A5103614130- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Genetics and Plant Breeding
- Smart Agriculture and AI
- Genetically Modified Organisms Research
- Semantic Web and Ontologies
- Species Distribution and Climate Change
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Molecular Biology Techniques and Applications
- Genetic diversity and population structure
- Plant Virus Research Studies
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Plant Pathogens and Resistance
- Remote Sensing in Agriculture
- Animal Genetics and Reproduction
- Invertebrate Taxonomy and Ecology
- Wheat and Barley Genetics and Pathology
- RNA modifications and cancer
Iowa State University
2015-2024
Institut thématique Génétique, génomique et bioinformatique
2015-2019
Computational Physics (United States)
2015
Ames National Laboratory
2015
CRISPR/Cas9 and Cas12a (Cpf1) nucleases are two of the most powerful genome editing tools in plants. In this work, we compared their activities by targeting maize glossy2 gene coding region that has overlapping sequences recognized both nucleases. We introduced constructs carrying SpCas9-guide RNA (gRNA) LbCas12a-CRISPR (crRNA) into inbred B104 embryos using Agrobacterium-mediated transformation. On-target mutation analysis showed 90%-100% Cas9-edited T0 plants carried indel mutations...
MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant model organism Zea mays ssp. mays. Although some form of maize community has existed over last 25 years, there have only been two major releases. In 1991, original genetics MaizeDB was created. 2003, combined contents sequence data from ZmDB were made accessible as single resource named MaizeGDB. Over next decade, became more driven while still maintaining traditional...
Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive changed the ability of improved cultivars maintain high across variable environments is unknown. Understanding genetic control phenotypic plasticity genotype by environment (G × E) interaction will enhance performance predictions diverse environments. Here we use data generated from Genomes Fields (G2F) Maize G E project assess effect on...
We created a new high-coverage, robust, and reproducible functional annotation of maize protein-coding genes based on Gene Ontology (GO) term assignments. Whereas the existing Phytozome Gramene GO sets only cover 41% 56% genes, respectively, this study provides annotations for 100% genes. also compared quality our newly derived with by comparing all three to manually annotated gold standard set 1,619 where were primarily inferred from direct assay or mutant phenotype. Evaluations indicate...
Targeted genome editing is now possible in nearly any organism and widely acknowledged as a biotech game-changer. Among available gene techniques, the CRISPR-Cas9 system current favorite because it has been shown to work many species, does not necessarily result addition of foreign DNA at target site, follows set simple design rules for selection. Use facilitated by availability an array CRISPR tools that vary specifications parameter choices, genomes, graphical visualization, downstream...
The CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein) has been used to generate targeted changes for direct modification of endogenous genes in an increasing number plant species; but development genome editing not yet fully considered potential off-target mismatches that may lead unintended within the genome. Assessing specificity efficiency as well unanticipated downstream effects from mutations is important regulatory consideration...
Abstract An important advantage of delivering CRISPR reagents into cells as a ribonucleoprotein (RNP) complex is the ability to edit genes without being integrated genome. Transient presence RNP molecules in can reduce undesirable off-target effects. One method for delivery plant use biolistic gun. To facilitate selection transformed during delivery, plasmid carrying selectable marker gene be co-delivered with enrich transformed/edited cells. In this work, we compare targeted mutagenesis...
The unfolded protein response (UPR) is a highly conserved that protects plants from adverse environmental conditions. UPR elicited by endoplasmic reticulum (ER) stress, in which and misfolded proteins accumulate within the ER. Here, we induced maize (
Genome assemblies are foundational for understanding the biology of a species. They provide physical framework mapping additional sequences, thereby enabling characterization of, example, genomic diversity and differences in gene expression across individuals tissue types. Quality metrics genome gauge both completeness contiguity an assembly help confidence downstream biological insights. To compare quality multiple assemblies, set common typically calculated then compared to one or more...
Abstract Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by identifying and trait such many environments (phenomics). Identifying the most critical opportunities challenges genome to phenome (G2P) research is focus of this paper. Previously (Genome Biol, 23(1):1–11, 2022), we laid out how Agricultural Genome Phenome Initiative (AG2PI) will coordinate activities with USA federal government agencies expand...
The accuracy of machine learning tasks critically depends on high quality ground truth data. Therefore, in many cases, producing good data typically involves trained professionals; however, this can be costly time, effort, and money. Here we explore the use crowdsourcing to generate a large number training quality. We an image analysis task involving segmentation corn tassels from images taken field setting. investigate accuracy, speed other metrics when is performed by students for academic...
