Agronomy and Crop Sciences Commons^™

Stress-Responsive Pathways And Small Rna Changes Distinguish Variable Developmental Phenotypes Caused By Msh1 Loss, Mon-Ray Shao, Sunil Kumar Kenchanmane Raju, John D. Laurie, Robersy Sanchez, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Background: Proper regulation of nuclear-encoded, organelle-targeted genes is crucial for plastid and mitochondrial function. Among these genes, MutS Homolog 1 (MSH1) is notable for generating an assortment of mutant phenotypes with varying degrees of penetrance and pleiotropy. Stronger phenotypes have been connected to stress tolerance and epigenetic changes, and in Arabidopsis T-DNA mutants, two generations of homozygosity with the msh1 insertion are required before severe phenotypes begin to emerge. These observations prompted us to examine how msh1 mutants contrast according to generation and phenotype by profiling their respective transcriptomes and small RNA populations.

Results: Using RNA-seq, we analyze …

Expression Of The Maize Dof1 Transcription Factor In Wheat And Sorghum, Pamela A. Pena, Truyen Quach, Shirley Sato, Zhengxiang Ge, Natalya Nersesian, Taity Changa, Ismail M. Dweikat, Madhavan Soundararajan, Tom E. Clemente

Department of Agronomy and Horticulture: Faculty Publications

Nitrogen is essential for plant growth and development. Improving the ability of plants to acquire and assimilate nitrogen more efficiently is a key agronomic parameter that will augment sustainability in agriculture. A transcription factor approach was pursued to address improvement of nitrogen use efficiency in two major commodity crops. To this end, the Zea mays Dof1 (ZmDof1) transcription factor was expressed in both wheat (Triticum aestivum) and sorghum (Sorghum bicolor) either constitutively, UBI4 promoter from sugarcane, or in a tissue specific fashion via the maize rbcS1 promoter. The primary transcription activation target of ZmDof1 …

Genomic-Enabled Prediction Accuracies Increased By Modeling Genotype × Environment Interaction In Durum Wheat, Sivakumar Sukumaran, Diego Jarquin, José Crossa, Matthew Reynolds

Department of Agronomy and Horticulture: Faculty Publications

Genomic prediction studies incorporating genotype × environment (G×E) interaction effects are limited in durum wheat. We tested the genomic-enabled prediction accuracy (PA) of Genomic Best Linear Unbiased Predictor (GBLUP) models—six non-G × E and three G × E models—on three basic cross-validation (CV) schemes— in predicting incomplete field trials (CV2), new lines (CV1), and lines in untested environments (CV0)— in a durum wheat panel grown under yield potential, drought stress, and heat stress conditions. For CV0, three scenarios were considered: (i) leave-one environment out (CV0-Env); (ii) leave one site out (CV0- Site); and (iii) leave 1 yr out (CV0-Year). The …

Genomic Prediction With Pedigree And Genotype X Environment Interaction In Spring Wheat Grown In South And West Asia, North Africa, And Mexico, Sivakumar Sukumaran, José Crossa, Diego Jarquin, Marta Lopes, Matthew P. Reynolds

Department of Agronomy and Horticulture: Faculty Publications

Developing genomic selection (GS) models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation (CV) scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY), thousand-grain weight (GW), grain number (GN), and thermal time for flowering (TTF) in 18 international environments (year-location combinations) in major wheat-producing countries in 2010 and 2011. Prediction models with genomic and pedigree information included main effects and interaction with environments. Two random CV schemes were applied to predict a …

The Effect Of Artificial Selection On Phenotypic Plasticity In Maize, Joseph L. Gage, Diego Jarquin, Cinta Romay, Aaron Lorenz, Edward S. Buckler, Shawn Kaeppler, Naser Alkhalifah, Martin Bohn, Darwin A. Campbell, Jode Edwards, David Ertl, Sherry Flint-Garcia, Jack Gardiner, Byron Good, Candice N. Hirsch, Jim Holland, David C. Hooker, Joseph Knoll, Judith Kolkman, Greg Kruger, Nick Lauter, Carolyn J. Lawrence-Dill, Elizabeth Lee, Jonathan Lynch, Seth C. Murray, Rebecca Nelson, Jane Petzoldt, Torbert Rocheford, James C. Schnable, Patrick S. Schnable, Brian Scully, Margaret Smith, Nathan M. Springer, Srikant Srinivasan, Renee Walton, Teclemariam Weldekidan, Randall J. Wisser, Wenwei Xu, Jianming Yu, Natalia De Leon

