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2019

Agronomy and Crop Sciences

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Full-Text Articles in Life Sciences

Canavalia And Dolichos Extracts For Sustainable Pest Biocontrol And Plant Nutrition Improvement In El Salvador, Carlos Martinez Oct 2019

Canavalia And Dolichos Extracts For Sustainable Pest Biocontrol And Plant Nutrition Improvement In El Salvador, Carlos Martinez

Theses, Dissertations, and Student Research in Agronomy and Horticulture

Botanical repellents and pesticides are now being rediscovered as new tools for integrated pest management in order to reduce the use of toxic chemicals in crop production. Canavalia gladiata and Dolichos lablab are two Fabaceae very well adapted to farmlands of El Salvador, effective as living barriers and mostly as cover crops, however, they are not yet very well disseminated. This document describes the potential for using the liquid extracts and the dry flour of raw seeds of those plants for economic benefit and practical convenience for pest management in Salvadorian agriculture under field conditions. Seed extracts were useful when ...


B.R. Wells Arkansas Rice Research Studies, R. J. Norman, K. A.K. Moldenhauer Aug 2019

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

Research Series

No abstract provided.


Tillage In 2001: Fall Strip-Tillage, Mahdi Al-Kaisi, H. Mark Hanna, Michael J. Tidman Jul 2019

Tillage In 2001: Fall Strip-Tillage, Mahdi Al-Kaisi, H. Mark Hanna, Michael J. Tidman

H. Mark Hanna

Every tillage practice has distinct advantages and disadvantages, requires specific equipment, and requires that you learn how to successfully implement the practice in your operation. In this article, we discuss the merits of fall strip-tillage and present some of the facts you need to consider to implement fall strip-tillage.


Tillage Implement Design And Its Effect On Soil, Mahdi Al-Kaisi, H. Mark Hanna, Michael Tidman Jul 2019

Tillage Implement Design And Its Effect On Soil, Mahdi Al-Kaisi, H. Mark Hanna, Michael Tidman

H. Mark Hanna

The weather is gradually improving and most Iowa producers are getting closer to working in the field. Some have already started fieldwork. However, there is still time to finalize preparation of tillage implements for spring fieldwork. Producers are encouraged to check and evaluate the design of soil-engaging components of their tillage implements, assess the potential for soil erosion, and think about their chances for a successful crop.


Tillage Equipment Maintenance, H. Mark Hanna, Mahdi Al-Kaisi, Michael J. Tidman Jul 2019

Tillage Equipment Maintenance, H. Mark Hanna, Mahdi Al-Kaisi, Michael J. Tidman

H. Mark Hanna

Many crop operations experience a lull in mid-winter. This lull is a great time to take a look at tillage equipment maintenance for the 2002 growing season and catch up on "little fixes" that were put off from last year. Proper setup and maintenance of tillage equipment can eliminate extra tillage trips through the field and increase equipment efficiency, which preserves crop residue and limits soil erosion.


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 Jul 2019

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 Jul 2019

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 Jul 2019

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 Jul 2019

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 ...


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 Jul 2019

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 ...


Laser Microdissection Of Narrow Sheath Mutant Maize Uncovers Novel Gene Expression In The Shoot Apical Meristem, Xiaolan Zhang, Shahinez Madi, Lisa Borsuk, Dan Nettleton, Robert J. Elshire, Brent Buckner, Diane Janick-Buckner, Jon Beck, Marja Timmermans, Patrick S. Schnable, Michael J. Scanlon Jul 2019

Laser Microdissection Of Narrow Sheath Mutant Maize Uncovers Novel Gene Expression In The Shoot Apical Meristem, Xiaolan Zhang, Shahinez Madi, Lisa Borsuk, Dan Nettleton, Robert J. Elshire, Brent Buckner, Diane Janick-Buckner, Jon Beck, Marja Timmermans, Patrick S. Schnable, Michael J. Scanlon

Dan Nettleton

Microarrays enable comparative analyses of gene expression on a genomic scale, however these experiments frequently identify an abundance of differentially expressed genes such that it may be difficult to identify discrete functional networks that are hidden within large microarray datasets. Microarray analyses in which mutant organisms are compared to nonmutant siblings can be especially problematic when the gene of interest is expressed in relatively few cells. Here, we describe the use of laser microdissection microarray to perform transcriptional profiling of the maize shoot apical meristem (SAM), a ~100-μm pillar of organogenic cells that is required for leaf initiation. Microarray analyses ...


