Department of Plant and Soil Sciences

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The Department of Plant and Soil Sciences has excellent teaching, research, and outreach programs in the areas of plant biology (cellular, genetics, genomics, microbial, molecular and physiology), agronomy (including pathology, soil management, and weed science), horticulture (sustainable landscapes, fruits, and vegetables), landscape architecture, and environmental soil sciences (biogeochemistry, hydrology, and plant-soil interactions). We have a distinguished faculty, known nationally and internationally for their research and outreach, and within the University of Delaware for their excellence in teaching, advising, and mentoring students.

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Killing Two Birds with One Stone: Natural Rice Rhizospheric Microbes Reduce Arsenic Uptake and Blast Infections in Rice
(Frontiers Media S.A., 10/13/16) Lakshmanan,Venkatachalam; Cottone,Jonathon; Bais,Harsh P.; Venkatachalam Lakshmanan, Jonathon Cottone and Harsh P.Bais; Harsh P.Bais
Our recent work has shown that a rice thizospheric natural isolate, a Paritoea sp (hereafter EA106) attenuates Arsenic (As) uptake in rice. In parallel, yet another natural rice rhizospheric isolate, a Pseuclomonas chlororaphis (hereafter EA105), was shown to inhibit rice blast pathogen Magnaporthe oryzae. Considering the above, we envisaged to evaluate the importance of mixed stress regime in rice plants subjected to both As toxicity and blast infections. Plants subjected to As regime showed increased susceptibility to blast infections compared to As-untreated plants. Rice blast pathogen M. oryzae showed significant resistance against As toxicity compared to other non host fungal pathogens. Interestingly, plants treated with EA106 showed reduced susceptibility against blast infections in plants pre-treated with As. This data also corresponded with lower As uptake in plants primed with EA106. In addition, we also evaluated the expression of defense related genes in host plants subjected to As treatment. The data showed that plants primed with EA106 upregulated defense-related genes with or without As treatment. The data shows the first evidence of how rice plants cope with mixed stress regimes. Our work highlights the importance of natural association of plant microbiome which determines the efficacy of benign microbes to promote the Developmentelopment of beneficial traits in plants.
Management Impacts on Carbon Dynamics in a Sierra Nevada Mixed Conifer Forest
(Public Library Science, 2/26/16) Dore,Sabina; Fry,Danny L.; Collins,Brandon M.; Vargas,Rodrigo; York,Robert A.; Stephens,Scott L.; Sabina Dore, Danny L. Fry, Brandon M. Collins, Rodrigo Vargas, Robert A. York, Scott L. Stephens; Vargas, Rodrigo
Forest ecosystems can act as sinks of carbon and thus mitigate anthropogenic carbon emissions. When forests are actively managed, treatments can alter forests carbon dynamics, reducing their sink strength and switching them from sinks to sources of carbon. These effects are generally characterized by fast temporal dynamics. Hence this study monitored for over a decade the impacts of management practices commonly used to reduce fire hazards on the carbon dynamics of mixed-conifer forests in the Sierra Nevada, California, USA. Soil CO2 efflux, carbon pools (i.e. soil carbon, litter, fine roots, tree biomass), and radial tree growth were compared among un-manipulated controls, prescribed fire, thinning, thinning followed by fire, and two clear-cut harvested sites. Soil CO2 efflux was reduced by both fire and harvesting (ca. 15%). Soil carbon content (upper 15 cm) was not significantly changed by harvest or fire treatments. Fine root biomass was reduced by clear-cut harvest (60-70%) but not by fire, and the litter layer was reduced 80% by clear-cut harvest and 40% by fire. Thinning effects on tree growth and biomass were concentrated in the first year after treatments, whereas fire effects persisted over the seven-year post-treatment period. Over this period, tree radial growth was increased (25%) by thinning and reduced (12%) by fire. After seven years, tree biomass returned to pre-treatment levels in both fire and thinning treatments; however, biomass and productivity decreased 30%-40% compared to controls when thinning was combined with fire. The clear-cut treatment had the strongest impact, reducing ecosystem carbon stocks and delaying the capacity for carbon uptake. We conclude that post-treatment carbon dynamics and ecosystem recovery time varied with intensity and type of treatments. Consequently, management practices can be selected to minimize ecosystem carbon losses while increasing future carbon uptake, resilience to high severity fire, and climate related stresses.
