Plant Breeding and Genetics Commons^™

Complete Mitogenomes Of Two Aragoa Species And Phylogeny Of Plantagineae (Plantaginaceae, Lamiales) Using Mitochondrial Genes And The Nuclear Ribosomal Rna Repeat, Jeffrey P. Mower, Lilly Hanley, Kirsten Wolff, Natalia Pabón-Mora, Favio González

Center for Plant Science Innovation: Faculty Publications

Aragoa, comprising 19 high-altitude North Andean species, is one of three genera in the Plantagineae (Plantaginaceae, Lamiales), along with Littorella and Plantago. Based primarily on plastid data and nuclear ITS, Aragoa is sister to a clade of Littorella + Plantago, but Plantagineae relationships have yet to be assessed using multigene datasets from the nuclear and mitochondrial genomes. Here, complete mitogenomes were assembled for two species of Aragoa (A. abietina and A. cleefii). The mitogenomes of both species have a typical suite of genes for 34 proteins, 17 tRNAs, and three rRNAs. The A. abietina mitogenome …

Inmut-Finder: A Software Tool For Insertion Identification In Mutagenesis Using Nanopore Long Reads, Rui Song, Ziyao Wang, Hui Wang, Han Zhang, Xuemeng Wang, Hanh Nguyen, David Holding, Bin Yu, Tom Clemente, Shangang Jia, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Background: Biological mutagens (such as transposon) with sequences inserted, play a crucial role to link observed phenotype and genotype in reverse genetic studies. For this reason, accurate and efficient software tools for identifying insertion sites based on the analysis of sequencing reads are desired. Results: We developed a bioinformatics tool, a Finder, to identify genome-wide Insertions in Mutagenesis (named as “InMut-Finder”), based on target sequences and flanking sequences from long reads, such as Oxford Nanopore Sequencing. InMut-Finder succeeded in identify > 100 insertion sites in Medicago truncatula and soybean mutants based on sequencing reads of whole-genome DNA or enriched …

3d Reconstruction Identifies Loci Linked To Variation In Angle Of Individual Sorghum Leaves, Michael C. Tross, Mathieu Gaillard, Mackenzie Zwiener, Chenyong Miao, Ryleigh J. Grove, Bosheng Li, Bedrich Benes, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quan- tification of the angle of each leaf for each plant. The resulting measurements are both heritable and …

Somatic Variants For Seed And Fruit Set In Grapevine, Laura Costantini, Paula Moreno-Sanz, Chinedu Charles Nwafor, Silvia Lorenzi, Annarita Marrano, Fabiana Cristofolini, Elena Gottardini, Stefano Raimondi, Paola Ruffa, Ivana Gribaudo, Anna Schneider, Maria Stella Grando

Center for Plant Science Innovation: Faculty Publications

Background: Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like seedlessness, berry and bunch size, cluster compactness and berry skin to pulp ratio. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with …

The Study Of Ppal And Its Role In The Development Of Physcomitrella Patens, Susana Perez-Martinez, Christine Chen, Mark P. Running

Undergraduate Arts and Research Showcase

Protein Prenylation is the addition of lipids to select proteins that play a key role during the development of plants. There are three enzymes that play a role in protein prenylation: protein farnesyltransferase (PFT), protein geranylgeranyl-transferase-I (PGGT), and Rab geranylgeranyltransferase (Rab-GGT). However, there is a protein called PPAL that has a similar alpha subunit of PFT, PGGT, and RAB-GGT but its biochemical function is unknown. Physconmitrella patens, a type of moss, was chosen to explore the role of PpPPAL in the development process. There are two copies of PPAL found in moss. PPAL1 and PPAL2. To study the role …

A Comparison Of Media To Determine Optimal Growth In Aquaponics: Prg Virtual Showcase January 2021, Rachel L. Fogle, Andrea Nagy, Claribel Asare, Steven Berry, Jordan Brown, Aquila Durham-Lewis

Harrisburg University Presidential Research Grants

No abstract provided.

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 …

Patterns Of Genetic Divergence Across Geographically Variable Populations Of Xanthisma Gracile (Asteraceae), Lavanya Challagundla, Lisa E. Wallace

Biological Sciences Faculty Publications

Premise of research. Numerous biotic and abiotic factors can contribute to local selection and lead to geographic structure and genetic divergence between populations. The southwestern United States contains many distinctive plant communities, ranging from woodlands to desert scrub, that are shaped by species adapting to local variation in elevation, precipitation, seasonality, and soils. Given this variation, species occurring across diverse habitats are expected to harbor high genetic diversity and exhibit significant genetic differences associated with environmental variation.

