Plant Breeding and Genetics Commons^™

Regulatory Landscapes: Transcriptome And Microrna Regulated Senescence And Dormancy In Grapevines And Gene Regulatory Networks In Nitrogen-Fixing Soybean Nodules, Ramandeep Kaur

Electronic Theses and Dissertations

Grapevine and soybean are two economically important crops, each with unique yet equally crucial physiological processes that profoundly influence their growth and productivity. Grapevine (Vitis sp.), a temperate fruit crop, employs dormancy to withstand winter challenges and can grow in various regions worldwide. Understanding the molecular mechanisms involved in dormancy in Vitis species, is crucial for improving grapevine selection for resilience in northern temperate regions. Dormancy induction is modulated by decreasing photoperiods in some Vitis species, enhancing their ability to prepare for winter stress conditions. Understanding the molecular underpinnings of response to photoperiod will provide potential markers for selecting genotypes …

Genome-Wide Association Studies And Advanced Genomic Selection Strategies: Towards The Optimization Of Oat (Avena Sativa L) Breeding, Girma Ayana

Electronic Theses and Dissertations

Oats are important cereal crops worldwide, primarily valued for their nutritional and health benefits. The primary goal of oat breeding programs is to accelerate genetic gain to develop oat varieties with the desired product profiles, with the aim of meeting the needs and expectations of growers, processors, and consumers. Achieving this goal involves conducting extensive and resource-intensive field trials, particularly for traits such as crop yield and grain quality, which are strongly influenced by environmental factors. The availability of cost-effective molecular markers and tools like genome-wide association studies (GWAS) and genomic selection have the potential to accelerate the oat breeding …

Genomics-Assisted Approaches To Improve Grain Yield And End-Use Quality In Hard Winter Wheat (Triticum Aestivum L.), Harsimardeep Singh Gill

Electronic Theses and Dissertations

Global wheat production needs to be increased by 60% to meet the future demand of feeding nine billion people by 2050. Simultaneously, it is important to improve the enduse quality to meet the requirements of producers, grain markets, processors, and consumers. Thus, the development of more productive wheat varieties with better enduse quality remains the primary focus for all wheat breeding programs. However, direct phenotypic selection for improving grain yield and end-use quality is difficult as it is highly influenced by environmental factors. This dissertation focuses on harnessing advancements in genomics applications, including genome-wide association studies (GWAS), for the genetic …

Berry Anthocyanin, Acid, And Volatile Trait Analyses In A Grapevine-Interspecific F2 Population Using An Integrated Gbs And Rhampseq Genetic Map, Dilmini Alahakoon, Anne Fennell, Zachary Helget, Terry Bates, Avainash Karn, David Manns, Anna Katherine Mansfield, Bruce I. Reisch, Gavin Sacks, Qi Sun, Cheng Zou, Lance Cadle-Dvidson, Jason P. Londo

Agronomy, Horticulture and Plant Science Faculty Publications

Increased map density and transferability of markers are essential for the genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F₂ population (VRS-F₂) that was derived by selfing a single F₁ from a Vitis riparia x ‘Seyval blanc’ cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera ‘PN40024’ genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq …

Development Of Genomic Resources In Vitis Riparia For Discoveries On Pre- And Post-Transcriptional Molecular Regulators Of Early Induction Into Endodormancy, Michael Robben

Electronic Theses and Dissertations

Grapevine is one of the most important fruit crops in the world, responsible for billions in global sales annually. The largest threat to grapevine and other crop production is global climate change resulting human activities. This brings unpredictable and drastic changes in ambient air temperatures to many climates in which grapes are grown. Lower temperatures and inclement weather are already responsible for millions in lost revenue due to tissue damage of established plants. Thus, protecting grapevine crops from weather-related damage is the biggest concern to growers aside from pathogen- and diseaserelated crop damage. The primary mechanism for winter survival in …

Genome-Wide Association Mapping And Genomic Prediction For Enhancing Fhb Resistance In Hard Winter Wheat, Jinfeng Zhang

Electronic Theses and Dissertations

Wheat is one of the most important staple crops providing 20% of energy for 35% of the world population. Fusarium head blight (FHB), primarily caused by the fugal Fusarium graminearum Schwabe, is a damaging disease in wheat that affects global wheat production every year and causes food safety issues. The disease not only reduces the grain yield and quality but also produces mycotoxin in the diseased kernels making them unsuitable for human consumption or as livestock feeds. Breeding FHB resistant cultivar is the most effective and economical approach to managing the disease. This study combines genome-wide association study (GWAS) and …

