Other Plant Sciences Commons^™

Selection For Silage Yield And Composition Did Not Affect Genomic Diversity Within The Wisconsin Quality Synthetic Maize Population, Aaron Lorenz, Timothy M. Beissinger, Renato Rodrigues Silva, Natalia De Leon

Department of Agronomy and Horticulture: Faculty Publications

Maize silage is forage of high quality and yield, and represents the second most important use of maize in the United States. The Wisconsin Quality Synthetic (WQS) maize population has undergone five cycles of recurrent selection for silage yield and composition, resulting in a genetically improved population. The application of high-density molecular markers allows breeders and geneticists to identify important loci through association analysis and selection mapping, as well as to monitor changes in the distribution of genetic diversity across the genome. The objectives of this study were to identify loci controlling variation for maize silage traits through association analysis …

A Roadmap For Functional Structural Variants In The Soybean Genome, Justin E. Anderson, Michael B. Kantar, Thomas Y. Kono, Fengli Fu, Adrian O. Stec, Qijian Song, Perry B. Cregan, James E. Specht, Brian W. Diers, Steven B. Cannon, Leah K. Mchale, Robert M. Stupar

Department of Agronomy and Horticulture: Faculty Publications

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less …

Overexpression Of The Transporters Atzip1 And Atmtp1 In Cassava Changes Zinc Accumulation And Partitioning, Eliana Gaitán-Solis, Nigel J. Taylor, Dimuth Siritunga, William Stevens, Daniel P. Schachtman

Department of Agronomy and Horticulture: Faculty Publications

Zinc deficiency in humans is a serious problem worldwide with an estimated one third of populations at risk for insufficient zinc in diet, which leads to impairment of cognitive abilities and immune system function. The goal of this research was to increase the bioavailable zinc in the edible portion of cassava roots to improve the overall zinc nutrition of populations that rely on cassava as a dietary staple. To increase zinc concentrations, two Arabidopsis thaliana genes coding for ZIP1 and MTP1 were overexpressed with a tuber-specific or constitutive promoter. Eighteen transgenic events from four constructs, out of a total of …

Differential Expression Analysis In Rna-Seq By A Naive Bayes Classifier With Local Normalization, Yongchao Dou, Xiaomei Guo, Lingling Yuan, David R. Holding, Chi Zhang

Department of Agronomy and Horticulture: Faculty Publications

To improve the applicability of RNA-seq technology, a large number of RNA-seq data analysis methods and correction algorithms have been developed. Although these new methods and algorithms have steadily improved transcriptome analysis, greater prediction accuracy is needed to better guide experimental designs with computational results. In this study, a new tool for the identification of differentially expressed genes with RNA-seq data, named GExposer, was developed. This tool introduces a local normalization algorithm to reduce the bias of nonrandomly positioned read depth. The naive Bayes classifier is employed to integrate fold change, transcript length, and GC content to identify differentially expressed …

Plants Coping Abiotic And Biotic Stresses: A Tale Of Diligent Management, Hatem Rouached, Sikander Pal, Shimon Rachmilevitch, Marc Libault, Lam-Son Phan Tran

Department of Agronomy and Horticulture: Faculty Publications

Plants unlike other living forms are sessile thereby facing severe biotic and abiotic stresses. Plants have evolved different efficient defence responses which thrive upon a number of intrinsic factors, such as genotypic and phenotypic constitutions and developmental circumstances, and extrinsic factors like severity and duration of the stresses. Stress management uses molecular and biochemical level controls, the competence, and speed, at which a stress signal is perceived and transmitted to generate stress signal molecules and activate stress-protective mechanisms. A well-concerted action of the plants’ competence at morphological, physiological, biochemical, and molecular strata regulates numerous adaptive responses to biotic and abiotic …

Identification Of Novel Qtl Governing Root Architectural Traits In An Interspecific Soybean Population, Lakshmi P. Manavalan, Silvas J. Prince, Theresa A. Musket, Julian Chaky, Rupesh Deshmukh, Tri D. Vuong, Li Song, Perry B. Cregan, James C. Nelson, J. Grover Shannon, James E. Specht, Henry T. Nguyen

Department of Agronomy and Horticulture: Faculty Publications

Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibited significant differences in root architecture and root-related traits. In this study, phenotypic variability for root traits among 251 BC₂F₅ backcross inbred lines (BILs) developed from the cross Dunbar/PI 326582A were identified. The root systems of the parents and BILs were evaluated in controlled environmental conditions using a cone system at seedling stage. The G. max parent Dunbar contributed phenotypically favorable alleles at a major quantitative trait locus on chromosome 8 (Satt315-I locus) that governed root traits (tap root length and …