Department of Agronomy and Horticulture: Faculty Publications

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize …

Validation Of Qtl Mapping And Transcriptome Profiling For Identification Of Candidate Genes Associated With Nitrogen Stress Tolerance In Sorghum, Malleswari Gelli, Anji Reddy Konda, Kan Liu, Chi Zhang, Thomas E. Clemente, David R. Holding, Ismail M. Dweikat

Department of Agronomy and Horticulture: Faculty Publications

Background: Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations. Also, with Illumina RNA-sequencing we checked the differential expression of …

The Trouble With Cover Crops: Farmers’ Experiences With Overcoming Barriers To Adoption, Gabrielle E. Roesch-Mcnally, Andrea D. Basche, J. G. Arbuckle, John C. Tyndall, Fernando E. Miguez, Troy Bowman, Rebecca Clay

Department of Agronomy and Horticulture: Faculty Publications

Cover crops are known to promote many aspects of soil and water quality, yet estimates find that in 2012 only 2.3% of the total agricultural lands in the Midwestern USA were using cover crops. Focus groups were conducted across the Corn Belt state of Iowa to better understand how farmers confront barriers to cover crop adoption in highly intensive agricultural production systems. Although much prior research has focused on analyzing factors that help predict cover crop use on farms, there is limited research on how farmers navigate and overcome field-level (e.g. proper planting of a cover crop) and structural barriers …

The Impact Of Continuous Living Cover On Soil Hydrologic Properties: A Meta-Analysis, Andrea D. Basche, Marcia Delonge

Department of Agronomy and Horticulture: Faculty Publications

Increased rainfall variability due to climate change threatens the efficacy of critical soil ecosystem services. One strategy to negate effects of too much or not enough rainfall is to improve soil water properties. Practices that offer “continuous living cover” can enhance soil water storage and other soil hydrologic properties relative to annual crop systems, but to what extent such benefits can accrue, under different conditions, remains under-quantified. To address these uncertainties, we conducted a meta-analysis that included 27 studies representing 93 paired observations measuring two soil hydrologic properties: porosity and the water retained at field capacity. All experiments compared the …

Gene Silencing Of Argonaute5 Negatively Affects The Establishment Of The Legume-Rhizobia Symbiosis, Maria Del Rocio Reyero-Saavedra, Zhenzhen Qiao, Maria Del Socorro Sanchez-Correa, M. Enrique Diaz-Pineda, Jose L. Reyes, Alejandra A. Covarrubias, Marc Libault, Oswaldo Valdes-Lopez

Department of Agronomy and Horticulture: Faculty Publications

The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also …

Reversing Resistance To Tembotrione In An Amaranthus Tuberculatus (Var. Rudis) Population From Nebraska, Usa With Cytochrome P450 Inhibitors, Maxwel C. Oliveira, Todd A. Gaines, Franck E. Dayan, Eric L. Patterson, Amit J. Jhala, Stevan Z. Knezevic

Department of Agronomy and Horticulture: Faculty Publications

Background: A population of Amaranthus tuberculatus (var. rudis) was confirmed resistant to 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitor herbicides (mesotrione, tembotrione, and topramezone) in a seed corn/soybean rotation in Nebraska. Further investigation confirmed a non-target-site resistance mechanism in this population. The main objective of this study was to explore the role of cytochrome P450 inhibitors in restoring the efficacy of HPPD-inhibitor herbicides on the HPPD-inhibitor resistant A. tuberculatus population from Nebraska, USA (HPPD-R).

