A5102025126- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Plant Disease Resistance and Genetics
- Plant Molecular Biology Research
- Plant and Fungal Interactions Research
- Chromosomal and Genetic Variations
- Genetic and phenotypic traits in livestock
- Genetics and Plant Breeding
- Plant Stress Responses and Tolerance
- Spectroscopy and Chemometric Analyses
- Wheat and Barley Genetics and Pathology
- Gene expression and cancer classification
- RNA modifications and cancer
- Plant nutrient uptake and metabolism
- Remote Sensing in Agriculture
- Rice Cultivation and Yield Improvement
- Machine Learning in Bioinformatics
- Spectroscopy Techniques in Biomedical and Chemical Research
- Legume Nitrogen Fixing Symbiosis
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Smart Agriculture and AI
- Plant biochemistry and biosynthesis
- Molecular Biology Techniques and Applications
- Genetic diversity and population structure
St. Jude Children's Research Hospital
2023-2024
North Dakota State University
2024
University of Nebraska–Lincoln
2016-2023
University of Minnesota
2020-2023
University of Minnesota System
2020-2022
Mississippi State University
2015-2016
Nitrogen (N) is an essential and often limiting nutrient to plant growth development. Previous studies have shown that the mRNA expressions of numerous genes are regulated by nitrogen supplies; however, little known about expressed non-coding elements, for example long RNAs (lncRNAs) control response maize (Zea mays L.) nitrogen. LncRNAs a class larger than 200 bp, which emerged as key regulators in gene expression.In this study, we surveyed intergenic/intronic lncRNAs B73 leaves at V7 stage...
Identifying interspecies changes in gene regulation, one of the two primary sources phenotypic variation, is challenging on a genome-wide scale. The use paired time-course data cold-responsive expression maize (Zea mays) and sorghum (Sorghum bicolor) allowed us to identify differentially regulated orthologs. While majority transcriptional regulation conserved pairs species specific, initial responses cold appear be more than later responses. In maize, promoters genes with tend contain...
Significance The same gene is often regulated differently in response to stress even closely related plant species. Directly measuring stress-responsive expression can be financially and logistically challenging nonmodel Here, we show that models trained using data on which genes respond cold one species predict will species, when the training target vary their degree of tolerance cold. prediction used require only genomic sequence models. As a result, from well-studied model may...
Abstract Background Maize (Zea mays ssp. mays) is 1 of 3 crops, along with rice and wheat, responsible for more than one-half all calories consumed around the world. Increasing yield stress tolerance these crops essential to meet growing need food. The cost speed plant phenotyping are currently largest constraints on breeding efforts. Datasets linking new types high-throughput data collected from plants performance same genotypes under agronomic conditions across a wide range environments...
Changes in gene expression are important for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes identifies many changes transcript abundance. We used comparisons multiple identify alleles with variable heat cold stress and distinguish examples cis- trans-regulatory variation stress-responsive changes. motifs enriched near the transcription start sites (TSSs) thermal genes develop predictive models responses. Prediction accuracies can be improved by...
Abstract Purpose: The purpose of the study was to design a pan-cancer gene panel for childhood malignancies and validate it using clinically characterized patient samples. Experimental Design: In addition 5,275 coding exons, SJPedPanel also covers 297 introns fusions/structural variations 7,590 polymorphic sites copy-number alterations. Capture uniformity limit detection are determined by targeted sequencing cell lines dilution experiment. We its coverage in silico analysis an established...
Abstract Pearl millet is a non-model grain and fodder crop adapted to extremely hot dry environments globally. In India, great deal of public private sectors’ investment has focused on developing pearl single cross hybrids based the cytoplasmic-genetic male sterility (CMS) system, while in Africa most production relies open pollinated varieties. lines were phenotyped for both inbred parents stage. Many breeding efforts focus phenotypic selection generate improved parental hybrids. This study...
Abstract Despite high cure rates of >90% for newly diagnosed childhood B-ALL, outcomes remain poor relapsed patients. Prior genomics studies have revealed 12 genes with mutations enriched at relapse. However, the resistance mechanisms >50% relapses elusive. Here we performed WGS and RNA sequencing on initial diagnostic, relapse, remission specimens from 183 patients enrolled in AALL1331 trial Children’s Oncology Group. In this cohort, 96 cases did not harbor a known mutation....