Scanning Microarrays At Multiple Intensities Enhances Discovery Of Differentially Expressed Genes, David S. Skibbe, Xiujuan Wang, Xuefeng Zhao, Lisa A. Borsuk, Dan Nettleton, Patrick S. Schnable Jul 2019

Scanning Microarrays At Multiple Intensities Enhances Discovery Of Differentially Expressed Genes, David S. Skibbe, Xiujuan Wang, Xuefeng Zhao, Lisa A. Borsuk, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Motivation: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been developed.

Results: Data from each of three scan intensities (low, medium, high) were analyzed separately using multiple scan and linear regression approaches to identify and compare the sets of genes that exhibit statistically significant differential expression. In the multiple scan approach only one-third of the differentially expressed genes were shared among the three intensities, and each scan intensity identified unique sets of differentially expressed genes. The set of differentially expressed genes from ...


The B73 Maize Genome: Complexity, Diversity, And Dynamics, Patrick S. Schnable, Doreen Ware, Kai Ying, Cheng-Ting Yeh, Scott J. Emrich, Yi Jia, Ananth Kalyanaraman, An-Ping Hsia, Yan Fu, Sanzhen Liu, Alan M. Myers, Dan Nettleton, Srinivas Aluru Jul 2019

The B73 Maize Genome: Complexity, Diversity, And Dynamics, Patrick S. Schnable, Doreen Ware, Kai Ying, Cheng-Ting Yeh, Scott J. Emrich, Yi Jia, Ananth Kalyanaraman, An-Ping Hsia, Yan Fu, Sanzhen Liu, Alan M. Myers, Dan Nettleton, Srinivas Aluru

Dan Nettleton

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and ...


Microdissection Of Shoot Meristem Functional Domains, Lionel Brooks Iii, Josh Strable, Xiaolan Zhang, Kazuhiro Ohtsu, Ruilian Zhou, Ananda Sarkar, Sarah Hargreaves, Robert J. Elshire, Douglas Eudy, Teresa Pawlowska, Doreen Ware, Diane Janick-Buckner, Brent Buckner, Marja C. P. Timmermans, Patrick S. Schnable, Dan Nettleton, Michael J. Scanlon Jul 2019

Microdissection Of Shoot Meristem Functional Domains, Lionel Brooks Iii, Josh Strable, Xiaolan Zhang, Kazuhiro Ohtsu, Ruilian Zhou, Ananda Sarkar, Sarah Hargreaves, Robert J. Elshire, Douglas Eudy, Teresa Pawlowska, Doreen Ware, Diane Janick-Buckner, Brent Buckner, Marja C. P. Timmermans, Patrick S. Schnable, Dan Nettleton, Michael J. Scanlon

Dan Nettleton

The shoot apical meristem (SAM) maintains a pool of indeterminate cells within the SAM proper, while lateral organs are initiated from the SAM periphery. Laser microdissection–microarray technology was used to compare transcriptional profiles within these SAM domains to identify novel maize genes that function during leaf development. Nine hundred and sixty-two differentially expressed maize genes were detected; control genes known to be upregulated in the initiating leaf (P0/P1) or in the SAM proper verified the precision of the microdissections. Genes involved in cell division/growth, cell wall biosynthesis, chromatin remodeling, RNA binding, and translation are especially upregulated in ...


