Genomics Commons^™

Development Of Functional Markers For Resistance To Smut And Identification Of Genes Differentially Expressed In Response To Brown Rust In Sugarcane, Jose David Cortes

LSU Doctoral Dissertations

Smut, caused by Sporisorium scitamineum and brown rust, caused by Puccinia melanocephala, are two of the most important diseases that affect sugarcane production in Louisiana and worldwide. Smut continues to cause losses in the breeding program in Louisiana. Therefore, a QTL analysis was conducted to identify molecular markers associated with resistance in F₁ progeny (162) of a biparental cross between susceptible cultivar L 99-233 and resistant HoCP 96-540. Using 1,574 single-dose SNP markers, a total of 253 linkage groups (LG) were obtained with a genome coverage of 24,580.15 cM. Six QTLs were localized on five LGs. The highest …

Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan Jimenez

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Wheat (Triticum aestivum L.) is a staple cereal that provides 20% of the calories and proteins in human intake (Ray et al., 2013). Global population is projected to increase to 9.7 billion by 2050. Food production must increase by 70% to feed this future population. Wheat production is in crisis due to political and environmental challenges and is projected to decline by 0.8% in 2022 (FAO, 2022). To ensure food security yield genetic gain must increase by around 1.4% annually. Taking advantage of heterosis, hybrid wheat has the potential to boost grain yield. However, hybrid wheat seed production systems …

Unraveling The Genetic Architecture Of Somatic Embryogenesis In Upland Cotton, Adam M. Canal

All Theses

Somatic embryogenesis is the de novo development of asexual embryos because of the plasticity of the plant cell. In tissue culture, the biochemical and genetic mechanisms of dedifferentiated callus tissues can be reprogrammed to transdifferentiate into developed, polarized embryos, which can ultimately regenerate into whole plants. Although this rarely occurs in nature, scientists have exploited this process for decades to regenerate whole plants following gene transformation or for micropropagation. While some species are amenable to in vitro regeneration, upland cotton is particularly recalcitrant, with regenerative potential being confined to only several genotypes. The lack of elite, regenerable genotypes greatly restricts …

Exploration Of Genes Controlling Grain Yield Heterosis In Hybrid Wheat (Triticum Aestivum L.) Utilizing 3ʹ Rna Sequencing, Nichole Miller

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The implementation and future success of hybrid wheat (Triticum aestivum L.) is impacted by breeders’ inability to create consistent high yielding, high heterosis hybrids. This research addresses this problem by conducting an exploration of transcriptomes from hybrids and parent lines to determine what genes are active in heterotic or non-heterotic hybrids and how their level of expression can explain the phenotype of grain yield heterosis. Using hybrids that showed positive mid-parent heterosis (MPH), classified as heterotic in our study, and negative or no difference MPH hybrids, classified as non-heterotic, differentially expressed genes (DEGs) potentially related to heterosis and hybrid …

Screening For Binding Partners And Protein-Protein Interactions Of A Fungal Transcription Factor- Xdr1, Nishadi Punsara Gallala Gamage

Masters Theses

Clarireedia spp. (formerly Sclerotinia homoeocarpaF.T. Bennett) is the causal agent dollar spot, the most economically important turfgrass disease impacting golf courses in North America. The most effective strategy for dollar spot control is repeated application of multiple classes of fungicides. However, reliance on chemical application has led to resistance to four classes of fungicides as well as multidrug resistance (MDR). Fungi are known to detoxify xenobiotics, like fungicides, through transcriptional regulation of three detoxification phases: modification, conjugation and secretion. Little is known, however, of the protein-protein interactions that facilitate these pathways. Following next-generation RNA sequencing of Clarireedia spp., a …

A Functional Genomics Approach To Overwintering Mechanisms In Insects, Emily Allison Wheeler Nadeau

Theses and Dissertations--Entomology

Insects living in temperate and polar environments have developed numerous adaptations to increase survival at low temperatures. A majority of insects are freeze-intolerant and die from internal ice formation, but some are freeze-tolerant and can survive ice formation in extracellular spaces. Both categories of insects prepare for winter with a combination of seasonal and rapid acclimation responses, which differ both in time course and in underlying mechanisms. In this dissertation, I examine adaptations for winter survival in several insect species with a specific focus on molecular mechanisms. To better understand the underpinning mechanisms of these adaptations, I leverage functional genomics …

Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum, Farren Smith

Graduate Theses, Dissertations, and Problem Reports

Plants are some of the most diverse organisms on earth, consisting of more than 350,000 different species. To understand the underlying processes that contributed to plant diversification, it is fundamental to identify the genetic and genomic components that facilitated various adaptations over evolutionary history. Most studies to date have focused on the underlying controls of above-ground traits such as grain and vegetation; however, little is known about the “hidden half” of plants. Root systems comprise half of the total plant structure and provide vital functions such as anchorage, resource acquisition, and storage of energy reserves. The execution of these key …

Has Maize Overtaken Our Reality? A Personal Briefing, Biochemical Comparison, Agrigenomics, And History Of Maize, Nader Pahlevan

Honors Theses

Maize (Zea mays ssp. Mays) is a revolutionary cereal grain that has raced to the world’s most popular staple crop, transforming societies and impacting history. This paper aims to build and portray the story maize has created through its journey to world domination. The important details that encompass this literature are maize’s cultural significance in my life’s story, the comparison of various starches broken down into amylose and amylopectin ratios, a summative historical account on maize’s spread throughout numerous parts of the old world, and the genetical analysis of maize that explains the key features that have led …

Extreme‐Phenotype Genome‐Wide Association Study (Xp‐Gwas): A Method For Identifying Trait‐Associated Variants By Sequencing Pools Of Individuals Selected From A Diversity Panel, Jinliang Yang, Haiying Jiang, Cheng-Ting Yeh, Jianming Yu, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Although approaches for performing genome‐wide association studies (GWAS) are well developed, conventional GWAS requires high‐density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP‐GWAS (extreme‐phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well‐characterized kernel row number trait, which was …

Beef Production Systems In The Nebraska Sandhills, Mckay Erickson

Department of Animal Science: Dissertations, Theses, and Student Research

Four studies were conducted to determine the effectiveness of improving production systems of beef cattle in the Sandhills region of Nebraska. These studies were to determine impacts of modified estrus synchronization protocols, genomic testing heifer calves for longevity, and evaluation of 2 differing calving systems (March or May) for improving biological outcome and improved production. Experiment 1 utilized 180 yearling heifers to determine the effectiveness of a second dose of prostaglandin F_2α(PGF) with those females not expressing estrus after an initial 14 d MGA-PG estrus synchronization protocol. The treatment of PGF did increase estrus expression, but did not …

Genetic Assessment Of Inbred Chicken Lines Indicates Genomic Signatures Of Resistance To Marek's Disease, Lingyang Xu, Yanghua He, George E. Liu, Huanmin Zhang, Hans H. Cheng, Robert L. Taylor Jr, Jiuzhou Song

Faculty & Staff Scholarship

Background: Marek’s disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. However, the mechanisms of genetic resistance for MD are complex and not fully understood. MD-resistant line 63 and MD-susceptible line 72 are two highly inbred progenitor lines of White Leghorn. Recombinant Congenic Strains (RCS) were developed from these two lines, which show varied susceptibility to MD.

Results: We investigated genetic structure and genomic signatures across the genome, including the line 63 and line 72, six RCSs, and two reciprocally crossed flocks between the lines 63 and 72 (F1 63 × 72 and F1 72 × …

All Roads Lead To Weediness: Stories About Weedy Rice Origins, Weedy Genes And Weed Competitiveness, Zhongyun Huang

Doctoral Dissertations

Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O.sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the ‘agricultural weed syndrome’, making this an ideal model to study the genetic basis of parallel evolution. Using population genetics analyses of South Asian and US weedy rice, my research reveals multiple independent evolution events giving rise to weed groups in the two geographic areas. Weeds in South Asia have highly heterogenous genetic backgrounds, with contributions from both cultivated varieties (aus and indica) …

Improvement Of Milling And Nutritional Quality Characteristics Of Oats Through Genomic Selection, Sudha Neupane Adhikari