Background: A population of Amaranthus tuberculatus (var. rudis) was confirmed resistant to 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitor herbicides (mesotrione, tembotrione, and topramezone) in a seed corn/soybean rotation in Nebraska. Further investigation confirmed …

Tgbs® Genotyping-By-Sequencing Enables Reliable Genotyping Of Heterozygous Loci, Alina Ott, Sanzhen Liu, James C. Schnable, Cheng-Ting 'Eddy' Yeh, Kai-Sin Wang, Patrick S. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Conventional genotyping-by-sequencing (cGBS) strategies suffer from high rates of missing data and genotyping errors, particularly at heterozygous sites. tGBS® genotyping-by-sequencing is a novel method of genome reduction that employs two restriction enzymes to generate overhangs in opposite orientations to which (single-strand) oligos rather than (double-stranded) adaptors are ligated. This strategy ensures that only doubledigested fragments are amplified and sequenced. The use of oligos avoids the necessity of preparing adaptors and the problems associated with inter-adaptor annealing/ligation. Hence, the tGBS protocol simplifies the preparation of high-quality GBS sequencing libraries. During polymerase chain reaction (PCR) amplification, selective nucleotides included at the 3'-end …

Can Cover Crop Use Allow Increased Levels Of Corn Residue Removal For Biofuel In Irrigated And Rainfed Systems?, S. J. Ruis, Humberto Blanco-Canqui, Paul J. Jasa, R. B. Ferguson, G. Slater

Department of Agronomy and Horticulture: Faculty Publications

Corn (Zea mays L.) residue removal at high rates can result in negative impacts to soil ecosystem services. The use of cover crops could be a potential strategy to ameliorate any adverse effects of residue removal while allowing greater removal levels. Hence, the objective of this study was to determine changes in water erosion potential, soil organic C (SOC) and total N concentration, and crop yields under early- and late-terminated cover crop (CC) combined with five levels of corn residue removal after 3 years on rainfed and irrigated no-till continuous corn in Nebraska. Treatments were no CC, early- and …

Using An Unmanned Aerial Vehicle To Evaluate Nitrogen Variability And Height Effect With An Active Crop Canopy Sensor, Brian Krienke, Richard B. Ferguson, Michael Schlemmer, Kyle Holland, David B. Marx, Kent M. Eskridge

Department of Agronomy and Horticulture: Faculty Publications

Ground-based active sensors have been used in the past with success in detecting nitrogen (N) variability within maize production systems. The use of unmanned aerial vehicles (UAVs) presents an opportunity to evaluate N variability with unique advantages compared to ground-based systems. The objectives of this study were to: determine if a UAV was a suitable platform for use with an active crop canopy sensor to monitor in-season N status of maize, if UAV’s were a suitable platform, is the UAV and active sensor platform a suitable substitute for current handheld methods, and is there a height effect that may be …

Plantcv V2: Image Analysis Software For High-Throughput Plant Phenotyping, Malia A. Gehan, Noah Fahlgren, Arash Abbasi, Jeffrey C. Berry, Steven T. Callen, Leonardo Chavez, Andrew N. Doust, Max J. Feldman, Kerrigan B. Gilbert, John G. Hodge, J. Steen Hoyer, Andy Lin, Suxing Liu, César Lizárraga, Argelia Lorence, Michael Miller, Eric Platon, Monica Tessman, Tony Sax

Department of Agronomy and Horticulture: Faculty Publications

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major …

Metabolism Of 2,4-Dichlorophenoxyacetic Acid Contributes To Resistance In A Common Waterhemp (Amaranthus Tuberculatus) Population, Marcelo R. A. Figueiredo, Lacy J. Leibhart, Zachary J. Reicher, Patrick J. Tranel, Scott J. Nissen, Philip Westra, Mark L. Bernards, Greg R. Kruger, Todd A. Gaines, Mithila Jugulam

Department of Agronomy and Horticulture: Faculty Publications

BACKGROUND: Synthetic auxins such as 2,4-D have been widely used for selective control of broadleaf weeds since the mid-1940s. In 2009, an Amaranthus tuberculatus (common waterhemp) population with 10-fold resistance to 2,4-D was found in Nebraska, USA. The 2,4-D resistance mechanism was examined by conducting [¹⁴C] 2,4-D absorption, translocation and metabolism experiments.