Multi-Dimensional Leaf Phenotypes Reflect Root System Genotype In Grafted Grapevine Over The Growing Season, Zachery N. Harris, Mani Awale, Niyati Bhaakta, Daniel H. Chitwood, Anne Fennell, Emma Frawley, Laura L. Klein, Laszlo G. Kovacs, Misha Kwasniewski, Jason P. Londo, Qin Ma, The Ohio State University Miogicovsky, Joel F. Swift, Allison J. Miller

Agronomy, Horticulture and Plant Science Faculty Publications

Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes …

Identification Of Loci Influencing Teosinte Crossing Barrier 1 (Tcb1) Efficacy In Maize By Quantitative Trait Loci (Qtl) Mapping And Genome-Wide Association Study (Gwas), Namrata Maharjan

Electronic Theses and Dissertations

Pollen cross-contamination has been a major problem for maize breeders. Various mechanical methods applied to avoid the contaminations are ineffective. The genetic factors related to maize fertilization can be used to develop an effective method to prevent pollen contamination. Pollen rejection ability controlled by Teosinte crossing barrier 1 (Tcb1) is such a genetic system. Silks possessing dominant Tcb1-s reject pollen possessing the recessive allele (tcb1). Successful fertilization occurs when Tcb1-s pollen falls upon tcb1 silks. The efficacy of dominant Tcb1-s was, however, reduced when repeatedly backcross with maize inbred lines, which suggests that there are modifiers to Tcb1-s. To find …

A Biocontrol Pesticide Derived From Mycovirus-Infected Sclerotinia Sclerotiorum Can Induce Plant Resistance, Connor Pedersen

Electronic Theses and Dissertations

Soybean leaf-associated gemycircularvirus-1 (SlaGemV-1) is a novel mycovirus discovered through the metagenomic sequencing of soybean leaves which is capable of inducing hypovirulence in the highly pathogenic fungus Sclerotinia sclerotiorum. RNASeq analysis techniques were used to determine the transcriptional changes caused by the infection of virus in S. sclerotiorum, as well as the transcriptional changes in Glycine max caused by the colonization of hypovirulent, SlaGemV-1-infected S. sclerotiorum. RNASeq results indicate that viral infection leading to hypovirulence may attenuate expression of genes relating to cell wall synthesis, microtubule formation, and metabolism of steroids and natural antibiotics. Cytochrome P450-related genes, kinesin domain genes, …

Genome-Wide Association Analysis Permits Characterization Of Stagonospora Nodorum Blotch (Snb) Resistance In Hard Winter Wheat, Rami Altameemi

Electronic Theses and Dissertations

Stagonospora nodorum blotch (SNB) is an economically important wheat disease caused by the necrotrophic fungus Parastagonospora nodorum. SNB resistance in wheat is controlled by several quantitative trait loci (QTLs). Thus, the identifying of novel resistance/susceptibility QTLs is crucial for continuous improvement of the SNB resistance. Here, the hard winter wheat association mapping panel (HWWAMP) comprising accessions from breeding programs in the Great Plains region of the US, was evaluated for SNB resistance and necrotrophic effectors (NEs) sensitivity at the seedling stage. A genome-wide association study (GWAS) was performed to identify singlenucleotide polymorphism (SNP) markers associated with SNB resistance and …

Genome Wide Association Study On Kernel Size In Avena Sativa (Oats), Koryne Ann Carlson

Electronic Theses and Dissertations

Kernel size is a vital milling characteristic for Avena sativa L. (oats), with larger kernel size being desirable for milling facilities. This project evaluated the effect of genotype, environment, and their genotype by environment interaction (G by E) on kernel width, length, and area for a set of 27 oat cultivars grown at multiple locations in South Dakota over three years. Findings indicated significant differences among oat varieties, and that environment had a substantial effect on kernel size. However, we did not see a strong influence of genotype by environment interaction on kernel size. The lack of impact for genotype …

Exploring Quantitative Trait Loci Mapping For Bud Fruitfulness And Bud Break Traits In Grapevine F2 Population, Seyma Bozkus

Electronic Theses and Dissertations

Grapevine (Vitis vinifera L. subsp. vinifera) is one of the most important and valuable fruit crops around the world and grape industries in the USA have been growing increasingly regarding the demand for highly productive and quality grapes that can be grown in the cold region around the USA. The development of new cultivars with these features is performed through grape breeding with the help of quantitative trait loci (QTL) mapping, marker-assisted selection (MAS), and and other technologies. In this study, we evaluated grapevine bud fruitfulness by position and bud break in controlled conditions. These traits are multi-genetic and understanding …