Genomic selection (GS) is an emerging methodology that helps select superior lines among experimental cultivars in plant breeding programs. It offers the opportunity to increase productivity of by delivering increased genetic gains and reducing cycles. This requires inexpensive sufficiently dense marker information be successful, with whole genome sequencing, it has become important tool many crops. The recent assembly pearl millet made possible employ GS models improve procedure Here, three...
Abstract Intact transposable elements (TEs) account for 65% of the maize genome and can impact gene function regulation. Although TEs comprise majority affect important phenotypes, genome-wide patterns TE polymorphisms in have only been studied a handful genotypes, due to challenging nature assessing highly repetitive sequences. We implemented method use short-read sequencing data from 509 diverse inbred lines classify presence/absence 445,418 nonredundant that were previously annotated four...
Abstract Background Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of gene across multiple varieties within same under abiotic Results By analyzing transcriptomes more than 100 maize inbreds, we reveal many cis - and trans -acting eQTLs influence expression response heat The in stress identified genes differential responses...
High-throughput phenotyping system has become more and popular in plant science research. The data analysis for such a typically involves two steps: feature extraction through image processing statistical the extracted features. current approach is to perform those steps on different platforms. We develop package “implant” R both robust functional analysis. For processing, provides methods including thresholding, hidden Markov random field model, morphological operations. analysis, this can...
Abstract Transposable elements (TEs) pervade most eukaryotic genomes. The repetitive nature of TEs complicates the analysis their expression. Evaluation expression both TE families (using unique and multi-mapping reads) specific uniquely mapping in leaf tissue three maize (Zea mays) inbred lines subjected to heat or cold stress reveals no evidence for genome-wide activation TEs; however, some generate transcripts only conditions. There is substantial variation which exhibit stress-responsive...
Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized variation as a result cross contamination stocks, unintentional crossing, residual heterozygosity within original or de novo mutation. 27 public, scale, RNA-seq datasets from 20 independent groups were to assess maize (Zea mays ssp. mays) inbred B73, four decade old variety which served reference genotype for genome sequencing project and is...
Linking natural genetic variation to trait can help determine the functional roles ofdifferent genes. Variations of one or several traits are often assessed separately. High-throughput phenotyping and data mining capture dozens hundreds from same individuals. Here, we test association between markers within a gene many simultaneously. This genome–phenome wide study (GPWAS) is both multi-marker multi-trait test. Genes identified using GPWAS with 260 phenotypic in maize were enriched for genes...
Abstract Severe cold, defined as a damaging cold beyond acclimation temperatures, has unique responses, but the signaling and evolution of these responses are not well understood. Production oligogalactolipids, which is triggered by cytosolic acidification in Arabidopsis (Arabidopsis thaliana), contributes to survival severe cold. Here, we investigated oligogalactolipid production species from bryophytes angiosperms. oligogalactolipids differed within each clade, suggesting multiple...
ABSTRACT Maize ( Zea mays ssp. ) is one of three crops, along with rice and wheat, responsible for more than 1/2 all calories consumed around the world. Increasing yield stress tolerance these crops essential to meet growing need food. The cost speed plant phenotyping currently largest constraint on breeding efforts. Datasets linking new types high throughput data collected from plants performance same genotypes under agronomic conditions across a wide range environments are developing...
The Heat Shock Factor (HSF) transcription factor family is a central and required component of plant heat stress responses acquired thermotolerance. HSF has dramatically expanded in lineages, often including repertoire 20 or more genes. Here we assess compare the composition, responsiveness, chromatin profiles families maize
Common purslane (Portulaca oleracea) integrates both C4 and crassulacean acid metabolism (CAM) photosynthesis pathways is a promising model plant to explore C4-CAM plasticity. Here, we report high-quality chromosome-level genome of nicotinamide adenine dinucleotide (NAD)-malic enzyme (ME) subtype common that provides evidence for 2 rounds whole-genome duplication (WGD) with an ancient WGD (P-β) in the ancestor Portulacaceae Cactaceae around 66.30 million years ago (Mya) another (Po-α)...
Abstract Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting functions these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to functions. As result, homology is widely used for function prediction. This means functional errors also propagate one species another. Several approaches based on machine learning classification algorithms were evaluated their ability accurately...