Plant Breeding and Genetics Commons^™

Analyzing Multigene Stacking And Genome Editing Strategies In Rice, Bhuvan Pathak

Graduate Theses and Dissertations

Crop improvement through biotechnology is an integrated effort, incorporating multiple approaches like integration of genes, editing of native genes, and removal of selection marker genes. Before streamlining the protocols, the efficiency and feasibility of the individual approach and their components must be tested. This study evaluated following approaches: 1) stacking an array of genes into a single locus by site-specific integration via Cre-lox recombination in rice, 2) determining the efficiency of I-SceI and the CCR5-ZFN in the targeted excisions of gene fragments in rice and Arabidopsis, and 3) determining the efficiency of CRISPR/Cas9 in generating targeted mutations for genome editing …

Qtl Mapping Of Panicle Architecture And Yield-Related Traits Between Two U.S. Rice Cultivars 'Lagrue' And 'Lemont', Adam D. Rice

Graduate Theses and Dissertations

Grain yield in rice consists of multiple yield components such as number of panicles/plant, number of tillers/plant, and number of seeds/panicle. Panicle architecture is an important yield trait yield as the number of seeds on a panicle greatly contributes to the overall panicle yield. A QTL analysis and mapping study on panicle architecture and yield-related traits was performed to identify major QTL and candidate genes associated with the traits. The first objective of the project was to do a yield study evaluating 15 agronomic traits between each of the four U.S. rice cultivars, ‘LaGrue’, ‘Lemont’, ‘Bengal’, and ‘Mars’, to determine …

Investigating The Connection Between Light, A Circadian Clock, And Pathogenesis In Cercospora Zeae-Maydis, John Byron Ridenour

Graduate Theses and Dissertations

Gray leaf spot is a globally important foliar disease of maize caused by the fungus Cercospora zeae-maydis. In C. zeae-maydis, light is a critical environmental signal linked to pathogenesis and secondary metabolism. However, the mechanisms by which the fungus senses and responds to light are not fully understood. Thus, the overarching goal of this project was to unravel the connection between light and pathogenesis in C. zeae-maydis. The conserved fungal protein White Collar-1 (WC-1), designated Crp1 in C. zeae-maydis, senses light and initiates physiological responses. In fungi, WC-1 functions in the White Collar Complex via interaction with White Collar-2 (WC-2). …

Influence Of Loss Of Function Of The Fatty Acid Desaturase 7 Gene On Photosynthetic Activity And Foliar Redox Status, Janithri Savindya Wickramanayake

Graduate Theses and Dissertations

Fatty Acid Desaturase7 (FAD7) is a chloroplast-localized enzyme that converts 16 and 18 carbon dienoic fatty acids to trienoic fatty acids. The suppressor of prosystemin-mediated response2 (spr2) mutant in tomato (Solanum lycopersicum) and the fad7-1 mutant in Arabidopsis (Arabidopsis thaliana) result in the loss of function of FAD7, which alter the fatty acid profiles of chloroplast membranes and enhance resistance against aphids. This research contributes toward the long-term goal of identifying factors that determine aphid resistance in FAD7 mutants. Previous data suggested constitutive differences between spr2 and WT including increased expression of genes associated with photosynthesis and differences in redox …

Linkage Mapping For Soybean (Glycine Max) Flood Tolerance, Wade Stiles Hummer

Graduate Theses and Dissertations

Flood tolerance in soybean (Glycine max) is not a well-characterized trait, yet flooding damage is second only to drought stress in terms of yield reduction. The objectives of this study were to determine genetic variation for flooding tolerance in two populations of soybean recombinant inbred lines (RILs) and to identify and confirm flood tolerant QTL. Population A (WHA) consisted of 111 RILs derived from the cross 5002T by 91210-350 and Population B (WHB) consisted of 79 RILs from the cross RA-452 by Osage. Experiments were conducted at the Rice Research and Extension Center (RREC) near Stuttgart, AR in 2015 and …

Identification And Characterization Of Salinity Tolerance Genes By Activation Tagging In Arabidopsis, Jawaher Alkahtani

Graduate Theses and Dissertations

Salinity often affects irrigated areas in arid and semi-arid regions of the world. The existence and accumulation of soluble salts in the soil layers limit the growth of crops essential for our food. Salt stress dramatically affects plant growth, plant development, as well as crop yield. Arabidopsis thaliana is the plant model that provides a comprehensive knowledge of plant development, genetics and physiology, and response to abiotic stresses such as salinity. The redundancy of genes due to duplication, even in the simple model genome of Arabidopsis, limits the value of knockout (KO) mutagenesis to provide complete information on gene function. …

