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Iowa State University

Plant Sciences

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Mapping Of Qtl For Kernel Abortion Caused By In Vivo Haploid Induction In Maize (Zea Mays L.), Yanzhi Qu, Penghao Wu, Jiaojiao Ren, Zonghua Liu, Jihua Tang, Thomas Lubberstedt, Haochuan Li, Shaojiang Chen Feb 2020

Mapping Of Qtl For Kernel Abortion Caused By In Vivo Haploid Induction In Maize (Zea Mays L.), Yanzhi Qu, Penghao Wu, Jiaojiao Ren, Zonghua Liu, Jihua Tang, Thomas Lubberstedt, Haochuan Li, Shaojiang Chen

Agronomy Publications

Kernel abortion is common phenomenon in vivo haploid induction and closely linked with haploid induction rate, but little information of kernel abortion is available and its genetic basis still unclear. We used two mapping populations including 186 and 263 F2.3 family lines to analyze the different degree of kernel abortion and identify quantitative trait loci (QTL) responsible for kernel abortion during haploid induction. In total 62 putative QTL, accounting for 3.27–14.70% of the phenotypic variation in kernel abortion traits, were detected across all 10 chromosomes. Ten QTL with over 10% contribution to phenotypic variation were affecting ...


Low Ribosomal Rna Genes Copy Number Provoke Genomic Instability And Chromosomal Segment Duplication Events That Modify Global Gene Expression And Plant-Pathogen Response, Ariadna Picart-Picolo, Stefan Grob, Nathalie Picault, Michal Franek, Thierry Halter, Tom R. Maier, Christel Llauro, Edouard Jobet, Panpan Zhang, Paramasivan Vijayapalani, Thomas J. Baum, Lionel Navarro, Martina Dvorackova, Marie Mirouze, Frederic Pontvianne Jan 2020

Low Ribosomal Rna Genes Copy Number Provoke Genomic Instability And Chromosomal Segment Duplication Events That Modify Global Gene Expression And Plant-Pathogen Response, Ariadna Picart-Picolo, Stefan Grob, Nathalie Picault, Michal Franek, Thierry Halter, Tom R. Maier, Christel Llauro, Edouard Jobet, Panpan Zhang, Paramasivan Vijayapalani, Thomas J. Baum, Lionel Navarro, Martina Dvorackova, Marie Mirouze, Frederic Pontvianne

Plant Pathology and Microbiology Publications

Among the hundreds of ribosomal RNA (rRNA) gene copies organized as tandem repeats in the nucleolus organizer regions (NORs), only a portion is usually actively expressed in the nucleolus and participate in the ribosome biogenesis process. The role of these extra-copies remains elusive, but previous studies suggested their importance in genome stability and global gene expression. Because the nucleolus is also a platform for nuclear organization, we tested the impact of a decreased amount of rRNA gene copies on the Arabidopsis thaliana 3D genome organization and stability, using an A. thaliana line only containing 20% of rRNA gene copies (20rDNA ...


Computer Vision And Machine Learning Enabled Soybean Root Phenotyping Pipeline, Kevin G. Falk, Talukder Z. Jubery, Seyed V. Mirnezami, Kyle A. Parmley, Soumik Sarkar, Arti Singh, Baskar Ganapathysubramanian, Asheesh K. Singh Jan 2020

Computer Vision And Machine Learning Enabled Soybean Root Phenotyping Pipeline, Kevin G. Falk, Talukder Z. Jubery, Seyed V. Mirnezami, Kyle A. Parmley, Soumik Sarkar, Arti Singh, Baskar Ganapathysubramanian, Asheesh K. Singh

Mechanical Engineering Publications

Background Root system architecture (RSA) traits are of interest for breeding selection; however, measurement of these traits is difficult, resource intensive, and results in large variability. The advent of computer vision and machine learning (ML) enabled trait extraction and measurement has renewed interest in utilizing RSA traits for genetic enhancement to develop more robust and resilient crop cultivars. We developed a mobile, low-cost, and high-resolution root phenotyping system composed of an imaging platform with computer vision and ML based segmentation approach to establish a seamless end-to-end pipeline - from obtaining large quantities of root samples through image based trait processing and ...


