Life Sciences Commons^™

Development Of Highly Variable Microsatellite Markers For The Tetraploid Silene Stellata (Caryophyllaceae), Juannan Zhou, Michele R. Dudash, Charles B. Fenster, Elizabeth A. Zimmer

Natural Resource Management Faculty Publications

Premise of the study:We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success.

Methods and Results: A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats. Genotyping results showed the number of alleles per locus ranged from six to 45 and expected heterozygosity ranged from 0.511 to 0.951. Five of these loci were successfully amplified in S. …

An Integrative And Applicable Phylogenetic Footprinting Framework For Cis-Regulatory Motifs Identification In Prokaryotic Genomes, Bingqiang Liu, Hanyuan Zhang, Chaun Zhou, Guojaun Li, Anne Fennell, Guanghui Wang, Yu Kang, Qi Liu

Agronomy, Horticulture and Plant Science Faculty Publications

Background: Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Results: Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP3 ). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, …

Growing South Dakota (Summer 2016), College Of Agriculture &. Biological Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

[Page] 2 Breaking New Ground SDSU Leads Nation With Precision Agriculture Initiative
[Page] 6 In The Driver's Seat Utility Vehicles Provide Students Hands-On Precision Ag Experience
[Page] 7 Introduction To Industry Travel To National Events Opens Opportunities For Students
[Page] 9 On The Ground SDSU Extension Specialists Have Vital Role In Bringing Data To Producers
[Page] 10 Curricula Collaboration SDSU Leaders Among Team Preparing Future Precision Ag Coursework
[Page] 12 Future Focus Ag 2020 Plan Prompts Important Reinvestments In State's Ag Experiment Station
[Page] 13 The Power Of Connections Connected Approach Helps Solve "Real-Life" Problems To Benefit Animal And …

Impacts Of Mowing Treatments On Smooth Bromegrass (Bromus Inermis) Belowground Bud Bank, L. Xu, J. Young, A. Boe, J. R. Hendrickson, N. H. Troelstrup Jr.

Natural Resource Management Faculty Publications

Introduced in the 1880s for improving forage production and controlling soil erosion, smooth bromegrass (Bromus inermis Leyss) has invaded and is threating numerous native prairie ecosystems and wildlife habitats in the Northern Great Plains. Land managers of the mixed-grass prairie ecosystems currently spend significant resources attempting to control invasive species and restore native grasslands with various management strategies including grazing, prescribed burning, herbicide application and seeding native species. Unfortunately, many studies have showed that such management efforts have minimal short-term effects. Without sustained effort, persistence and resurgence of smooth bromegrass is inevitable.

Physiological And Molecular Characterisation Of Lucerne (Medicago Sativa L.) Germplasm With Improved Seedling Freezing Tolerance, M. Rokebul Anowar, Anne Fennell, Arvid Boe, Ivan W. Mott, Michael D. Peel, Yajun Wu

Agronomy, Horticulture and Plant Science Faculty Publications

We conducted greenhouse experiments to compare 14 lucerne (alfalfa, Medicago sativa L.) germplasms for their survival following freezing. Some are collections adapted to the Grand River National Grasslands in South Dakota. We hypothesised that these collections might have developed a tolerance to survive the frigid growth conditions common there. Two of these collections, River side (RS) and Foster ranch (FR), showed greater freezing tolerance than the other germplasms tested, based on their consistent survival rates with or without cold acclimation. In multiple freezing studies, RS and FR had average survival rates of 74% and 79%, respectively, in contrast to the …

Research Update: Bud Bank Ecology For Understanding Perennial Grass Persistence, Lan Xu

Natural Resource Management Faculty Publications

Grassland ecosystems often demonstrate very remarkable resiliency to severe natural and anthropogenic disturbances. Such resiliency following disturbances comes from either seed banks (germinable seeds in the soil) or bud banks (meristems or buds, such as bulbs, bulbils, and buds on rhizomes, corms, and tubers, that generate vegetative tissues). Although seeds are important for dispersal, initial colonization, and maintenance of genetic diversity; few grass seeds persist in the soil more than five years, plus seed production often is unreliable under grazing. Recent studies have demonstrated that >99% of aboveground stems in undisturbed tallgrass prairie were recruited from the bud bank while <1% were recruited from the seed bank. Even under grazed or disturbed sites in tallgrass prairie, belowground buds make a significantly larger contribution (80%) to plant recruitment than do seeds (20%).