Association Mapping And Genomic Selection For Yield And Agronomic Traits In Soft Winter Wheat, Dennis Bulusan Lozada

Graduate Theses and Dissertations

Tools such as genome-wide association study (GWAS) and genomic selection (GS) have expedited the development of crops with improved genetic potential. While GWAS aims to identify significant markers associated with a trait of interest, the goal of GS is to utilize all marker effects to predict the performance of new breeding lines prior to testing. A GWAS for grain yield (GY), yield components, and agronomic traits was conducted using a diverse panel of 239 soft winter wheat (SWW) lines evaluated in eight site-years in Arkansas and Oklahoma. Broad sense heritability of GY (H2=0.48) was moderate compared to other traits including …

Dissection Of Soil Waterlogging Tolerance In Soft Red Winter Wheat Using Genomic Approaches, Marlovi Andrea Acuna-Galindo

Graduate Theses and Dissertations

Genomic methods including genome wide association analysis (GWAS), genomic selection (GS) and RNA-seq allow for faster selection of superior breeding lines and for identification and resolution of candidate genes. A panel of 240 soft red winter wheat (Triticum aestivum L.) cultivars and breeding lines were subjected to soil waterlogging stress over two seasons at Stuttgart, AR and St. Joseph, LA, US. Total concentrations of P, K, Ca, Mg, Mn, Fe, Al, B, Cu, Na, S and Zn were determined in wheat shoots post-waterlogging using inductively coupled plasma spectroscopy. Yield components kernel number per spike (KNPS), kernel weight per spike (KWS) …

Effect Of Allelic Variation In Rht Loci On Plant Height And Grain Yield Of Soft Red Winter Wheat (Triticum Aestivum L.), Habib Hayat

Graduate Theses and Dissertations

Plant height in wheat (Triticum aestivum L.) is controlled in large part by two major Rht genes, Rht-B1 and Rht-D1, which pleiotropically impact lodging and grain yield. Prior to the Green Revolution, wheat varieties contained only ‘wild-type’ Rht alleles (Rht-B1a and Rht-D1a) and were tall and prone to lodging. Introgression of a semi-dominant mutation at either of these two loci (Rht-B1b or Rht-D1b) results in a semi-dwarf phenotype and reduced plant height. When combined (Rht-B1b and Rht-D1b) an extremely short double-dwarf phenotype is observed. The objective of this study was to determine the impact of allelic variation in Rht-B1 and …

An Evaluation Of Breeding, Agronomic, And Processing Methodologies Of Vegetable Soybean (Edamame) To Increase Domestic Production In The United States Market, David Octor Moseley

Graduate Theses and Dissertations

Edamame is a food-grade soybean (Glycine max (L.) Merrill) that is either harvested immature (R6 stage) or after plant maturity (R8 stage). At R6, the premium product will have crescent- shaped large green pods and gray pubescence. At R8, the seed will either have stayed green or will have turned yellow, black, or brown. Edamame is a healthy snack with a sweet flavor and firm texture. The edamame market is growing in the United States, creating a need for more adapted varieties. The genetic diversity is low among adapted large-seeded breeding lines. Finding diverse accessions will help develop larger and …

A Genome Wide Association Study For Fusarium Head Blight Resistance In Southern Soft Red Winter Wheat, Amanda Holder

Graduate Theses and Dissertations

Fusarium head blight (FHB) is a disease of small grains caused by the fungal pathogen Fusarium graminearum. FHB poses potential economic losses and health risks due to the accumulation of the mycotoxin deoxynivalenol (DON) on infected seed heads. The objectives of this study are: 1) evaluate soft red winter wheat (SRWW) lines for resistance to FHB in terms of resistance to initial inoculum (incidence); resistance to spread within the head (severity); resistance to DON accumulation; and resistance to Fusarium damaged kernels (FDK), 2) determine the frequency and effect of known FHB resistance genes and quantitative trait loci (QTL), and 3) …

Genetic And Phytopathological Studies On Charcoal Rot Resistance In Soybean [Glycine Max (L) Merr.], Marcos Paulo Da Silva

Graduate Theses and Dissertations

Charcoal rot of soybean (Glycine max (L.), caused by Macrophomina phaseolina is a disease of economic significance in the United States. The identification and quantification of the resistance is difficult, and very little is known about the genetics and markers linked to the charcoal rot (CR) resistance genes. Current assay methods can be time consuming, and data may vary between tests. The objectives of this study were to 1) create a robust seed plate assay (SPA) for CR resistance by comparing results with cut-stem and CFUI assays; 2) correlate and compare field data disease assessments with SPA; 3) identify QTLs …

