Botany Commons^™

Managing Wicked Herbicide-Resistance: Lessons From The Field, Jill Schroeder, Michael Barrett, David R. Shaw, Amy B. Asmus, Harold Coble, David Ervin, Raymond A. Jussaume Jr., Michael D. K. Owen, Ian Burke, Cody F. Creech, A. Stanley Culpepper, William S. Curran, Darrin M. Dodds, Todd A. Gaines, Jeffrey L. Gunsolus, Bradley D. Hanson, Prashant Jha, Annie E. Klodd, Andrew R. Kniss, Ramon G. Leon, Sandra Mcdonald, Don W. Morishita, Brian J. Schutte, Christy L. Sprague, Phillip W. Stahlman, Larry E. Steckel, Mark J. Vangessel

Department of Agronomy and Horticulture: Faculty Publications

Herbicide resistance is ‘wicked’ in nature; therefore, results of the many educational efforts to encourage diversification of weed control practices in the United States have been mixed. It is clear that we do not sufficiently understand the totality of the grassroots obstacles, concerns, challenges, and specific solutions needed for varied crop production systems. Weed management issues and solutions vary with such variables as management styles, regions, cropping systems, and available or affordable technologies. Therefore, to help the weed science community better understand the needs and ideas of those directly dealing with herbicide resistance, seven half-day regional listening sessions were held …

Genome-Wide Association Study Reveals Novel Genomic Regions For Grain Yield And Yield-Related Traits In Drought-Stressed Synthetic Hexaploid Wheat, Madhav Bhatta, Alexey Morgounov, Vikas Belamkar, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x = 14, DD, Aegilops tauschii Coss.) and is reported to have significant novel alleles-controlling biotic and abiotic stresses resistance. A genome-wide association study (GWAS) was conducted to unravel these loci [marker–trait associations (MTAs)] using 35,648 genotyping-by-sequencing-derived single nucleotide polymorphisms in 123 SHWs. We identified 90 novel MTAs (45, 11, and 34 on the A, B, and D …

Wheat Height Estimation Using Lidar In Comparison To Ultrasonic Sensor And Uas, Wenan Yuan, Jiating Li, Madhav Bhatta, Yeyin Shi, P. Stephen Baenziger, Yufeng Ge

Department of Agronomy and Horticulture: Faculty Publications

As one of the key crop traits, plant height is traditionally evaluated manually, which can be slow, laborious and prone to error. Rapid development of remote and proximal sensing technologies in recent years allows plant height to be estimated in more objective and efficient fashions, while research regarding direct comparisons between different height measurement methods seems to be lagging. In this study, a ground-based multi-sensor phenotyping system equipped with ultrasonic sensors and light detection and ranging (LiDAR) was developed. Canopy heights of 100 wheat plots were estimated five times during a season by the ground phenotyping system and an unmanned …

Genetic Architecture Of Common Bunt Resistance In Winter Wheat Using Genome-Wide Association Study, Amira M. I. Mourad, Ahmed Sallam, Vikas Belamkar, Ezzat Mahdy, Bahy Bakheit, Atif Abo El-Wafaa, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Background: Common bunt (caused by Tilletia caries and T. foetida) has been considered as a major disease in wheat (Triticum aestivum) following rust (Puccinia spp.) in the Near East and is economically important in the Great Plains, USA. Despite the fact that it can be easily controlled using seed treatment with fungicides, fungicides often cannot or may not be used in organic and low-input fields. Planting common bunt resistant genotypes is an alternative.

Results: To identify resistance genes for Nebraska common bunt race, the global set of differential lines were inoculated. Nine differential lines carrying nine …

Cc-Type Glutaredoxins Mediate Plant Response And Signaling Under Nitrate Starvation In Arabidopsis, Ji-Yul Jung, Ji Hoon Ahn, Daniel P. Schachtman

Department of Agronomy and Horticulture: Faculty Publications

Background: Nitrogen is an essential nutrient in plants. Despite the importance of nitrogen for plant growth and agricultural productivity, signal transduction pathways in response to nitrate starvation have not been fully elucidated in plants.