Methodology. Here, we studied the genetic divergence of populations of Xanthisma gracile (Asteraceae) across Arizona using amplified fragment length polymorphisms and evaluated associations …

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 …

Arkansas Corn And Grain Sorghum Performance Tests 2020, J. F. Carlin, R. D. Bond, R. B. Morgan

Arkansas Agricultural Experiment Station Research Series

Corn and grain sorghum performance tests are conducted each year in Arkansas by the University of Arkansas System Division of Agriculture. The tests provide information to companies marketing seed within the state and aid the Arkansas Cooperative Extension Service in formulating recommendations for producers.

The 2020 corn performance tests contained 85 hybrids and were conducted at the Northeast Research and Extension Center (NEREC) at Keiser, the Lon Mann Cotton Research Station (LMCRS) near Marianna, the Bell Farming Company (BFC) near Des Arc, the Pine Tree Research Station (PTRS) near Colt, the Rohwer Research Station (RRS) near Rohwer, and the Rice …

Arkansas Soybean Performance Tests 2020, J. F. Carlin, R. D. Bond, R. B. Morgan

Arkansas Agricultural Experiment Station Research Series

Soybean variety and strain performance tests are conducted each year in Arkansas by the University of Arkansas System Division of Agriculture’s Arkansas Crop Variety Improvement Program. The tests provide information to companies developing varieties and/or marketing seed within the State, and aid the Arkansas Cooperative Extension Service in formulating variety recommendations for soybean producers.

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 …

Optical Seed Sorter-Based Selection Lowers Deoxynivalenol Accumulation In Soft Red Winter Wheat, William Jesse Carmack

Theses and Dissertations--Plant and Soil Sciences

Fusarium head blight (FHB) of wheat (Triticum aestivum L.) results in discolored grain contaminated with deoxynivalenol (DON). DON accumulation, an indicator of FHB resistance, can be quantified and used as the basis for direct phenotypic selection, but testing is expensive. The primary objective of this study was to evaluate an optical seed sorter as an alternative to DON testing for FHB resistance breeding. Three hundred F4 derived soft red winter wheat (SRWW) breeding lines were grown in an inoculated FHB nursery over several years in Lexington, KY. Grain from each breeding line was sorted using an optical seed sorter calibrated …

Genomic Selection Strategies To Predict Grain Yield And Disease Resistance Traits In A Wheat Breeding Program, Virginia Laura Verges

Theses and Dissertations--Plant and Soil Sciences

Genomic selection (GS) is a form of marker-assisted selection (MAS) that simultaneously estimates all locus, haplotype or marker effects across the entire genome to calculate genomic estimated breeding values (GEBVs). Since its inception, it has had the attention of breeders keen on finding tools to accelerate genetic gain and reduce phenotyping costs in the breeding program. A first objective of this study was to evaluate strategies to design the training population (TP) and validating population (VP) to estimate GEBVs for grain yield and agronomic traits for wheat breeding lines. Our results demonstrate that, despite the small family size, an approach …

Genetic Structure Of Pseudoroegneria Spicata In The Northern Palouse Prairie And Channeled Scablands, Ethan Timothy Bean

EWU Masters Thesis Collection

Establishing genetically diverse communities that can adapt to dynamic selective pressures is crucial in ecological restoration. However, the genetic structure of native plant species used for restoration is often poorly understood. Pseudoroegneria spicata, is a keystone species of the Inland Northwestern US that has become a staple in commercially available restoration seed mixes. It is abundant in remnant prairies of the endangered Palouse Prairie ecoregion, which is characterized by rolling hills of deep loess soil. Less than 1% of native Palouse Prairie is left, due to agricultural conversion, with remnants highly fragmented and isolated. P. spicata is also common in …

Traditional And Modern Breeding Strategies Towards Developing Resilient Crops: Two Case Studies In Tomato, Estefania Tavares Flores

Graduate Theses, Dissertations, and Problem Reports (ETD)

Crop designing for resilience traits to produce satisfactorily under adverse conditions and scenarios is a priority for the future of global food security. In this thesis, two different approaches addressing major stress factors for tomato cropping are presented. We first aimed to domesticate tomato de novo as a high-salinity resistant crop using the wild relative, S. cheesmaniae via gene editing. We conducted single-gene and multiplex knock-out strategies using CRISPR/Cas9 genome editing to create loss-of-function alleles for the domestication-related genes BIF, CycB, J2, EJ2, MULTI, SP, SP5G, and FW11.3 in order to create a novel, halophyte tomato harboring an inherent high-salinity …