RESULTS: No differences were found in 2,4-D absorption or translocation between the resistant and susceptible A. tuberculatus. Resistant plants metabolized [¹⁴C] 2,4-D more rapidly than did susceptible plants. The half-life of [¹⁴C] 2,4-D in susceptible plants was 105 h, compared to …

Dissecting The Genetic Basis Of Local Adaptation In Soybean, Nonoy B. Bandillo, Justin E. Anderson, Michael B. Kantar, Robert M. Stupar, James E. Specht, George L. Graef, Aaron J. Lorenz

Department of Agronomy and Horticulture: Faculty Publications

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep …

Assessment Of Canopy Chlorophyll Content Retrieval In Maize And Soybean: Implications Of Hysteresis On The Development Of Generic Algorithms, Yi Peng, Anthony L. Nguy-Robertson, Timothy J. Arkebauer, Anatoly A. Gitelson

Department of Agronomy and Horticulture: Faculty Publications

Canopy chlorophyll content (Chl) closely relates to plant photosynthetic capacity, nitrogen status and productivity. The goal of this study is to develop remote sensing techniques for accurate estimation of canopy Chl during the entire growing season without re-parameterization of algorithms for two contrasting crop species, maize and soybean. These two crops represent different biochemical mechanisms of photosynthesis, leaf structure and canopy architecture. The relationships between canopy Chl and reflectance, collected at close range and resampled to bands of the Multi Spectral Instrument (MSI) aboard Sentinel-2, were analyzed in samples taken across the entirety of the growing seasons in three irrigated …

Rooting For Food Security In Sub-Saharan Africa, Nicolas Guilpart, Patricio Grassini, Justin Van Wart, Haishun Yang, Martin K. Van Ittersum, Lenny G.J. Van Bussel, Joost Wolf, Lieven Claessens, Johan G.B. Leenaars, Kenneth G. Cassman

Department of Agronomy and Horticulture: Faculty Publications

There is a persistent narrative about the potential of Sub-Saharan Africa (SSA) to be a ‘grain breadbasket’ because of large gaps between current low yields and yield potential with good management, and vast land resources with adequate rainfall. However, rigorous evaluation of the extent to which soils can support high, stable yields has been limited by lack of data on rootable soil depth of sufficient quality and spatial resolution. Here we use location-specific climate data, a robust spatial upscaling approach, and crop simulation to assess sensitivity of rainfed maize yields to root-zone water holding capacity. We find that SSA could …

Can Yield Gap Analysis Be Used To Inform R & D Prioritisation?, P. A. J. Van Oort, K. Saito, I. Dieng, P. Grassini, K. G. Cassman, M. K. Van Ittersum

Department of Agronomy and Horticulture: Faculty Publications

The phrase “biggest bang for a buck” is associated with the policy making question that governments and development agencies face: “Where and which crops should receive highest priority for improving local and global food supply?”. A first step of prioritisation is to identify region x crop combinations for which high impact can be anticipated. We developed a new method for this prioritisation exercise and applied it to data from the Global Yield Gap and Water Productivity Atlas (GYGA). Our prioritisation distinguishes between two policy objectives (humanitarian and economic) and builds upon the relative yield gap and climate risk. Results of …

Multisite Evaluation Of Apex For Water Quality: I. Best Professional Judgment Parameterization, Claire Baffaut, Nathan O. Nelson, John A. Lory, G.M.M.M. Anomaa Senaviratne, Ammar B. Bhandari, Ranjith P. Udawatta, Daniel W. Sweeney, Matt J. Helmers, M. W. Van Liew, Antonio P. Mallarino, Charles S. Wortmann

Department of Agronomy and Horticulture: Faculty Publications

The Agricultural Policy Environmental eXtender (APEX) model is capable of estimating edge-of-field water, nutrient, and sediment transport and is used to assess the environmental impacts of management practices. The current practice is to fully calibrate the model for each site simulation, a task that requires resources and data not always available. The objective of this study was to compare model performance for flow, sediment, and phosphorus transport under two parameterization schemes: a best professional judgment (BPJ) parameterization based on readily available data and a fully calibrated parameterization based on site-specific soil, weather, event flow, and water quality data. The analysis …