Electronic Theses and Dissertations

Oats can lower cholesterol, reduce risks of type-2 diabetes, and help prevent heart diseases when consumed daily. Therefore, it is important to evaluate and select breeding lines with desirable milling and nutritional quality traits. Genomic selection, which uses genotyping data to predict the breeding value of an individual, is a promising method to increase genetic gain by selecting for quality traits earlier in the line development process. In this study, we collected phenotypic data for three nutritional traits (protein, β- glucan, and fat content) and five milling quality traits (percent plumps, percent thins, percent plump groat, groat percent and thousand …

Novel Advancements For Improving Sprout Safety, Kyle S. Landry

Doctoral Dissertations

All varieties of bean sprouts (mung bean, alfalfa, broccoli, and radish) are classified as a “super-food” and are common staples for health conscious consumers. Along with the proposed health benefits, there is also an inherent risk of foodborne illness. When sprouts are cooked, there is little risk of illness. The purpose of this dissertation was to explore novel techniques to minimize or prevent the incidence of foodborne illness associated with the consumption of sprouts. Three areas were investigated: 1) the use of a biocontrol organism, 2) the use of a novel spontaneous carvacrol nanoemulsion, and 3) the influence of the …

Biology, Gene Flow, And Management Of Glyphosate-Resistant Common Waterhemp (Amaranthus Rudis Sauer) In Nebraska, Debalin Sarangi

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Common waterhemp is the most troublesome weed in the midwestern United States. Growers from Nebraska reported failure to control common waterhemp following sequential applications of glyphosate in glyphosate-tolerant corn and soybean, which led to moderate to severe yield loss; justifying the need to confirm resistance and study the biology and management of common waterhemp. The objectives of this research were: 1) to confirm the presence of glyphosate-resistant (GR) common waterhemp biotypes in Nebraska and to evaluate their sensitivity to herbicides belonging to alternative sites-of-action; 2) to evaluate the response of common waterhemp to water stress; 3) to quantify pollen-mediated gene …

Variation In Avian Pathogenic Escherichia Coli Colonization Levels In Chickens, Melissa Monson, Michael Kaiser, Susan Lamont

Melissa Monson

Colonization levels in five tissues after avian pathogenic Escherichia coli (APEC) inoculation were investigated in chickens to generate phenotypic data for a genome wide association study (GWAS). Bacterial loads were measured in 370 birds and varied among individuals and tissues. Mean bacterial levels were significantly different between tissues (right lung > spleen > left lung and liver > blood). There were also significant correlations in bacterial load between tissues. These data suggest that colonization levels could be used as phenotypes in GWAS and could help identify markers associated with poultry resistance to APEC infections. After verification, these markers could be used for genetic …

Genomic Prediction Of Gene Bank Wheat Landraces, José Crossa, Diego Jarquin, Jorge Franco, Paulino Pérez-Rodríguez, Juan Burgueño, Carolina Saint-Pierre, Prashant Vikram, Carolina Sansaloni, Cesar Petroli, Denis Akdemir, Clay Sneller, Matthew Reynolds, Maria Tattaris, Thomas Payne, Carlos Guzman, Roberto J. Peña, Peter Wenzl, Sukhwinder Singh

Department of Agronomy and Horticulture: Faculty Publications

This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% …

The Effects Of Manufactured Nanomaterial Transformations On Bioavailability, Toxicity And Transcriptomic Responses Of Caenorhabditis Elegans, Daniel L. Starnes

Theses and Dissertations--Plant and Soil Sciences

In recent decades, there has been a rapid expansion in the use of manufactured nanoparticles (MNPs). Experimental evidence and material flow models predict that MNPs enter wastewater treatment plants and partition to sewage sludge and majority of that sludge is land applied as biosolids. During wastewater treatment and after land application, MNPs undergo biogeochemical transformations (aging). The primary transformation process for silver MNPs (Ag-MNPs) is sulfidation, while zinc oxide MNPs (ZnO-MNPs) most likely undergo phosphatation and sulfidation. Our overall goal was to assess bioavailability and toxicogenomic impacts of both pristine, defined as-synthesized, and aged Ag- and ZnO-MNPs, as well as …

Differential Expression Of Cyb5a In Chinese And European Pig Breeds Due To Genetic Variations In The Promoter Region..Pdf, Ying Bai, Jibin Zhang, Y Xue, Yl Peng, Gang Chen, Meiying Fang

