A5071816450- Soybean genetics and cultivation
- Legume Nitrogen Fixing Symbiosis
- Advanced Data Storage Technologies
- Parallel Computing and Optimization Techniques
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Distributed and Parallel Computing Systems
- Agricultural pest management studies
- Genetic Mapping and Diversity in Plants and Animals
- Algorithms and Data Compression
- Genetic and Environmental Crop Studies
- Plant Molecular Biology Research
- Meat and Animal Product Quality
- Distributed systems and fault tolerance
- Genetics, Bioinformatics, and Biomedical Research
- Plant Virus Research Studies
- Plant nutrient uptake and metabolism
- Molecular Biology Techniques and Applications
- Radiomics and Machine Learning in Medical Imaging
- Peanut Plant Research Studies
- Genetic Associations and Epidemiology
- Bioinformatics and Genomic Networks
- Research Data Management Practices
- Embedded Systems Design Techniques
- Biochemical Analysis and Sensing Techniques
Agricultural Research Service
2012-2024
Harvard University
2020
United States Department of Agriculture
2010-2019
Harvard University Press
2019
Iowa State University
2011-2018
University of Illinois Urbana-Champaign
2011
National Center for Genome Resources
2011
Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets chromosomes from two ancestral species. Here we report sequence show after its origin, evolved through mobile-element activity, deletions by flow genetic information between corresponding (that is, homeologous recombination). Uniformity patterns recombination at ends favors single for wild counterpart A. monticola. However, much genome,...
The Soybean Consensus Map 4.0 facilitated the anchoring of 95.6% soybean whole genome sequence developed by Joint Genome Institute, Department Energy, but its marker density was only sufficient to properly orient 66% scaffolds. discovery and genetic mapping more single nucleotide polymorphism (SNP) markers were needed anchor remaining sequence. To that end, next generation sequencing high-throughput genotyping combined obtain a much higher resolution map could be used most help validate...
Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and information major crop model legumes. With more than two-dozen domesticated species, there are numerous specialists working on particular also GDPs these species. has been redesigned in last three years both better integrate sets across legumes, accommodate specialized that serve To sets, genome map viewers, holds synteny mappings among all...
The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation growth response to environmental stresses. Many HD-Zip are characterized Arabidopsis (Arabidopsis thaliana), members being investigated for abiotic stress responses rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) cucumber (Cucmis sativus). Findings these species suggest as high priority candidates crop...
Abstract SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genomic data, which is integrated made accessible to researchers breeders. The site several reference genome assemblies, as well maps, thousands of mapped traits, expression epigenetic pedigree information, extensive variant genotyping data sets. SoyBase displays include genetic, genomic, maps the genome. Gene presented in viewer heat pictorial tabular gene report pages. Millions sequence variants...
The nutritional and economic value of many crops is effectively a function seed protein oil content. Insight into the genetic molecular control mechanisms involved in deposition these constituents developing needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) soybean (Glycine max (L.) Merrill) has striking effect content.A near-isogenic line (NIL) pair contrasting differing an introgressed genomic segment containing LG QTL was used as resource...
A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 FLX/454 and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant assembly, referred to as CcTA v2, comprised 21 434 transcript contigs (TACs) with an N50 of 1510 bp, the largest one being ∼8 kb. Of TACs, 622 (77.5%) could be mapped on soybean genome build 1.0.9 under fairly stringent alignment parameters. Based knowledge...
The objective of this study was to determine how prenatal and postnatal dietary omega-3 fatty acids alter white blood cell (leukocyte) DNA methylation offspring. Fifteen gilts (n = 5 per treatment) were selected from one three treatments: (i) control diet throughout gestation, lactation nursery phase (CON); (ii) algal acid supplementation enriched in EPA DHA (Gromega™ ) fed (Cn3); or (iii) Gromega™ maternally, during gestation only, the (Mn3). At 11 weeks age after 8 post-weaning feeding,...