Development And Characterization Of Rice Genotypes For Water Use Efficiency And Drought Resistance, Anuj Kumar

Graduate Theses and Dissertations

Rice, the second largest staple food crop, uses 30% of global fresh water to complete its life cycle worldwide. Water deficits worldwide have become a serious problem affecting rice growth and ultimately grain yield. To solve the water problem globally, improvement of water use efficiency (WUE) and other drought resistance (DR) traits in rice genotypes would be a useful strategy using advanced genomics tools. In this study, our objectives were to 1) analyze phenotypes of the USDA rice mini-core collection (URMC) for WUE and DR related traits, 2) correlate drought response phenes for physiological traits and grain yield in the …

Genomic And Physiological Approaches To Improve Drought Tolerance In Soybean, Avjinder Kaler

Graduate Theses and Dissertations

Drought stress is a major global constraint for crop production, and improving crop tolerance to drought is of critical importance. Direct selection of drought tolerance among genotypes for yield is limited because of low heritability, polygenic control, epistasis effects, and genotype by environment interactions. Crop physiology can play a major role for improving drought tolerance through the identification of traits associated with drought tolerance that can be used as indirect selection criteria in a breeding program. Carbon isotope ratio (δ13C, associated with water use efficiency), oxygen isotope ratio (δ18O, associated with transpiration), canopy temperature (CT), canopy wilting, and canopy coverage …

Association Mapping Of Seed Weight, Protein, And Sucrose Content; And Kinetics Of Edamame Under Infrared Treatment, Laura Melissa Lara Santisteban

Graduate Theses and Dissertations

Edamame is a specialty large-seeded soybean (Glycine max L. Merr.) harvested at an immature stage (R6) that has become the second largest consumed soyfood. Although United States is the largest soybean producer, majority of edamame is imported from Asia, highlighting the importance of developing new edamame varieties. Association mapping (AM) provides an alternative to bi-parental linkage mapping method to detect quantitative trait loci (QTL) adding higher resolution and broader germplasm information. Seed weight, sucrose, and protein are quantitative traits of value when selecting edamame lines. However molecular mechanisms controlling each of these traits are still inconclusive and have not been …

Quantitative Trait Loci Mapping, Genome-Wide Association Analysis, And Gene Expression Of Salt Tolerance In Soybean, Ailan Zeng

Graduate Theses and Dissertations

Salt stress is a common abiotic stress causing yield reduction in soybean. There are differential responses, namely tolerance (excluder) and intolerance (includer), among soybean germplasm. However, the genetic and physiological mechanism for salt tolerance is not clear. Identification of novel QTL for salt tolerance and genes that are differentially expressed under salt stress would help elucidate the salt tolerance mechanism and facilitate the development of salt tolerant cultivars through marker assisted selection (MAS). The objectives of this study were to identify new QTL or genes responsible for salt tolerance using three approaches: QTL mapping, association analysis, and RNA sequencing (RNA-seq). …

Phenotypic And Gene Expression Analysis Of Diverse Rice Genotypes In Response To Drought, Miranti Rahmaningsih

Graduate Theses and Dissertations

Drought is one of the most limiting factors for rice (Oryza sativa L.) growth and development with vegetative and reproductive stages the most sensitive and distinct phases. During the vegetative stage, drought can cause reduction in growth and biomass accumulation. Moreover, water stress at reproductive stage can reduce yield significantly. Plants are protected against drought by three different mechanisms: drought avoidance, drought tolerance, and drought escape. An integrated approach combining physiology, breeding, and genomics could be an effective way to characterize and mitigate this problem. The objectives of this research were to (1) screen a diverse set of rice genotypes …

Genetic Basis Of Biosynthesis And Cytotoxic Activity Of Medicago Truncatula Triterpene Saponins, Brynn Kathleen Lawrence

Graduate Theses and Dissertations

Saponins are a large family of specialized metabolites produced in many plants. They can have negative effects on a number of plant pests and are thought to play a role in plant defense. With current and possible future uses in industry and agriculture, saponins have also been shown to be hypocholesterolemic, hypoglycemic, immunostimulatory, antioxidative, anti-inflammatory, and cytotoxic. In spite of their usefulness, our understanding of the genetic basis for saponin biosynthesis is still incomplete. We generated recombinant populations with parents from genetically distinct accessions of Medicago truncatula, with either high or low accumulation and varying profiles of saponins. Primers for …

Genetic Determinism Of Xanthomonas Arboricola Pv. Pruni (Xap) Resistance, Fruit Quality, And Phenological Traits In Peach And Incorporation Of Marker-Assisted Selection (Mas) In The University Of Arkansas Peach And Nectarine Breeding Program, Terrence James Frett

Graduate Theses and Dissertations

For over two decades the incorporation of marker-assisted selection (MAS) has been discussed as an innovative approach to increase peach breeding efficiency. Although hundreds of quantitative trait loci (QTLs) have been identified, only a few have been converted into usable MAS tools. This highlights a disconnect between genomic discoveries and practical application in breeding programs, which has delayed use of MAS.

