Botany Commons^™

Soybean Seed Amino Acid Content Qtl Detected Using The Universal Soy Linkage Panel 1.0 With 1,536 Snps, Benjamin D. Fallen, Catherine N. Hatcher, Fred L. Allen, Dean A. Kopsell, Arnold M. Saxton, Pengyin Chen, Stella K. Kantartzi, P. B. Cregan, D. L. Hyten, Vincent R. Pantalone

Department of Agronomy and Horticulture: Faculty Publications

Soybean [Glycine max (L.) Merr.] is the primary source of meal used in animal feed in the U.S. However, few studies have been conducted to evaluate genomic regions controlling amino acid composition is soybean. Designing soybean seed compositions that will benefit animal production is essential. The objective of this study was to identify genomic regions controlling essential and non-essential amino acid composition in soybean seed proteins. To achieve this objective, 282 F_5:9 recombinant inbred lines (RILs) developed from a cross of Essex × Williams 82 were used. Ground soybean seed samples were analyzed for amino acids and statistically …

Development And Evaluation Of Soysnp50k, A High-Density Genotyping Array For Soybean, Qijian Song, D. L. Hyten, Gaofeng Jia, Charles V. Quigley, Edward W. Fickus, Randall L. Nelson, P. B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

The objective of this research was to identify single nucleotide polymorphisms (SNPs) and to develop an Illumina Infinium BeadChip that contained over 50,000 SNPs from soybean (Glycine max L. Merr.). A total of 498,921,777 reads 35–45 bp in length were obtained from DNA sequence analysis of reduced representation libraries from several soybean accessions which included six cultivated and two wild soybean (G. soja Sieb. et Zucc.) genotypes. These reads were mapped to the soybean whole genome sequence and 209,903 SNPs were identified. After applying several filters, a total of 146,161 of the 209,903 SNPs were determined to be …

The Plant Science Decadal Vision: Response To The Martin Commentary, David Stern, Sally Ann Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

The plant science community is being called upon as never before to carry out research that addresses challenges in food, climate, and health, to educate a populace inundated with science misinformation, and to excite and recruit a new generation of scientists from among that populace, all while investments in basic research are stagnant or even declining in many countries. The Decadal Vision (Plant Science Research Summit, 2013) represents a response from that community, one that launches a meaningful and ongoing dialogue about how best to accomplish these goals. In that spirit, we welcome this thoughtful commentary by Cathie Martin (Martin, …

Chloroplast Division Protein Arc3 Regulates Chloroplast Ftsz-Ring Assembly And Positioning In Arabidopsis Through Interaction With Ftsz2, Min Zhang, Aaron J. Schmitz, Deena K. Kadirjan-Kalbach, Allan D. Terbush, Katherine W. Osteryoung

Department of Agronomy and Horticulture: Faculty Publications

Chloroplast division is initiated by assembly of a mid-chloroplast FtsZ (Z) ring comprising two cytoskeletal proteins, FtsZ1 and FtsZ2. The division-site regulators ACCUMULATION AND REPLICATION OF CHLOROPLASTS3 (ARC3), MinD1, and MinE1 restrict division to the mid-plastid, but their roles are poorly understood. Using genetic analyses in Arabidopsis thaliana, we show that ARC3 mediates division-site placement by inhibiting Z-ring assembly, and MinD1 and MinE1 function through ARC3. ftsZ1 null mutants exhibited some mid-plastid FtsZ2 rings and constrictions, whereas neither constrictions nor FtsZ1 rings were observed in mutants lacking FtsZ2, suggesting FtsZ2 is the primary determinant of Z-ring assembly in vivo. arc3 …

Resource Allocation For Maximizing Prediction Accuracy And Genetic Gain Of Genomic Selection In Plant Breeding: A Simulation Experiment, Aaron Lorenz

Department of Agronomy and Horticulture: Faculty Publications

Allocating resources between population size and replication affects both genetic gain through phenotypic selection and quantitative trait loci detection power and effect estimation accuracy for marker-assisted selection (MAS). It is well known that because alleles are replicated across individuals in quantitative trait loci mapping and MAS, more resources should be allocated to increasing population size compared with phenotypic selection. Genomic selection is a form of MAS using all marker information simultaneously to predict individual genetic values for complex traits and has widely been found superior to MAS. No studies have explicitly investigated how resource allocation decisions affect success of genomic …

