Plant Breeding and Genetics Commons^™

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 …

Non-Homology-Based Prediction Of Gene Functions In Maize (Zea Mays Ssp. Mays), Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James Schnable, Pinghua Li

Center for Plant Science Innovation: Faculty Publications

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions.As a result, homology is widely used for gene function prediction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random forest-based prediction consistently provided the most accurate gene function prediction. …

Patterns Of Genetic Diversity In Highly Invasive Species: Cogongrass (Imperata Cylindrica) Expansion In The Invaded Range Of The Southern United States (Us), Rima D. Lucardi, Lisa E. Wallace, Gary N. Ervin

Biological Sciences Faculty Publications

The spatial expansions of invasive organisms in the novel range are generally expected to follow an isolation-by-distance relationship (IBD) if the invasion is biologically driven; however, many invasions are facilitated anthropogenically. This research focused on the extant expansion patterns of cogongrass (Imperata cylindrica). Cogongrass is a widespread invasive species throughout the southern United States (US). Patterns of infestation vary among US states. Cogongrass is pyrogenic, and its invasion threatens softwood (Pinus spp.) plantations, a substantial economic market for this US region. Over 600 individuals were sampled from seven invaded US states, using amplified fragment length polymorphisms (AFLPs) …

Genetic Control Of Arbuscular Mycorrhizal Colonization In Helianthus Annuus, Katherine Stahlhut

Honors Undergraduate Theses

Plant symbiosis with arbuscular mycorrhizal (AM) fungi provides many benefits for plants, including increased nutrient uptake, drought tolerance, and belowground pathogen resistance. In order to have a better understanding of the genetic architecture of mycorrhizal symbiosis, we conducted a genome-wide association study (GWAS) by phenotyping a diversity panel of cultivated sunflower (Helianthus annuus) for root colonization under inoculation with the AM fungus Rhizophagus intraradices. This mapping panel consists of 261 inbred lines that capture approximately 90% of the genetic diversity present in the cultivated sunflower germplasm. Using a mixed linear model approach with a high-density genetic map, we …

Floral Trait Architecture In Crop Sunflower (Helianthus Annuus) Under Drought Conditions, Lauren Segarra

All Master's Theses

Longer and more intense droughts are predicted to become more common in the coming century due to anthropogenic climate change. Drought can reduce crop yield and decrease food security. In order to mitigate the negative effects of drought on crop production, it is important to elucidate the underlying mechanisms that promote drought stress resistance in crop plants. Floral traits impact yield, especially in oilseed crops such as sunflower (Helianthus annuus), but their susceptibility to drought stress is understudied. The goal of this study was to describe the floral trait architecture of H. annuus crop lines under drought versus …

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 …

Asparagus Cultivar Trial – Selinsgrove, Pa, Carl Cantaluppi

Midwest Vegetable Trial Reports

This paper reports on yields of three asparagus varieties in Pennsylvania harvested one year after planting one-year-old crowns.

Arthropod Resistant Tomatoes: Screening Tools, Yield And Nutritional Quality Of Interspecific Hybrids, Mohammad Hasan Salman Ali Dawood

Theses and Dissertations--Plant and Soil Sciences

Tomato (Solanum lycopersicum) is one of the most economically important vegetable crops grown around globe but is a host for numerous pests and pathogens. In the future, tomato breeders will have to focus on increasing fruit quantity and on enhancing pest resistance. Many accessions of the wild relative of tomato, S. habrochaites display high levels of resistance towards arthropods such as spider mites. The presence of the sesquiterpene hydrocarbon, 7-epi-zingiberene, found in S. habrochaites type IV trichomes has been associated with arthropod resistance. However, the presence of other compounds in its trichome secretions may also be related …

Functional Characterization Of Petiolule-Like Pulvinus (Plp) Gene In Abscission Zone Development In Medicago Truncatula And Its Application To Genetic Improvement Of Alfalfa, Juan Du, Shaoyun Lu, Maofeng Chai, Chuanen Zhou, Liang Sun, Yuhong Tang, Jin Nakashima, Jaydeep Kolape, Zhaozhu Wen, Marjan Behzadirad, Tianxiu Zhong, Juan Sun, Yunwei Zhang, Zeng-Yu Wang