The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic growth. Meristems show a striking diversity in shape size. How this morphological relates to variation plant architecture molecular circuitries driving it are unclear. By generating high-resolution gene expression atlas of vegetative maize apex, we here that distinct sets genes govern regulation identity cells versus Arabidopsis. Cell identities SAM...
Abstract Annotating gene structures and functions to genome assemblies is necessary make assembly resources useful for biological inference. Gene Ontology (GO) term assignment the most used functional annotation system, new methods GO have improved quality of GO-based function predictions. The Meta Annotator Plants (GOMAP) an optimized, high-throughput, reproducible pipeline genome-scale plants. We containerized GOMAP increase portability reproducibility also optimized its performance HPC...
Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? alleles specific genes are required for optimal performance each environment? Such datasets also leveraged to predict cultivar performance, even uncharacterized environments. The maize Genomes Fields (G2F) Initiative is a multi-institutional organization scientists working...
Background: The availability of gene function prediction datasets helps researchers to consider possible functions for uncharacterized genes hypothesis generation, candidate prioritization, and many other applications. Many such are based on the Gene Ontology (GO) graph. For plants this can be problematic because most specific GO terms available often derived from biology non-plant taxa (e.g., nerve would not seem likely map plant biological processes given that lack nerves). To balance need...
Phenotyping plants in a field environment can involve variety of methods including the use automated instruments and labor-intensive manual measurement scoring. Researchers also collect language-based phenotypic descriptions controlled vocabularies structures such as ontologies to enable computation on descriptive phenotype data, determine similarities. In this study, spoken were collected observers instructed their own vocabulary describe plant features that present visible. Further, these...
Abstract We present a novel approach to genome-wide association studies (GWAS) by leveraging unstructured, spoken phenotypic descriptions identify genomic regions associated with maize traits. Utilizing the Wisconsin Diversity panel, we collected of Zea mays ssp. traits, converting these qualitative observations into quantitative data amenable GWAS analysis. First, determined that visually striking phenotypes could be detected from unstructured descriptions. Next, developed two methods...
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype environment are highly heterogeneous thus difficult to find integrate. One approach likely improve status quo involves use ontologies standardize link about environments. Specifying linking through will allow researchers increase scope flexibility large-scale analyses aided by modern computing methods. Investments in this...
Abstract Background Assessing the impact of environment on plant performance requires growing plants under controlled environmental conditions. Plant phenotypes are a product genotype × (G E), and Enviratron at Iowa State University is facility for testing conditions effects growth development. Crop (including maize) can be grown to maturity in Enviratron, different monitored 24 h per day, 7 days week throughout cycle. Results The an array custom-designed chambers that simulate coupled with...
Natural language descriptions of plant phenotypes are a rich source information for genetics and genomics research. We computationally translated into structured representations that can be analyzed to identify biologically meaningful associations. These include the EQ (Entity-Quality) formalism, which uses terms from biological ontologies represent in standardized, semantically-rich format, as well numerical vector generated using Language Processing (NLP) methods (such bag-of-words...
Background: An organism can be described by its observable features (phenotypes) and the genes genomic information (genotypes) that cause these phenotypes. For many decades, researchers have tried to find relationships between genotypes phenotypes great strides been made. However, improved methods tools for discovering visualizing phenotypic are still needed. The maize genetics genomics database (MaizeGDB, www.maizegdb.org) provides an array of useful resources diverse data types including...
Biotech news coverage in English-language Russian media fits the profile of information warfare strategy described recent military reports. This raises question whether Russia views dissemination anti-GMO as just one many divisive issues it can exploit part its war, or if GMOs serve more expansive disruptive purposes. Distinctive patterns provide evidence a coordinated campaign that could turn public opinion against genetic engineering. The branding agriculture ecologically clean alternative...
Abstract Background Genome assemblies are foundational for understanding the biology of a species. They provide physical framework mapping additional sequences, thereby enabling characterization of, example, genomic diversity and differences in gene expression across individuals tissue types. Quality metrics genome gauge both completeness contiguity an assembly help confidence downstream biological insights. To compare quality multiple assemblies, set common typically calculated then...
Abstract The accuracy of machine learning tasks critically depends on high quality ground truth data. Therefore, in many cases, producing good data typically involves trained professionals; however, this can be costly time, effort, and money. Here we explore the use crowdsourcing to generate a large number training quality. We an image analysis task involving segmentation corn tassels from images taken field setting. investigate accuracy, speed other metrics when is performed by students for...