Evaluation Of Public Sweet Sorghum A-Lines For Use In Hybrid Production, Jeffrey F. Pedersen, Scott E. Sattler, William F. Anderson

Department of Agronomy and Horticulture: Faculty Publications

A fundamental need for commercialization of sweet sorghum [Sorghum bicolor (L.) Moench] as a bioenergy crop is an adequate seed supply, which will require development of hybrid varieties using dwarf seed-parent lines. A set of six public sweet sorghum A-lines (Dwarf Kansas Sourless, KS9, N36, N38, N39, and N4692) were crossed with a set of six public sweet sorghum cultivars (Brawley, Kansas Collier, Dale, Sugar Drip, Waconia, and Wray). Grain, fiber, and sugar yields were determined, and conversion formulas were applied to estimate ethanol yields. Hybrids were grown in fields at Ithaca, NE, USA, in 1983– 1984 fertilized with …

Yield Gap Analysis—Rationale, Methods And Applications—Introduction To The Special Issue, M.K. Van Ittersum, Kenneth Cassman

Department of Agronomy and Horticulture: Faculty Publications

Yield gap analysis is an increasingly popular concept. It is a powerful method to reveal and understand the biophysical opportunities to meet the projected increase in demand for agricultural products towards 2050, and to support decision making on research, policies, development and investment that is needed. This Special Issue presents the state-of-the-art about concepts, methods and applications of yield gap analysis. The methodological papers emphasize the need for agronomically sound and relevant analyses, from local to global scales. The fourteen papers provide examples of applications to different crops, climate zones and production conditions, at various spatial extents and with different …

Agricultural Innovation To Protect The Environment, Jeffrey Sayer, Kenneth Cassman

Department of Agronomy and Horticulture: Faculty Publications

In a world of 9.5 billion people, global demand for food, fiber, and biofuels has to be met with minimal possible increases in land, water, fossil fuels, and the minerals used to produce fertilizers (1–4). The problem is debated at three levels: first, that agriculture will not be able to produce enough because it will come up against both biophysical and environmental limits that restrict yields (3, 5, 6); second, that the need to expand and intensify agriculture will destroy the broader environmental values of forests, wetlands, marine systems, and their associated biodiversity (7–9); and third, that there are institutional …

New Technologies Reduce Greenhouse Gas Emissions From Nitrogenous Fertilizer In China, Wei-Feng Feng, Zheng-Xia Dou, Pan He, Xiao-Tang Ju, David Powlson, Dave Chadwick, David Norse, Yue-Lai Lu, Ying Zhang, Liang Wu, Xin-Ping Chen, Kenneth Cassman, Fu-Suo Zhang

Department of Agronomy and Horticulture: Faculty Publications

Synthetic nitrogen (N) fertilizer has played a key role in enhancing food production and keeping half of the world’s population adequately fed. However, decades of N fertilizer overuse in many parts of the world have contributed to soil, water, and air pollution; reducing excessive N losses and emissions is a central environmental challenge in the 21st century. China’s participation is essential to global efforts in reducing N-related greenhouse gas (GHG) emissions because China is the largest producer and consumer of fertilizer N. To evaluate the impact of China’s use of N fertilizer, we quantify the carbon footprint of China’s N …

Influence Of Two Herbicides On Soybean Cyst Nematode (Heterodera Glycines) Reproduction On Henbit (Lamium Amplexicaule) Roots, Rodrigo Werle, Mark L. Bernards, Loren J. Giesler, John L. Lindquist

Department of Agronomy and Horticulture: Faculty Publications

Soybean cyst nematode (SCN) is the most yield-limiting pathogen of soybean in the United States. Henbit is a prevalent winter annual weed species in no-till fields and is reported to be an alternative host of SCN. A greenhouse study was conducted to evaluate how the development of SCN on henbit roots was affected by herbicide mode of action and time of herbicide application. Henbit plants were grown in watertight pots placed in a water bath bench that kept soil temperature constant (27 6 1 C) during the study. Ten d after transplanting, pots were inoculated with approximately 1,000 SCN eggs. …