The Rna Of Maize Chlorotic Mottle Virus - The Essential Virus In Maize Lethal Necrosis Disease - Is Translated Via A Panicum Mosaic Virus-Like Cap-Independent Translation Element, Elizabeth Carino, Kay Scheets, W. Allen Miller Jan 2020

The Rna Of Maize Chlorotic Mottle Virus - The Essential Virus In Maize Lethal Necrosis Disease - Is Translated Via A Panicum Mosaic Virus-Like Cap-Independent Translation Element, Elizabeth Carino, Kay Scheets, W. Allen Miller

Plant Pathology and Microbiology Publications

Maize chlorotic mottle virus (MCMV) combines with a potyvirus in maize lethal necrosis disease (MLND), an emerging disease worldwide that often causes catastrophic yield loss. To inform resistance strategies, we characterized the translation initiation mechanism of MCMV. We report that, like other tombusvirids, MCMV RNA contains a cap-independent translation element (CITE) in its 3’ untranslated region (UTR). The MCMV 3’ CITE (MTE) was mapped to nucleotides 4164-4333 in the genomic RNA. SHAPE probing revealed that the MTE is a variant of the panicum mosaic virus-like 3’ CITE (PTE). Like the PTE, electrophoretic mobility shift assays (EMSAs) indicated that eukaryotic translation ...


Milkweed (Asclepias Syriaca) Plant Detection Using Mobile Cameras, Koray Ozcan, Anuj Sharma, Steven P. Bradbury, Dana Schweitzer, Teresa Blader, Sue Blodgett Jan 2020

Milkweed (Asclepias Syriaca) Plant Detection Using Mobile Cameras, Koray Ozcan, Anuj Sharma, Steven P. Bradbury, Dana Schweitzer, Teresa Blader, Sue Blodgett

Natural Resource Ecology and Management Publications

Milkweed (Asclepias spp.) are host plants of monarch butterflies (Danaus plexippus). It is important to detect milkweed plant locations to assess the status and trends of monarch habitat in support of monarch conservation programs. In this paper, we describe autonomous detection of milkweed plants using cameras mounted to vehicles. For detection, we used both aggregated channel features (ACF) for running the detectors on embedded computing platforms with central processing unit and faster region‐based convolutional neural network (Faster R‐CNN) with a ResNet architecture‐based detector that is suitable for graphics processing unit optimized processing. The ACF‐based model produced ...


Efficacy Of A Cry1ab Gene For Control Of Maruca Vitrata (Lepidoptera: Crambidae) In Cowpea (Fabales: Fabaceae), Prince C. Addae, Mohammad F. Ishiyaku, Jean-Batiste Tignegre, Malick N. Ba, Joseph B. Bationo, Ibrahim D. K. Atokple, Mumuni Abudulai, Clémentine L. Dabiré-Binso, Fousséni Traore, Mohammed Saba, Muhammed L. Umar, Gloria A. Adazebra, Francis N. Onyekachi, Margaret A. Nemeth, Joseph E. Huesing, Larry R. Beach, Thomas J. V. Higgins, Richard L. Hellmich, Barry R. Pittendrigh Jan 2020

Efficacy Of A Cry1ab Gene For Control Of Maruca Vitrata (Lepidoptera: Crambidae) In Cowpea (Fabales: Fabaceae), Prince C. Addae, Mohammad F. Ishiyaku, Jean-Batiste Tignegre, Malick N. Ba, Joseph B. Bationo, Ibrahim D. K. Atokple, Mumuni Abudulai, Clémentine L. Dabiré-Binso, Fousséni Traore, Mohammed Saba, Muhammed L. Umar, Gloria A. Adazebra, Francis N. Onyekachi, Margaret A. Nemeth, Joseph E. Huesing, Larry R. Beach, Thomas J. V. Higgins, Richard L. Hellmich, Barry R. Pittendrigh

Entomology Publications

Cowpea [Vigna unguiculata (L) Walp.] is an important staple legume in the diet of many households in sub-Saharan Africa. Its production, however, is negatively impacted by many insect pests including bean pod borer, Maruca vitrata F., which can cause 20–80% yield loss. Several genetically engineered cowpea events that contain a cry1Ab gene from Bacillus thuringiensis (Bt) for resistance against M. vitrata were evaluated in Nigeria, Burkina Faso, and Ghana (West Africa), where cowpea is commonly grown. As part of the regulatory safety package, these efficacy data were developed and evaluated by in-country scientists. The Bt-cowpea lines were planted in ...