Results: Gene expression analysis and ectopic expression were used to discover that many CC-type glutaredoxins (ROXYs) are differentially expressed in response to nitrate deprivation. A gain-of-function approach showed that ROXYs may play a role in nutrient sensing through the regulation of chlorophyll content, root hair growth, and transcription of nitrate-related genes such as NRT2.1 under low or high nitrate conditions. Reactive oxygen species (ROS) …

Identification Of Quantitative Trait Loci Conferring Resistance To Tan Spot In A Biparental Population Derived From Two Nebraska Hard Red Winter Wheat Cultivars, Gayan K. Kariyawasam, Waseem Hussain, Amanda Easterly, Mary Guttieri, Vikas Belamkar, Jesse Poland, Jorge Venegas, Stephen Baenziger, Francois Marais, Jack B. Rasmussen, Zhaohui Liu

Department of Agronomy and Horticulture: Faculty Publications

Tan spot, caused by Pyrenophora triticirepentis (Ptr), is a destructive foliar disease in all types of cultivated wheat worldwide. Genetics of tan spot resistance in wheat is complex, involving insensitivity to fungal-produced necrotrophic effectors (NEs), major resistance genes, and quantitative trait loci (QTL) conferring race-nonspecific and race-specific resistance. The Nebraska hard red winter wheat (HRWW) cultivar ‘Wesley’ is insensitive to Ptr ToxA and highly resistant to multiple Ptr races, but the genetics of resistance in this cultivar is unknown. In this study, we used a recombinant inbred line (RIL) population derived from a cross between Wesley and another …

Active-Optical Reflectance Sensing Corn Algorithms Evaluated Over The United States Midwest Corn Belt, G. M. Bean, N. R. Kitchen, J. J. Camberato, R. B. Ferguson, F. G. Fernandez, D. W. Franzen, C. A. M. Laboski, E. D. Nafziger, J. E. Sawyer, P. C. Scharf, J. Schepers, J. S. Shanahan

Department of Agronomy and Horticulture: Faculty Publications

Uncertainty exists with corn (Zea mays L.) N management due to year-to-year variation in crop N need, soil N supply, and N loss from leaching, volatilization, and denitrification. Activeoptical reflectance sensing (AORS) has proven effective in some fields for generating N fertilizer recommendations that improve N use efficiency, but locally derived (e.g., within a US state) AORS algorithms have not been tested simultaneously across a broad region. The objective of this research was to evaluate locally developed AORS algorithms across the US Midwest Corn Belt region for making in-season corn N recommendations. Forty-nine N response trials were conducted across …

Lignocellulosic-Based Bioenergy And Water Quality Parameters: A Review, Bharat Sharma Acharya, Humberto Blanco-Canqui

Department of Agronomy and Horticulture: Faculty Publications

High rates of crop residue removal as biofuel feedstocks could increase losses of nonpoint source pollutants, negatively affecting water quality. An alternative to residue removal can be growing dedicated bioenergy crops such as warm season grasses (WSGs) and short-rotation woody crops (SRWCs). Yet, our understanding of the implications of growing dedicated bioenergy crops on water quality is limited. Thus, we (i) synthesized and compared the impacts of crop residue removal, WSGs, and SRWCs on water quality parameters (i.e., sediment and nutrient runoff, and nutrient leaching) and (ii) identified research gaps for growing dedicated energy crops. Literature indicates that residue removal …

Epigenomic Plasticity Of Arabidopsis Msh1 Mutants Under Prolonged Cold Stress, Sunil Kumar Kenchanmane Raju, Mon-Ray Shao, Yashitola Wamboldt, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Dynamic transcriptional and epigenetic changes enable rapid adaptive benefit to environmental fluctuations. However, the underlying mechanisms and the extent to which this occurs are not well known. MutS Homolog 1 (MSH1) mutants cause heritable developmental phenotypes accompanied by modulation of defense, phytohormone, stress‐response, and circadian rhythm genes, as well as heritable changes in DNA methylation patterns. Consistent with gene expression changes, msh1 mutants display enhanced tolerance for abiotic stress including drought and salt stress, while showing increased susceptibility to freezing temperatures. Despite changes in defense and biotic stress‐response genes, msh1 mutants showed increasing susceptibility to the bacterial pathogen Pseudomonas syringae. …

