A5015912463- Plant Disease Resistance and Genetics
- Chromosomal and Genetic Variations
- Spectroscopy and Chemometric Analyses
- Plant Pathogens and Fungal Diseases
- Genetic Mapping and Diversity in Plants and Animals
- Smart Agriculture and AI
- Genomics and Phylogenetic Studies
- Turfgrass Adaptation and Management
- Wheat and Barley Genetics and Pathology
- Plant Pathogens and Resistance
- Leaf Properties and Growth Measurement
- Crop Yield and Soil Fertility
- Food composition and properties
- Plant-Microbe Interactions and Immunity
- Remote Sensing in Agriculture
- Genetics and Plant Breeding
- Plant Molecular Biology Research
- Plant responses to elevated CO2
- Mycotoxins in Agriculture and Food
- Plant and fungal interactions
- Plant and Fungal Interactions Research
- Yeasts and Rust Fungi Studies
- Potato Plant Research
- Legume Nitrogen Fixing Symbiosis
- Spectroscopy Techniques in Biomedical and Chemical Research
University of Minnesota
2015-2024
University of Minnesota System
2020-2024
Twin Cities Orthopedics
2024
Plant (United States)
2019-2023
Donald Danforth Plant Science Center
2023
United States Department of Agriculture
2020
Agricultural Research Service
2020
Minot State University
2017
Michigan State University
2013
University of Wisconsin–Madison
2009-2012
Significance RNA-directed DNA methylation (RdDM) provides a system for targeting to asymmetric CHH (H = A, C, or T) sites. This RdDM activity is often considered mechanism transcriptional silencing of transposons. However, many the targets in maize genome are located near genes regulatory elements. We find that regions elevated methylation, termed mCHH islands, boundaries between highly methylated (CG, CHG), silenced chromatin and more active chromatin. Analysis mutants suggests function...
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute production hybrids, we generated a draft assembly line PH207 complement compare with existing B73 reference sequence. is founder Stiff Stalk germplasm pool, while Iodent germplasm, both which have contributed substantially temperate commercial are combined make...
Parasexuality contributes to diversity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct nuclei). Newly emerged strains the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, a major threat global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation nuclear between dikaryons. Fully...
Abstract Cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, has been bred for distinct market classes, including fresh market, pigmented, and processing varieties. Breeding efforts have relied on phenotypic selection of populations developed from intra- intermarket class crosses introgressions wild cultivated Solanum relatives. To retrospectively explore the effects breeding at genome level, we used 8303 single-nucleotide polymorphism markers to genotype...
Plants respond to abiotic stress through a variety of physiological, biochemical, and transcriptional mechanisms. Many genes exhibit altered levels expression in response stress, which requires concerted action both cis- trans-regulatory features. In order study the variability transcriptome RNA sequencing was performed using 14-day-old maize seedlings inbreds B73, Mo17, Oh43, PH207 B37 under control, cold heat conditions. Large numbers that responded differentially between parental inbred...
Potato is the world's third most important crop, and becoming increasingly in developing countries. Cultivated potato a highly heterozygous tetraploid (2 n = 4 x 48) suffers from significant inbreeding depression when selfed. As can be vegetatively propagated, breeding has been based primarily on phenotypic selection F1 populations. However, recent advances genome sequencing genotyping methods have resulted development of large genomic, genetic, datasets that will enable more efficient rapid...
In many regions of the world, wheat is vulnerable to severe yield and quality losses from fungus disease Fusarium head blight (FHB). The development resistant cultivars one means ameliorating devastating effects this disease, but breeding process requires evaluation hundreds lines each year for reaction disease. These field evaluations are laborious, expensive, time-consuming, prone rater error. A phenotyping cart that can quickly capture images spikes their level FHB infection would greatly...
Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization content. Most maize composed TEs. We developed an approach to define shared variable TE insertions across assemblies applied this method four (B73, W22, Mo17 PH207) with uniform structural annotations Among these we identified approximately 400 000 TEs that polymorphic, encompassing 1.6 Gb sequence. These polymorphic include a combination recent transposition events as...
Fusarium head blight (FHB) is a devastating disease of wheat worldwide. In addition to reducing the yield crop, causal pathogens also produce mycotoxins that can contaminate grain. The development resistant varieties one best ways reduce impact FHB. To develop such varieties, breeders must expose germplasm lines pathogen in field and assess reaction. Phenotyping breeding materials for resistance FHB time-consuming, labor-intensive, expensive when using conventional protocols. reliable...
Subtelomeric domains immediately adjacent to telomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes. A common feature associated with subtelomeric different eukaryotes is presence long arrays tandemly repeated satellite sequences. However, studies on molecular organization evolution repeats are rare. We isolated two repeats, CL14 CL34, from potato (Solanum tuberosum). The CL34 organized as independent arrays, up 1-3 Mb, 182 bp 339 monomers,...