Nebraska Center for Biotechnology: Faculty and Staff Publications

Alfalfa (Medicago sativa L.) is one of the most important forage crops throughout the world. Maximizing leaf retention during the haymaking process is critical for achieving superior hay quality and maintaining biomass yield. Leaf abscission process affects leaf retention. Previous studies have largely focused on the molecular mechanisms of floral organ, pedicel and seed abscission but scarcely touched on leaf and petiole abscission. This study focuses on leaf and petiole abscission in the model legume Medicago truncatula and its closely related commercial species alfalfa. By analysing the petiolule-like pulvinus (plp) mutant in M. truncatula at phenotypic level (breakstrength and …

The Balancing Act Of Cytokinin In Environmental Stress Tolerance, Sumudu Sandeepani Karunadasa

Theses and Dissertations--Plant and Soil Sciences

Cytokinin, long known as a phytohormone that regulates plant growth and development, has been recently recognized as an important regulator of stress responses. However, our current knowledge about the mechanisms by which cytokinin regulates stress responses is fragmentary, as many of the studies in this field yielded conflicting results. Most of the work described here has focused on analyses of the molecular mechanisms of cytokinin-dependent regulation of growth and development under stress conditions, with an emphasis on the role of cytokinin-dependent regulation of protein synthesis in development and stress tolerance.

One of the important contributions of this study is the …

The Morphological, Physiological, And Genetic Underpinnings Of Intraspecific Salinity Tolerance In Sorghum Bicolor, Ashley N. Henderson

Graduate Theses, Dissertations, and Problem Reports (ETD)

Decreases in land quality and quantity threaten the efficient production of agriculturally and economically pivotal crops. Such reductions in arable lands are a consequence of population growth and urbanization, and often result in the introduction of various abiotic stresses. The most common abiotic stressors include water limitation (drought), water logging (over watering), poor water quality (salinity), and extreme temperatures (cold, frost, heat). Each of these stressors negatively impact plant growth, development, and yield. Soil salinity, specifically, is a considerable constraint affecting lands used in agriculture. Salts in the soil rise both naturally and through anthropogenic factors making the abundance a …

Pengaruh Cekaman Kekeringan Terhadap Hasil Dan Sensitivitas Tiga Genotip Jawawut, Sheli Mustikasari Dewi, Yuyun Yuwariah, Warid Ali Qosim, Dedi Ruswandi

Jurnal Kultivasi

Jawawut merupakan salah satu tanaman serealia lokal Indonesia yang dapat dikembangkan dan dimanfaatkan sebagai sumber pangan. Tujuan dari penelitian ini adalah untuk mendapatkan genotip jawawut yang memberikan hasil paling baik dan sensitivitas paling rendah pada berbagai tingkat pemberian air di rumah plastik. Penelitian dilaksanakan pada bulan Juni sampai dengan bulan September 2017 di kebun percobaan Fakultas Pertanian UNPAD. Penelitian ini menggunakan Rancangan Petak Terbagi (Split Plot Design) dengan 3 ulangan. Petak utama terdiri dari tiga macam genotip, yaitu genotip 44, 46, dan 48. Anak petak terdiri dari tiga taraf kadar air tanah, yaitu 75%, 50%, dan 25% dari kapasitas lapang. …

Phenotypic Study Of Anthracnose Resistance In Black Walnut And Building A Mapping Population, Sadie D. Land

Graduate Theses/Dissertations

Black walnut anthracnose, caused by Gnomonia leptostyla, is the most widespread and destructive disease affecting black walnut trees (Juglans nigra). Breeding cultivars for a higher resistance to anthracnose is a natural and efficient strategy for improving the health and production quality of black walnut trees. The two goals of this study were to reveal that the ‘Sparrow’ cultivar of black walnut contains a significantly higher resistance to anthracnose than the ‘Football’ cultivar when separated from environmental factors, and to expand the ‘Football’ × ‘Sparrow’ F1 mapping population to evaluate how the trait of resistance is inherited in the progeny. A …

An Evaluation Of Hybrid Traits, Yield, And Major Qtl Effect On Heterosis In Hybrid Soft Red Winter Wheat, Zachary James Winn