Genetic And Molecular Characterization Of Submergence Response Identifies Subtol6 As A Major Submergence Tolerance Locus In Maize, Malachy T. Campbell, Christopher A. Proctor, Yongchao Dou, Aaron J. Schmitz, Piyaporn Phansak, Greg R. Kruger, Chi Zhang, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Maize is highly sensitive to short term flooding and submergence. Early season flooding reduces germination, survival and growth rate of maize seedlings. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling and linkage analysis of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18Wand M162W) and sensitive (B97 and B73) genotypes were identified. Tolerant lines exhibited delayed senescence and lower oxidative stress levels compared to sensitive lines. Transcriptome analysis was performed on these inbreds to provide …

Allmaps: Robust Scaffold Ordering Based On Multiple Maps, Haibo Tang, Xingtan Zhang, Chenyong Miao, Jisen Zhang, Ray Ming, James C. Schnable, Patrick S. Schnable, Eric Lyons, Jianguo Lu

Department of Agronomy and Horticulture: Faculty Publications

The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.

From Field To Atlas: Upscaling Of Location-Specific Yield Gap Estimates, Lenny G.J. Van Bussel, Patricio Grassini, Justin Van Wart, Joost Wolf, Lieven Claessens, Haishun Yang, Hendrik Boogaard, Hugo De Groot, Kazuki Saito, Kenneth Cassman, Martin K. Van Ittersum

Department of Agronomy and Horticulture: Faculty Publications

Accurate estimation of yield gaps is only possible for locations where high quality local data are available,which are, however, lacking in many regions of the world. The challenge is how yield gap estimates based on location-specific input data can be used to obtain yield gap estimates for larger spatial areas. Hence,insight about the minimum number of locations required to achieve robust estimates of yield gaps at larger spatial scales is essential because data collection at a large number of locations is expensive and time consuming. In this paper we describe an approach that consists of a climate zonation scheme supplemented …

Effects Of Sowing Date On Phenotypic Plasticity Of Fitness-Related Traits In Two Annual Weeds On The Songnen Plain Of China, Haiyan Li, John L. Lindquist, Yunfei Yang

Department of Agronomy and Horticulture: Faculty Publications

Background Phenotypic plasticity of fitness-related traits is vital for plant species to adapt to variable environments. Chenopodium glaucum L. and Amaranthus retroflexus L. are two common weed species globally. Understanding the plasticity in life-history traits, especially in reproductive allocation, within and among these species is important for predicting their success and for managing them in different environments.

Methodology/Principal Findings Seeds of the two plant species were sown every 10 days from 26 Jun to 15 Aug. Life-history and fitness-related traits of both phenology and morphology were measured, and dry biomass of roots, stems, leaves, and reproductive tissues was determined at …

Assessment Of Rice Self-Sufficiency In 2025 In Eight African Countries, P. A.J. Van Oort, K. Saito, E. Amovin-Assagba, Lenny G.J. Van Bussel, Justin Van Wart, Hugo De Groot, Martin K. Van Ittersum, Kenneth Cassman, M. C.S. Wopereis

Department of Agronomy and Horticulture: Faculty Publications

Most African countries are far from self-sufficient in meeting their rice consumption; in eight countries the production: consumption ratio, ranged from 0.16 to 1.18 in 2012. We show that for the year 2025, with population growth, diet change and yield increase on existing land (intensification), countries cannot become fully self-sufficient in rice. This implies that for the future, a mixture of area expansion and imports will be needed on top of yield gap closure. Further research is needed for identification of most suitable new land for rice area expansion and areas that should be protected.

Fall Seed Guide 2015, Teshome Regassa, P. Stephen Baenziger, Stephen N. Wegulo, Greg Kruger, Dipak K. Santra

Department of Agronomy and Horticulture: Faculty Publications

Crops included in this guide are winter wheat, winter barley, and triticale. You may receive this guide in the mail or through the University of Nebraska Extension network. The data and other information this guide is can be found at our web site: http://cropwatch.unl.edu/varietytest/ and http://www.unl.edu/ncia. Additional information is available at the wheat variety virtual tour web site http://cropwatch.unl.edu/wheat/virtual or the winter wheat variety selection tool page http:// citnews.unl.edu/winter_wheat_tool/index.shtml. The last season was hard on Nebraska winter wheat. Emergence was poor in the west due to dry conditions. On the other hand, some plots in the east had to be …