Patterns Of Gene Expression In Western Corn Rootworm (Diabrotica Virgifera Virgifera) Neonates, Challenged With Cry34ab1, Cry35ab1 And Cry34/35ab1, Based On Next-Generation Sequencing, Haichuan Wang, Seong-Il Eyun, Kanika Arora, Sek Yee Tan, Premchand Gandra, Etsuko N. Moriyama, Chitvan Khajuria, Jessica D. Jurzenski, Huarong Li, Maia Donahue, Kenneth E. Narva, Blair Siegfried

Department of Agronomy and Horticulture: Faculty Publications

With Next Generation Sequencing technologies, high-throughput RNA sequencing (RNAseq) was conducted to examine gene expression in neonates of Diabrotica virgifera virgifera (LeConte) (Western Corn Rootworm, WCR) challenged with individual proteins of the binary Bacillus thuringiensis insecticidal proteins, Cry34Ab1 and Cry35Ab1, and the combination of Cry34/Cry35Ab1, which together are active against rootworm larvae. Integrated results of three different statistical comparisons identified 114 and 1300 differentially expressed transcripts (DETs) in the Cry34Ab1 and Cry34/35Ab1 treatment, respectively, as compared to the control. No DETs were identified in the Cry35Ab1 treatment. Putative Bt binding receptors previously identified in other insect species were not identified …

Mapping And Characterization Of The Fefe Gene That Controls Iron Uptake In Melon (Cucumis Melo L.), Raghuprakash Kastoori Ramamurthy, Brian M. Waters

Department of Agronomy and Horticulture: Faculty Publications

Iron (Fe) deficiency in plants limits crop growth and productivity. Molecular mechanisms that plants use to sense and respond to Fe deficiency by coordinated expression of Feuptake genes are not fully understood. The C940-fe chlorotic melon (Cucumis melo) mutant known as fefe is unable to upregulate Fe-uptake genes, however, the FeFe gene had not been identified. In this study, we used two F₂ mapping populations to map and identify the FeFe gene as bHLH38, a homolog of subgroup Ib bHLH genes from Arabidopsis thaliana that are involved in transcriptional regulation of Feuptake genes in partnership with the …

Interaction Of 2,4-D Or Dicamba With Glufosinate For Control Of Glyphosate-Resistant Giant Ragweed (Ambrosia Trifida L.) In Glufosinate-Resistant Maize (Zea Mays L.), Zahoor A. Ganie, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Glyphosate-resistant (GR) giant ragweed is a problematic broadleaf weed in crops including maize and soybean in the Midwestern United States. Commercialization of crops with 2,4-D or dicamba and glufosinate resistance will allow post-emergence (POST) applications of these herbicides. Therefore, information is needed on how 2,4-D/dicamba will interact with glufosinate in various rate combinations. The objectives of this study were to evaluate the interaction of glufosinate plus 2,4-D and/or dicamba for control of GR giant ragweed, and to determine their effect on GR giant ragweed density, biomass, maize injury, and yield. Field experiments were conducted in 2013 and 2014 in a …

Changes In Soil Microbial Communities After 10 Years Of Winter Wheat Cultivation Versus Fallow In An Organic-Poor Soil In The Loess Plateau Of China, Hui Tian, Hui Wang, Xiaoli Hui, Zhaohui Wang, Rhae A. Drijber, Jinshan Liu

Department of Agronomy and Horticulture: Faculty Publications

Agricultural management methods, such as cultivation or fallowing, have led to significant changes in soil fertility and hence, crop yield. Such changes may have stemmed from changes in soil microbial communities and associated biogeochemical processes. This phenomenon is particularly true in organic-poor soil in the Loess Plateau of China. In this study, we examined three existing soil management regimes as part of a 10-year field experiment and evaluated their effects on fungal and bacterial community structures by performing high-throughput 454 pyrosequencing. These management regimes were (i) fertilized winter wheat (Triticum aestivum L.) (FW), (ii) continuous …