Maize, Switchgrass, And Ponderosa Pine Biochar Added To Soil Increased Herbicide Sorption And Decreased Herbicide Efficacy, Sharon A. Clay, Kaitlynn K. Krack, Stephanie A. Bruggeman, Sharon Papiernik, Thomas E. Schumacher

Agronomy, Horticulture and Plant Science Faculty Publications

Biochar, a by-product of pyrolysis made from a wide array of plant biomass when producing biofuels, is a proposed soil amendment to improve soil health. This study measured herbicide sorption and efficacy when soils were treated with low (1% w/w) or high (10% w/w) amounts of biochar manufactured from different feedstocks [maize (Zea mays) stover, switchgrass (Panicum vigatum), and ponderosa pine (Pinus ponderosa)], and treated with different post-processing techniques. Twenty-four hour batch equilibration measured sorption of ¹⁴C-labelled atrazine or 2,4-D to two soil types with and without biochar amendments. Herbicide efficacy was measured …

Greater Bud Outgrowth Of Bromus Inermis Than Pascopyrum Smithii Under Multiple Environmental Conditions, Jacqueline P. Ott, Jack L. Butler, Yuping Rong, Lan Xu

Natural Resource Management Faculty Publications

Tiller recruitment of perennial grasses in mixed-grass prairie primarily occurs from belowground buds. Environmental conditions, such as temperature, soil moisture and grazing can affect bud outgrowth of both invasive and native perennial grasses. Differential bud outgrowth responses of native and invasive species to climate change and grazing could alter competitive interactions that have implications for future land management. The aims of this work were to (i) compare how spring temperature altered bud outgrowth of native Pascopyrum smithii (Rydb.) Á. Löve (western wheatgrass) and introduced Bromus inermis Leyss.(smooth brome), (ii) compare how watering frequency altered bud outgrowth of these two species …

Mapping Temperate Vegetation Climate Adaptation Variability Using Normalized Land Surface Phenology, Liang Liang, Mark D. Schwartz, Xiaoyang Zhang

GSCE Faculty Publications

Climate influences geographic differences of vegetation phenology through both contemporary and historical variability. The latter effect is embodied in vegetation heterogeneity underlain by spatially varied genotype and species compositions tied to climatic adaptation. Such long-term climatic effects are difficult to map and therefore often neglected in evaluating spatially explicit phenological responses to climate change. In this study we demonstrate a way to indirectly infer the portion of land surface phenology variation that is potentially contributed by underlying genotypic differences across space. The method undertaken normalized remotely sensed vegetation start-of-season (or greenup onset) with a cloned plants-based phenological model. As the …

Growing South Dakota (Winter 2016), College Of Agriculture &. Biological Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

This issue includes the 2015 SDSU Extension Annual Report.

[Page] 2 Contours Program Launched: Aims to Provide Insights & Prompt Discussions
[Page] 4 Local Momentum: Formation of State's First “Food Hub” Comes To Fruition [Page] 6 Spotlight On Soil Health: New Coalition Formed
[Page] 8 Exploring A Range Of Options: Youth Programs Cultivate Interest In Natural Resource Careers
[Page] 9 Profiles In Leadership: Our Mission Continues… Ensuring All Citizens Have Access To Education & Emerging Innovation
[Page] 10 Encouraging Animal Well-Being Workshops & Trainings Help Livestock Producers Become Better Stewards
[Page] 12 Wellness Wisdom: Variety Of Efforts Available To Encourage …

Invasive Grasses Consistently Create Similar Plant-Soil Feedback Types In Soils Collected From Geographically Distant Locations, Lora B. Perkins, Gary Hatfield, Erin K. Espeland

Natural Resource Management Faculty Publications

Aims Plants of similar life forms and closely related species have been observed to create similar types of plant–soil feedbacks (PSFs). However, investigations of the consistency of PSFs within species have not yielded clear results. For example, it has been reported that species create different types of PSFs in their native and introduced ranges. The aim of this project is to examine if four species create similar PSF types from soils collected from widely distributed areas within their introduced range. The soil for this project was collected from three areas in western North America. With this design, we aim to …

Next Generation Mapping Of Enological Traits In An F2 Interspecific Grapevine Hybrid Family, Shanshan Yang, Jonathan Fresnedo-Ramírez, Qi Sun, David C. Manns, Gavin L. Sacks, Anna Katherine Mansfield, James L. Luby, Jason Londo, Bruce I. Reisch, Lance Cadle-Davidson, Anne Y. Fennell