De Novo Transcriptome Of Phakopsora Pachyrhizi Uncovers Putative Effector Repertoire During Infection, Manjula G. Elmore, Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven A. Whitham Jan 2020

De Novo Transcriptome Of Phakopsora Pachyrhizi Uncovers Putative Effector Repertoire During Infection, Manjula G. Elmore, Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven A. Whitham

Plant Pathology and Microbiology Publications

Phakopsora pachyrhizi, which causes Asian soybean rust (ASR), secretes effector proteins to manipulate host immunity and promote disease. To date, only a small number of effectors have been identified from transcriptome studies. To obtain a more comprehensive understanding of P. pachyrhizi candidate secreted effector proteins (CSEPs), we sequenced the transcriptome using two next-generation sequencing technologies. Short-read Illumina RNA-Seq data was used for reducing base-calling errors for long-read PacBio Iso-Seq. After initial de novo assemblies for RNA-seq and error correction of transcripts for Iso-Seq followed by filtering, we obtained 8,528, 27,647, 26,895, and 17,141 non-plant, non-soybean transcripts ...


Forecasting Corn Yield With Machine Learning Ensembles, Mohsen Shahhosseini, Guiping Hu, Sotirios Archontoulis Jan 2020

Forecasting Corn Yield With Machine Learning Ensembles, Mohsen Shahhosseini, Guiping Hu, Sotirios Archontoulis

Industrial and Manufacturing Systems Engineering Publications

The emerge of new technologies to synthesize and analyze big data with high-performance computing, has increased our capacity to more accurately predict crop yields. Recent research has shown that Machine learning (ML) can provide reasonable predictions, faster, and with higher flexibility compared to simulation crop modeling. The earlier the prediction during the growing season the better, but this has not been thoroughly investigated as previous studies considered all data available to predict yields. This paper provides a machine learning based framework to forecast corn yields in three US Corn Belt states (Illinois, Indiana, and Iowa) considering complete and partial in-season ...


Soil Depth And Grassland Origin Cooperatively Shape Microbial Community Co‐Occurrence And Function, Racheal N. Upton, Aleksandra Checinska Sielaff, Kirsten S. Hofmockel, Xia Xu, H. Wayne Polley, Brian J. Wilsey Jan 2020

Soil Depth And Grassland Origin Cooperatively Shape Microbial Community Co‐Occurrence And Function, Racheal N. Upton, Aleksandra Checinska Sielaff, Kirsten S. Hofmockel, Xia Xu, H. Wayne Polley, Brian J. Wilsey

Ecology, Evolution and Organismal Biology Publications

Many soils are deep, yet soil below 20 cm remains largely unexplored. Exotic plants can have shallower roots than native species, so their impact on microorganisms is anticipated to change with depth. Using environmental DNA and extracellular enzymatic activities, we studied fungal and bacterial community composition, diversity, function, and co-occurrence networks between native and exotic grasslands at soil depths up to 1 m. We hypothesized (1) the composition and network structure of both fungal and bacterial communities will change with increasing depth, and diversity and enzymatic function will decrease; (2) microbial enzymatic function and network connectedness will be lower in ...


Spectrally Derived Values Of Community Leaf Dry Matter Content Link Shifts In Grassland Composition With Change In Biomass Production, H. Wayne Polley, Chenghai Yang, Brian J. Wilsey, Philip A. Fay Jan 2020

Spectrally Derived Values Of Community Leaf Dry Matter Content Link Shifts In Grassland Composition With Change In Biomass Production, H. Wayne Polley, Chenghai Yang, Brian J. Wilsey, Philip A. Fay

Ecology, Evolution and Organismal Biology Publications

Leaf traits link environmental effects on plant species abundances to changes in ecosystem processes but are a challenge to measure regularly and over large areas. We used measurements of canopy reflectance from grassland communities to derive a regression model for one leaf trait, leaf dry matter content (LDMC). Partial least squares regression (PLSR) analysis was used to model community‐weighted (species abundance‐weighted) values of LDMC as a function of canopy reflectance in visible and near‐infrared (NIR) wavebands. The PLSR model then was applied to airborne measurements of canopy reflectance to determine how community LDMC interacts with inter‐annual ...