Jibin Zhang

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species⁴. RNA-seq analysis showed that one gene, PPTG_16698 has the 5^th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of …

Epigenetics Of Stress Adaptation In Arabidopsis: The Case Of Histone Modifications, Behnaz Najafi Majdabadi Farahani

Electronic Thesis and Dissertation Repository

Changes in the epigenetic status of plants, which contribute to changes in gene expression, in response to abiotic stress are well documented. However, their stability and transmission to subsequent generations, and their incorporation into plant stress adaptation are still a matter for debate. Using chromatin immuno-precipitation and Next Generation Sequencing (ChIP-seq), we compared genome wide enrichment of two histone marks, H3K9ac and H3K4me2, in the progeny of salt stressed and control Arabidopsis plants. Data showed less enrichment of the H3K9ac in the chromatin of the progeny of salt stressed plants, but no changes were detected in the enrichment of the …

Escape From Preferential Retention Following Repeated Whole Genome Duplications In Plants, James C. Schnable, Xiaowu Wang, J. Chris Pires, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

The well supported gene dosage hypothesis predicts that genes encoding proteins engaged in dose–sensitive interactions cannot be reduced back to single copies once all interacting partners are simultaneously duplicated in a whole genome duplication. The genomes of extant flowering plants are the result of many sequential rounds of whole genome duplication, yet the fraction of genomes devoted to encoding complex molecular machines does not increase as fast as expected through multiple rounds of whole genome duplications. Using parallel interspecies genomic comparisons in the grasses and crucifers, we demonstrate that genes retained as duplicates following a whole genome duplication have only …

Phylogenetics Of Morus (Moraceae) Inferred From Its And Trnl-Trnf Sequence Data., Madhav Nepal

Madhav Nepal

Genome-Wide Analysis Of Syntenic Gene Deletion In The Grasses, James C. Schnable, Michael Freeling, Eric Lyons

Department of Agronomy and Horticulture: Faculty Publications

The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost …

High-Resolution Mapping Of Open Chromatin In The Rice Genome, Wenli Zhang, Yufeng Wu, James C. Schnable, Zixian Zeng, Michael Freeling, Gregory E. Crawford, Jiming Jiang

Department of Agronomy and Horticulture: Faculty Publications

Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa). Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions. We found 58% more DH sites in …

Screening Synteny Blocks In Pairwise Genome Comparisons Through Integer Programming, Haibao Tang, Eric Lyons, Brent S. Pedersen, James C. Schnable, Andrew H. Paterson, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Background:

It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple “subgenomes” derived from genome duplications, we need to relax the traditional requirements of “one-to-one” syntenic matchings of genomic regions in order to reflect “one-to-many” or more generally “many-to-many” matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we …

Genes Identified By Visible Mutant Phenotypes Show Increased Bias Toward One Of Two Subgenomes Of Maize, James C. Schnable, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these ‘‘classical’’ maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that …

Dose–Sensitivity, Conserved Non-Coding Sequences, And Duplicate Gene Retention Through Multiple Tetraploidies In The Grasses, James C. Schnable, Brent S. Pedersen, Sabarinath Subramaniam, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein–protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This …

Following Tetraploidy In Maize, A Short Deletion Mechanism Removed Genes Preferentially From One Of The Two Homeologs, Margaret R. Woodhouse, James C. Schnable, Brent S. Pedersen, Eric Lyons, Damon Lisch, Shabarinath Subramaniam, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Previous work in Arabidopsis showed that after an ancient tetraploidy event, genes were preferentially removed from one of the two homeologs, a process known as fractionation. The mechanism of fractionation is unknown. We sought to determine whether such preferential, or biased, fractionation exists in maize and, if so, whether a specific mechanism could be implicated in this process. We studied the process of fractionation using two recently sequenced grass species: sorghum and maize. The maize lineage has experienced a tetraploidy since its divergence from sorghum approximately 12 million years ago, and fragments of many knocked-out genes retain enough sequence similarity …

3hsds1和17hsds7基因5'上游区转录活性研究.Pdf, Xinxing Dong, Yi Xin, Ying Bai, Yunzhou Yang, Jibin Zhang, Meiying Fang, Gang Chen

Jibin Zhang