Studies On Genetic Characterization Of Agronomic Traits And Disease Resistance In Bread Wheat, Jyotirmoy Halder

Electronic Theses and Dissertations

A steady increase in wheat yield is vital to feed the continuously rising world population. Systematic exploitation of wheat germplasm and a better understanding of the underlying genetic control could be pivotal in accelerating the genetic gain for yield and disease management. Various modern techniques such as genome-wide association study (GWAS), genomic selection (GS), fine mapping, and cloning can expedite wheat improvement and broaden our understanding of the complex wheat genome. In the first objective of this study, we evaluated the Watkins core set of 121 landrace cultivars (LCs) to identify novel sources of resistance against the tan spot, Stagonospora …

Examining The Utility Of Dna Barcodes For The Identification Of Tallgrass Prairie Flora, Sarah A. Herzog, Maribeth Latvis

Natural Resource Management Faculty Publications

Premise
The tallgrass prairies of North America are one of the most threatened ecosystems in the world, making efficient species identification essential for understanding and managing diversity. Here, we assess DNA barcoding with high‐throughput sequencing as a method for rapid plant species identification.
Methods
Using herbarium collections representing the tallgrass prairie flora of Oak Lake Field Station, South Dakota, USA, we amplified and examined four common nuclear and plastid barcode regions (ITS, matK, psbA‐trnH, and rbcL), individually and in combination, to test their success in identifying samples to family, genus, and species levels using BLAST searches of …

Reverse Genetic Analysis Of Ehd1 For An Association Between Flowering Time And Seed Dormancy In Rice (Oryza Sativa L.), Yeter Karakoc

Electronic Theses and Dissertations

This research aimed to understand the evolutionary mechanism of seed dormancy and flowering time and to provide basic knowledge for the manipulation of germination features in crop breeding. Flowering time and seed dormancy are two adaptive traits for flowering plants. Seed dormancy (SD) helps regulate the timing of germination to promote the survival of seed-bearing plants in adverse environments. Cereal crops and weedy/wild relatives, such as Asian cultivated rice and weedy rice (Oryza sativa L.), have weak and strong seed dormancy, respectively. Thus, weedy and cultivated rice has been used as a model system to investigate mechanisms of seed dormancy …

Functional Analysis Of Squamosa-Promoter Binding Protein Like 13 In Controlling Flowering Time, Plant Architecture, Grain Size, And Grain Number In Wheat, Ajay Gupta

Electronic Theses and Dissertations

Higher and stable yield is always a major objective of wheat genetic improvement programs. The SQUAMOSA-promoter binding protein-like (SPL) genes constitute a small family of plant-specific transcription factors with diverse functions in plant development and growth and have great potential in improving yield and other major agronomic traits. However, the functional characterization of the SPL gene family in wheat is far behind other cereal crops such as rice. Using phylogenetic analysis, we identified 56 wheat orthologues of rice SPL genes belonging to 19 homoeologous groups. Among these 19 orthologous TaSPL genes, nine harbor the micro RNA 156 recognition element (MRE) …

Assembly Of Triticum Boeoticum Ssp. Aegilopoides And Triticum Monoccocum Genomes, Mustafa Aljadi

Electronic Theses and Dissertations

Wheat is ancient cereal. Wheat has n = 7 chromosomes which is belong to genus Triticum. The group Triticum monococcum sp. aegilopoides(boeoticum) is a diploid wheat (2n = 14). It has a morphology aspect of having narrow, flat spike which usually shatters before harvesting time. The domesticated type of T.boeoticum known as a diploid wheat of Triticum monococcum L. In this research we want to generate a high quality assembly of wild and domesticated type of Einkorn wheat. Our method is using Illumina short sequence reads assembled by both CLC, and W2RAP(Wheat/Whole- genome Robust Assembly Pipeline) software’s. In our approach …

Analysis Of Two Maize Mutations That Arose After Exposure To Radiation From A Plutonium-Beryllium Source And Developing Molecular Markers For Antimorph Aei1-5180, An Alternative To Aei To Increase Amylose Content In Maize Endosperm, Prameela Awale

Electronic Theses and Dissertations

This thesis consists of two independent projects dealing with two different aspects of maize. The first project is about the maize reproduction, where we try to uncover the candidate genes of two mutations that affect pollen viability and successful fertilization. The second project is about maize endosperm starch, where we developed molecular markers to characterize a mutant allele that knocks a major starch branching enzyme in maize.

