A5068163827- Genomics and Phylogenetic Studies
- Legume Nitrogen Fixing Symbiosis
- Soybean genetics and cultivation
- Molecular Biology Techniques and Applications
- Plant tissue culture and regeneration
- Plant Virus Research Studies
- CRISPR and Genetic Engineering
- Genetic Mapping and Diversity in Plants and Animals
- Bioinformatics and Genomic Networks
- Plant Disease Resistance and Genetics
- Plant nutrient uptake and metabolism
- Genetically Modified Organisms Research
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Chromosomal and Genetic Variations
- Agronomic Practices and Intercropping Systems
- Genetic and phenotypic traits in livestock
- Plant Genetic and Mutation Studies
- Wheat and Barley Genetics and Pathology
- Plant-Microbe Interactions and Immunity
- Plant responses to water stress
- Plant Molecular Biology Research
- Nematode management and characterization studies
- Genetic and Environmental Crop Studies
- Genetics and Plant Breeding
University of Minnesota
2013-2023
University of Missouri
2023
Center for Life Sciences
2023
Ho Chi Minh City University of Science
2023
Vietnam National University Ho Chi Minh City
2023
Can Tho University
2023
University of Minnesota System
2015-2017
Nicolaus Copernicus University
2013
The CRISPR/Cas9 system is rapidly becoming the reagent of choice for targeted mutagenesis and gene editing in crop species. There are currently intense research efforts sciences to identify efficient platforms carry out projects. These typically result incremental tweaking various platform components including identification crop-specific promoters terminators optimal expression Cas9 enzyme CRISPR guide RNA. In this report, we demonstrate development an online web tool fast target loci...
Processing of double-stranded RNA precursors into small RNAs is an essential regulator gene expression in plant development and stress response. Small processing requires the combined activity a functionally diverse group molecular components. However, most species, there are insufficient mutant resources to characterize each encoding gene. Here, mutations loci protein machinery involved soya bean Medicago truncatula were generated using CRISPR/Cas9 TAL-effector nuclease (TALEN) mutagenesis...
Genome-wide association studies (GWAS) have identified loci linked to hundreds of traits in many different species. Yet, because linkage equilibrium implicates a broad region surrounding each locus, the causal genes often remain unknown. This problem is especially pronounced nonhuman, nonmodel species, where functional annotations are sparse and there frequently little information available for prioritizing candidate genes. We developed computational approach, Camoco, that integrates by GWAS...
Abstract Soybean is the world’s leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but genetic architecture yield key agronomic traits poorly understood. We developed a 40-mating nested association mapping (NAM) population 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers six in field trials 22 environments. Analysis agronomic, SNP data revealed 23 significant marker-trait...
Abstract Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast are not well understood. Here, we examine variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from large neutron-mutagenized population. While deletion rates were similar previous reports, surprisingly high segmental duplication also found throughout genome. Duplication coverage extended across entire...
The safety of mutagenized and genetically transformed plants remains a subject scrutiny. Data gathered communicated on the phenotypic molecular variation induced by gene transfer technologies will provide scientific-based means to rationally address such concerns. In this study, genomic structural (e.g. large deletions duplications) single nucleotide polymorphism rates were assessed among sample soybean cultivars, fast neutron-derived mutants, five developed through Agrobacterium based...
The soybean [Glycine max (L.) Merr.] chlorophyll-deficient line MinnGold is a spontaneous mutant characterized by yellow foliage. Map-based cloning and transgenic complementation revealed that the phenotype caused nonsynonymous nucleotide substitution in third exon of Mg-chelatase subunit gene (ChlI1a) on chromosome 13. This was selected as candidate for different foliage mutant, T219H (Y11y11), had been previously mapped to Although phenotypes are clearly distinct, sequencing ChlI1a...
Abstract Mutagenesis is a useful tool in many crop species to induce heritable genetic variability for trait improvement and gene discovery. In this study, forward screening of soybean fast neutron (FN) mutant population identified an individual that produced seed with nearly twice the amount sucrose (8.1% on dry matter basis) less than half oil (8.5% as compared wild type. Bulked segregant analysis (BSA), comparative genomic hybridization, genome resequencing were used associate composition...
