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Aquatic Coarse Woody Debris, Erin C. Rowekamp, Julia I. Chapman, Ryan W. McEwan 2019 University of Dayton

Aquatic Coarse Woody Debris, Erin C. Rowekamp, Julia I. Chapman, Ryan W. Mcewan

Ryan McEwan

No abstract provided.


Biofilm Ash Free Dry Mass And Chlorophyll A, Kevin W. Custer, Sean D. Mahoney, Mitchell J. Kukla, Corey Kuminecz, Joseph Murphy, Julia I. Chapman, Ryan W. McEwan 2019 University of Dayton

Biofilm Ash Free Dry Mass And Chlorophyll A, Kevin W. Custer, Sean D. Mahoney, Mitchell J. Kukla, Corey Kuminecz, Joseph Murphy, Julia I. Chapman, Ryan W. Mcewan

Ryan McEwan

No abstract provided.


Adjusting For Spatial Effects In Genomic Prediction, Xiaojun Mao, Somak Dutta, Raymond K. W. Wong, Dan Nettleton 2019 Fudan University

Adjusting For Spatial Effects In Genomic Prediction, Xiaojun Mao, Somak Dutta, Raymond K. W. Wong, Dan Nettleton

Statistics Publications

This paper investigates the problem of adjusting for spatial effects in genomic prediction. Despite being seldomly considered in genome-wide association studies (GWAS), spatial effects often affect phenotypic measurements of plants. We consider a Gaussian random field (GRF) model with an additive covariance structure that incorporates genotype effects, spatial effects and subpopulation effects. An empirical study shows the existence of spatial effects and heterogeneity across different subpopulation families while simulations illustrate the improvement in selecting genotypically superior plants by adjusting for spatial effects in genomic prediction.


Mid To Late Season Weed Detection In Soybean Production Fields Using Unmanned Aerial Vehicle And Machine Learning, Arun Narenthiran Veeranampalayam Sivakumar 2019 University of Nebraska - Lincoln

Mid To Late Season Weed Detection In Soybean Production Fields Using Unmanned Aerial Vehicle And Machine Learning, Arun Narenthiran Veeranampalayam Sivakumar

Biological Systems Engineering--Dissertations, Theses, and Student Research

Mid-late season weeds are those that escape the early season herbicide applications and those that emerge late in the season. They might not affect the crop yield, but if uncontrolled, will produce a large number of seeds causing problems in the subsequent years. In this study, high-resolution aerial imagery of mid-season weeds in soybean fields was captured using an unmanned aerial vehicle (UAV) and the performance of two different automated weed detection approaches – patch-based classification and object detection was studied for site-specific weed management. For the patch-based classification approach, several conventional machine learning models on Haralick texture features were compared ...


Determining The Functions Of Novel Genes Required For Photosynthesis, Gillian Gomer, Moshe Kafri, Martin Jonikas 2019 University of Central Florida

Determining The Functions Of Novel Genes Required For Photosynthesis, Gillian Gomer, Moshe Kafri, Martin Jonikas

Gillian Gomer

As land available for agriculture remains limited, it is becoming more necessary to explore methods to improve the efficiency of crop production in order to support Earth’s growing populations. Newly characterized photosynthetic genes could improve our understanding of the way organisms convert light energy into fuel, allowing improvements in plant growth and environmental resistance. Using an insertion mutant library of the unicellular algae, Chlamydomonas reindhartii, that covers 83% of its genome, we are identifying and characterizing the hundreds of genes associated with photosynthesis. Chlamydomonas can be grown with or without a light source, which allows us to identify mutants ...


Molecular And Morphological Variation Among Populations Of Pediomelum Tenuiflorum (Pursh) A.N. Egan (Fabaceae) In Nebraska, Usa, Chauncey L. Kellar Jr., Roxi Kellar 2019 University of Nebraska at Omaha

Molecular And Morphological Variation Among Populations Of Pediomelum Tenuiflorum (Pursh) A.N. Egan (Fabaceae) In Nebraska, Usa, Chauncey L. Kellar Jr., Roxi Kellar

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Individuals of Pediomelum tenuiflorum, “wild alfalfa”, from disjunct populations in Nebraska vary extensively in their overall gestalt. Those in the western and central part of the state have a very slender growth habit, with thin stems and few, small flowers; whereas, those in the southeast have a very robust growth habit with heavy-looking stems and many tightly clustered flowers. For nearly 200 years, taxonomists have alternated between splitting P. tenuiflorum into two species, with the many-flowered morphotype named P. floribundum, and lumping all the morphological variants into one species as they are now. In this study, we investigated morphological and ...