Establishing Winter Annual Cover Crops By Interseeding Into Maize And Soybean, Yesuf Assen Mohammed, Heather L. Matthees, Russ W. Gesch, Swetabh Patel, Frank Forcella, Kyle Aasand, Nicholas Steffl, Burton L. Johnson, M. Scott Wells, Andrew W. Lenssen Jan 2020

Establishing Winter Annual Cover Crops By Interseeding Into Maize And Soybean, Yesuf Assen Mohammed, Heather L. Matthees, Russ W. Gesch, Swetabh Patel, Frank Forcella, Kyle Aasand, Nicholas Steffl, Burton L. Johnson, M. Scott Wells, Andrew W. Lenssen

Agronomy Publications

The limited time available for cover crop establishment after maize (Zea mays L.) and soybean [Glycine max (L.) Merr.] harvest is one of the main reasons for low cover crop adoption in the upper Midwest. Therefore, a 2‐yr multilocation study was conducted to evaluate winter annual cover crops establishment, their effect on main crop grain yields, and soil water content when interseeded into standing maize and soybean. Treatments were three interseeding dates (broadcasting at R4, R5, and R6 growth stages for maize, and R6, R7, and R8 for soybean) and three cover crops (winter camelina [WC] [Camelina sativa L ...


Whole-Profile Soil Organic Matter Content, Composition, And Stability Under Cropping Systems That Differ In Belowground Inputs, Hanna J. Poffenbarger, Daniel C. Olk, Cynthia Cambardella, Jordan Kersey, Matthew Z. Liebman, Antonio Mallarino, Johan Six, Michael J. Castellano Jan 2020

Whole-Profile Soil Organic Matter Content, Composition, And Stability Under Cropping Systems That Differ In Belowground Inputs, Hanna J. Poffenbarger, Daniel C. Olk, Cynthia Cambardella, Jordan Kersey, Matthew Z. Liebman, Antonio Mallarino, Johan Six, Michael J. Castellano

Agronomy Publications

Subsoils have been identified as a potential carbon sink because they typically have low soil organic carbon (SOC) concentrations and high SOC stability. One proposed strategy to increase SOC stocks is to enhance C inputs to the subsoil by increasing crop rotation diversity with deep-rooted perennial crops. Using three long-term field trials in Iowa (study durations of 60, 35, and 12 years), we examined the effects of contrasting cropping systems [maize (Zea mays L.)-soybean (Glycine max (L.) Merr) (= two-year system) vs. maize-soybean-oat (Avena sativa L.)/alfalfa (Medicago sativa L.)-alfalfa or maize-maize-oat/alfalfa-alfalfa (= four-year system)] on above- and below-ground ...


Predicting Crop Yields And Soil‐Plant Nitrogen Dynamics In The Us Corn Belt, Sotirios V. Archontoulis, Michael J. Castellano, Mark A. Licht, Virginia Nichols, Mitch Baum, Isaiah Huber, Rafael Martinez-Feria, Laila Puntel, Raziel A. Ordonez, Javed Iqbal, Emily E. Wright, Ranae N. Dietzel, Matthew Helmers, Andy Vanloocke, Matt Liebman, Jerry L. Hatfield, Daryl Herzmann, S. Carolina Córdova, Patrick Edmonds, Kaitlin Togliatti, Ashlyn Kessler, Gerasimos Danalatos, Heather Pasley, Carl Pederson, Kendall R. Lamkey Jan 2020

Predicting Crop Yields And Soil‐Plant Nitrogen Dynamics In The Us Corn Belt, Sotirios V. Archontoulis, Michael J. Castellano, Mark A. Licht, Virginia Nichols, Mitch Baum, Isaiah Huber, Rafael Martinez-Feria, Laila Puntel, Raziel A. Ordonez, Javed Iqbal, Emily E. Wright, Ranae N. Dietzel, Matthew Helmers, Andy Vanloocke, Matt Liebman, Jerry L. Hatfield, Daryl Herzmann, S. Carolina Córdova, Patrick Edmonds, Kaitlin Togliatti, Ashlyn Kessler, Gerasimos Danalatos, Heather Pasley, Carl Pederson, Kendall R. Lamkey

Agronomy Publications

We used the Agricultural Production Systems sIMulator (APSIM) to predict and explain maize and soybean yields, phenology, and soil water and nitrogen (N) dynamics during the growing season in Iowa, USA. Historical, current and forecasted weather data were used to drive simulations, which were released in public four weeks after planting. In this paper, we 1) describe the methodology used to perform forecasts; 2) evaluate model prediction accuracy against data collected from 10 locations over 4-years; and 3) identify inputs that are key in forecasting yields and soil N dynamics. We found that the predicted median yield at planting was ...