A new approach for annotation of transposable elements using small RNA mapping
(Oxford University Press, 2015-03-15) El Baidouri, Moaine; Do Kim, Kyung; Abernathy, Brian; Arikit, Siwaret; Maumus, Florian; Panaud, Olivier; Meyers, Blake C.; Jackson, Scott A.; Moaine El Baidouri, Kyung Do Kim, Brian Abernathy, Siwaret Arikit, Florian Maumus, Olivier Panaud, Blake C. Meyers and Scott A. Jackson; Arikit, Siwaret; Meyers, Blake C. (orcid.org/0000-0003-3436-6097)
Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants.
Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population
(Frontiers Media S.A., 2015-04-22) Labonté, Jessica M.; Field, Erin K.; Lau, Maggie; Chivian, Dylan; Van Heerden, Esta; Wommack, K. Eric; Kieft, Thomas L.; Onstott, Tullis C.; Stepanauskas, Ramunas; Jessica M. Labonté, Erin K.Field, Maggie Lau, Dylan Chivian, Esta Van Heerden, K. Eric Wommack, Thomas L. Kieft, Tullis C.Onstott and Ramunas Stepanauskas; Wommack, K. Eric
A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.
Sea Surface Temperature Influence on Terrestrial Gross Primary Production along the Southern California Current
(Public Library of Science (PLOS), 2015-04-29) Reimer, Janet J.; Vargas, Rodrigo; Rivas, David; Gaxiola-Castro, Gilberto; Hernandez-Ayon, J. Martin; Lara-Lara, Ruben; Janet J. Reimer, Rodrigo Vargas, David Rivas, Gilberto Gaxiola-Castro, J. Martin Hernandez-Ayon, Ruben Lara-Lara; Reimer, Janet J.; Vargas, Rodrigo
Some land and ocean processes are related through connections (and synoptic-scale teleconnections) to the atmosphere. Synoptic-scale atmospheric (El Niño/Southern Oscillation [ENSO], Pacific Decadal Oscillation [PDO], and North Atlantic Oscillation [NAO]) decadal cycles are known to influence the global terrestrial carbon cycle. Potentially, smaller scale land-ocean connections influenced by coastal upwelling (changes in sea surface temperature) may be important for local-to-regional water-limited ecosystems where plants may benefit from air moisture transported from the ocean to terrestrial ecosystems. Here we use satellite-derived observations to test potential connections between changes in sea surface temperature (SST) in regions with strong coastal upwelling and terrestrial gross primary production (GPP) across the Baja California Peninsula. This region is characterized by an arid/ semiarid climate along the southern California Current. We found that SST was correlated with the fraction of photosynthetic active radiation (fPAR; as a proxy for GPP) with lags ranging from 0 to 5 months. In contrast ENSO was not as strongly related with fPAR as SST in these coastal ecosystems. Our results show the importance of local-scale changes in SST during upwelling events, to explain the variability in GPP in coastal, water-limited ecosystems. The response of GPP to SST was spatially-dependent: colder SST in the northern areas increased GPP (likely by influencing fog formation), while warmer SST at the southern areas was associated to higher GPP (as SST is in phase with precipitation patterns). Interannual trends in fPAR are also spatially variable along the Baja California Peninsula with increasing secular trends in subtropical regions, decreasing trends in the most arid region, and no trend in the semi-arid regions. These findings suggest that studies and ecosystem process based models should consider the lateral influence of local-scale ocean processes that could influence coastal ecosystem productivity.
Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in Arabidopsis
(PLOS (Public Library of Science), 2015-04-30) Tu, Bin; Liu, Li; Xu, Chi; Zhai, Jixian; Li, Shengben; Lopez, Miguel A.; Zhao, Yuanyuan; Yu, Yu; Ramachandran, Vanitharani; Ren, Guodong; Yu, Bin; Li, Shigui; Meyers, Blake C.; Mo, Beixin; Chen, Xuemei; Bin Tu1, Li Liu, Chi Xu, Jixian Zhai, Shengben Li, Miguel A. Lopez, Yuanyuan Zhao, Yu Yu, Vanitharani Ramachandran, Guodong Ren, Bin Yu, Shigui Li, Blake C. Meyers, Beixin Mo, Xuemei Chen; Zhai, Jixian; Meyers, Blake C.
3’ uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes. 2’-O-methylation on the 3’ terminal ribose protects micro(mi)RNAs from 3’ truncation and 3’ uridylation in Arabidopsis. Previously, we identified HESO1 as the nucleotidyl transferase that uridylates most unmethylated miRNAs in vivo, but substantial 3’ tailing of miRNAs still remains in heso1 loss-of-function mutants. In this study, we found that among nine other potential nucleotidyl transferases, UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) is the single most predominant nucleotidyl transferase that tails miRNAs. URT1 and HESO1 prefer substrates with different 3’ end nucleotides in vitro and act cooperatively to tail different forms of the same miRNAs in vivo. Moreover, both HESO1 and URT1 exhibit nucleotidyl transferase activity on AGO1-bound miRNAs. Although these enzymes are able to add long tails to AGO1-bound miRNAs, the tailed miRNAs remain associated with AGO1. Moreover, tailing of AGO1-bound miRNA165/6 drastically reduces the slicing activity of AGO1-miR165/6, suggesting that tailing reduces miRNA activity. However, monouridylation of miR171a by URT1 endows the miRNA the ability to trigger the biogenesis of secondary siRNAs. Therefore, 3’ tailing could affect the activities of miRNAs in addition to leading to miRNA degradation.
miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing
(BioMed Central Ltd., 2015-05-16) Belli Kullan, Jayakumar; Paim Pinto, Daniela Lopes; Bertolini, Edoardo; Fasoli, Marianna; Zenoni, Sara; Battista Tornielli, Giovanni; Pezzotti, Mario; Meyers, Blake C.; Farina, Lorenzo; Pè, Mario Enrico; Mica, Erica; Jayakumar Belli Kullan, Daniela Lopes Paim Pinto, Edoardo Bertolini, Marianna Fasoli, Sara Zenoni, Giovanni Battista Tornielli, Mario Pezzotti, Blake C. Meyers, Lorenzo Farina, Mario Enrico Pè and Erica Mica.; Meyers, Blake C.
Background miRNAs are the most abundant class of small non-coding RNAs, and they are involved in post-transcriptional regulations, playing a crucial role in the refinement of genetic programming during plant development. Here we present a comprehensive picture of miRNA regulation in Vitis vinifera L. plant during its complete life cycle. Furthering our knowledge about the post-transcriptional regulation of plant development is fundamental to understand the biology of such an important crop. Results We analyzed 70 small RNA libraries, prepared from berries, inflorescences, tendrils, buds, carpels, stamens and other samples at different developmental stages. One-hundred and ten known and 175 novel miRNAs have been identified and a wide grapevine expression atlas has been described. The distribution of miRNA abundance reveals that 22 novel miRNAs are specific to stamen, and two of them are, interestingly, involved in ethylene biosynthesis, while only few miRNAs are highly specific to other organs. Thirty-eight miRNAs are present in all our samples, suggesting a role in key regulatory circuit. On the basis of miRNAs abundance and distribution across samples and on the estimated correlation, we suggest that miRNA expression define organ identity. We performed target prediction analysis and focused on miRNA expression analysis in berries and inflorescence during their development, providing an initial functional description of the identified miRNAs. Conclusions Our findings represent a very extensive miRNA expression atlas in grapevine, allowing the definition of how the spatio-temporal distribution of miRNAs defines organ identity. We describe miRNAs abundance in specific tissues not previously described in grapevine and contribute to future targeted functional analyses. Finally, we present a deep characterization of miRNA involvement in berry and inflorescence development, suggesting a role for miRNA-driven hormonal regulation.