Loss Of Rna–Dependent Rna Polymerase 2 (Rdr2) Function Causes Widespread And Unexpected Changes In The Expression Of Transposons, Genes, And 24-Nt Small Rnas, Yi Jia, Damon R. Lisch, Kazuhiro Ohtsu, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable Jul 2019

Loss Of Rna–Dependent Rna Polymerase 2 (Rdr2) Function Causes Widespread And Unexpected Changes In The Expression Of Transposons, Genes, And 24-Nt Small Rnas, Yi Jia, Damon R. Lisch, Kazuhiro Ohtsu, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most ...


Comparative Gene Expression Profiles Between Heterotic And Non-Heterotic Hybrids Of Tetraploid Medicago Sativa, Xuehui Li, Yanling Wei, Dan Nettleton, E. Charles Brummer Jul 2019

Comparative Gene Expression Profiles Between Heterotic And Non-Heterotic Hybrids Of Tetraploid Medicago Sativa, Xuehui Li, Yanling Wei, Dan Nettleton, E. Charles Brummer

Dan Nettleton

Background: Heterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis.

Results: We tested these hypotheses in three Medicago sativa (alfalfa) genotypes and their three hybrids, two of which expressed heterosis for biomass yield and a third that did not, using Affymetrix M. truncatula GeneChip arrays. Alfalfa hybridized to approximately 47 ...


Use Of Legume Green Manures As Nitrogen Sources For Corn Production, Matt Liebman, Rhonda L. Graef, Daniel Nettleton, Cynthia A. Cambardella Jul 2019

Use Of Legume Green Manures As Nitrogen Sources For Corn Production, Matt Liebman, Rhonda L. Graef, Daniel Nettleton, Cynthia A. Cambardella

Dan Nettleton

Recent volatility in supplies and prices of natural gas and synthetic nitrogen (N) fertilizer suggests a need to develop and refine alternative strategies for supplying N to corn. In this study, conducted in north-eastern Iowa, we examined the use of red clover and alfalfa green manures as means of supplying N to a succeeding corn crop. Red clover intercropped with oat produced significantly more biomass and contained more N than alfalfa intercropped with oat. Tilling green manures in the fall or delaying tillage until the following spring did not have a consistent effect on green manure N content. Without N ...


Complementation Contributes To Transcriptome Complexity In Maize (Zea Mays L.) Hybrids Relative To Their Inbred Parents, Anja Paschold, Yi Jia, Caroline Marcon, Steve Lund, Nick B. Larson, Cheng-Ting Yeh, Stephan Ossowski, Christa Lanz, Dan Nettleton, Patrick S. Schnable, Frank Hochholdinger Jul 2019

Complementation Contributes To Transcriptome Complexity In Maize (Zea Mays L.) Hybrids Relative To Their Inbred Parents, Anja Paschold, Yi Jia, Caroline Marcon, Steve Lund, Nick B. Larson, Cheng-Ting Yeh, Stephan Ossowski, Christa Lanz, Dan Nettleton, Patrick S. Schnable, Frank Hochholdinger

Dan Nettleton

Typically, F1-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two ...


The Maize Brown Midrib2 (Bm2) Gene Encodes A Methylenetetrahydrofolate Reductase That Contributes To Lignin Accumulation, Ho Man Tang, Sanzhen Liu, Sarah Hill-Skinner, Wei Wu, Danielle Reed, Cheng-Ting Yeh, Dan Nettleton, Patrick S. Schnable Jun 2019

The Maize Brown Midrib2 (Bm2) Gene Encodes A Methylenetetrahydrofolate Reductase That Contributes To Lignin Accumulation, Ho Man Tang, Sanzhen Liu, Sarah Hill-Skinner, Wei Wu, Danielle Reed, Cheng-Ting Yeh, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

The midribs of maize brown midrib (bm) mutants exhibit a reddish‐brown color associated with reductions in lignin concentration and alterations in lignin composition. Here, we report the mapping, cloning, and functional and biochemical analyses of the bm2 gene. The bm2 gene was mapped to a small region of chromosome 1 that contains a putative methylenetetrahydrofolate reductase (MTHFR) gene, which is down‐regulated in bm2 mutant plants. Analyses of multiple Mu‐induced bm2‐Mu mutant alleles confirmed that this constitutively expressed gene is bm2. Yeast complementation experiments and a previously published biochemical characterization show that the bm2 gene encodes a ...