Deconstructing The Genetic Architecture Of Iron Deficiency Chlorosis In Soybean Using Genome-Wide Approaches, Teshale Assefa, Jiaoping Zhang, R. V. Chowda-Reddy, Adrienne N. Moran Lauter, Arti Singh, Jamie A. O'Rourke, Michelle A. Graham, Asheesh K. Singh Jan 2020

Deconstructing The Genetic Architecture Of Iron Deficiency Chlorosis In Soybean Using Genome-Wide Approaches, Teshale Assefa, Jiaoping Zhang, R. V. Chowda-Reddy, Adrienne N. Moran Lauter, Arti Singh, Jamie A. O'Rourke, Michelle A. Graham, Asheesh K. Singh

Agronomy Publications

Background: Iron (Fe) is an essential micronutrient for plant growth and development. Iron deficiency chlorosis (IDC), caused by calcareous soils or high soil pH, can limit iron availability, negatively affecting soybean (Glycine max) yield. This study leverages genome-wide association study (GWAS) and a genome-wide epistatic study (GWES) with previous gene expression studies to identify regions of the soybean genome important in iron deficiency tolerance.

Results: A GWAS and a GWES were performed using 460 diverse soybean PI lines from 27 countries, in field and hydroponic iron stress conditions, using more than 36,000 single nucleotide polymorphism (SNP) markers. Combining this ...


Dynamics Of Corn Dry Matter Content And Grain Quality After Physiological Maturity, Md Rasel Parvej, Charles R. Hurburgh, H. Mark Hanna, Mark A. Licht Jan 2020

Dynamics Of Corn Dry Matter Content And Grain Quality After Physiological Maturity, Md Rasel Parvej, Charles R. Hurburgh, H. Mark Hanna, Mark A. Licht

Agronomy Publications

Delayed corn (Zea mays L.) harvest after physiological maturity (PM) is a universal practice in the U.S. Corn Belt to reduce grain drying cost. However, corn yield is speculated to be lost due to kernel dry matter loss from seed respiration. We evaluated the impact of in‐field dry down on corn dry matter content and grain quality after PM at two locations in Iowa during 2016 and 2017. Each site‐year consisted of two planting dates and three hybrids where ears were collected six to eight times from PM to harvest. Regardless of site‐year and hybrid, grain ...


Long-Term Impact Of Poultry Manure On Crop Yield, Soil And Water Quality, And Crop Revenue, Natasha L. Hoover, Ji Yeow Law, Leigh Ann M. Long, Rameshwar S. Kanwar, Michelle L. Soupir Dec 2019

Long-Term Impact Of Poultry Manure On Crop Yield, Soil And Water Quality, And Crop Revenue, Natasha L. Hoover, Ji Yeow Law, Leigh Ann M. Long, Rameshwar S. Kanwar, Michelle L. Soupir

Agricultural and Biosystems Engineering Publications

A long-term poultry manure fertilizer study was initiated in 1998 and continued until 2009 under corn-soybean (CS) rotation. To match changing landscape trends, the plots were switched to continuous corn (CC) from 2010 to 2017. In both CS and CC phases, poultry manure (PM) was applied at the crop rotation recommended agronomic N rate and either half (CC phase) or double (CS phase) the recommended rate. Urea-ammonium nitrate (UAN) was applied to comparison plots at the crop recommended application rate (168 kg N ha−1 and 224 kg N ha−1 for the CS and CC phases, respectively) throughout the ...


Assessing Plant Performance In The Enviratron, Yin Bao, Scott Zarecor, Dylan Shah, Taylor Tuel, Darwin A. Campbell, Antony V. E. Chapman, David Imberti, Daniel Kiekhaefer, Henry Imberti, Thomas Lubberstedt, Yanhai Yin, Dan Nettleton, Carolyn J. Lawrence-Dill, Steven A. Whitham, Lie Tang, Stephen H. Howell Dec 2019

Assessing Plant Performance In The Enviratron, Yin Bao, Scott Zarecor, Dylan Shah, Taylor Tuel, Darwin A. Campbell, Antony V. E. Chapman, David Imberti, Daniel Kiekhaefer, Henry Imberti, Thomas Lubberstedt, Yanhai Yin, Dan Nettleton, Carolyn J. Lawrence-Dill, Steven A. Whitham, Lie Tang, Stephen H. Howell

Agricultural and Biosystems Engineering Publications

Background: Assessing the impact of the environment on plant performance requires growing plants under controlled environmental conditions. Plant phenotypes are a product of genotype × environment (G × E), and the Enviratron at Iowa State University is a facility for testing under controlled conditions the effects of the environment on plant growth and development. Crop plants (including maize) can be grown to maturity in the Enviratron, and the performance of plants under different environmental conditions can be monitored 24 h per day, 7 days per week throughout the growth cycle.

