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Phomopsis Stem Canker Of Sunflower In North America: Correlation With Climate And Solutions Through Breeding And Management, Brent S. Hulke, Samuel G. Markell, Nolan C. Kane, Febina M. Mathew 2019 USDA-Agricultural Research Service

Phomopsis Stem Canker Of Sunflower In North America: Correlation With Climate And Solutions Through Breeding And Management, Brent S. Hulke, Samuel G. Markell, Nolan C. Kane, Febina M. Mathew

Febina Mathew

Climate change is occurring in the central US and is interacting with agroecological factors to increase biotic stress in sunflower. Certain species of Diaporthe cause Phomopsis stem canker in sunflower and other dicotyledonous weeds and crops. The increase in precipitation already observed in the states of North Dakota, South Dakota, and Minnesota have increased the chances of outbreaks of necrotrophic pathogens, like Diaporthe. We discuss how climate trends, combined with technological, management, and economic interactions, are correlated with increasing incidence of Phomopsis stem canker in these and adjacent areas in North America. Further, we discuss management options and the role ...


Candidate Effectors From Uromyces Appendiculatus, The Causal Agent Of Rust On Common Bean, Can Be Discriminated Based On Suppression Of Immune Responses, Mingsheng Qi, Yu Mei, James P. Grayczyk, Luana M. Darben, Martin E. G. Rieker, Janina M. Seitz, Ralf T. Voegele, Steven A. Whitham, Tobias I. Link 2019 Iowa State University

Candidate Effectors From Uromyces Appendiculatus, The Causal Agent Of Rust On Common Bean, Can Be Discriminated Based On Suppression Of Immune Responses, Mingsheng Qi, Yu Mei, James P. Grayczyk, Luana M. Darben, Martin E. G. Rieker, Janina M. Seitz, Ralf T. Voegele, Steven A. Whitham, Tobias I. Link

Plant Pathology and Microbiology Publications

Rust fungi are devastating pathogens for several important crop plants. The biotrophic lifestyle of rust fungi requires that they influence their host plants to create a favorable environment for growth and reproduction. Rust fungi secrete a variety of effector proteins that manipulate host target proteins to alter plant metabolism and suppress defense responses. Because of the obligate biotrophic lifestyle of rust fungi, direct evidence for effector function is difficult to obtain, and so suites of experiments utilizing expression in heterologous systems are necessary. Here, we present results from a yeast cell death suppression assay and assays for suppression of PAMP-triggered ...


Summaries Of Arkansas Cotton Research 2018, Fred Bourland 2019 University of Arkansas, Fayetteville

Summaries Of Arkansas Cotton Research 2018, Fred Bourland

Research Series

Arkansas ended the 2018 season ranked 5th nationally in harvested acres (480,000 acres), 4th in lint yield (1150 lb/acre), and 4th in total production (1,150,000 bales). The string of consecutive years with good yields is helping to drive the increase in cotton acres. Harvest and ginning capacity is a major limiting factor for acre expansion. Cotton planting intentions for 2019 released in late March are at 580,000 acres, up 20% from the 485,000 acres planted in 2018. This continues to push the ginning capacity of 28 gins in 2018 and on-farm picker capacity to ...


Nature-Guided Synthesis Of Advanced Bio-Lubricants, Trevor Romsdahl, Asghar Shirani, Robert E. Minto, Chunyu Zhang, Edgar B. Cahoon, Kent D. Chapman, Diana Berman 2019 University of North Texas

Nature-Guided Synthesis Of Advanced Bio-Lubricants, Trevor Romsdahl, Asghar Shirani, Robert E. Minto, Chunyu Zhang, Edgar B. Cahoon, Kent D. Chapman, Diana Berman

Faculty Publications from the Center for Plant Science Innovation

Design of environmentally friendly lubricants derived from renewable resources is highly desirable for many practical applications. Here, Orychophragmus violaceus (Ov) seed oil is found to have superior lubrication properties, and this is based on the unusual structural features of the major lipid species— triacylglycerol (TAG) estolides. Ov TAG estolides contain two non-hydroxylated, glycerol-bound fatty acids (FAs) and one dihydroxylated FA with an estolide branch. Estolide branch chains vary in composition and length, leading to their thermal stability and functional properties. Using this concept, nature-guided estolides of castor oil were synthesized. As predicted, they showed improved lubrication properties similar to Ov ...


Qqs Orphan Gene And Its Interactor Nf‐Yc4 Reduce Susceptibility To Pathogens And Pests, Mingsheng Qi, Wenguang Zheng, Xuefeng Zhao, Jessica D. Hohenstein, Yuba Kandel, Seth O’Conner, Yifan Wang, Chuanlong Du, Dan Nettleton, Gustavo C. Macintosh, Gregory L. Tylka, Eve Syrkin Wurtele, Steven A. Whitham, Ling Li 2019 Iowa State University

Qqs Orphan Gene And Its Interactor Nf‐Yc4 Reduce Susceptibility To Pathogens And Pests, Mingsheng Qi, Wenguang Zheng, Xuefeng Zhao, Jessica D. Hohenstein, Yuba Kandel, Seth O’Conner, Yifan Wang, Chuanlong Du, Dan Nettleton, Gustavo C. Macintosh, Gregory L. Tylka, Eve Syrkin Wurtele, Steven A. Whitham, Ling Li

Ling Li

Enhancing the nutritional quality and disease resistance of crops without sacrificing productivity is a key issue for developing varieties that are valuable to farmers and for simultaneously improving food security and sustainability. Expression of the Arabidopsis thaliana species‐specific AtQQS (Qua‐Quine Starch) orphan gene or its interactor, NF‐YC4 (Nuclear Factor Y, subunit C4), has been shown to increase levels of leaf/seed protein without affecting the growth and yield of agronomic species. Here, we demonstrate that overexpression of AtQQS and NF‐YC4 in Arabidopsis and soybean enhances resistance/reduces susceptibility to viruses, bacteria, fungi, aphids, and soybean cyst ...