Root And Shoot Contribution To Carbon And Nitrogen Inputs In The Topsoil Layer In No-Tillage Crop Systems Under Subtropical Conditions, Marciel Redin, Sylvie Recous, Celso Aita, Bruno Chaves, Ismael Cristiano Pfeifer, Leonardo Mendes Bastos, Getulio Elias Pilecco, Sandro Jose Giacomini

Department of Agronomy and Horticulture: Faculty Publications

Recycling of carbon (C) and nitrogen (N) from plants into soils is decisive for maintaining soil organic matter and soil fertility. Therefore, we quantified plant biomass and C and N in the shoots and roots from the topsoil layer for a wide range of annual crops grown under subtropical conditions. We grew 26 species, 13 main crops, and 13 cover crops, in the field in standard sowing arrangements. Root biomass was recovered from the 0.00-0.20 m soil layer at flowering, and shoot biomass was measured at flowering for all crops and at maturity only for the main crops. Root dry …

Improving Fertilizer Recommendations For Nepalese Farmers With The Help Of Soil-Testing Mobile Van, Sunil Pandey, Netra Prasad Bhatta, Prakash Paudel, Rajan Pariyar, Kiran Hari Maskey, Janardan Khadka, Tuk Bahadur Thapa, Balaram Rijal, Dinesh Panday

Department of Agronomy and Horticulture: Faculty Publications

Smallholder farmers dominate agriculture in Nepal. These farmers have poor knowledge about agriculture and lack of support for soil management and integrated plant-nutrient systems. Focusing on the importance and need for soil-fertility management, a soil-testing mobile van program has recently been introduced in Nepal by Soil Management Directorate, Hariharbhawan. With the introduction of the mobile lab, famers can get their soil tested for nutrient deficiencies and fertilizer requirements at their doorsteps. Using mobile lab, spatial distributions of chemical properties, including pH, organic matter (OM), total nitrogen (N), available phosphorus (as P₂O₅), and available potassium (as K …

Genotype Imputation In Winter Wheat Using First-Generation Haplotype Map Snps Improves Genome-Wide Association Mapping And Genomic Prediction Of Traits, Moses Nyine, Shichen Wang, Kian Kiani, Katherine Jordan, Shuyu Liu, Patrick Byrne, Scott Haley, Stephen Baenziger, Shiaoman Chao, Robert Bowden, Eduard Akhunov

Department of Agronomy and Horticulture: Faculty Publications

Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study …

Genomic Selection In Preliminary Yield Trials In A Winter Wheat Breeding Program, Vikas Belamkar, Mary J. Guttieri, Waseem Hussain, Diego Jarquin, Ibrahim El-Basyoni, Jesse Poland, Aaron J. Lorenz, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Genomic prediction (GP) is now routinely performed in crop plants to predict unobserved phenotypes. The use of predicted phenotypes to make selections is an active area of research. Here, we evaluate GP for predicting grain yield and compare genomic and phenotypic selection by tracking lines advanced. We examined four independent nurseries of F_3:6 and F_3:7 lines trialed at 6 to 10 locations each year. Yield was analyzed using mixed models that accounted for experimental design and spatial variations. Genotype-by-sequencing provided nearly 27,000 high-quality SNPs. Average genomic predictive ability, estimated for each year by randomly masking lines as missing …

Genome-Wide Association Study Reveals Novel Genomic Regions Associated With 10 Grain Minerals In Synthetic Hexaploid Wheat, Madhav Bhatta, P. Stephen Baenziger, Brian M. Waters, Rachana Poudel, Vikas Belamkar, Jesse Poland, Alexey Morgounov

Department of Agronomy and Horticulture: Faculty Publications

Synthetic hexaploid wheat (SHW; Triticum durum L. x Aegilops tauschii Coss.) is a means of introducing novel genes/genomic regions into bread wheat (T. aestivum L.) and a potential genetic resource for improving grain mineral concentrations. We quantified 10 grain minerals (Ca, Cd, Cu, Co, Fe, Li, Mg, Mn, Ni, and Zn) using an inductively coupled mass spectrometer in 123 SHWs for a genome-wide association study (GWAS). A GWAS with 35,648 single nucleotide polymorphism (SNP) markers identified 92 marker-trait associations (MTAs), of which 60 were novel and 40 were within genes, and the genes underlying 20 MTAs had annotations suggesting …