Oat crown rust, caused by the fungus
Abstract Developing the resilient crops of future will require access to a broad set tools. While advances in sequencing and marker technologies have facilitated marker‐trait associations ability predict phenotype an individual from its genotypic information, other tools such as high‐throughput phenotyping are still their infancy. Advances sensors, aeronautics, computing enabled progress. Here, we review current platforms sensors available for top‐down field with focus on unoccupied aerial...
Increasing the tolerance of maize seedlings to low-temperature episodes could mitigate effects increasing climate variability on yield. To aid progress toward this goal, we established a growth chamber-based system for subjecting 40 inbred genotypes defined, temporary cold stress while collecting digital profile images over 9-daytime course. Image analysis performed with PlantCV software quantified shoot height, area, 14 other morphological traits, and necrosis identified by color analysis....
Centromeres in eukaryotic species are defined by the presence of a centromere-specific histone H3 variant, CENH3. CENH3 plays key role recruiting other centromeric proteins; thus, it is central component kinetochore formation and centromere function. The proteins several plant animal were found to be under positive selection, which was hypothesized respond rapid changing repetitive DNA sequences associated with centromeres. Here, we report expression evolution CenH3 genes two allotetraploid...
Technology and software improvements in the last decade now provide methodologies to access genome sequence of not only a single accession, but also multiple accessions plant species. This provides means interrogate species diversity at level. Ample among collection can be found, including single-nucleotide polymorphisms, insertions deletions, copy number variation presence/absence variation. For with small, non-repetitive rich genomes, re-sequencing query is robust, highly informative,...
Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in maize genome. Due to their repetitive nature, genomic studies TEs complicated by difficulty properly attributing multi-mapped short reads specific loci. Here, we utilize a method attribute RNA-seq TE families rather than particular loci order characterize transcript abundance for We applied this assess per-family expression transposable >800 published libraries representing range development,...
Single-parent expression (SPE) is defined as gene in only one of the two parents. SPE can arise from differential between parental alleles, termed non-presence/absence (non-PAV) SPE, or physical absence a parent, PAV SPE. We used transcriptome data diverse Zea mays (maize) inbreds and hybrids, including 401 samples five different tissues, to test for differences these types genes. Although commonly observed, highly genotype tissue specific. A positive correlation was observed genetic...
Grape berry color is an economically important trait that controlled by two major genes influencing anthocyanin synthesis in the skin. Color often described qualitatively using six categories; however, this a subjective rating fails to describe variation within these classes. To investigate minor color, image analysis was used quantify different spaces. An pipeline developed and utilized segregating hybrid wine grape population across years. Images were collected from clusters immediately...
Abstract Canopy cover is an important agronomic trait influencing photosynthesis, weed suppression, biomass accumulation, and yield. Conventional methods to quantify canopy are time labor-intensive. As such, little known about how develops over time, the stability of across environments, or genetic architecture cover. We used unoccupied aerial vehicle-mediated image capture plot-level coverage in maize throughout growing season. Images 501 diverse inbred lines were acquired between 300 1300...
Summary The field of genomics has grown rapidly with the advent massively parallel sequencing technologies, allowing for novel biological insights regards to genomic, transcriptomic, and epigenomic variation. One widely utilized application high‐throughput is transcriptional profiling using RNA ( seq). Understanding limitations a technology critical accurate interpretations, clear interpretation seq data can be difficult in species complex genomes. To understand expression levels we...
Bacterial leaf streak (BLS) of wheat and barley has been a disease increasing concern in the Upper Midwest over past decade. In this study, intra- interfield genetic pathogenic diversity bacteria causing BLS Minnesota was evaluated. 2015, 89 strains were isolated from 100 samples collected two fields naturally infected with BLS. Virulence assays multilocus sequence alignments four housekeeping genes supported pathovar identifications. All on belonged to same lineage as Xanthomonas...
Fine fescues (Festuca L., Poaceae) are turfgrass species that perform well in low-input environments. Based on morphological characteristics, the most commonly-utilized fine divided into five taxa: three subspecies within F. rubra L. and remaining two treated as ovina complex. Morphologically, these taxa very similar, both identification classification of remain challenging. In an effort to develop methods for fescues, we used flow cytometry estimate genome size sequenced chloroplast all...
Precise segmentation of wheat spikes from a complex background is necessary for obtaining image-based phenotypic information traits such as yield estimation and spike morphology. A new instance method based on Hybrid Task Cascade model was proposed to solve the detection problem with improved results. In this study, images were collected fields where environment varied both spatially temporally. Res2Net50 adopted backbone network, combined multi-scale training, deformable convolutional...