How Good Is Good Enough? Data Requirements For Reliable Crop Yield Simulations And Yield-Gap Analysis, Patricio Grassini, Lenny G.J. Van Bussel, Justin Van Wart, Joost Wolf, Lieven Claessens, Haishun Yang, Hendrik Boogaard, Hugo De Groot, Martin K. Van Ittersum, Kenneth Cassman

Department of Agronomy and Horticulture: Faculty Publications

Numerous studies have been published during the past two decades that use simulation models to assess crop yield gaps (quantified as the difference between potential and actual farm yields), impact of climate change on future crop yields, and land-use change. However, there is a wide range in quality and spatial and temporal scale and resolution of climate and soil data underpinning these studies, as well as widely differing assumptions about cropping-system context and crop model calibration. Here we present an explicit rationale and methodology for selecting data sources for simulating crop yields and estimating yield gaps at specific locations that …

Selective Genotyping For Marker Assisted Selection Strategies For Soybean Yield Improvement, Benjamin D. Fallen, Fred L. Allen, Dean A. Kopsell, Arnold M. Saxton, Leah Mchale, J. Grover Shannon, Stella K. Kantartzi, Andrea J. Cardinal, P. B. Cregan, D. L. Hyten, Vincent R. Pantalone

Department of Agronomy and Horticulture: Faculty Publications

Using molecular markers in soybean [Glycine max (L.) Merr.] has lead to the identification of major loci controlling quantitative and qualitative traits that include: disease resistance, insect resistance and tolerance to abiotic stresses. Yield has been considered as one of the most important quantitative traits in soybean breeding. Unfortunately, yield is a very complex trait and most yield quantitative trait loci (QTL) that have been identified have had only limited success for marker assisted selection (MAS). The objective of this study was to identify QTL associated with soybean seed yield in preliminary yield trials grown in different environments and …

Using A Simple Leaf Color Chart To Estimate Leaf And Canopy Chlorophyll A Content In Maize (Zea Mays), Anthony Nguy-Robertson, Yi Peng, Timothy Arkebauer, David Scoby, James Schepers, Anatoly Gitelson

Department of Agronomy and Horticulture: Faculty Publications

This study utilized a leaf color chart (LCC) to characterize the variation in leaf chlorophyll and estimate canopy chlorophyll in maize (Zea mays). The LCC consisted of four levels of greenness and was used to sort maize leaves in 2011 for three fields near Mead, Nebraska, USA. Leaf chlorophyll content for each color chart class was determined using two leaf-level sensors. The variation within each LCC class was reasonable (CV < 56%). The darkest color class predominated and indicated adequate fertilization rates using a SPAD. Canopy chlorophyll content was estimated using destructively measured leaf area index (LAI) and the LCC. This approach was verified with a method utilizing canopy reflectance collected by both satellite imagery and a four-band radiometer. The error between the two methods was reasonable (RMSE = 0.55-0.88 g m^-2; CV = 25.6-50.4%), indicating that both leaf and canopy chlorophyll can be estimated cheaply without a wet lab or field-based sensors.

Overexpression Of Sbmyb60 Impacts Phenylpropanoid Biosynthesis And Alters Secondary Cell Wall Composition In Sorghum Bicolor, Erin D. Scully, Tammy Gries, Gautam Sarath, Nathan A. Palmer, Lisa Baird, Michelle J. Serapiglia, Bruce S. Dien, Akwasi A. Boateng, Zhengxiang Ge, Deanna L. Funnell-Harris, Paul Twigg, Thomas E. Clemente, Scott E. Sattler

Department of Agronomy and Horticulture: Faculty Publications

The phenylpropanoid biosynthetic pathway that generates lignin subunits represents a significant target for altering the abundance and composition of lignin. The global regulators of phenylpropanoid metabolism may include MYB transcription factors, whose expression levels have been correlated with changes in secondary cell wall composition and the levels of several other aromatic compounds, including anthocyanins and flavonoids. While transcription factors correlated with downregulation of the phenylpropanoid biosynthesis pathway have been identified in several grass species, few transcription factors linked to activation of this pathway have been identified in C4 grasses, some of which are being developed as dedicated bioenergy feedstocks. In …