Results: The Enviratron is an array of custom-designed plant growth chambers that ...


Using A Crop Modeling Framework For Precision Cost-Benefit Analysis Of Variable Seeding And Nitrogen Application Rates, Gabriel Mcnunn, Emily Heaton, Sotirios Archontoulis, Mark A. Licht, Andy Vanloocke Dec 2019

Using A Crop Modeling Framework For Precision Cost-Benefit Analysis Of Variable Seeding And Nitrogen Application Rates, Gabriel Mcnunn, Emily Heaton, Sotirios Archontoulis, Mark A. Licht, Andy Vanloocke

Agronomy Publications

A key goal of precision agriculture is to achieve the maximum crop yield while minimizing inputs and loses from cropping systems. The challenge for precision agriculture is that these factors interact with one another on a subfield scale. Seeding density and nitrogen (N) fertilizer application rates are two of the most important inputs influencing agronomic, economic and environmental outcomes in cropping systems including yield, return on investment (ROI), and nitrate (NO3−) leaching. Here a cropping system model framework is used to predict site-specific subfield optimum seeding density and (N) fertilizer application rates based on publicly available data sources. The framework ...


Machine Learning Approach For Prescriptive Plant Breeding, Kyle A. Parmley, Race H. Higgins, Baskar Ganapathysubramanian, Soumik Sarkar, Asheesh K. Singh Nov 2019

Machine Learning Approach For Prescriptive Plant Breeding, Kyle A. Parmley, Race H. Higgins, Baskar Ganapathysubramanian, Soumik Sarkar, Asheesh K. Singh

Mechanical Engineering Publications

We explored the capability of fusing high dimensional phenotypic trait (phenomic) data with a machine learning (ML) approach to provide plant breeders the tools to do both in-season seed yield (SY) prediction and prescriptive cultivar development for targeted agro-management practices (e.g., row spacing and seeding density). We phenotyped 32 SoyNAM parent genotypes in two independent studies each with contrasting agro-management treatments (two row spacing, three seeding densities). Phenotypic trait data (canopy temperature, chlorophyll content, hyperspectral reflectance, leaf area index, and light interception) were generated using an array of sensors at three growth stages during the growing season and seed ...


Considerations For Continuous Corn, Mark A. Licht Nov 2019

Considerations For Continuous Corn, Mark A. Licht

Integrated Crop Management News

Continuous corn is a "three strikes and you’re out" situation. And the first strike is automatic – high residue volume. This is how a farmer recently described it to me.


A Meta-Analysis Of Global Fungal Distribution Reveals Climate-Driven Patterns, Tomáš Větrovský, Petr Kohout, Martin Kopecký, Antonin Machac, Matěj Man, Barbara Doreen Bahnmann, Vendula Brabcová, Jinlyung Choi, Lenka Meszárošová, Zander Rainier Human, Clémentine Lepinay, Salvador Lladó, Rubén López-Mondéjar, Tijana Martinović, Tereza Mašínová, Daniel Morais, Diana Navrátilová, Iñaki Odriozola, Martina Štursová, Karel Švec, Vojtěch Tláskal, Michaela Urbanová, Joe Wan, Lucia Žifčáková, Adina Howe, Joshua Ladau, Kabir Gabriel Peay, David Storch, Jan Wild, Petr Baldrian Nov 2019

A Meta-Analysis Of Global Fungal Distribution Reveals Climate-Driven Patterns, Tomáš Větrovský, Petr Kohout, Martin Kopecký, Antonin Machac, Matěj Man, Barbara Doreen Bahnmann, Vendula Brabcová, Jinlyung Choi, Lenka Meszárošová, Zander Rainier Human, Clémentine Lepinay, Salvador Lladó, Rubén López-Mondéjar, Tijana Martinović, Tereza Mašínová, Daniel Morais, Diana Navrátilová, Iñaki Odriozola, Martina Štursová, Karel Švec, Vojtěch Tláskal, Michaela Urbanová, Joe Wan, Lucia Žifčáková, Adina Howe, Joshua Ladau, Kabir Gabriel Peay, David Storch, Jan Wild, Petr Baldrian

Agricultural and Biosystems Engineering Publications

The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes ...