Analysis of two maize mutations that arose after exposure to radiation from a plutonium-beryllium source
Maize is a monoecious and diclinous plant. Sexual reproduction takes place by the fusion of haploid male and …

Exploring Phenotypic Diversity And Quantitative Trait Loci Mapping For Root Architecture, Freezing Tolerance, Chilling Fulfillment, And Photoperiod Traits In Grapevine Populations, Dilmini Alahakoon

Electronic Theses and Dissertations

Grapevine (Vitis species) is one of the most valuable fruit crops widely cultivated throughout the United States of America (USA). Grape and wine industries in the northern USA have been expanding rapidly with the demand for quality wine grapes that can be grown in Northern cold climate regions. As most popular cultivars are freezing sensitive, the development of new cultivars for the region continues through breeding. In this study, we evaluated grapevine root system architecture, freezing tolerance, and bud break in different genetic backgrounds in natural or controlled environments. The dissertation research objectives were to explore trait phenotypic variation and …

Varying Weed Densities Alter The Corn Transcriptome, Highlighting A Core Set Of Weed-Induced Genes And Processes With Potential For Manipulating Weed Tolerance, David P. Horvath, Sharon A. Clay, Stephanie A. Bruggeman, James V. Anderson, Wun S. Chao, Kathleen Yeater

Agronomy, Horticulture and Plant Science Faculty Publications

The phenological responses of corn (Zea mays L.) to competition with increasing densities of winter canola (Brassica napus L.) as the weedy competitor were investigated. Changes in the corn transcriptome resulting from varying weed densities were used to identify genes and processes responsive to competition under controlled conditions where light, nutrients, and water were not limited. Increasing densities of weeds resulted in decreased corn growth and development and increased the number and expression intensity of competition-responsive genes. The physiological processes identified in corn that were consistently induced by competition with weeds included protein synthesis and various transport functions. …

Qtl × Environment Interactions Underlie Adaptive Divergence In Switchgrass Across A Large Latitudinal Gradient, David B. Lowry, John T. Lovell, Li Zhang, Jason Bonnette, Philip A. Fay, Robert B. Mitchell, John Lloyd-Reilley, Arvid R. Boe, Et. Al

Agronomy, Horticulture and Plant Science Faculty Publications

Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify the benefits and costs of locally adaptive loci across 17° of latitude in a four-grandparent outbred mapping population in outcrossing switchgrass (Panicum virgatum L.), …

Phomopsis Stem Canker Of Sunflower In North America: Correlation With Climate And Solutions Through Breeding And Management, Brent S. Hulke, Samuel G. Markell, Nolan C. Kane, Febina M. Mathew

Agronomy, Horticulture and Plant Science Faculty Publications

Climate change is occurring in the central US and is interacting with agroecological factors to increase biotic stress in sunflower. Certain species of Diaporthe cause Phomopsis stem canker in sunflower and other dicotyledonous weeds and crops. The increase in precipitation already observed in the states of North Dakota, South Dakota, and Minnesota have increased the chances of outbreaks of necrotrophic pathogens, like Diaporthe. We discuss how climate trends, combined with technological, management, and economic interactions, are correlated with increasing incidence of Phomopsis stem canker in these and adjacent areas in North America. Further, we discuss management options and the …

Iris-Eda: An Integrated Rna-Seq Interpretation System For Gene Expression Data Analysis, Brandon Monier, Adam Mcdermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma

Agronomy, Horticulture and Plant Science Faculty Publications

Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies. While these analyses can provide invaluable information related to gene expression, integration and interpretation of the results can prove challenging. Here we present a tool called IRIS-EDA, …

Native Grass And Legume Biology And Establishment, Arvid A. Boe, P. J. Johnson

Oak Lake Field Station 30th Anniversary Retreat Presentations

No abstract provided.