Agronomy, Horticulture and Plant Science Faculty Publications

In winegrapes (Vitis spp.), fruit quality traits such as berry color, total soluble solids content (SS), malic acid content (MA), and yeast assimilable nitrogen (YAN) affect fermentation or wine quality, and are important traits in selecting new hybrid winegrape cultivars. Given the high genetic diversity and heterozygosity of Vitis species and their tendency to exhibit inbreeding depression, linkage map construction and quantitative trait locus (QTL) mapping has relied on F₁ families with the use of simple sequence repeat (SSR) and other markers. This study presents the construction of a genetic map by single nucleotide polymorphisms identified through genotyping-by-sequencing …

A Next-Generation Marker Genotyping Platform (Ampseq) In Heterozygous Crops: A Case Study For Marker-Assisted Selection In Grapevine, Shanshan Yang, Jonathan Fresnedo-Ramírez, Minghui Wang, Linda Cote, Peter Schweitzer, Paola Barba, Elizabeth M. Takacs, Matthew Clark, James Luby, David C. Manns, Gavin Sacks, Anna Katharine Mansfield, Jason Londo, Anne Fennell Dr, David Gadoury, Bruce Reisch, Lance Cadle-Davidson, Qi Sun

Agronomy, Horticulture and Plant Science Faculty Publications

Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates traitassociated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and …

Reproductive Biology Of American Licorice (Glycyrrhiza Lepidota Pursh) In Western South Dakota With New Seed Insect Associations, Arvid Boe

Native Plant Focused Publications

American licorice (Glycyrrhiza lepidota Pursh) is a long-lived rhizomatous native legume that is common on moist prairies and meadows in the northern Great Plains and further west. This species is of interest for remediation and conservation because it is a legume that is fairly well adapted to moist saline soils. It is browsed by deer and pronghorn and its seeds are consumed by birds, rodents, and insects. Acanthoscelides aureolus (Horn) (Coleoptera: Chrysomelidae)] and Bruchophagus grisselli McDaniel & Boe (Hymenoptera: Eurytomidae) can decimate seed production in natural populations. Our objectives were to determine seed yield components (i.e., seeds per pod and …

Seed Source May Determine Field-Specific Germination And Emergence: The Source By Planting Environment Interaction, Erin K. Espeland, Lora B. Perkins, Matthew E. Horning, Richard C. Johnson

Natural Resource Management Faculty Publications

Farm environmental conditions and management practices can result in within-cultivar differences in seed quality and lead to transgenerational plasticity (farm-specific effects on offspring, or TGP) that affect germination and emergence in transplant fields. We used three perennial bunchgrasses, [green needlegrass (Nassella viridula) ‘Lodorm’, slender wheatgrass (Elymus trachycaulus) ‘Pryor’, and bluebunch wheatgrass (Pseudoregneria spicata) prevariety registered germplasm P-7] to determine if seeds exhibited TGP. We also determined if TGP was affected by the interaction between production farms and planting environments (farm × environment interaction, or context-dependent TGP), using four laboratory temperature regimes to test germination response and four field environments to …

Growing South Dakota (Winter 2016), College Of Agriculture &. Biological Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

This issue includes the 2015 South Dakota Agricultural Experiment Station Annual Report.

[Page] 2 Director's Message
[Page] 3 Concentrating On Cattle: Researcher Studying Mechanics To Improve Reproduction Efficiency In Beef Cattle
[Page] 5 At The Forefront: SDSU Diagnostic Lab Scientists Sequence Avian Influenza Genome
[Page] 6 Seeking Superior Wheat: Breeder Using Extensive Genome Testing To Improve Winter Wheat Cultivars
[Page] 8 Profiles In Leadership: Plant And Fungi Interactions May Offer New Plant Production Possibilities
[Page] 9 Targeting Emerging Diseases: Plant Pathologists Working To Better Manage Soybean & Sunflower Diseases
[Page] 10 Compelling New Crop: Carinata Offers Potential For Crop Diversity, …

Distribution And Characterization Of The Soybean Cyst Nematode, Heterodera Glycines (Hg) Types In South Dakota, Krishna Acharya

Electronic Theses and Dissertations

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is an endoparasitic nematode and one of the major pests of soybean (Glycine max L.) in the United State and all over the world where soybean is grown. SCN is ranked first among the biological factors that cause yield loss in soybean. The estimated yield loss by this nematode is $1b annually in the United States alone. SCN is thought to have been first found in China. It was first identified in the United States in 1954 in North Carolina and in South Dakota in 1995. To date, SCN continues to spread …