An invisible soil acidification: Critical role of soil carbonate and its impact on heavy metal bioavailability
(Nature Publishing Group, 2015-07-31) Wang, Cheng; Li, Wei; Yang, Zhongfang; Chen, Yang; Shao, Wenjing; Ji, Junfeng; Cheng Wang, Wei Li, Zhongfang Yang, Yang Chen, Wenjing Shao & Junfeng Ji; Li, Wei
It is well known that carbonates inhibit heavy metals transferring from soil to plants, yet the mechanism is poorly understood. Based on the Yangtze River delta area, we investigated bioaccumulation of Ni and Cd in winter wheat as affected by the presence of carbonates in soil. This study aimed to determine the mechanism through which soil carbonates restrict transport and plant uptake of heavy metals in the wheat cropping system. The results indicate that soil carbonates critically influenced heavy metal transfer from soil to plants and presented a tipping point. Wheat grains harvested from carbonates-depleted (due to severe leaching) soils showed Ni and Cd concentrations 2–3 times higher than those of the wheat grains from carbonates-containing soils. Correspondingly, the incidence of Ni or Cd contamination in the wheat grain samples increased by about three times. With the carbonate concentration >1% in soil, uptake and bioaccumulation of Ni and Cd by winter wheat was independent with the soil pH and carbonate content. The findings suggest that soil carbonates play a critical role in heavy metal transfer from soil to plants, implying that monitoring soil carbonate may be necessary in addition to soil pH for the evaluating soil quality and food safety.
pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature
(PLOS (Public Library of Science), 2015-08-10) Ding, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.; Ruoyao Ding, Cecilia N. Arighi, Jung-Youn Lee, Cathy H. Wu, K. Vijay-Shanker; Ding, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.
BACKGROUND Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. METHODS In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. RESULTS We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9%(Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly
pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature
(Public Library of Science, 2015-08-10) Ding, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.; Ruoyao Ding, Cecilia N. Arighi, Jung-Youn Lee, Cathy H. Wu, K. Vijay-Shanker; Dina, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.
BACKGROUND Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. METHODS In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. RESULTS We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9%(Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource. org/iprolink/).
The influence of environmental conditions on kinetics of arsenite oxidation by manganese‑oxides
(BIOMED CENTRAL LTD, 2015-09-16) Fischel, Matthew H. H.; Fischel, Jason S.; Lafferty, Brandon J.; Sparks, Donald L.; Matthew H. H. Fischel, Jason S. Fischel, Brandon J. Lafferty and Donald L. Sparks; Fischel, Matthew H. H.; Fischel, Jason S.; Sparks, Donald L.