Allelic Variants Of Oshkt1;1 Underlie The Divergence Between Indica And Japonica Subspecies Of Rice (Oryza Sativa) For Root Sodium Content, Malachy T. Campbell, Nonoy Bandillo, Fouad Razzaq A. Al Shiblawi, Sandeep Sharma, Kan Liu, Qian Du, Aaron J. Schmitz, Chi Zhang, Anne-Alienor Very, Aaron J. Lorenz, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Salinity is a major factor limiting crop productivity. Rice (Oryza sativa), a staple crop for the majority of the world, is highly sensitive to salinity stress. To discover novel sources of genetic variation for salt tolerance-related traits in rice, we screened 390 diverse accessions under 14 days of moderate (9 dS m^-1) salinity. In this study, shoot growth responses to moderate levels of salinity were independent of tissue Na⁺ content. A significant difference in root Na+ content was observed between the major subpopulations of rice, with indica accessions displaying higher root Na⁺ and japonica …

Robust Spatial Frameworks For Leveraging Research On Sustainable Crop Intensification, Patricio Grassini, Cameron M. Pittelkow, Kenneth Cassman, Haishun S. Yang, Sotirios Archontoulis, Mark Licht, Kendall R. Lamkey, Ignacio A. Ciampitti, Jeffrey A. Coulter, Sylvie M. Brouder, Jeffrey J. Volenec, Noemi Guindin-Garcia

Department of Agronomy and Horticulture: Faculty Publications

Meeting demand for food, fiber, feed, and fuel in a world with 9.7 billion people by 2050 without negative environmental impact is the greatest scientific challenge facing humanity. We hypothesize that this challenge can only be met with current and emerging technologies if guided by proactive use of a broad array of relevant data and geospatial scaling approaches to ensure local to global relevance for setting research priorities and implementing agricultural systems responsive to real-time status of weather, soils, crops, and markets. Despite increasing availability of field-scale agricultural data, robust spatial frameworks are lacking to convert these data into actionable …

Genome-Guided Phylo-Transcriptomic Methods And The Nuclear Phylogentic Tree Of The Paniceae Grasses, Jacob D. Washburn, James C. Schnable, Gavin C. Conant, Thomas P. Brutnell, Ying Shao, Yang Zhang, Martha Ludwig, Gerrit Davidse, J. Chris Pires

Department of Agronomy and Horticulture: Faculty Publications

The past few years have witnessed a paradigm shift in molecular systematics from phylogenetic methods (using one or a few genes) to those that can be described as phylogenomics (phylogenetic inference with entire genomes). One approach that has recently emerged is phylo-transcriptomics (transcriptome-based phylogenetic inference). As in any phylogenetics experiment, accurate orthology inference is critical to phylo-transcriptomics. To date, most analyses have inferred orthology based either on pure sequence similarity or using gene-tree approaches. The use of conserved genome synteny in orthology detection has been relatively under-employed in phylogenetics, mainly due to the cost of sequencing genomes. While current trends …

Genome-Wide Characterization Of Non-Reference Transposable Element Insertion Polymorphisms Reveals Genetic Diversity In Tropical And Temperate Maize, Xianjun Lai, James C. Schnable, Zhengqiao Liao, Jie Xu, Gengyun Zhang, Chuan Li, Erliang Hu, Tingzhao Rong, Yunbi Xu, Yanli Li

Department of Agronomy and Horticulture: Faculty Publications

Background: Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation. Recent advances in sequencing technology have made it possible to study variation in transposon content and insertion location in large sets of …

Long-Term Tillage Impact On Soil Hydraulic Properties, Humberto Blanco-Canqui, Brian J. Weinhold, Virginia L. Jin, Marty R. Schmer, Leonard C. Kibet

Department of Agronomy and Horticulture: Faculty Publications

An improved understanding of the impact of tillage systems on soil hydraulic properties is necessary to conserve and manage soil water under a changing climate. The objective of this study was to specifically measure soil hydraulic properties (total porosity, water infiltration, saturated hydraulic conductivity, and water retention characteristics) in no-till, chisel plow, disk, and moldboard plow systems under rainfed continuous corn (Zea mays L.) after 35 yr on silty clay loam soils in eastern Nebraska. We measured ponded water infiltration (positive soil water pressure) and tension (-1 kPa matric potential) infiltration to exclude macropore (>125 mm diameter) flow. …