Senescence Of Native Perennial Warm Season Grasses Senescence Associated Switchgrass Transcriptome, Michaellong Tran

Electronic Theses and Dissertations

Senescence of perennial crops enable continuous harvests after one sowing event. Perennials senesce at adapted rates of their native environments; however, early senescencing crops do not maximize the growing season as nutrient reallocation takes precedence. Chlorophyll degradation and nitrogen reallocation was observed to occur rapidly between mid to late September. Transcriptome analysis on early and late senescencing switchgrass cultivars reveals upregulation of starch metabolism, light reactions, Calvin-Benson Cycle, and anthocyanin synthesis in late senescencing switchgrass. Morphological variations between the two germplasms prolong the growing season of late senescencing switchgrass, maximizing yield. Expression of mRNA as senescence progresses and between the …

Soil Salinity Study In Northern Great Plains Sodium Affected Soil, Tulsi P. Kharel

Electronic Theses and Dissertations

Climate and land-use changes when combined with the marine sediments that underlay portions of the Northern Great Plains have increased the salinization and sodification risks. The objectives of this dissertation were to compare three chemical amendments (calcium chloride, sulfuric acid and gypsum) remediation strategies on water permeability and sodium (Na) transport in undisturbed soil columns and to develop a remote sensing technique to characterize salinization in South Dakota soils. Fortyeight undisturbed soil columns (30 cm x 15 cm) collected from White Lake, Redfield, and Pierpont were used to assess the chemical remediation strategies. In this study the experimental design was …

Evaluation And Identification Of Soybean Aphid Resistance Sources And Mapping Of Soybean Aphid Resistance Loci In Early Maturing Soybean Germplasm Accessions, Siddhi Jeewan Bhusal

Electronic Theses and Dissertations

Soybean aphid (Aphis glycines Matsumura) has been a major pest of soybean [Glycine max (L.) Merr.] in North America particularly in the northern United States and three Canadian provinces. At least four biotypes of soybean aphid have been confirmed in the United States. Identification of soybean aphid resistance sources in early-maturing soybeans and genetic characterization of new sources of resistance will facilitate to expand the gene pool of soybean aphid resistance and thus will help to develop soybean aphid resistant cultivars. To identify new sources of resistance in early maturing soybeans, 330 soybean germplasm accessions from Maturity Group (MG) I, …

Cooperation And Punishment In The Arbuscular Mycorrhizal Symbiosis: Implications For Resource Exchange & Biological Market Dynamics, Jerry A. Mensah

Electronic Theses and Dissertations

The arbuscular mycorrhizal (AM) symbiosis is arguably the world’s most abundant and important mutualism, and brings together the roots of the majority of land plants and AM fungi to great mutual advantage. The AM symbiosis can increase the uptake of nutrients, such as phosphorus (P) and nitrogen (N), and improves the abiotic and biotic stress resistance of the host plant. AM fungi have the potential to act as biofertilizers and bioprotectors in sustainable agriculture. However, despite its significance, the mechanisms that control the resource exchange between both partners in the arbuscular mycorrhizal symbiosis are largely unknown. The main aim of …

Evaluation Of Tillage, Crop Rotation, And Cover Crop Impacts On Corn Nitrogen Requirements In Southeastern South Dakota, Sara Louise Berg

Electronic Theses and Dissertations

Nitrogen (N) is a vital factor of corn (Zea mays) production. Previous work in South Dakota has shown that there is uncertainty as to whether nitrogen requirements are the same for corn raised under no-till (NT) versus conventional till (CT) production systems. The objective of this study was to evaluate whether N requirements continue to be greater under long-term NT versus CT production systems in southeastern South Dakota, while also considering effects from cover crops and crop rotation. This was a two year study conducted at the SDSU Southeast Research Farm near Beresford, SD; it was superimposed on a long-term …

Evaluation Of Flame Weeding In Southeastern South Dakota, Benjamin William Arlt

Electronic Theses and Dissertations

Weed management is the main yield-limiting factor in production of organic crops. Currently, organic producers have limited resources available for in-row weed management. Flame weeding has been recognized for its potential as one part of an integrated approach at weed management in organic systems. Flame weeding uses propane fueled torches to heat plant tissue and denature proteins, thus injuring or destroying the affected tissue. When properly timed, flame weeding can effectively be used for weed control in corn and soybean fields. Corn and soybean have both shown tolerances to flame weeding and minimal yield loss with well-managed and timed flame …