Stolon Development And Cultural Production Practices Of Winter-Grown Strawberries, Donna M. Morrison, Erin Blankenship, Paul Read, Ellen Paparozzi

Department of Agronomy and Horticulture: Faculty Publications

The four experiments described here are part of a 5-year program focused on determining whether day-neutral and short-day strawberries would be suitable for commercial offseason/ winter (temperate climate) production in greenhouses. All research was performed using container-grown plants fertigated through a capillary mat production system with heat supplied under the benches. The first experiment focused on stolon development. The second experiment investigated the influence of stolon removal on berry production and included the removal of flowers for the first three weeks. The third and fourth experiments were conducted as a comparison of university research (experiment 3) versus a commercial operation …

An Exome-Seq Based Tool For Mapping And Selection Of Candidate Genes In Maize Deletion Mutants, Shangang Jia, Kyla Morton, Chi Zhang, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 X Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA …

Genetic Architecture Of Soybean Yield And Agronomic Traits, Brian W. Diers, Jim Specht, Katy Martin Rainey, Perry Cregan, Qijian Song, Vishnu Ramasubramanian, George Graef, Randall L. Nelson, William Schapaugh, Dechun Wang, Grover Shannon, Leah Mchale, Stella K. Kantartzi, Alencar Xavier, Rouf Mian, Robert M. Stupar, Jean-Michel Michno, Yong-Qiang Charles An, Wolfgang Goettel, Russell Ward, Carolyn Fox, Alexander E. Lipka, David Hyten, Troy Cary, William D. Beavis

Department of Agronomy and Horticulture: Faculty Publications

Soybean is the world’s leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key agronomic traits is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. …

Impact Of Drought On Chemical Composition And Sugar Yields From Dilute-Acid Pretreatment And Enzymatic Hydrolysis Of Miscanthus, A Tall Fescue Mixture, And Switchgrass, Amber Hoover, Rachel Emerson, Allison Ray, Daniel Stevens, Sabrina Morgan, Marnie Cortez, Robert Kallenbach, Matthew Sousek, Rodney Farris, Dayna Daubaras

Department of Agronomy and Horticulture: Faculty Publications

Environmental factors like drought impact the quality of biomass entering a bioconversion process. Drought often reduces the sugar content in lignocellulosic biomass, which could have economic impacts, particularly when compounded with losses in dry biomass yield; however, the effects on conversion efficiency are not completely understood. This study investigated how drought may impact biomass composition and sugar yields from dilute-acid pretreatment and enzymatic hydrolysis of Miscanthus, a tall fescue mixture, and switchgrass from Nebraska, Missouri, and Oklahoma, respectively, grown as part of Regional Feedstock Partnership field trials. Samples were grown and harvested in 2010 during non-drought conditions and in …

Influence Of Harvest Date On Seed Yield And Quality In Forage Kochia, Cody F. Creech, Blair L. Waldron, Corey V. Ransom, Dale R. Zobell, Joseph Earl Creech

Department of Agronomy and Horticulture: Faculty Publications

Forage kochia (Bassia prostrata) is used for rangeland reclamation and livestock and wildlife forage, but limited research has been conducted on its seed production. Therefore, this research evaluated the effect of harvest date on seed weight, germination, and seed yield of forage kochia subspecies virescens and grisea. Seed was harvested from individual plants for 3 years during October, November, and December. October harvest had the lightest 100-seed weights, with the November harvest slightly heavier than December, for most accessions. Cultivar Snowstorm and breeding line Sahsel, both subsp. grisea, had the greatest 100-seed weights in November, 155 …

Sequences Involved In Plant Yield And Methods Of Using, Harkamal Walia, Dante Placido, Thomas E. Clemente

Department of Agronomy and Horticulture: Faculty Publications

Nucleic acid sequences involved in plant yield are provided, as are methods of using such nucleic acid sequences .