Graduate Theses and Dissertations

Wheat (Triticum aestivum L.) is a self-pollinating species that is most often bred as a recombinant inbred line. When two inbred individuals are crossed, they produce progeny which experience heterosis; heterosis is the increased robustness experienced due to the reintroduction of heterozygosity. Hybrid wheat may be produced through the use of chemical hybridization agents, yet the structure of wheat flowers decreases the efficiency of outcrossing. The objectives of this study were to: assess the amount of heterosis experienced by a population of hybrid wheat and observe the effect of major gene loci on yield and yield components, phenotype anthers extruded …

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 …

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. …

Identification Of Quantitative Trait Loci (Qtls) For Resistance To Fusarium Head Blight (Fhb) In Wheat Variety Ags 2060 And Evaluation Of The Effect Of Fhb1 Resistance Gene On Fhb Reaction In A Louisiana Wheat Breeding Population, Alejandro Castro Aviles

LSU Doctoral Dissertations

Fusarium head blight (FHB), caused by the fungus Fusarium spp., is a disease that attacks several grass species, including wheat. Wheat variety AGS 2060 has remained moderately susceptible to FHB and is regularly found in pedigrees of resistant breeding lines. Quantitative trait loci (QTL) mapping was conducted to find sources of resistance to FHB in AGS 2060. A 90K SNP chip was used to genotype a double haploid mapping population produced from a cross between wheat varieties AGS 2060 and AGS 2035. There were highly significant differences between lines in the population for Fusarium damaged kernels (FDK) rating and deoxynivalenol …

Supersweet Sweet Corn Cultivar Evaluation For Northern Indiana, 2019, Elizabeth Maynard

Midwest Vegetable Trial Reports

This paper reports on fifteen bicolor, four yellow, and one white supersweet sweet corn entries that were evaluated at the Pinney Purdue Agricultural Center in Wanatah, Indiana.

Molecular Systematics Of Isoëtes (Isoëtaceae) In Eastern North America, Peter William Schafran

Biological Sciences Theses & Dissertations

Isoëtes (Isoëtaceae, Isoetales, Lycopodiophyta) is a cosmopolitan genus of aquatic lycophytes, occurring on every continent except Antarctica. Of approximately 200 total taxa, about half are in a clade of species mostly occurring in North and South America. Eastern North America accounts for 22% of global taxonomic diversity, containing 32 fertile taxa and 16 named hybrids. This taxonomic diversity is built upon relatively little morphological difference, and even combined with phylogenetic analysis using several nuclear and chloroplast DNA markers, no well-resolved systematic treatment within this clade exists.

This study aims to clarify the relationships between all species and subspecies of Isoëtes …

Summaries Of Arkansas Cotton Research 2018, Fred Bourland

Arkansas Agricultural Experiment Station Research Series

Arkansas ended the 2018 season ranked 5th nationally in harvested acres (480,000 acres), 4th in lint yield (1150 lb/acre), and 4th in total production (1,150,000 bales). The string of consecutive years with good yields is helping to drive the increase in cotton acres. Harvest and ginning capacity is a major limiting factor for acre expansion. Cotton planting intentions for 2019 released in late March are at 580,000 acres, up 20% from the 485,000 acres planted in 2018. This continues to push the ginning capacity of 28 gins in 2018 and on-farm picker capacity to the limit. Optimism for cotton is …

Nature-Guided Synthesis Of Advanced Bio-Lubricants, Trevor Romsdahl, Asghar Shirani, Robert E. Minto, Chunyu Zhang, Edgar B. Cahoon, Kent D. Chapman, Diana Berman

Center for Plant Science Innovation: Faculty Publications

Design of environmentally friendly lubricants derived from renewable resources is highly desirable for many practical applications. Here, Orychophragmus violaceus (Ov) seed oil is found to have superior lubrication properties, and this is based on the unusual structural features of the major lipid species— triacylglycerol (TAG) estolides. Ov TAG estolides contain two non-hydroxylated, glycerol-bound fatty acids (FAs) and one dihydroxylated FA with an estolide branch. Estolide branch chains vary in composition and length, leading to their thermal stability and functional properties. Using this concept, nature-guided estolides of castor oil were synthesized. As predicted, they showed improved lubrication properties similar to Ov …