Scn-Resistant Soybean Varieties For 2020, Gregory L. Tylka Nov 2019

Scn-Resistant Soybean Varieties For 2020, Gregory L. Tylka

Integrated Crop Management News

Resistant varieties continue to be a key tool for managing the soybean cyst nematode (SCN). With financial support from the soybean checkoff through the Iowa Soybean Association, Iowa State University annually compiles a list of SCN-resistant soybean varieties that are available for use in Iowa.


Corn Residue Breakdown As Affected By Tillage And N Application, Mahdi Al-Kaisi Nov 2019

Corn Residue Breakdown As Affected By Tillage And N Application, Mahdi Al-Kaisi

Integrated Crop Management News

Crop residue serves an important role in physically protecting soil from erosion during rain events or high winds, as well as enhancing the soil biological activity by providing sources of organic carbon and nitrogen for its energy needs. In order to understand how residue decomposes, we need to understand how the degradation processes are influenced by environmental and soil conditions; namely, air and soil temperatures, soil moisture availability, soil pH, oxygen, and type of microbial community. The composition of crop residue includes lignin, cellulose, hemicellulose, and macro and micronutrients. Certain biological and enzymatic processes, controlled by a wide range of ...


Managing Scn For 2020 Should Begin Now, Gregory L. Tylka Nov 2019

Managing Scn For 2020 Should Begin Now, Gregory L. Tylka

Integrated Crop Management News

Now that the 2019 corn and soybean harvest is in full swing, it is not too early to start thinking about and planning for the 2020 growing season as well. For soybean farmers in Iowa, a critically important fall activity that can pay large dividends is soil sampling to determine soybean cyst nematode (SCN) population densities in fields in which soybeans will be grown in 2020. Also, some farmers might consider sampling fields for SCN in which soybeans were grown in 2019 that produced disappointing yields for no apparent reason. Often, SCN infestations are found in areas of fields in ...


The Genome Sequence Of Gossypioides Kirkii Illustrates A Descending Dysploidy In Plants, Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, Justin L. Conover, Daojun Yuan, Corrinne E. Grover, Lei Gong, Mark A. Arick Ii, Rick E. Masonbrink, Daniel G. Peterson, Jonathan F. Wendel Nov 2019

The Genome Sequence Of Gossypioides Kirkii Illustrates A Descending Dysploidy In Plants, Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, Justin L. Conover, Daojun Yuan, Corrinne E. Grover, Lei Gong, Mark A. Arick Ii, Rick E. Masonbrink, Daniel G. Peterson, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n = 12 (the Hawaiian Kokia and the East African and Madagascan Gossypioides). We generated a high-quality genome sequence of Gossypioides kirkii (n = 12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n = 12) and Gossypium diploids (n = 13). Previous analysis demonstrated that ...


Protein Expression And Gene Editing In Monocots Using Foxtail Mosaic Virus Vectors, Yu Mei, Bliss Beernink, Evan E. Ellison, Eva Konečná, Anjanasree K. Neelakandan, Daniel F. Voytas, Steven A. Whitham Nov 2019

Protein Expression And Gene Editing In Monocots Using Foxtail Mosaic Virus Vectors, Yu Mei, Bliss Beernink, Evan E. Ellison, Eva Konečná, Anjanasree K. Neelakandan, Daniel F. Voytas, Steven A. Whitham

Plant Pathology and Microbiology Publications

Plant viruses can be engineered to carry sequences that direct silencing of target host genes, expression of heterologous proteins, or editing of host genes. A set of foxtail mosaic virus (FoMV) vectors was developed that can be used for transient gene expression and single guide RNA delivery for Cas9‐mediated gene editing in maize, Setaria viridis, and Nicotiana benthamiana. This was accomplished by duplicating the FoMV capsid protein subgenomic promoter, abolishing the unnecessary open reading frame 5A, and inserting a cloning site containing unique restriction endonuclease cleavage sites immediately after the duplicated promoter. The modified FoMV vectors transiently expressed green ...


