Genomics Commons^™

Vines In The Neotropics: Phylogenomics, Biogeography And Systematics In Passion Flowers (Passiflora Subgenus Decaloba Section Decaloba), Serena Acha

Dissertations

With 600 species, Passiflora is a large, morphologically complex and broadly distributed genus in Passifloraceae that represents a major challenge to scientists interested in understanding the evolutionary history of tropical vines. Passiflora has been divided into subgenera, super sections and sections. One of the most enigmatic and species-rich (~120 spp.) groups in Passiflora is section Decaloba, which occurs in the Neotropics and is particularly diverse in Andean montane forests. In this study, we used phylogenomic and population genomic approaches to investigate the evolutionary history, biologeography, species boundaries, and taxonomy of Passiflora section Decaloba. We sampled herbarium specimens, extracted …

The Role Of Chromatin State Transitions In Modulating Early Phosphate-Deficiency Response Genes In Plants, Maryam Foroozani

LSU Doctoral Dissertations

Phosphorus (P) is an essential plant macronutrient vital to fundamental metabolic processes. Plant-available P is low in most soils, making it a frequent limiter of growth. Declining P reserves for fertilizer production exasperates this agricultural challenge. Plants modulate complex responses to fluctuating P levels via global transcriptional regulatory networks. Although chromatin structure plays a substantial role in controlling gene expression, the chromatin-level mechanisms involved in regulating P homeostasis have not been determined.

In this work, I used chromatin immunoprecipitation (ChIP) combined with next-generation DNA sequencing (ChIP-seq) to map the distribution of H3K4me3 in rice (Oryza sativa L.) during both …

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 …

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

MSU Graduate Theses

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 …

Root Hair Single Cell Type Specific Profiles Of Gene Expression And Alternative Polyadenylation Under Cadmium Stress, Jingyi Cao, Congting Ye, Guijie Hao, Carole Dabney-Smith, Arthur G. Hunt, Qingshun Q. Li

Plant and Soil Sciences Faculty Publications

Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic stress by increasing the heterogeneity at mRNA 3′-ends. Heavy metals like cadmium pollute water and soil due to mining and industry applications. Understanding how plants cope with heavy metal stress remains an interesting question. The Arabidopsis root hair was chosen as a single cell model to investigate the functional role of APA in cadmium stress response. Primary root growth inhibition and defective root hair morphotypes were observed. Poly(A) tag (PAT) libraries from single cell types, i.e., root …

Improved Draft Genome Sequence Of Bacillus Sp. Strain Yf23, Which Has Plant Growth-Promoting Activity, Ye Xia, Seth Debolt, Qin Ma, Adam Mcdermaid, Cankun Wang, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides

Horticulture Faculty Publications

We report here the improved draft genome sequence of Bacillus sp. strain YF23, a bacterium originally isolated from switchgrass (Panicum virgatum) plants and shown to exhibit plant growth-promoting activity. The genome comprised 5.82 Mbp, containing 5,933 genes, with 193 as RNA genes, and a GC content of 35.10%.

Distribution And Population Structure Of The Invasive Nitellopsis Obtusa (Desv. In Loisel.) J. Groves And Native Species Of Characeae In The Northeast U.S.A., Robin Sleith

Dissertations, Theses, and Capstone Projects

Freshwater ecosystems are some of the most biologically diverse environments on Earth. Billions of humans rely on functioning freshwater ecosystems for drinking water and many other services. These ecosystems are increasingly threatened by human impacts including nutrient pollution, invasive species, and climate change. Here I contribute four research chapters that investigate freshwater diversity and ecosystem threats using the Characeae, a family of freshwater green macroalgae, as a study system. Characeae are a diverse and ancient group with more than 500 extant species and a fossil history spanning at least 250 million years. These algae are macrophytes in freshwater ecosystems, and …