Abstract The Legume Information System (LIS; https://legumeinfo.org ) houses genetic and genomic data, integrated in various online tools to allow comparative analyses. website database maintain data for more than two dozen species, particularly focusing on crop model species holding other diverse of taxonomic interest. Major analysis features include genome browsers, sequence‐search tools, legume‐focused gene families a phylogenetic tree viewer, annotation service (which places submitted...
epiSNP is a program for identifying pairwise single nucleotide polymorphism (SNP) interactions (epistasis) in quantitative-trait genome-wide association studies (GWAS). A parallel MPI version (EPISNPmpi) was created 2008 to address this computationally expensive analysis on large data sets with many quantitative traits and SNP markers. However, the falling cost of genotyping has led an explosion large-scale GWAS that challenge EPISNPmpi’s ability compute results reasonable amount time....
Studies have indicated that exon and intron size intergenic distance are correlated with gene expression levels breadth. Previous reports on these correlations in plants animals been conflicting. In this study, next-generation sequence data, which has shown to be more sensitive than previous profiling technologies, were generated analyzed from 14 tissues. Our results revealed a novel dichotomy. At the low level, an increase breadth transcript because of number exons introns. No significant...
Abstract For species with potential as new crops, rapid improvement may be facilitated by genomic methods. Apios ( americana Medik.), once a staple food source of Native American Indians, produces protein-rich tubers, tolerates wide range soils, and symbiotically fixes nitrogen. We report the first high-quality de novo transcriptome assembly, an expression atlas, set 58,154 SNP 39,609 gene markers (GEMs) for characterization breeding collection. Both SNPs GEMs identify six genotypic clusters...
The PCIT method is an important technique for detecting interactions between networks. algorithm has been used in the biological context to infer complex regulatory mechanisms and genetic networks, genome wide association studies, other similar problems. In this work, re-implemented with exemplary parallel, vector, I/O, memory instruction optimizations today's multi- many-core architectures. evolution performance of new code targets processor architectures Stampede supercomputer, but will...
epiSNP is a program for identifying pairwise single nucleotide polymorphism (SNP) interactions (epistasis) that affect quantitative traits in genome-wide association studies (GWAS). A parallel MPI version (EPISNPmpi) was created 2008 to address this computationally-expensive analysis on data sets with many and markers. However, the explosion genome sequencing will lead creation of large-scale overwhelm EPISNPmpi's ability compute results reasonable amount time. Thus, rewritten efficiently...
SUMMARY The partial correlation coefficient with information theory (PCIT) method is an important technique for detecting interactions between networks. PCIT algorithm has been used in the biological context to infer complex regulatory mechanisms and genetic networks, genome wide association studies, other similar problems. In this work, re‐implemented exemplary parallel, vector, input/output (I/O), memory, instruction optimizations today's multi‐core many‐core architectures. evolution...
Identification of allelic or corresponding genes (pan-genes) within a species genus is important for discovery biologically significant genetic conservation and variation. Similarly, identification orthologs (gene families) across wider evolutionary distances understanding the basis similar differing traits. Especially in plants, several complications make pan-genes gene families challenging, including whole-genome duplications, rate differences among lineages, varying qualities assemblies...
As sequencing prices drop, genomic data accumulates—seemingly at a steadily increasing pace. Most potentially have value beyond the initial purpose—but only if shared with scientific community. This, of course, is often easier said than done. Some challenges in sharing include volume (raw file sizes and number files), complexities, formats, nomenclatures, metadata descriptions, choice repository. In this paper, we describe 10 quick tips for open data.
Consumers are becoming increasingly conscientious about the nutritional value of their food. Consumption some fatty acids has been associated with human health traits such as blood pressure and cardiovascular disease. Therefore, it is important to investigate genetic variation in content present meat. Previously publications reported regions cattle genome that additively acid content. This study evaluated epistatic interactions, which could account for additional Epistatic interactions 44 a...
Recently, the combination of new projection technology, fast, low-cost graphics cards, and Linux-powered personal computers has made it possible to provide a stereoprojection stereoviewing system that is much more affordable than previous commercial solutions. These Geowall systems are visualization built with commodity off-the-shelf components, run on open-source (and other) operating systems, using applications software. In short, they "Beowulf-class" cost-effective way for U. S....
Powerful high performance computing systems of the future are expected to have higher failure rates than current systems. As a result, HPC applications running on such more likely encounter system today's machines. Application fault tolerance is therefore becoming important avoid costly waste resources associated with rerunning failed applications. The MPI 3.1 standard does not address issue process failures. Checkpoint/restart commonly used add However, there can be complicated issues...