Maternal Environment Effects On Phenolic Defenses In Abutilon Theophrasti Seeds, Brian J. Schutte, Sam E. Wortman, John L. Lindquist, Adam S. Davis

Department of Agronomy and Horticulture: Faculty Publications

A class of phenolic compounds, ortho-dihydroxyphenols (hereafter “o-DHP”), has been implicated with seed survival. Based on expectations of the growth-differentiation balance hypothesis, we predicted that seed o-DHP concentration exhibits a curvilinear response to increasing resource availability in the maternal environment, with maximum o-DHP occurring at moderate resource levels. To test this hypothesis, Abutilon theophrasti seeds were produced under field conditions at two locations. Each location included twelve maternal environments established through factorial combinations of soil compost (+/−), species assemblage (A. theophrasti with and without maize), and soil nitrogen fertilizer (0, 0.5× or 1× local …

Seed Burial Physical Environment Explains Departures From Regional Hydrothermal Model Of Giant Ragweed (Ambrosia Trifida) Seedling Emergence In U.S. Midwest, Adam S. Davis, Sharon Clay, John Cardina, Anita Dille, Frank Forcella, John Lindquist, Christy Sprague

Department of Agronomy and Horticulture: Faculty Publications

Robust predictions of weed seedling emergence from the soil seedbank are needed to aid weed management. A common seed accession (Illinois) of giant ragweed was buried in replicate experimental gardens over 18 site years in Illinois, Michigan, Kansas, Nebraska, Ohio, and South Dakota to examine the importance of site and climate variability by year on seedling emergence. In a nonlinear mixed-effects modeling approach, we used a flexible sigmoidal function (Weibull) to model giant ragweed cumulative seedling emergence in relation to hydrothermal time accumulated in each site-year. An iterative search method across a range of base temperature (T_b) …

Genetic Dissection Of Yield And Its Component Traits Using High-Density Composite Map Of Wheat Chromosome 3a: Bridging Gaps Between Qtls And Underlying Genes, Sachin Rustgi, Mustafa N. Shafqat, Neeraj Kumar, P. Stephen Baenziger, M. Liakat Ali, Ismail M. Dweikat, B. Todd Campbell, Kulvinder Singh Gill

Department of Agronomy and Horticulture: Faculty Publications

Earlier we identified wheat (Triticum aestivum L.) chromosome 3A as a major determinant of grain yield and its component traits. In the present study, a high-density genetic linkage map of 81 chromosome 3A-specific markers was developed to increase the precision of previously identified yield component QTLs, and to map QTLs for biomass-related traits. Many of the previously identified QTLs for yield and its component traits were confirmed and were localized to narrower intervals. Four novel QTLs one each for shoot biomass (Xcfa2262-Xbcd366), total biomass (wPt2740-Xcfa2076), kernels/spike (KPS) (Xwmc664-Xbarc67), and Pseudocercosporella induced lodging ( …

Dna Fingerprinting And Anastomosis Grouping Reveal Similar Genetic Diversity In Rhizoctonia Species Infecting Turfgrasses In The Transition Zone Of Usa, B. S. Amaradasa, B. J. Horvath, D. K. Lakshman, S. E. Warnke

Department of Agronomy and Horticulture: Faculty Publications

Rhizoctonia blight is a common and serious disease of many turfgrass species. The most widespread causal agent, Thanatephorus cucumeris (anamorph: R. solani), consists of several genetically different subpopulations. In addition, Waitea circinata varieties zeae, oryzae and circinata (anamorph: Rhizoctonia spp.) also can cause the disease. Accurate identification of the causal pathogen is important for effective management of the disease. It is challenging to distinguish the specific causal pathogen based on disease symptoms or macroscopic and microscopic morphology. Traditional methods such as anastomosis reactions with tester isolates are time consuming and sometimes difficult to interpret. In the present study universally …

Distinguishing Between Yield Advances And Yield Plateaus In Historical Crop Production Trends, Patricio Grassini, Kent M. Eskridge, Kenneth Cassman