Identification And Characterization Of Mitogen-Activated Protein Kinase (Mapk) Genes In Sunflower (Helianthus Annuus L.), Surendra Neupane, Sarah E. Schweitzer, Achal Neupane, Ethan J. Anderson, Anne Fennell, Ruanbao Zhou, Madhav P. Nepal

Agronomy, Horticulture and Plant Science Faculty Publications

Mitogen-Activated Protein Kinase (MAPK) genes encode proteins that regulate biotic and abiotic stresses in plants through signaling cascades comprised of three major subfamilies: MAP Kinase (MPK), MAPK Kinase (MKK), and MAPKK Kinase (MKKK). The main objectives of this research were to conduct genome-wide identification of MAPK genes in Helianthus annuus and examine functional divergence of these genes in relation to those in nine other plant species (Amborella trichopoda, Aquilegia coerulea, Arabidopsis thaliana, Daucus carota, Glycine max, Oryza sativa, Solanum lycopersicum, Sphagnum fallax, and Vitis vinifera), representing diverse taxonomic groups of …

Development And Characterization Of Wheat-Thinopyrum Junceiforme Chromosome Addition Lines, Dilkaran Singh

Electronic Theses and Dissertations

Production of wheat is challenged by dynamic biotic and abiotic stresses. Genetic improvement via alien gene transfer is an effective approach to tackle such challenges. Alien gene transfer played an important role in the history of wheat crop improvement. Sea wheatgrass (SWG; Thinopyrum junceiforme, 2n = 28, genomes J1J1J2J2) is a wild relative of wheat. In our previous work, we have developed a complete amphiploid between cultivated emmer and SWG and shown that SWG is resistant to wheat streak mosaic virus, Fusarium head blight and wheat stem sawflies (due to the solid stem) and tolerant to waterlogging, salinity, heat, and …

Disease Resistance In Wheat And Its Relatives, Ethan James Andersen

Electronic Theses and Dissertations

Plants have evolved a complex defense system against pests and pathogens utilizing many types of receptors, signaling factors, and defense compounds to detect pathogen presence and respond effectively. Since many pathogens have evolved immunesuppressing effectors used to reduce plant resistance, plants have evolved a family of receptors that detect pathogenic effectors as a result of an evolutionary arms race. These receptors contain Nucleotide-Binding Site and Leucine-Rich Repeat domains and are called NBS-LRR or NLR proteins. Many grasses possess huge genomes with hundreds of NLR-encoding genes, often found in clusters at the extra-pericentromeric regions of chromosomes, where unequal crossing over causes …

Identification And Characterization Of Stress Responsive Genes In Soybean And Sunflower, Surendra Neupane

Electronic Theses and Dissertations

Stress responsive genes encode proteins involved in plants’ response to abiotic and biotic stresses. Among such stress responsive proteins, proteins encoded by resistance genes (R genes) or nucleotide binding site-leucine-rich repeats (NBS-LRRs) and mitogen-activated protein kinases (MAPKs) are the major groups of proteins regulating biotic and abiotic stresses, respectively. Previous studies in Nepal’s lab at SDSU identified and characterized coiled coil (CC)-NBS-LRRs (CNLs), resistance to powdery mildew8 (RPW8)-NBS-LRRs (RNLs), NBS-LRR (NLs), and MAPK proteins in soybean. This study focuses on R and MAPK genes in the recently sequenced genome of sunflower as well as the toll-interleukin-1 receptor-like nucleotide-binding site leucine-rich …

Validation Of Candidate Loci For Maize Regrowability And Selection Of Near Isogenic Lines For The Loci, Tajbir Raihan

Electronic Theses and Dissertations

Developing perennial grain crops is an effective way for sustainable agriculture and it can be a tool for the betterment of the overall ecosystem. To understand how perenniality works in perennial species, we made a cross between Zea diploperennis and maize (Z. mays) inbred line B73. F1 hybrids produced from this cross were selfed to get the F2 population and later the F2 population underwent Genotyping-By- Sequencing (GBS) analysis. Based on the candidate loci identified on chromosome 2 and chromosome 7 from GBS, SNP-specific markers were developed from the candidate locus interval and used to genotype the F2 …

Development Of Computational Techniques For Identification Of Regulatory Dna Motif, Cankun Wang

Electronic Theses and Dissertations

Identifying precise transcription factor binding sites (TFBS) or regulatory DNA motif (motif) plays a fundamental role in researching transcriptional regulatory mechanism in cells and helping construct regulatory networks for biological investigation. Chromatin immunoprecipitation combined with sequencing (ChIP-seq) and lambda exonuclease digestion followed by high-throughput sequencing (ChIP-exo) enables researchers to identify TFBS on a genome-scale with improved resolution. Several algorithms have been developed to perform motif identification, employing widely different methods and often giving divergent results. In addition, these existing methods still suffer from prediction accuracy. Thesis focuses on the development of improved regulatory DNA motif identification techniques. We designed an …