CORE IDEAS: 'Fiskeby III' harbors a combination of abiotic stress traits, including iron deficiency chlorosis (IDC) tolerance. An IDC quantitative trait locus on chromosome Gm05 was identified in genome-wide association studies and biparental populations. Fine-mapping resolved 137-kb interval containing strong candidate genes. Iron is an important nutrient for soybean [Glycine max (L.) Merr.] grown high-pH soils. Despite numerous agronomic attempts to alleviate IDC, genetic tolerance remains...
Abstract Background As with many plant species, current genome editing strategies in soybean are initiated by stably transforming a gene that encodes an engineered nuclease into the genome. Expression of transgene results double-stranded break and repair at targeted locus, oftentimes resulting mutation(s) intended site. is self-pollinating species 20 chromosome pairs, transgene(s) T0 generally expected to be unlinked mutation(s), transgene(s)/mutation(s) should independently assort T1...
Perennial crops show promise for sustainable agricultural production while providing ecosystem services (maintaining healthy soil, controlling erosion, improving water quality, and enhancing wildlife habitat). could also provide economically viable cropping option to farmers. Sunflower (Helianthus annuus L.) is an ideal crop perennialization because of existing genetic resources a wide variety end-uses. The objective this research was evaluate interspecific hybrids between perennial...
Small nonprotein-coding microRNAs (miRNAs) are present in most eukaryotes and central effectors of RNA silencing-mediated mechanisms for gene expression regulation. In plants, DICER-LIKE1 (DCL1) is the founding member a highly conserved family RNase III-like endonucleases that function as core machinery proteins to process hairpin-like precursor transcripts into mature miRNAs, small regulatory RNAs, 21-22 nucleotides length. Zinc finger nucleases (ZFNs) were used generate single...
Abstract Background Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each these new genome assemblies shares significant portions synteny between other, annotated structure gene models regions can differ. Of particular concern are split-gene misannotations, which a single is incorrectly as two distinct genes or gene. These misannotations major impacts on functional prediction,...
Wheat stem rust disease caused by Puccinia graminis f. sp. tritici ( Pgt ) is a global threat to wheat production. Fast evolving populations of limit the efficacy plant genetic resistance and constrain management strategies. Understanding molecular mechanisms that lead infection susceptibility could deliver novel strategies deploy crop through loss susceptibility. We used comparative transcriptome-based orthology-guided approaches characterize gene expression changes associated with in...
The advent of -omics technologies has enabled the resolution fine molecular differences among individuals within a species. DNA sequence variations, such as single nucleotide polymorphisms or small deletions, can be tabulated for many kinds genotype comparisons. However, experimental designs and analytical approaches are replete with ways to overestimate level variation present given sample. Analytical pipelines that do not apply proper thresholds nor assess reproducibility samples...
Abstract Background Genome wide association studies (GWAS) have identified thousands of loci linked to hundreds traits in many different species. However, because linkage equilibrium implicates a broad region surrounding each locus, the causal genes often remain unknown. This problem is especially pronounced non-human, non-model species where functional annotations are sparse and there frequently little information available for prioritizing candidate genes. Results To address this issue, we...
Abstract Genome‐wide association studies (GWAS) have proven to be a valuable approach for identifying genetic intervals associated with phenotypic variation in Medicago truncatula . These can vary size, depending on the historical local recombination. Typically, significant span numerous gene models, limiting ability resolve high‐confidence candidate genes underlying trait of interest. Additional genomic data, including co‐expression networks, combined mapping information successfully...
Differentially expressed transcript derived fragments (TDFs) of bovine pituitary gland tissue at different developmental ages Limousine and Hereford bulls were identified by cDNA-AFLP technique. Study revealed comparatively higher differentially transcripts in 6-month 12-month bulls. The BLASTn/p analysis 3 21 predicted genes which gave significant e-values for respectively, assembled Bos taurus genome. showed their mapped positions on chromosomes: BTA2, 3, 5, 8, 9, 11, 12, 15-23, 26, 28,...
ABSTRACT Genome-wide association studies (GWAS) have proven to be a valuable approach for identifying genetic intervals associated with phenotypic variation in Medicago truncatula . These can vary size, depending on the historical local recombination near each significant interval. Typically, span numerous gene models, limiting ability resolve high-confidence candidate genes underlying trait of interest. Additional genomic data, including co-expression networks, combined mapping information...
Abstract Background Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each these new genome assemblies shares significant portions synteny between other, annotated structure gene models regions can differ. Of particular concern are split-gene misannotations, which a single is incorrectly as two distinct genes or gene. These misannotations major impacts on functional prediction,...