B.R. Wells Arkansas Rice Research Studies, R. J. Norman, K. A.K. Moldenhauer 2019 University of Arkansas, Fayetteville

B.R. Wells Arkansas Rice Research Studies, R. J. Norman, K. A.K. Moldenhauer

Research Series

No abstract provided.


The Database Of Identified Root-Specific Genes And Their Promoters In Maize, Sorghum, And Soybean, Gleb Moisseyev, Divith Rajagopal, Alix Cui, Kiyoul Park, Edgar B. Cahoon, Chi Zhang 2019 University of Nebraska - Lincoln

The Database Of Identified Root-Specific Genes And Their Promoters In Maize, Sorghum, And Soybean, Gleb Moisseyev, Divith Rajagopal, Alix Cui, Kiyoul Park, Edgar B. Cahoon, Chi Zhang

Faculty Publications from the Center for Plant Science Innovation

Root genes are essential to plants as they dictate factors such as the strength of the plant, reproductivity success, etc. However, in status quo studies on roots genes are simply inefficient. To be more specific, currently there are very few online databases of roots genes and promoters, which essentially deters root gene studies from being successful. To fix this problem, our lab constructed and coded an online database that contains information about the roots of maize, soybean, and sorghum. We collected 1200 root genes and assessed the strength and success of a given gene. This online database of these crops ...


A Sugarcane Mosaic Virus Vector For Gene Expression In Maize, Yu Mei, Guanjun Liu, Chunquan Zhang, John H. Hill, Steven A. Whitham 2019 Iowa State University

A Sugarcane Mosaic Virus Vector For Gene Expression In Maize, Yu Mei, Guanjun Liu, Chunquan Zhang, John H. Hill, Steven A. Whitham

Plant Pathology and Microbiology Publications

Zea mays L. ssp. mays (maize) is an important crop plant as well as model system for genetics and plant biology. The ability to select among different virus‐based platforms for transient gene silencing or protein expression experiments is expected to facilitate studies of gene function in maize and complement experiments with stable transgenes. Here, we describe the development of a sugarcane mosaic virus (SCMV) vector for the purpose of protein expression in maize. An infectious SCMV cDNA clone was constructed, and heterologous genetic elements were placed between the protein 1 (P1) and helper component‐proteinase (HC‐Pro) cistrons in ...


Assessing Anthocyanin Biosynthesis In Solanaceae As A Model Pathway For Secondary Metabolism, Zou Li, Trisha Vickrey, Moira G. McNally, Shirley J. Sato, Thomas E. Clemente, Jeffrey P. Mower 2019 University of Nebraska - Lincoln & Guangdong Academy of Agricultural Sciences

Assessing Anthocyanin Biosynthesis In Solanaceae As A Model Pathway For Secondary Metabolism, Zou Li, Trisha Vickrey, Moira G. Mcnally, Shirley J. Sato, Thomas E. Clemente, Jeffrey P. Mower

Faculty Publications from the Center for Plant Science Innovation

Solanaceae have played an important role in elucidating how flower color is specified by the flavonoid biosynthesis pathway (FBP), which produces anthocyanins and other secondary metabolites. With well-established reverse genetics tools and rich genomic resources, Solanaceae provide a robust framework to examine the diversification of this well-studied pathway over short evolutionary timescales and to evaluate the predictability of genetic perturbation on pathway flux. Genomes of eight Solanaceae species, nine related asterids, and four rosids were mined to evaluate variation in copy number of the suite of FBP enzymes involved in anthocyanin biosynthesis. Comparison of annotation sources indicated that the NCBI ...


Network‐Based Feature Selection Reveals Substructures Of Gene Modules Responding To Salt Stress In Rice, Qian Du, Malachy Campbell, Huihui Yu, Kan Liu, Harkamal Walia, Qi Zhang, Chi Zhang 2019 University of Nebraska - Lincoln

Network‐Based Feature Selection Reveals Substructures Of Gene Modules Responding To Salt Stress In Rice, Qian Du, Malachy Campbell, Huihui Yu, Kan Liu, Harkamal Walia, Qi Zhang, Chi Zhang

Faculty Publications from the Center for Plant Science Innovation

Rice, an important food resource, is highly sensitive to salt stress, which is directly related to food security. Although many studies have identified physiological mechanisms that confer tolerance to the osmotic effects of salinity, the link between rice genotype and salt tolerance is not very clear yet. Association of gene co‐expression network and rice phenotypic data under stress has penitential to identify stress‐responsive genes, but there is no standard method to associate stress phenotype with gene co‐expression network. A novel method for integration of gene co‐expression network and stress phenotype data was developed to conduct a ...


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 ...


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 ...


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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