BACGROUND: Manganese-oxides are one of the most important minerals in soil due to their widespread distribution and high reactivity. Despite their invaluable role in cycling many redox sensitive elements, numerous unknowns remain about the reactivity of different manganese-oxide minerals under varying conditions in natural systems. By altering temperature, pH, and concentration of arsenite we were able to determine how manganese-oxide reactivity changes with simulated environmental conditions. The interaction between manganese-oxides and arsenic is particularly important because manganese can oxidize mobile and toxic arsenite into more easily sorbed and less toxic arsenate. This redox reaction is essential in understanding how to address the global issue of arsenic contamination in drinking water. RESULTS: The reactivity of manganese-oxides in ascending order is random stacked birnessite, hexagonal birnessite, biogenic manganese-oxide, acid birnessite, and δ-MnO2. Increasing temperature raised the rate of oxidation. pH had a variable effect on the production of arsenate and mainly impacted the sorption of arsenate on δ-MnO2, which decreased with increasing pH. Acid birnessite oxidized the most arsenic at alkaline and acidic pHs, with decreased reactivity towards neutral pH. The δ-MnO2 showed a decline in reactivity with increasing arsenite concentration, while the acid birnessite had greater oxidation capacity under higher concentrations of arsenite. The batch reactions used in this study quantify the impact of environmental variances on different manganese-oxides’ reactivity and provide insight to their roles in governing chemical cycles in the Critical Zone. CONCLUSIONS: The reactivity of manganese-oxides investigated was closely linked to each mineral’s crystallinity, surface area, and presence of vacancy sites. δ-MnO2 and acid birnessite are thought to be synthetic representatives of naturally occurring biogenic manganese-oxides; however, the biogenic manganese-oxide exhibited a lag time in oxidation compared to these two minerals. Reactivity was clearly linked to temperature, which provides important information on how these minerals react in the subsurface environment. The pH affected oxidation rate, which is essential in understanding how manganese-oxides react differently in the environment and their potential role in remediating contaminated areas. Moreover, the contrasting oxidative capacity of seemingly similar manganese-oxides under varying arsenite concentrations reinforces the importance of each manganese-oxide mineral’s unique properties.
Polymer Coated Urea in Turfgrass Maintains Vigor and Mitigates Nitrogen's Environmental Impacts
(Public Library of Science (PLOS), 2016-01-14) LeMonte, Joshua J.; Jolley, Von D.; Summerhays, Jeffrey S.; Terry, Richard E.; Hopkins, Bryan G.; Joshua J. LeMonte, Von D. Jolley, Jeffrey S. Summerhays, Richard E. Terry, Bryan G. Hopkins; LeMonte, Joshua J.
Polymer coated urea (PCU) is a N fertilizer which, when added to moist soil, uses temperature- controlled diffusion to regulate N release in matching plant demand and mitigate environmental losses. Uncoated urea and PCU were compared for their effects on gaseous (N2O and NH3) and aqueous (NO3 -) N environmental losses in cool season turfgrass over the entire PCU N-release period. Field studies were conducted on established turfgrass sites with mixtures of Kentucky bluegrass (Poa pratensis L.) and perennial ryegrass (Lolium perenne L.) in sand and loam soils. Each study compared 0 kg N ha-1 (control) to 200 kg N ha-1 applied as either urea or PCU (Duration 45CR1). Application of urea resulted in 127–476% more evolution of measured N2O into the atmosphere, whereas PCU was similar to background emission levels from the control. Compared to urea, PCU reduced NH3 emissions by 41–49% and N2O emissions by 45–73%, while improving growth and verdure compared to the control. Differences in leachate NO3 - among urea, PCU and control were inconclusive. This improvement in N management to ameliorate atmospheric losses of N using PCU will contribute to conserving natural resources and mitigating environmental impacts of N fertilization in turfgrass.
Spontaneous Detachment of Colloids from Primary Energy Minima by Brownian Diffusion
(Public Library of Science (PLOS), 2016-01-19) Wang, Zhan; Jin, Yan; Shen, Chongyang; Li, Tiantian; Huang, Yuanfang; Li, Baoguo; Zhan Wang, Yan Jin, Chongyang Shen, Tiantian Li, Yuanfang Huang, Baoguo Li; Jin, Yan
The Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energy profile has been frequently used to interpret the mechanisms controlling colloid attachment/detachment and aggregation/disaggregation behavior. This study highlighted a type of energy profile that is characterized by a shallow primary energy well (i.e., comparable to the average kinetic energy of a colloid) at a small separation distance and a monotonic decrease of interaction energy with separation distance beyond the primary energy well. This energy profile is present due to variations of height, curvature, and density of discrete physical heterogeneities on collector surfaces. The energy profile indicates that colloids can be spontaneously detached from the shallow primary energy well by Brownian diffusion. The spontaneous detachment from primary minima was unambiguously confirmed by conducting laboratory column transport experiments involving flow interruptions for two model colloids (polystyrene latex microspheres) and engineered nanoparticles (fullerene C60 aggregates). Whereas the spontaneous detachment has been frequently attributed to attachment in secondary minima in the literature, our study indicates that the detached colloids could be initially attached at primary minima. Our study further suggests that the spontaneous disaggregation from primary minima is more significant than spontaneous detachment because the primary minimum depth between colloid themselves is lower than that between a colloid and a collector surface.