Growing On A Scar: Genetic Variation Of Achillea Millefolium Near Meeker, Colorado, Ace Spitzer 2019 University of Northern Colorado

Growing On A Scar: Genetic Variation Of Achillea Millefolium Near Meeker, Colorado, Ace Spitzer

Ursidae: The Undergraduate Research Journal at the University of Northern Colorado

Mining operations deposit high concentrations of heavy metals such as lead, cadmium, arsenic, and vanadium into the topsoil of an ecosystem. These toxic metals can affect plant health and behavior, causing local extinction and shifts in ecosystem dynamics. However, genetic analyses of some plants growing on toxic soil conditions indicate higher genetic diversity than would be expected in that environment. Determining the effects of soil pollution on plants is important to determine a species’ utility in conservation and restoration. This investigation compared the genetic diversity of western yarrow (Achillea millefolium, Asteraceae), growing near a mine with vanadium and arsenic contamination ...


Identifying Brachypodium Distachyon Proteins Interacting With Histone Deacetylase Bdhd1, Alberto Giovanni Torrez 2019 The University of Western Ontario

Identifying Brachypodium Distachyon Proteins Interacting With Histone Deacetylase Bdhd1, Alberto Giovanni Torrez

Electronic Thesis and Dissertation Repository

Current evidence has revealed the involvement of epigenetic mechanisms, including histone deacetylases (HDACs), in plant stress responses. In Arabidopsis thaliana, HDA19, belonging to the RPD3/HDA1 class, interacts with transcription factors to form repressor complexes. HDAC research mainly exists for dicotyledons, whereas research on monocotyledons is limited. Brachypodium distachyon is used as a model plant to investigate questions unique to monocot crops. BdHD1 is the closest homologous gene to HDA19 in B. distachyon. This study investigated potential protein-protein interactions between BdHD1 and each of BdMYB22, BdWRKY24, and BdHOS15. Protein interactions were investigated using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation ...


Gene Expression Programs During Shoot, Root, And Callus Development In Arabidopsis Tissue Culture, Ping Che, Sonia Lall, Dan Nettleton, Stephen H. Howell 2019 Iowa State University

Gene Expression Programs During Shoot, Root, And Callus Development In Arabidopsis Tissue Culture, Ping Che, Sonia Lall, Dan Nettleton, Stephen H. Howell

Dan Nettleton

Shoots can be regenerated from Arabidopsis (Arabidopsis thaliana) root explants in tissue culture through a two-step process requiring preincubation on an auxin-rich callus induction medium. Regenerating tissues can be directed along different developmental pathways leading to the formation of shoots, new roots, or callus by transferring to the appropriate organ induction medium. Using gene-profiling methods, we identified groups of genes that serve as molecular signatures of the different developmental processes, i.e. genes that were specifically up- or down-regulated on one developmental pathway, but not on others. One transcription factor gene that was up-regulated during early shoot development was RAP2 ...


Transcript-Based Cloning Of Rrp46, A Regulator Of Rrna Processing And R Gene–Independent Cell Death In Barley–Powdery Mildew Interactions, Liu Xi, Matthew J. Moscou, Yan Meng, Weihui Xu, Rico A. Caldo, Miranda Shaver, Dan Nettleton, Roger P. Wise 2019 Iowa State University

Transcript-Based Cloning Of Rrp46, A Regulator Of Rrna Processing And R Gene–Independent Cell Death In Barley–Powdery Mildew Interactions, Liu Xi, Matthew J. Moscou, Yan Meng, Weihui Xu, Rico A. Caldo, Miranda Shaver, Dan Nettleton, Roger P. Wise