A Dedicated Type Ii Nadph Dehydrogenase Performs The Penultimate Step In The Biosynthesis Of Vitamin K1 In Synechocystis And Arabidopsis, Abdelhak Fatihi, Scott Latimer, Stefan Schmollinger, Anna Block, Patrick Dussault, Wim F.J. Vermaas, Sabeeha S. Merchant, Gilles J. Basset

Department of Agronomy and Horticulture: Faculty Publications

Mutation of Arabidopsis thaliana NAD(P)H DEHYDROGENASE C1 (NDC1; At5g08740) results in the accumulation of demethylphylloquinone, a late biosynthetic intermediate of vitamin K₁. Gene coexpression and phylogenomics analyses showed that conserved functional associations occur between vitamin K biosynthesis and NDC1 homologs throughout the prokaryotic and eukaryotic lineages. Deletion of Synechocystis ndbB, which encodes for one such homolog, resulted in the same defects as those observed in the cyanobacterial demethylnaphthoquinone methyltransferase knockout. Chemical modeling and assay of purified demethylnaphthoquinone methyltransferase demonstrated that, by virtue of the strong electrophilic nature of S-adenosyl-Lmethionine, the transmethylation of the demethylated precursor …

Soil And Crop Response To Stover Removal From Rainfed And Irrigated Corn, Ian Kenney, Humberto Blanco-Canqui, Deann R. Presley, Charles W. Rice, Keith Janssen, Brian Olson

Department of Agronomy and Horticulture: Faculty Publications

Excessive corn (Zea mays L.) stover removal for biofuel and other uses may adversely impact soil and crop production. We assessed the effects of stover removal at 0, 25, 50, 75, and 100% from continuous corn on water erosion, corn yield, and related soil properties during a 3-year study under irrigated and no-tillage management practice on a Ulysses silt loam at Colby, irrigated and strip till management practice on a Hugoton loam at Hugoton, and rainfed and no-tillage management practice on a Woodson silt loam at Ottawa in Kansas, USA. The slope of each soil was <1%. One year after removal, complete (100%) stover removal resulted in increased losses of sediment by 0.36–0.47 Mg ha-1 at the irrigated sites, but, at the rainfed site, removal at rates as low as 50% resulted in increased sediment loss by 0.30 Mg ha-1 and sediment-associated carbon (C) by 0.29 kg ha-1. Complete stover removal reduced wet aggregate stability of the soil at the irrigated sites in the first year after removal, but, at the rainfed site, wet aggregate stability was reduced in all years. Stover removal at rates ≥ 50%resulted in reduced soil water content, increased soil temperature in summer by 3.5–6.8 °C, and reduced tem-perature in winter by about 0.5 °C. Soil C pool tended to decrease and crop yields tended to increase with an increase in stover removal, but 3 years after removal, differences were not significant. Overall, stover removal at rates ≥50% may enhance grain yield but may increase risks of water erosion and negatively affect soil water and temperature regimes in this region.

High Tunnel Design, Site Development, And Construction, Stacy A. Adams, Kim Todd

Department of Agronomy and Horticulture: Faculty Publications

High tunnels are low technology plant growing structures that provide opportunity for season extension, severe weather protection, and modified environments to increase productivity and visual quality of harvested plant products. This publication describes high tunnel components, site selection, development, covering materials, installation, and operation.

Experienced specialty plant growers can increase the quality of their products and the duration of their marketing of high- value crops through the use of high tunnels. High tunnels give growers the opportunity to plant earlier and include more sequential planting dates. This can result in early- season, high- dollar returns and the ability to offer …

Genetic Control Of Morphometric Diversity In The Maize Shoot Apical Meristem, Samuel Leiboff, Xianran Li, Heng-Cheng Hu, Natalie Todt, Jinliang Yang, Xiao Li, Xiaoqing Yu, Gary J. Muehlbauer, Marja C.P. Timmermans, Jianming Yu, Patrick S. Schnable, Michael J. Scanlon

Department of Agronomy and Horticulture: Faculty Publications

The maize shoot apical meristem (SAM) comprises a small pool of stem cells that generate all above-ground organs. Although mutational studies have identified genetic networks regulating SAM function, little is known about SAM morphological variation in natural populations. Here we report the use of high-throughput image processing to capture rich SAM size variation within a diverse maize inbred panel. We demonstrate correlations between seedling SAM size and agronomically important adult traits such as flowering time, stem size and leaf node number. Combining SAM phenotypes with 1.2 million single nucleotide polymorphisms (SNPs) via genome-wide association study reveals unexpected SAM morphology candidate …