In this dissertation, three sequential steps were performed with the objective to bridge this gap and develop breeding-relevant DNA tests for MAS of fruit bacterial spot resistance (Xap1 and Xap6), fruit quality [blush (Rf), acidity (D), and acidity and …

Consumer Willingness To Pay For Genetically Engineered Edamame, Elijah John Wolfe

Graduate Theses and Dissertations

This study examined the effect of GM labeling on consumer willingness to pay (WTP) for edamame. It also investigated how people reacted to different messages and whether the order of receiving positive or negative information about GM technology impacted their willingness to pay (WTP). The study had three components: (1) a sensory test of GM and non-GM labeled products; (2) a non-hypothetical experimental auction to assess WTP for GM, non-GM and unlabeled products; and (3) a questionnaire to collect demographics and other information from the participants. Results of the sensory evaluation revealed no statistically significant difference between GM and non-GM …

Gene Expression And Physiological Analysis To Study Differences Between Oryza Sativa Cultivars Susceptible And Resistant To Chalky Grain Formation Subjected To High Nighttime Temperatures., Nicholas Lawson

Graduate Theses and Dissertations

Starch composition and grain quality of rice is greatly influenced by genotype and environmental factors. The detrimental effects of high nighttime temperatures on rice yield and quality has recently become apparent, with some of the warmest average nighttime temperatures being recorded in the past few years. One of the most notable effects of this stress, an increase in grain chalk formation, correlates with a decrease in quality. This effect varies greatly between cultivars as some show less temperature-sensitive quality reduction than others. The goal of this research is to elucidate fundamental changes that occur in developing plants and grains as …

Preserving Rice Quality: Fine-Mapping And Introgressing A Fissure Resistance Locus, Haley Marie Sater

Graduate Theses and Dissertations

Rice (Oryza sativa L.) kernel fissuring is a major concern of both rice producers and millers. Fissures are small cracks in rice kernels that increase breakage of kernels when milled, and decrease the value of processed rice. This study employed molecular gene tagging methods to fine-map a fissure resistance (FR) locus found in ‘Cybonnet’, a semidwarf tropical japonica cultivar, as well as transfer this trait to rice genotypes of taller, non-semidwarf plant height that are better adapted to some rice production systems. Three QTLs for FR were previously reported; the FR locus with strongest effect resides near the semidwarf sd-1 …

Influence Of Fatty Acids And Their Derivatives On Aphid Resistance In Arabidopsis And Tomato, Jiamei Li

Graduate Theses and Dissertations

Fatty acid desaturases (FADs) are enzymes that act in the chloroplast or the endoplasmic reticulum (ER) to incorporate double bonds into the acyl chains of fatty acids, and recent evidence indicates that at least one of these enzymes, FAD7, also influences plant resistance to aphids. FAD7 is an enzyme in the chloroplast that is found throughout the plant kingdom and that desaturates 16- and 18-carbon fatty acids (FAs) with two double bonds (dienoic acids) to generate FAs with three double bonds (trienoic acids). In tomato (Solanum lycopersicum) and the model plant Arabidopsis thaliana, mutants with impaired FAD7 function are more …

Genetic Analysis Of Soybean Mosaic Virus (Smv) Resistance Genes In Soybean [Glycine Max (L.) Merr.], Mariola Klepadlo

Graduate Theses and Dissertations

Soybean mosaic virus (SMV) causes the most serious viral disease in soybean worldwide. Seven SMV strains, G1 - G7, and three independent multi-allelic loci for SMV resistance, Rsv1, Rsv3, and Rsv4, have been identified. In the initial study, 299 soybean germplasm lines were genotyped for Rsv4 region, inoculated with SMV-G1 and G7 strains, and classified into several resistance groups. The Glyma.02g121400 locus was sequenced from ten soybean accessions, and alignment of the sequences revealed three SNPs displaying 100% polymorphic consistency when a soybean genotype carrying the Rsv4 gene was present. A cross between V94-5152 × Lee 68 was made to …