Department of Agronomy and Horticulture: Faculty Publications

Food security and land required for food production largely depend on rate of yield gain of major cereal crops. Previous projections of food security are often more optimistic than what historical yield trends would support. Many econometric projections of future food production assume compound rates of yield gain, which are not consistent with historical yield trends. Here we provide a framework to characterize past yield trends and show that linear trajectories adequately describe past yield trends, which means the relative rate of gain decreases over time. Furthermore, there is evidence of yield plateaus or abrupt decreases in rate of yield …

Updated Manuscript Submission Guidelines For The Prairie Naturalist, Christopher N. Jacques, Troy W. Grovenburg, Jonathan A. Jenks

The Prairie Naturalist

These guidelines present updated policies and procedures for submitting scientific manuscripts for consideration for publication in The Prairie Naturalist (PNAT). These guidelines incorporate substantial changes that have occurred following a change in Editorial staff during January 2009, and update the online “Suggestions for Contributors” guidelines provided on the PNAT website (http://www.sdstate.edu/nrm/organizations/gpnss/tpn/index.cfm); these instructions supersede all previous guidelines.

Tables and appendices are included for common word expressions with superfluous wording (Table 1), examples of correct format and style guidelines for tables accompanying manuscripts (Table 2, Appendix A), guidance in properly preparing Research notes (Appendix B) and citing literature (Appendix …

Terrestrial And Semi-Aquatic Vertebrates In Diets Of Largemouth Bass In Central Nebraska, Seth A. Lundgren, Keith Geluso, Casey W. Schoenebeck

The Prairie Naturalist

Largemouth bass (Micropterus salmoides) are opportunistic predators often feeding in littoral areas during crepuscular periods (Snow 1971). Adult largemouth bass primarily are piscivorous, whereas juveniles generally consume zooplankton, insects, and small fish (Zweiacker and Summerfelt 1974, Carlander 1977, Post 2003). Age-0 largemouth bass generally consume zooplankton and macroinvertebrates (Keast and Webb 1966, Keast 1985, Phillips et al. 1995, Post 2003) and shift to piscivory at 50-70 mm in length (Phillips et al. 1995, Olson 1996, Post 2003). Few studies have documented detailed accounts of other vertebrates besides fish in diets of largemouth bass, which include amphibians (Hodgson and …

The Incentive And Benefits To Publish Research, Christopher N. Jacques

The Prairie Naturalist

In the northern Great Plains, December is a month marked by the end of the year and a period of much-needed rest and relaxation during the start of the winter season. Landscapes will soon be blanketed with snow and local floral and faunal species have adapted to the ensuing winter months ahead. Winter is a season that reminds you who you live in the Plains states, and as such, should expect bitter cold temperatures, strong winds, and blowing and drifting snow. However, December is a great time to enjoy the outdoors across the Great Plains, a time to reflect on …

Interior Least Tern Powerline Collision On The Lower Platte River, Lauren R. Dinan, Joel G. Jorgensen, Mary Bomberger Brown

The Prairie Naturalist

Collisions with electrical powerlines are a well-known documented cause of avian mortality (Avian Power Line Interaction Committee [APLIC] 1994, Savereno et al. 1996). Mortality caused by collisions with powerlines can be an important concern for many bird species, but is a serious conservation problem for threatened and endangered species because any mortality can have biological and legal ramifications (Janss 2000). Loss of individuals, particularly breeding adults, from an already small population may impede a species’ recovery by reducing reproduction and recruitment into the breeding population. The death of an individual from a threatened or endangered species as a result of …

Avian Diversity And Habitat Use On Wetland Reserve Program Lands In The Lower Missouri River Valley, Eric C. Hopps

The Prairie Naturalist

A primary objective of the Wetland Reserve Program (WRP) is to provide habitat for migratory birds throughout all seasons of the year. Comprehensive avian assessments are lacking and limit our ability to evaluate the benefits of the WRP to continental bird populations. I investigated avian species occurrence on WRP lands within the Lower Missouri River Valley (LMRV), Nebraska, USA, from March 2010 to February 2011. Ten WRP habitat types are described based on plant community assemblages and observed hydrological regimes. Estimates of avian species richness were greatest in lowland forest (n = 115), lowland woodland (n = 83) and upland …