Corncob Grit Application As An Alternative To Control Weeds In Two Crop Production Systems, Mauricio Erazo-Barradas

Electronic Theses and Dissertations

Weed management is one of the most challenging production problems in organic cropping systems because of limited weed control methods. Grits, derived from agricultural residues, have been demonstrated to control weed seedlings selectively in corn. This research examined weed efficacy and crop yield of an integrated air-propelled abrasive corncob grit (for in-row weed control) at varying timings and frequencies and flame-weeding or cultivation (for between-row weed control) system in two corn production systems. In the first study efficacy of weed control was assessed with this approach in an organic corn silage production system established in Morris, MN in 2013 and …

Quantitative Trait Loci Analysis Of Low Temperature Responses In Grapevine F2 Population, Mani Awale

Electronic Theses and Dissertations

Freezing injury, caused by freezing temperatures in the late fall, midwinter, or early spring, can result in significant loss to grape growers. The damage may range from the partial damage of parts of the plants to the total death of the plant, and may vary between years. Freezing tolerance is a multi-genetic, complex quantitative trait that involves many related traits like dormancy induction, growth cessation, acclimation, deacclimation and bud break. Developing an understanding of the genetics behind the complex trait requires connecting the phenotype with the genotype to enable discovering the underlying genes that can contribute to quantifiable differences between …

Effects Of Seed Applied Fungicide On Arbuscular Mycorrhizal Colonization Of South Dakota Cultivars Of Oat, Soybean, And Corn, Jesse Cameron

Electronic Theses and Dissertations

Arbuscular mycorrhizal fungi (AMF) are obligate symbionts that form a mutualistic relationship with approximately 80% of terrestrial plant species. These obligate symbionts have a generally beneficial effect on their host such as increased nutrient acquisition, better tolerance to biotic and abiotic stresses, and the improvement of soil qualities. Due to the recent, widespread use of seed applied fungicides on row crops in the U.S. Midwest, there are concerns that the fungicides will inhibit these beneficial mycorrhizae. This study was conducted to evaluate what effect different commonly used seed applied fungicides have on AMF in the presence of different varieties of …

Igrow Corn: Best Management Practices, David E. Clay, Gregg G. Carlson, Sharon A. Clay, Emmanuel Byamukama

Agronomy, Horticulture, and Plant Science Books

No abstract provided.

The Efficacy Of Allopurinol In Suppressing Hypersensitive-Like Symptoms In Wheat (Triticum Aestivum L.) And In Suppressing Sunflower Rust (Puccinia Helianthi) Symptoms, Thumbiko Walker Gambler Mkandawire

Electronic Theses and Dissertations

A mutant wheat (Triticum aestivum L.) genotype can constitutively produce hypersensitive-like flecks in the absence of any pathogen. The lesions of the mutant are thought to be the result of Reactive Oxygen Species (ROS), which are similarly implicated in hypersensitive reactions to fungal pathogens. Allopurinol can suppress ROS. Consequently, allopurinol was applied to a wheat lesion mutant to test the hypothesis that the same ROS are involved, regardless of the presence of the pathogen. ‘Ning7840’, a lesion mutant and ‘Alsen’, a related genotype that does not express the mutant phenotype were treated with different concentrations of allopurinol under controlled …

Soybean Yield And Plant Response To Phosphorus Fertilization, Rebecca L. Helget

Electronic Theses and Dissertations

Phosphorus (P) is a key limiting nutrient for soybean production in South Dakota. Soil tests have been used as a baseline indicator for plant available P and fertilizer recommendations for over a century. Plant nutrient analysis may be used to complement a soil test as a way to validate fertilizer and management practices. Soybean nutrient sufficiency ranges have only been slightly adjusted since they were published in the 1960’s. The objectives of this study were to update the soil test P and soybean plant P sufficiency level in South Dakota and to recognize implications of improper plant sampling. We also …

Response Of Soil And Water Quality To Winter Manure Application From Small Agricultural Watersheds In South Dakota, Shikha Singh

Electronic Theses and Dissertations

The extreme winter conditions prevailing in the state of South Dakota make it difficult for the livestock producers to manage the manure generated at the farm. The South Dakota Department of Environmental and Natural Resources does not recommend manure application in the state during the winter months when the ground is frozen. Thus, producers are left with the options such as storing the manure over a longer period until summer or spreading on snow or frozen ground. Storing manure for longer duration leads to increased risks of concentrated spills into the streams. Thus, it is important to develop management strategies …