Shared Genetic Control Of Root System Architecture Between Zea Mays And Sorghum Bicolor, Zihao Zheng, Stefan Hey, Talukder Jubery, Huyu Liu, Yu Yang, Lisa Coffey, Chenyong Miao, Brandi Sigmon, James C. Schnable, Frank Hochholdinger, Baskar Ganapathysubramanian, Patrick Schnable Nov 2019

Shared Genetic Control Of Root System Architecture Between Zea Mays And Sorghum Bicolor, Zihao Zheng, Stefan Hey, Talukder Jubery, Huyu Liu, Yu Yang, Lisa Coffey, Chenyong Miao, Brandi Sigmon, James C. Schnable, Frank Hochholdinger, Baskar Ganapathysubramanian, Patrick Schnable

Mechanical Engineering Publications

Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed CREAMD (Core Root Excavation using Compressed-air), a high-throughput pipeline for the cleaning of field-grown roots, and COFE (Core Root Feature Extraction), a semi-automated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize (Zea mays) and sorghum (Sorghum bicolor), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from >3,300 maize roots and >1,470 sorghum roots. SNP-based GWAS identified 87 ...


Corn Yield Response To Row Spacing And Plant Population In Iowa, Mark A. Licht, M. R. Parvej, Emily E. Wright Nov 2019

Corn Yield Response To Row Spacing And Plant Population In Iowa, Mark A. Licht, M. R. Parvej, Emily E. Wright

Agronomy Publications

Corn (Zea mays L.) planted in narrow row spacing (<30-inch) with high plant population has become a recent interest in the US Corn Belt to increase grain yield. We evaluated the impact of row spacing and plant population on corn grain yield across 22 site-years in Iowa from 2009 to 2018. Experiments were designed as a split-plot with two row spacings, 20- and 30-inch, as the main-plot and three to four plant populations, ranging from 30,000 to 42,000 plants acre–1, as subplot. Grain yield was affected in 73% of the site-years: 13 site-years by row spacing, six site-years by plant population, and 2 site-years by the interaction of both. Corn in 20-inch rows yielded 5 to 19 bu acre–1 more in 11 site-years and 10 to 14 bu acre–1 less in two site-years compared to 30-inch rows. In both 20- and 30-inch row spacings, corn yield decreased linearly at 0.4 to 1.7 bu acre–1 per thousand increase in plant population in four site-years and responded ...


Fall Fertilizer Nitrogen Application, John E. Sawyer Oct 2019

Fall Fertilizer Nitrogen Application, John E. Sawyer

Integrated Crop Management News

Fall nitrogen (N) fertilizer application continues to be popular for several reasons, including lower cost, time for application, equipment availability, often better soil conditions, and competing springtime field activities. Success, compared to spring or sidedress timing, can be enhanced by following several long-standing suggestions: only use anhydrous ammonia; apply in late fall after soils cool to 50 degrees F (4-inch depth) and are trending cooler (the colder the better); consider an effective nitrification inhibitor to further slow nitrification to nitrate; and avoid fall application to soils that are more prone to wetness or leaching (poorly or excessively drained soils).


The Influence Of Concrete Grinding Residue On Soil Physical Properties And Plant Growth, Chenyi Luo, Zhuangji Wang, Farnaz Kordbacheh, Yang Zhang, Bo Yang, Sunghwan Kim, Bora Cetin, Halil Ceylan, Robert Horton Oct 2019

The Influence Of Concrete Grinding Residue On Soil Physical Properties And Plant Growth, Chenyi Luo, Zhuangji Wang, Farnaz Kordbacheh, Yang Zhang, Bo Yang, Sunghwan Kim, Bora Cetin, Halil Ceylan, Robert Horton

Civil, Construction and Environmental Engineering Publications

Diamond grinding is a concrete pavement maintenance technique, and concrete grinding residue (CGR) is the byproduct. Concrete grinding residue deposited along roadsides affects soil chemical properties, but impacts of CGR on soil physical properties and plant growth are rarely studied. In this study, a controlled field experiment was performed to determine the influence of CGR on selected soil physical properties (i.e., bulk density [ρb], saturated hydraulic conductivity [Ks], and water infiltrability [It]) and on plant biomass and plant coverage under four application rates (0, 2.24, 4.48, and 8.96 kg m−2). Field measurements ...