A5064231059- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Wheat and Barley Genetics and Pathology
- Genetics and Plant Breeding
- Plant Disease Resistance and Genetics
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Plant Gene Expression Analysis
- Genetic and phenotypic traits in livestock
- Molecular Biology Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Plant tissue culture and regeneration
- Plant Virus Research Studies
- Plant Genetic and Mutation Studies
- Microtubule and mitosis dynamics
- Telomeres, Telomerase, and Senescence
- Machine Learning in Bioinformatics
- Fungal and yeast genetics research
- Biomedical Text Mining and Ontologies
- Genomics and Chromatin Dynamics
- Plant Reproductive Biology
- Plant nutrient uptake and metabolism
University of Missouri
2007-2024
Iowa State University
2010-2018
University of Arizona
2004-2015
Florida State University
2011
Plant Gene Expression Center
2011
DuPont (United States)
2004
Incyte (United States)
2004
Pediatrics and Genetics
2004
Maize (Zea mays L.) is one of the most important cereal crops and a model for study genetics, evolution, domestication. To better understand maize genome organization to build framework sequencing, we constructed sequence-ready fingerprinted contig-based physical map that covers 93.5% genome, which 86.1% aligned genetic map. The contig contains 25,908 genic markers enabled us align nearly 73% anchored rice genome. distribution pattern expressed sequence tags correlates recombination. In...
Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support sequenced genomes of many maize inbred lines in addition B73 reference genome assembly. Curation development efforts have targeted high quality datasets tools trait analysis, germplasm genetic studies, breeding. MaizeGDB hosts a wide range data including recent new types metadata, RNA-seq, proteomics, synteny, large-scale diversity. To improve access visualization several been implemented to:...
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...
Abstract Research in the past decade has demonstrated that a single reference genome is not representative of species’ diversity. MaizeGDB introduces pan-genomic approach to hosting genomic data, leveraging large number diverse maize genomes and their associated datasets quickly efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural transposable elements, diversity data across so researchers can easily track functional differences locus its orthologs...
Abstract A map derived from restriction fragment length polymorphisms (RFLPs) in maize (Zea mays L.) is presented. The was constructed an immortalized Tx303 x CO159 F2 mapping population that allowed for unlimited number of markers to be mapped and pooled F3 seed distributed other laboratories. total 215 consisting 159 genomic clones, 16 isozymes 35 cloned genes defined function have been placed on 10 chromosomes. An examination segregation data has revealed several regions with aberrant...
Abstract Background Heterosis is the superior performance of F 1 hybrid progeny relative to parental phenotypes. Maize exhibits heterosis for a wide range traits, however magnitude highly variable depending on choice parents and trait(s) measured. We have used expression profiling determine whether level, or types, non-additive gene vary in maize hybrids with different levels genetic diversity heterosis. Results observed that distributions better parent among series 25 generally do not...
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...
A framework for understanding the synthesis and catalysis of metabolites other biochemicals by proteins is crucial unraveling physiology cells. To create such a Zea mays L. subsp. (maize), we developed MaizeCyc, metabolic network enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary plant products, annotating genes identified in maize reference genome sequenced from B73 variety. MaizeCyc version 2.0.2 collection 391 pathways involving 8889 mapped to 2110 reactions 1468...
Abstract Our goal is to construct a robust physical map for maize (Zea mays) comprehensively integrated with the genetic map. We have used two-dimensional 24 × overgo pooling strategy anchor expressed sequence tagged (EST) unigenes 165,888 bacterial artificial chromosomes (BACs) on high-density filters. A set of 70,716 public ESTs seeded derivation 10,723 EST unigene assemblies. From these assemblies, 10,642 sequences 40 bp were applied as hybridization probes. BAC addresses obtained 9,371...
First released in 1991 with the name MaizeDB, Maize Genetics and Genomics Database, now MaizeGDB, celebrates its 20th anniversary this year. MaizeGDB has transitioned from a focus on comprehensive curation of literature, genetic maps stocks to paradigm that accommodates recent release reference maize genome sequence, multiple diverse genomes sequence-based gene expression data sets. The Team is relatively small, relies heavily research community provide data, nomenclature standards most...
Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these were designed for audiences, they frequently contain language details tailored to investigators with research objectives backgrounds. Although comparisons across have long been possible on a small scale, comprehensive queries analyses that span broad set reference species, disciplines, knowledge domains continue be severely limited by the absence common semantic...
Crop plant research is poised to make revolutionary strides including the following: cloning target genes based on their function and/or position in genome; documenting all and interplay; defining exploring existing genetic diversity a species; using
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...
Sequence-indexed insertional libraries in maize (Zea mays) are fundamental resources for functional genetics studies. Here, we constructed a Mutator (Mu) library the B73 inbred background designated BonnMu. A total of 1,152 Mu-tagged F2-families were sequenced using Mu-seq approach. We detected 225,936 genomic Mu insertion sites and 41,086 high quality germinal insertions covering 16,392 annotated genes (37% B73v4 genome). On average, each F2-family BonnMu captured 37 Filtered Gene Set...
Abstract Three maize (Zea mays) bacterial artificial chromosome (BAC) libraries were constructed from inbred line B73. High-density filter sets all three libraries, made using different restriction enzymes (HindIII,EcoRI, and MboI, respectively), evaluated with a set of complex probes including the185-bp knob repeat, ribosomal DNA, two telomere-associated repeat sequences, four centromere repeats, the mitochondrial genome, multifragment chloroplast DNA probe, bacteriophage λ. The results...
Single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) are becoming important genetic markers for major crop species. In this study we demonstrate their utility locating fingerprint contigs (FPCs) to the map. To derive SNP InDel markers, amplified genomic regions corresponding 3000 unigenes across 12 maize ( Zea mays L.) lines, of which 194 (6.4%) showed size polymorphism InDels between B73 Mo17 on agarose gels. The analysis these in 83 diverse inbred lines that often...
Abstract Pan-genomes, encompassing the entirety of genetic sequences found in a collection genomes within clade, are more useful than single reference for studying species diversity. This is especially true like Zea mays, which has particularly diverse and complex genome. Presenting pan-genome data, analyses, visualization challenging, species, but so when pan-genomic data linked to extensive gene model including classical information, markers, insertions, expression proteomic protein...
Abstract Background Molecular markers serve three important functions in physical map assembly. First, they provide anchor points to genetic maps facilitating functional genomic studies. Second, reduce the overlap required for BAC contig assembly from 80 50 percent. Finally, validate assemblies based solely on fingerprints. We employed a six-dimensional pooling strategy combination with high-throughput PCR-based screening method maize and maps. Results A total of 110,592 clones (~ 6x haploid...
MaizeMine is the data mining resource of Maize Genetics and Genome Database (MaizeGDB). It enables researchers to create export customized annotation datasets that can be merged with their own research for use in downstream analyses. uses InterMine warehousing system integrate genomic sequences gene annotations from Zea mays B73 RefGen_v3 RefGen_v4 genome assemblies, Gene Ontology annotations, single nucleotide polymorphisms, protein homologs, pathways precomputed expression levels based on...