Fish Assemblage Structure In Black Hills, South Dakota Streams, Luke D. Schultz, Sarah J. Lewis, Katie Nicole Bertrand

The Prairie Naturalist

Understanding factors structuring fish assemblages in a particular area is valuable to both sport fishery management and native species conservation. Fish assemblages in the Black Hills are unique to South Dakota because they contain economically valuable introduced salmonids as well as native species of conservation need. Our objective was to examine the relationship between fish assemblages and geomorphic and reach-scale habitat features across multiple stream reaches in the Black Hills. Canonical correspondence analysis, a direct gradient ordination analysis, indicated that factors operating at multiple spatial scales interacted to structure fish assemblages. There also was indication of segregation between native species …

Walleye Trophic Position Before And After A Gizzard Shad Extirpation, Bethany J. Bethke, Justin A. Vandehey, Mark J. Fincel, Brian D.S. Graeb, Mark T. Porath

The Prairie Naturalist

Walleye (Sander vitreus) are an ecologically and recreationally important sport fish species. Reduced growth and condition in walleye can occur when prey availability is limited. In two Nebraska reservoirs, walleye consumed gizzard shad (Dorosoma cepedianum) as their primary prey until a winterkill extirpated the gizzard shad in 2001. Because of the winterkill, walleye in the two reservoirs had to change to alternative prey items. Our objective was to determine if stable isotope analysis on archived walleye scales can be used to detect a known food web shift in two reservoir food webs. We quantified the changes …

Marketing Contracts, Overconfidence, And Timing In The Canadian Wheat Market, Fabio L. Mattos, Stefanie A. Fryza

Department of Agronomy and Horticulture: Faculty Publications

This paper investigates factors that impact marketing performance in the Canadian wheat market. Using data provided by the Canadian Wheat Board (CWB) for six crop years, results indicate that producers were not able to profitably use all marketing contracts offered by the CWB, earlier pricing tended to generate better performance, there was a negative relationship between activeness and performance (suggesting overconfidence in marketing skills), and performance was generally worse in volatile crop years. Further analysis reveals some of these findings differ when outperforming and underperforming producers are investigated separately, particularly with respect to activeness and volatility.

Review Of The Midwestern Native Garden: Native Alternatives To Nonnative Flowers And Plants, An Illustrated Guide By Charlotte Adelman And Bernard L. Schwartz, Stephen L. Young

Great Plains Research: A Journal of Natural and Social Sciences (through 2013)

Native plants are important for maintaining biodiversity and supporting birds, mammals, and insects in a particular region. The interaction of plants with other organisms is what makes up food webs, and a shift in one will result in change in the other, change that is often detrimental to both. Invasive plant species, which include many nonnative types, can alter ecosystems with lasting effects on hydrology, nutrient cycling, and habitat. Similar to other regions, the Central Plains is increasingly threatened by the establishment of invasive plant species. The reintroduction of native plant species not only in large natural areas, but also …

Monitoring Standing Herbage Of The Sands And Choppy Sands Ecological Vegetation Types In The Nebraska Sandhills, Daniel W. Uresk

Great Plains Research: A Journal of Natural and Social Sciences (through 2013)

A modified Robel pole with white and gray alternating bands (2.54 cm) was used to measure vegetation on sands and choppy sands ecological types in the Sandhills of Nebraska. Objectives were to determine the relationship between visual obstruction readings (VOR) and clipped standing herbage, develop guidelines for monitoring standing herbage, and provide sample size estimates. Visual obstruction measurements of standing herbage were linear, and regression coefficients were significant (P< 0.001) for 125 transects (R² = 0.60, SE = 496 kg/ha). Clipped standing herbage ranged from 293 to 4389 kg/ha with a mean of 1,559 kg/ha. A minimum of four transects (20 stations/transect with four …

Initial Changes In Species Cover Following Savanna Restoration Treatments In Western Iowa, David A. Mckenzie, Thomas B. Bragg, David M. Sutherland