High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time
(Public Library of Science, 2017-01-03) Jamann, Tiffany M; Sood, Shilpa; Wisser, Randall J; Holland, James B; Tiffany M. Jamann; Shilpa Sood; Randall J. Wisser; James B. Holland; Wisser, RJ
Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions. We report the use of a multiplexed panel of 319 PCR assays that target 20 candidate loci associated with photoperiod sensitivity in maize while requiring 25 ng or less of starting DNA per sample. Enriched regions had an average on-target sequence read depth of 105 with 98% of the sequence data mapping to the maize ‘B73’ reference and 80% of the reads mapping to the target interval. Sequence reads were aligned to B73 and 1,486 and 1,244 variants were called using SAMtools and GATK, respectively. Of the variants called by both SAMtools and GATK, 30% were not previously reported in maize. Due to the high sequence read depth, heterozygote genotypes could be called with at least 92.5% accuracy in hybrid materials using GATK. The genetic data are congruent with previous reports of high total genetic diversity and substantial population differentiation among maize landraces. In conclusion, semiconductor sequencing of highly multiplexed PCR reactions is a cost-effective strategy for resequencing targeted genomic loci in diverse maize materials.
SoilGrids250m: Global gridded soil information based on machine learning
(PLOS (Public Library of Science), 2017-02-16) Heng, Tomislav; Mendes de Jesus, Jorge; Heuvelink, Gerard B. M.; Ruiperez Gonzalez, Maria; Kilibarda, Milan; Blagotić, Aleksandar; Shangguan, Wei; Wright, Marvin N.; Geng, Xiaoyuan; Bauer-Marschallinger, Bernhard; Guevara, Mario Antonio; Vargas, Rodrigo; MacMillan, Robert A.; Batjes, Niels H.; Leenaars, Johan G. B.; Ribeiro, Eloi; Wheeler, Ichsani; Mantel, Stephan; Kempen, Bas; Tomislav Hengl, Jorge Mendes de Jesus, Gerard B. M. Heuvelink, Maria Ruiperez Gonzalez, Milan Kilibarda, Aleksandar Blagotić, Wei Shangguan, Marvin N. Wright, Xiaoyuan Geng, Bernhard Bauer-Marschallinger, Mario Antonio Guevara, Rodrigo Vargas, Robert A. MacMillan, Niels H. Batjes, Johan G. B. Leenaars, Eloi Ribeiro, Ichsani Wheeler, Stephan Mantel, Bas Kempen; Guevara, Mario Antonio; Vargas, Rodrigo
This paper describes the technical development and accuracy assessment of the most recent and improved version of the SoilGrids system at 250m resolution (June 2016 update). SoilGrids provides global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm), in addition to predictions of depth to bedrock and distribution of soil classes based on the World Reference Base (WRB) and USDA classification systems (ca. 280 raster layers in total). Predictions were based on ca. 150,000 soil profiles used for training and a stack of 158 remote sensing-based soil covariates (primarily derived from MODIS land products, SRTM DEM derivatives, climatic images and global landform and lithology maps), which were used to fit an ensemble of machine learning methodsÐrandom forest and gradient boosting and/or multinomial logistic regressionÐas implemented in the R packages ranger, xgboost, nnet and caret. The results of 10±fold cross-validation show that the ensemble models explain between 56% (coarse fragments) and 83% (pH) of variation with an overall average of 61%. Improvements in the relative accuracy considering the amount of variation explained, in comparison to the previous version of SoilGrids at 1 km spatial resolution, range from 60 to 230%. Improvements can be attributed to: (1) the use of machine learning instead of linear regression, (2) to considerable investments in preparing finer resolution covariate layers and (3) to insertion of additional soil profiles. Further development of SoilGrids could include refinement of methods to incorporate input uncertainties and derivation of posterior probability distributions (per pixel), and further automation of spatial modeling so that soil maps can be generated for potentially hundreds of soil variables. Another area of future research is the development of methods for multiscale merging of SoilGrids predictions with local and/or national gridded soil products (e.g. up to 50 m spatial resolution) so that increasingly more accurate, complete and consistent global soil information can be produced. SoilGrids are available under the Open Data Base License.
ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis
(Public Library of Science (PLoS), 2017-02-23) Yu, Yu; Ji, Lijuan; Le, Brandon H.; Zhai, Jixian; Chen, Jiayi; Lusche, Elizabeth; Gao, Lei; Liu, Chunyan; Cao, Xiaofeng; Mo, Beixin; Ma, Jinbiao; Meyers, Blake C.; Chen, Xuemei; Yu Yu, Lijuan Ji, Brandon H. Le, Jixian Zhai, Jiayi Chen, Elizabeth Luscher, Lei Gao, Chunyan Liu, Xiaofeng Cao, Beixin Mo, Jinbiao Ma, Blake C. Meyers, Xuemei Chen; Zhai, Jixian; Meyers, Blake C.
The degradation of small RNAs in plants and animals is associated with small RNA 30 truncation and 30 uridylation and thus relies on exonucleases and nucleotidyl transferases. ARGONAUTE (AGO) proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. AGO1 is the microRNA (miRNA) effector in Arabidopsis, and its closest homolog, AGO10, maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we show that SMALL RNA DEGRADING NUCLEASES (SDNs) initiate miRNA degradation by acting on AGO1-bound miRNAs to cause their 30 truncation, and the truncated species are uridylated and degraded. We report that AGO10 reduces miR165/6 accumulation by enhancing its degradation by SDN1 and SDN2 in vivo. In vitro, AGO10-bound miR165/6 is more susceptible to SDN1-mediated 30 truncation than AGO1-bound miR165/ 6. Thus, AGO10 promotes the degradation of miR165/6, which is contrary to the stabilizing effect of AGO1. Our work identifies a class of exonucleases responsible for miRNA 30 truncation in vivo and uncovers a mechanism of specificity determination in miRNA turnover. This work, together with previous studies on AGO10, suggests that spatially regulated miRNA degradation underlies stem cell maintenance in plants.
Phloem unloading in Arabidopsis roots is convective and regulated by the phloem- pole pericycle
(eLIFE Sciences Publications, 2017-02-23) Ross-Elliott, Timothy J.; Jensen, Kaare H.; Haaning, Katrine S.; Wager, Brittney M.; Knoblauch, Jan; Howell, Alexander H.; Mullendore, Daniel L.; Monteith, Alexander G.; Paultre, Danae; Yan, Dawei; Otero, Sofia; Bourdon, Matthieu; Sager, Ross; Lee, Jung-Youn; Helariutta, Yka¨; Knoblauch, Michael; Oparka, Karl J.; Timothy J Ross-Elliott, Kaare H Jensen, Katrine S Haaning, Brittney M Wager, Jan Knoblauch, Alexander H Howell, Daniel L Mullendore, Alexander G Monteith, Danae Paultre, Dawei Yan, Sofia Otero, Matthieu Bourdon, Ross Sager, Jung-Youn Lee, Yka¨ Helariutta, Michael Knoblauch, Karl J Oparka; Sager, Ross; Lee, Jung-Youn
In plants, a complex mixture of solutes and macromolecules is transported by the phloem. Here, we examined how solutes and macromolecules are separated when they exit the phloem during the unloading process. We used a combination of approaches (non-invasive imaging, 3D-electron microscopy, and mathematical modelling) to show that phloem unloading of solutes in Arabidopsis roots occurs through plasmodesmata by a combination of mass flow and diffusion (convective phloem unloading). During unloading, solutes and proteins are diverted into the phloem-pole pericycle, a tissue connected to the protophloem by a unique class of ‘funnel plasmodesmata’. While solutes are unloaded without restriction, large proteins are released through funnel plasmodesmata in discrete pulses, a phenomenon we refer to as ‘batch unloading’. Unlike solutes, these proteins remain restricted to the phloem-pole pericycle. Our data demonstrate a major role for the phloem-pole pericycle in regulating phloem unloading in roots.
ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing
(Nature Publishing Group, 2017-03-16) Francis, Felix; Dumas, Michael D.; Wisser, Randall J.; Felix Francis, Michael D. Dumas & Randall J. Wisser; Francis, Felix; Dumas, Michael D.; Wisser, Randall J.
Isolating and sequencing specific regions in a genome is a cornerstone of molecular biology. This has been facilitated by computationally encoding the thermodynamics of DNA hybridization for automated design of hybridization and priming oligonucleotides. However, the repetitive composition of genomes challenges the identification of target-specific oligonucleotides, which limits genetics and genomics research on many species. Here, a tool called ThermoAlign was developed that ensures the design of target-specific primer pairs for DNA amplification. This is achieved by evaluating the thermodynamics of hybridization for full-length oligonucleotide-template alignments — thermoalignments — across the genome to identify primers predicted to bind specifically to the target site. For amplificationbased resequencing of regions that cannot be amplified by a single primer pair, a directed graph analysis method is used to identify minimum amplicon tiling paths. Laboratory validation by standard and long-range polymerase chain reaction and amplicon resequencing with maize, one of the most repetitive genomes sequenced to date (≈85% repeat content), demonstrated the specificity-by-design functionality of ThermoAlign. ThermoAlign is released under an open source license and bundled in a dependency-free container for wide distribution. It is anticipated that this tool will facilitate multiple applications in genetics and genomics and be useful in the workflow of high-throughput targeted resequencing studies.
ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing
(Nature Publishing Group, 2017-03-16) Francis, Felix; Dumas, Michael D.; Wisser, RJ; Felix Francis, Michael D. Dumas and Randall J.Wisser; Wisser, Randall Jerome
Isolating and sequencing specific regions in a genome is a cornerstone of molecular biology. This has been facilitated by computationally encoding the thermodynamics of DNA hybridization for automated design of hybridization and priming oligonucleotides. However, the repetitive composition of genomes challenges the identification of target-specific oligonucleotides, which limits genetics and genomics research on many species. Here, a tool called ThermoAlign was developed that ensures the design of target-specific primer pairs for DNA amplification. This is achieved by evaluating the thermodynamics of hybridization for full-length oligonucleotide-template alignments — thermoalignments — across the genome to identify primers predicted to bind specifically to the target site. For amplificationbased resequencing of regions that cannot be amplified by a single primer pair, a directed graph analysis method is used to identify minimum amplicon tiling paths. Laboratory validation by standard and long-range polymerase chain reaction and amplicon resequencing with maize, one of the most repetitive genomes sequenced to date (≈85% repeat content), demonstrated the specificity-by-design functionality of ThermoAlign. ThermoAlign is released under an open source license and bundled in a dependency-free container for wide distribution. It is anticipated that this tool will facilitate multiple applications in genetics and genomics and be useful in the workflow of high-throughput targeted resequencing studies.
Historic Fort DuPont Nature Trail
(2019-01) Ruggiero, Emma

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