Dan Nettleton

Programmed cell death (PCD) plays a pivotal role in plant development and defense. To investigate the interaction between PCD and R gene–mediated defense, we used the 22K Barley1 GeneChip to compare and contrast time-course expression profiles of Blumeria graminis f. sp hordei (Bgh) challenged barley (Hordeum vulgare) cultivar C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast neutron–derived Bgh-induced tip cell death1 mutant, bcd1. Mixed linear model analysis identified genes associated with the cell death phenotype as opposed to Rgene–mediated resistance. One-hundred fifty genes were found at the threshold P value < 0.0001 and a false discovery rate bcd1mutant. Gene Ontology and rice (Oryza ...


Hierarchical Modeling And Differential Expression Analysis For Rna-Seq Experiments With Inbred And Hybrid Genotypes, Andrew Lithio, Dan Nettleton 2019 Iowa State University

Hierarchical Modeling And Differential Expression Analysis For Rna-Seq Experiments With Inbred And Hybrid Genotypes, Andrew Lithio, Dan Nettleton

Dan Nettleton

The performance of inbred and hybrid genotypes is of interest in plant breeding and genetics. High-throughput sequencing of RNA (RNA-seq) has proven to be a useful tool in the study of the molecular genetic responses of inbreds and hybrids to environmental stresses. Commonly used experimental designs and sequencing methods lead to complex data structures that require careful attention in data analysis. We demonstrate an analysis of RNA-seq data from a split-plot design involving drought stress applied to two inbred genotypes and two hybrids formed by crosses between the inbreds. Our generalized linear modeling strategy incorporates random effects for whole-plot experimental ...


Nested Hierarchical Functional Data Modeling And Inference For The Analysis Of Functional Plant Phenotypes, Yuhang Xu, Yehua Li, Dan Nettleton 2019 University of Nebraska - Lincoln

Nested Hierarchical Functional Data Modeling And Inference For The Analysis Of Functional Plant Phenotypes, Yuhang Xu, Yehua Li, Dan Nettleton

Dan Nettleton

In a plant science Root Image Study, the process of seedling roots bending in response to gravity is recorded using digital cameras, and the bending rates are modeled as functional plant phenotype data. The functional phenotypes are collected from seeds representing a large variety of genotypes and have a three-level nested hierarchical structure, with seeds nested in groups nested in genotypes. The seeds are imaged on different days of the lunar cycle, and an important scientific question is whether there are lunar effects on root bending. We allow the mean function of the bending rate to depend on the lunar ...


Toward Mass Spectrometry Imaging In The Metabolomics Scale: Increasing Metabolic Coverage Through Multiple On-Tissue Chemical Modifications, Maria Emilia Dueñas, Evan A. Larson, Young Jin Lee 2019 Iowa State University

Toward Mass Spectrometry Imaging In The Metabolomics Scale: Increasing Metabolic Coverage Through Multiple On-Tissue Chemical Modifications, Maria Emilia Dueñas, Evan A. Larson, Young Jin Lee

Chemistry Publications

Exploring the metabolic differences directly on tissues is essential for the comprehensive understanding of how multicellular organisms function. Mass spectrometry imaging (MSI) is an attractive technique toward this goal; however, MSI in metabolomics scale has been hindered by multiple limitations. This is most notable for single cell level high-spatial resolution imaging because of the limited number of molecules in small sampling size and the low ionization yields of many metabolites. Several on-tissue chemical derivatization approaches have been reported to increase MSI signals of targeted compounds, especially in matrix-assisted laser desorption/ionization (MALDI)- MSI. Herein, we adopt a combination of chemical ...