Extreme‐Phenotype Genome‐Wide Association Study (Xp‐Gwas): A Method For Identifying Trait‐Associated Variants By Sequencing Pools Of Individuals Selected From A Diversity Panel, Jinliang Yang, Haiying Jiang, Cheng-Ting Yeh, Jianming Yu, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable Jun 2019

Extreme‐Phenotype Genome‐Wide Association Study (Xp‐Gwas): A Method For Identifying Trait‐Associated Variants By Sequencing Pools Of Individuals Selected From A Diversity Panel, Jinliang Yang, Haiying Jiang, Cheng-Ting Yeh, Jianming Yu, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Although approaches for performing genome‐wide association studies (GWAS) are well developed, conventional GWAS requires high‐density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP‐GWAS (extreme‐phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well‐characterized kernel row number ...


Extensive Tissue-Specific Transcriptomic Plasticity In Maize Primary Roots Upon Water Deficit, Nina Opitz, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Ronny Brandt, Hans-Peter Piepho, Dan Nettleton, Frank Hochholdinger Jun 2019

Extensive Tissue-Specific Transcriptomic Plasticity In Maize Primary Roots Upon Water Deficit, Nina Opitz, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Ronny Brandt, Hans-Peter Piepho, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, <3% (50 genes) of water deficit-responsive genes (1915) were consistently regulated in all tissues, while >75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the ...


Transcriptomic And Anatomical Complexity Of Primary, Seminal, And Crown Roots Highlight Root Type-Specific Functional Diversity In Maize (Zea Mays L.), Huanhuan Tai, Xin Lu, Nin Opitz, Caroline Marcon, Anja Paschold, Andrew Lithio, Dan Nettleton, Frank Hochholdinger Jun 2019

Transcriptomic And Anatomical Complexity Of Primary, Seminal, And Crown Roots Highlight Root Type-Specific Functional Diversity In Maize (Zea Mays L.), Huanhuan Tai, Xin Lu, Nin Opitz, Caroline Marcon, Anja Paschold, Andrew Lithio, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across ...


Non-Syntenic Genes Drive Rtcs-Dependent Regulation Of The Embryo Transcriptome During Formation Of Seminal Root Primordia In Maize (Zea Mays L.), Huanhuan Tai, Nina Opitz, Andrew Lithio, Xin Lu, Dan Nettleton, Frank Hochholdinger Jun 2019

Non-Syntenic Genes Drive Rtcs-Dependent Regulation Of The Embryo Transcriptome During Formation Of Seminal Root Primordia In Maize (Zea Mays L.), Huanhuan Tai, Nina Opitz, Andrew Lithio, Xin Lu, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Seminal roots of maize are pivotal for early seedling establishment. The maize mutant rootless concerning crown and seminal roots (rtcs) is defective in seminal root initiation during embryogenesis. In this study, the transcriptomes of wild-type and rtcs embryos were analyzed by RNA-Seq based on histological results at three stages of seminal root primordia formation. Hierarchical clustering highlighted that samples of each genotype grouped together along development. Determination of their gene activity status revealed hundreds of genes specifically transcribed in wild-type or rtcs embryos, while K-mean clustering revealed changes in gene expression dynamics between wild-type and rtcs during embryo development. Pairwise ...