The Role Of G-Protein Signaling In Pathogenesis In Cercospora Zeae-Maydis, Brant Smith

Graduate Theses and Dissertations

Gray leaf spot, caused by Cercospora zeae-maydis, is one of the most destructive foliar diseases of maize worldwide. C. zeae-maydis orients hyphal growth towards stomata (stomatal tropism) and forms infectious structures (appressoria) that are necessary for successful infection. Although some genes involved in pathogenesis in C. zeae-maydis have been identified, the molecular mechanisms are not well understood. In fungi, heterotrimeric G-proteins consist of three subunits (α, β, and γ) and mediate responses to environmental stimuli. They regulate diverse functions, including nutrient detection, virulence, fungal development, conidiation, secondary metabolism, and pathogenesis in many plant pathogenic fungi. This research explored the role …

Analysis Of Ac/Ds Activation Tagged Mutants In Tomato (Solanum Lycopersicum), Ipeleng Randome

Graduate Theses and Dissertations

Tomato (Solanum lycopersicum) is a crop of immense economic and nutritional importance worldwide and also a good model organism for genomic studies of other dicot species. The recent completion of the tomato genome sequence is a great milestone towards learning about the tomato genome. Elucidation of the function of the different genes using different functional genomic tools is therefore important in adding to this resource. To this end, we have developed an Ac-Ds transposon ‘activation tagging’ (ATag) system to be able to transpose transposon inserts, bearing a strong 35S-enhancer element, all around the genome. An Ac-Ds ATag construct was used …

Applying Molecular And Phenotypic Tools To Characterize Flesh Texture And Acidity Traits In The Arkansas Peach Breeding Program And Understanding The Crispy Texture In The Arkansas Blackberry Breeding Program, Alejandra Andrea Salgado Rojas

Graduate Theses and Dissertations

Quantitative trait loci (QTL) utilizing a pedigree-based analysis (PBA) approach was performed in the peach breeding program for the first time. The pedigree consisted of seven-F1 populations, their parents, ancestors, and cultivars. Flesh firmness and titratable acidity (TA) were examined in 2011, 2012, and 2013. For TA, a consistent and strong QTL was identified on the proximal end of linkage group (LG) 5 of the peach genome. For flesh firmness, two QTLs were located on LG 4. The first QTL was located on the chromosomal region where the slow-melting flesh (SMF) DNA test was identified, and the second QTL was …

Cotton Injury Due To Soil- Or Foliar-Applied Herbicides: An Assessment Based On The Influences Of Genetic, Agronomic, And Environmental Factors, Brandon William Schrage

Graduate Theses and Dissertations

Increasing populations of glyphosate-resistant weeds, such as Palmer amaranth, have prompted growers to pursue alternative means of weed control in cotton. In many cropping systems, this means the utilization of older chemistries and residual herbicides. The goal of this research was to evaluate and understand the agronomic and environmental factors that affect the inconsistent injury often associated with these herbicides as well as determine the impact of Palmer amaranth emergence date on seed production, biomass, and cotton yield. Experiments were conducted in three counties in Arkansas giving a distinct range of climate and soil texture. Injury, biomass, and number of …

Association Mapping For Elemental Concentration Resulting From Vegetative Stage Soil Waterlogging Stress In Wheat (Triticum Aestivum L.), Maria Nelly Arguello-Blanco

Graduate Theses and Dissertations

Soil waterlogging (WL) affects wheat production worldwide, including the southern of the U.S. Little is known about the genetics of tolerance mechanisms to WL, particularly of potentially toxic elements such as aluminum, iron and sodium. The objectives of this study were to use association mapping (AM) to identify SNP associated with the EC in the vegetative tissue of a set of 240 diverse soft winter wheat genotypes (AM panel) grown under field WL and to determine the impact of WL on wheat yield (GY) and yield components in a set 28 adapted cultivars (YT)

YT study showed reductions in GY …

Physiological Responses Of Cotton Genotypes To Water-Deficit Stress During Reproductive Development, Cristiane Pilon

Graduate Theses and Dissertations

Drought stress is one of the major abiotic factors affecting crop growth and limiting production worldwide. Cotton genotypes vary in drought tolerance, and the effects of drought stress on the anatomy and physiology of cotton leaves and roots have been reported. However, information on physiological and metabolic processes of leaves and flowers of modern cotton cultivars under water-deficit stress during reproductive development is not well elucidated. It was hypothesized that water-deficit stress during squaring and flowering stages would impair stomatal conductance and photosynthetic efficiency of leaves, which consequently would result in osmotic adjustment through accumulation of compatible solutes, increased activity …