Root Type-Specific Reprogramming Of Maize Pericycle Transcriptomes By Local High Nitrate Results In Disparate Lateral Root Branching Patterns, Peng Yu, Jutta A. Baldauf, Andrew Lithio, Caroline Marcon, Dan Nettleton, Chunjian Li, Frank Hochholdinger 2019 China Agricultural University

Root Type-Specific Reprogramming Of Maize Pericycle Transcriptomes By Local High Nitrate Results In Disparate Lateral Root Branching Patterns, Peng Yu, Jutta A. Baldauf, Andrew Lithio, Caroline Marcon, Dan Nettleton, Chunjian Li, Frank Hochholdinger

Dan Nettleton

The adaptability of root system architecture to unevenly distributed mineral nutrients in soil is a key determinant of plant performance. The molecular mechanisms underlying nitrate dependent plasticity of lateral root branching across the different root types of maize are only poorly understood. In this study, detailed morphological and anatomical analyses together with cell type-specific transcriptome profiling experiments combining laser capture microdissection with RNA-seq were performed to unravel the molecular signatures of lateral root formation in primary, seminal, crown, and brace roots of maize (Zea mays) upon local high nitrate stimulation. The four maize root types displayed divergent branching patterns of ...


Stability Of Single-Parent Gene Expression Complementation In Maize Hybrids Upon Water Deficit Stress, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Jutta A. Baldauf, Lena Altrogge, Nina Opitz, Christa Lanz, Heiko Schoof, Dan Nettleton, Hans-Peter Piepho, Frank Hochholdinger 2019 University of Bonn

Stability Of Single-Parent Gene Expression Complementation In Maize Hybrids Upon Water Deficit Stress, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Jutta A. Baldauf, Lena Altrogge, Nina Opitz, Christa Lanz, Heiko Schoof, Dan Nettleton, Hans-Peter Piepho, Frank Hochholdinger

Dan Nettleton

Heterosis is the superior performance of F1 hybrids compared with their homozygous, genetically distinct parents. In this study, we monitored the transcriptomic divergence of the maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrid progeny in primary roots under control and water deficit conditions simulated by polyethylene glycol treatment. Single-parent expression (SPE) of genes is an extreme instance of gene expression complementation, in which genes are active in only one of two parents but are expressed in both reciprocal hybrids. In this study, 1,997 genes only expressed in B73 and 2,024 genes only expressed ...


Ontogeny Of The Maize Shoot Apical Meristem, Elizabeth M. Takacs, Jie Li, Chuanlong Du, Lalit Ponnala, Diane Janick-Buckner, Jianming Yu, Gary J. Muehlbauer, Patrick S. Schnable, Marja C. P. Timmermans, Qi Sun, Dan Nettleton, Michael J. Scanlon 2019 Cornell University

Ontogeny Of The Maize Shoot Apical Meristem, Elizabeth M. Takacs, Jie Li, Chuanlong Du, Lalit Ponnala, Diane Janick-Buckner, Jianming Yu, Gary J. Muehlbauer, Patrick S. Schnable, Marja C. P. Timmermans, Qi Sun, Dan Nettleton, Michael J. Scanlon

Dan Nettleton

The maize (Zea mays) shoot apical meristem (SAM) arises early in embryogenesis and functions during stem cell maintenance and organogenesis to generate all the aboveground organs of the plant. Despite its integral role in maize shoot development, little is known about the molecular mechanisms of SAM initiation. Laser microdissection of apical domains from developing maize embryos and seedlings was combined with RNA sequencing for transcriptomic analyses of SAMontogeny. Molecular markers of key events during maize embryogenesis are described, and comprehensive transcriptional data from six stages in maize shoot development are generated. Transcriptomic profiling before and after SAM initiation indicates ...


Nonsyntenic Genes Drive Highly Dynamic Complementation Of Gene Expression In Maize Hybrids, Anja Paschold, Nick B. Larson, Caroline Marcon, James C. Schnable, Cheng-Ting Yeh, Christa Lanz, Dan Nettleton, Hans-Peter Piepho, Patrick S. Schnable, Frank Hochholdinger 2019 University of Bonn

Nonsyntenic Genes Drive Highly Dynamic Complementation Of Gene Expression In Maize Hybrids, Anja Paschold, Nick B. Larson, Caroline Marcon, James C. Schnable, Cheng-Ting Yeh, Christa Lanz, Dan Nettleton, Hans-Peter Piepho, Patrick S. Schnable, Frank Hochholdinger

Dan Nettleton

Maize (Zea mays) displays an exceptional level of structural genomic diversity, which is likely unique among higher eukaryotes. In this study, we surveyed how the genetic divergence of two maize inbred lines affects the transcriptomic landscape in four different primary root tissues of their F1-hybrid progeny. An extreme instance of complementation was frequently observed: genes that were expressed in only one parent but in both reciprocal hybrids. This single-parent expression (SPE) pattern was detected for 2341 genes with up to 1287 SPE patterns per tissue. As a consequence, the number of active genes in hybrids exceeded that of their parents ...