Complexity And Specificity Of The Maize (Zea Mays L.) Root Hair Transcriptome, Stefan Hey, Jutta Baldauf, Nina Opitz, Andrew Lithio, Asher Pasha, Nicholas Provart, Dan Nettleton, Frank Hochholdinger Jun 2019

Complexity And Specificity Of The Maize (Zea Mays L.) Root Hair Transcriptome, Stefan Hey, Jutta Baldauf, Nina Opitz, Andrew Lithio, Asher Pasha, Nicholas Provart, Dan Nettleton, Frank Hochholdinger

Dan Nettleton

Root hairs are tubular extensions of epidermis cells. Transcriptome profiling demonstrated that the single cell-type root hair transcriptome was less complex than the transcriptome of multiple cell-type primary roots without root hairs. In total, 831 genes were exclusively and 5585 genes were preferentially expressed in root hairs [false discovery rate (FDR) ≤1%]. Among those, the most significantly enriched Gene Ontology (GO) functional terms were related to energy metabolism, highlighting the high energy demand for the development and function of root hairs. Subsequently, the maize homologs for 138 Arabidopsis genes known to be involved in root hair development were identified and ...


Empirical Comparisons Of Different Statistical Models To Identify And Validate Kernel Row Number-Associated Variants From Structured Multi-Parent Mapping Populations Of Maize, Jinliang Yang, Cheng-Ting “Eddy” Yeh, Raghuprakash Kastoori Ramamurthy, Xinshuai Qi, Rohan L. Fernando, Jack C. M. Dekkers, Dorian J. Garrick, Dan Nettleton, Patrick S. Schnable Jun 2019

Empirical Comparisons Of Different Statistical Models To Identify And Validate Kernel Row Number-Associated Variants From Structured Multi-Parent Mapping Populations Of Maize, Jinliang Yang, Cheng-Ting “Eddy” Yeh, Raghuprakash Kastoori Ramamurthy, Xinshuai Qi, Rohan L. Fernando, Jack C. M. Dekkers, Dorian J. Garrick, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Advances in next generation sequencing technologies and statistical approaches enable genome-wide dissection of phenotypic traits via genome-wide association studies (GWAS). Although multiple statistical approaches for conducting GWAS are available, the power and cross-validation rates of many approaches have been mostly tested using simulated data. Empirical comparisons of single variant (SV) and multi-variant (MV) GWAS approaches have not been conducted to test if a single approach or a combination of SV and MV is effective, through identification and cross-validation of trait-associated loci. In this study, kernel row number (KRN) data were collected from a set of 6,230 entries derived from ...


Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable Jun 2019

Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Background: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

Results: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a ...


Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel Jun 2019

Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel

Dan Nettleton

Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to ...


Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable Jun 2019

Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable

Dan Nettleton

The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mutransposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional ...


Maize Inbreds Exhibit High Levels Of Copy Number Variation (Cnv) And Presence/Absence Variation (Pav) In Genome Content, Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng-Ting Yeh, Yi Jia, Wei Wu, Todd Richmond, Jacob Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Daniel S. Nettleton, Patrick S. Schnable Jun 2019

Maize Inbreds Exhibit High Levels Of Copy Number Variation (Cnv) And Presence/Absence Variation (Pav) In Genome Content, Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng-Ting Yeh, Yi Jia, Wei Wu, Todd Richmond, Jacob Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Daniel S. Nettleton, Patrick S. Schnable

Dan Nettleton

Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that ...


A Systems Biology Approach Toward Understanding Seed Composition In Soybean, Ling Li, Manhoi Hur, Joon-Yong Lee, Wenxu Zhou, Zhihong Song, Nick Ransom, Cumhur Yusuf Demirkale, Daniel S. Nettleton, Mark E. Westgate, Zebulun Wayne Arendsee, Vidya Vaancheeswaran Iyer, Jacqueline V. Shanks, Basil Nikolau, Eve Wurtele Jun 2019

A Systems Biology Approach Toward Understanding Seed Composition In Soybean, Ling Li, Manhoi Hur, Joon-Yong Lee, Wenxu Zhou, Zhihong Song, Nick Ransom, Cumhur Yusuf Demirkale, Daniel S. Nettleton, Mark E. Westgate, Zebulun Wayne Arendsee, Vidya Vaancheeswaran Iyer, Jacqueline V. Shanks, Basil Nikolau, Eve Wurtele

Dan Nettleton

Background

The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks.

Results

With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and ...