Great Plains Research: A Journal of Natural and Social Sciences (through 2013)

Study areas in the Iowa Loess Hills were used to evaluate short-term responses of understory species to three treatment methods designed to facilitate restoration of Quercus macrocarpa savanna. Treatments included burning alone, burning with thinning, and burning with clear-cutting. Plant abundance and diversity were compared before treatment and one year after treatment. Ninety-nine plant species were identified during the study, of which 40 were new following treatment, although most of these were forest associates. Increases in diversity of understory species were observed after treatment, particularly in plots with combined burning and thinning. The forb group was most consistent in response …

Monitoring Standing Herbage Of Mid-Grass Prairie On The Fort Pierre National Grassland, South Dakota, Daniel W. Uresk

The Prairie Naturalist

Monitoring vegetation with a modified Robel pole on the Fort Pierre National Grassland was evaluated for combined shallow clay and loamy overflow ecological sites (dominated by warm-season grasses), and for clayey ecological sites (dominated by cool-season grasses). My objectives were to 1) develop a relationship between visual obstruction readings (VOR) and standing herbage, 2) provide guidelines for vegetation monitoring, and 3) evaluate vegetation monitoring during the growing season for clayey ecological sites. The relationship between visual obstruction readings and standing herbage was linear and regression coefficients were highly significant (P < 0.001) for both ecological types. Cluster analyses for shallow clay and loamy overflow ecological sites grouped the VOR and standing herbage (kg•ha-1) into 4 resource categories. Monitoring with 4 transects will provide adequate information to estimate standing herbage within 259 ha (1 section). Three resource categories (VOR + herbage) for clayey ecological sites were defined by cluster analyses. Monitoring with 4 transects was determined to provide reliable estimates of standing herbage. July validation of vegetation with the developed clayey ecological site model will provide reliable monitoring of standing herbage from July through November for this ecological site.

Germination Response Of Prairie Dropseed And Hairy Goldaster To Stratification And Temperature, Aurora R. Roemmich, Jack L. Bulter, Gary E. Larson, E. Brent Turnipseed

The Prairie Naturalist

The unique vegetation assemblage of the Black Hills in conjunction with the frequent occurrence of natural and anthropogenic disturbances emphasizes the need to use locally adapted native species in a wide variety of restoration efforts. However, a general lack of information regarding germination and propagation requirements for most native plant species has restricted their usage. A better understanding of dormancy and germination patterns for native species will increase their availability and affordability. We selected two common native species, hairy goldaster (Heterotheca villosa) and prairie dropseed (Sporobolus heterolepis), to determine their optimum germination conditions. We hand-harvested seeds during 2007–2009 for use …

Review: Mammals Of Colorado. Second Edition. David M. Armstrong, James P. Fitzgerald, And Carron A. Meaney., Thomas J. O'Shea

The Prairie Naturalist

In my view, the second edition of Mammals of Colorado is among the finest state-level books on mammals available. The book is a major revision of the first edition (Fitzgerald et al. 1994) and is a reference worth having, even if the first edition is already at hand. In this review, T summarize aspects of the new volume and provide comparisons to the first edition in an effort to persuade the reader that this is indeed the case.

The first four chapters of the second edition include background information and updated material about Colorado environments, mammals in general, the history …

Five New Records Of Ants (Hymenoptera: Formicidae) For Nebraska, Kristine T. Nemec, James C. Trager, Elizabeth Manley, Craig R. Allen

The Prairie Naturalist

Ants are ubiquitous and influential organisms in terrestrial ecosystems. About 1,000 ant species occur in North America, where they are found in nearly every habitat (Fisher and Cover 2007). Ants are critical to ecological processes and structure. Ants affect soils via tunneling activity (Baxter and Hole 1967), disperse plant seeds (Lengyel et al. 2009), prey upon a variety of insects and other invertebrates (Way and Khoo 1992, Folgarait 1998), are often effective primary consumers through their prodigious consumption of floral and especially extrafloral nectar, and honeydew (Tobin 1994), and serve as prey for invertebrates (Gotelli 1996, Gastreich 1999) and vertebrates …