Interaction-Dependent Gene Expression In Mla-Specified Response To Barley Powdery Mildew, Rico A. Caldo, Dan Nettleton, Roger P. Wise 2019 Iowa State University

Interaction-Dependent Gene Expression In Mla-Specified Response To Barley Powdery Mildew, Rico A. Caldo, Dan Nettleton, Roger P. Wise

Dan Nettleton

Plant recognition of pathogen-derived molecules influences attack and counterattack strategies that affect the outcome of host–microbe interactions. To ascertain the global framework of host gene expression during biotrophic pathogen invasion, we analyzed in parallel the mRNA abundance of 22,792 host genes throughout 36 (genotype × pathogen × time) interactions between barley (Hordeum vulgare) and Blumeria graminis f. sp hordei (Bgh), the causal agent of powdery mildew disease. A split-split-plot design was used to investigate near-isogenic barley lines with introgressed Mla6, Mla13, and Mla1 coiled-coil, nucleotide binding site, Leu-rich repeat resistance alleles challenged with Bgh isolates 5874 (AvrMla6 and AvrMla1) and ...


Barleybase—An Expression Profiling Database For Plant Genomics, Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, Julie A. Dickerson 2019 Iowa State University

Barleybase—An Expression Profiling Database For Plant Genomics, Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, Julie A. Dickerson

Dan Nettleton

BarleyBase (BB) ( www.barleybase.org ) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. BB houses raw and normalized expression data from the two publicly available Affymetrix genome arrays, Barley1 and Arabidopsis ATH1 with plans to include the new Affymetrix 61K wheat, maize, soybean and rice arrays, as they become available. BB contains a broad set of query and display options at all data levels, ranging from experiments to individual hybridizations to probe sets down to individual probes. Users can perform cross-experiment queries on probe sets based on observed expression profiles and/or ...


Analysis Of The Genetic Architecture Of Maize Kernel Size Traits By Combined Linkage And Association Mapping, Min Liu, Xiaolong Tan, Yan Yang, Peng Liu, Xiaoxiang Zhang, Yinchao Zhang, Lei Wang, Yu Hu, Langlang Ma, Zhaoling Li, Yanling Zhang, Chaoying Zou, Haijian Lin, Shibin Gao, Michael Lee, Thomas Lubberstedt, Guangtang Pan, Yaou Shen 2019 Sichuan Agricultural University

Analysis Of The Genetic Architecture Of Maize Kernel Size Traits By Combined Linkage And Association Mapping, Min Liu, Xiaolong Tan, Yan Yang, Peng Liu, Xiaoxiang Zhang, Yinchao Zhang, Lei Wang, Yu Hu, Langlang Ma, Zhaoling Li, Yanling Zhang, Chaoying Zou, Haijian Lin, Shibin Gao, Michael Lee, Thomas Lubberstedt, Guangtang Pan, Yaou Shen

Thomas Lubberstedt

Kernel size‐related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P < 2.25 × 10−6) associated with these three traits in the association panel under four environments. Furthermore, 50 quantitative trait loci (QTL) controlling these traits were detected in seven environments in the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, of which eight were repetitively identified in at least three environments. Combining the two mapping populations revealed that 56 SNPs (P < 1 × 10−3) fell within 18 of the QTL confidence intervals. According to the top significant SNPs, stable‐effect SNPs and the co‐localized SNPs by association analysis and linkage mapping, a total of 73 candidate genes were identified, regulating seed development. Additionally, seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co‐localized SNPs, of which zma‐miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1, CUC2 and NAC6 in vitro. Overexpression of zma‐miR164e resulted in the down‐regulation of these genes above and the failure of seed formation in Arabidopsis pods, with the increased branch number. These findings provide insights into the mechanism of ...


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