The Database Of Identified Root-Specific Genes And Their Promoters In Maize, Sorghum, And Soybean, Gleb Moisseyev, Divith Rajagopal, Alix Cui, Kiyoul Park, Edgar B. Cahoon, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Root genes are essential to plants as they dictate factors such as the strength of the plant, reproductivity success, etc. However, in the status quo, studies on root genes are simply ineffective. To be more specific, currently, there are very few online databases of root genes and promoters, which essentially deters root gene studies from being successful. To fix this problem, our lab constructed and coded an online database that contains information about the roots of maize, soybean, and sorghum. We collected 1200 root genes and assessed the strength and success of a given gene. This online database of these …

B.R. Wells Arkansas Rice Research Studies 2018, R. J. Norman, K. A.K. Moldenhauer

Arkansas Agricultural Experiment Station Research Series

No abstract provided.

Assessing Anthocyanin Biosynthesis In Solanaceae As A Model Pathway For Secondary Metabolism, Zou Li, Trisha Vickrey, Moira G. Mcnally, Shirley J. Sato, Thomas E. Clemente, Jeffrey P. Mower

Center for Plant Science Innovation: Faculty Publications

Solanaceae have played an important role in elucidating how flower color is specified by the flavonoid biosynthesis pathway (FBP), which produces anthocyanins and other secondary metabolites. With well-established reverse genetics tools and rich genomic resources, Solanaceae provide a robust framework to examine the diversification of this well-studied pathway over short evolutionary timescales and to evaluate the predictability of genetic perturbation on pathway flux. Genomes of eight Solanaceae species, nine related asterids, and four rosids were mined to evaluate variation in copy number of the suite of FBP enzymes involved in anthocyanin biosynthesis. Comparison of annotation sources indicated that the NCBI …

Network‐Based Feature Selection Reveals Substructures Of Gene Modules Responding To Salt Stress In Rice, Qian Du, Malachy Campbell, Huihui Yu, Kan Liu, Harkamal Walia, Qi Zhang, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Rice, an important food resource, is highly sensitive to salt stress, which is directly related to food security. Although many studies have identified physiological mechanisms that confer tolerance to the osmotic effects of salinity, the link between rice genotype and salt tolerance is not very clear yet. Association of gene co‐expression network and rice phenotypic data under stress has penitential to identify stress‐responsive genes, but there is no standard method to associate stress phenotype with gene co‐expression network. A novel method for integration of gene co‐expression network and stress phenotype data was developed to conduct a system analysis to link …

Economic Contribution Of The Agricultural Sector To The Arkansas Economy In 2017, Leah English, Jennie Popp, Wayne Miller

AAES Research Reports and Research Bulletins

Agriculture and associated agricultural activities are major contributors to the Arkansas economy. Agriculture is defined as the sum of agricultural production and processing activities, unless otherwise specified, and includes crop and animal production and processing, agricultural support industries, forestry and forest products, and textile goods. Agriculture contributes to the economy through direct agricultural production and value-added processing, and also leads to economic activity in other parts of the economy. This report is the eleventh in a series of reports examining agriculture’s economic contribution to the Arkansas economy. The total economic contribution of agriculture (direct, indirect, and induced effects) on value …

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.), …

Mapping A New Disease Resistance Locus In An F1 Progeny Derived From Two Grape Wild Relatives, Gaurab Bhattarai

Graduate Theses/Dissertations

Linkage maps and quantitative trait loci (QTL) analysis have become essential tools for the positional cloning of agronomically important genes and for marker-assisted breeding. In this study, two North American grape species, Vitis rupestris and Vitis riparia, and their 294 F₁ progeny were used to construct parental linkage maps and to perform QTL analysis for downy mildew resistance. Single nucleotide polymorphism (SNP) discovery was accomplished using genotyping-by-sequencing (GBS) and resulted in 348,888 SNPs. Of these, 11,063 informative SNP markers (3.17% of the original SNP dataset) were derived after filtering for various quality parameters and missing data. A two-way …