaped plants and plants with and without flowers to test the stability of the algorithm, and accuracies greater than 94% were obtained.