Ethalinda K. S. Cannon's research while affiliated with Agricultural Research Service and other places

Publications (34)

Preprint
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The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing re-use of annotation data, this flexibility has become an obstacle for standardized downstream processing. Common...
Article
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The fatty acid composition of seed oil is a major determinant of the flavor, shelf-life, and nutritional quality of peanuts. Major QTLs controlling high oil content, high oleic content, and low linoleic content have been characterized in several seed oil crop species. Here, we employ genome-wide association approaches on a recently genotyped collec...
Article
An a-maize-ing set of genomes Maize is an important crop cultivated worldwide. As maize spread across the world, selection for local environments resulted in variation, but the impact on differences between the genome has not been quantified. By producing high-quality genomic sequences of the 26 lines used in the maize nested association mapping pa...
Article
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Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tre...
Preprint
Full-text available
The fatty acid composition of seed oil is a major determinant of the flavor, shelf-life, and nutritional quality of peanuts. Major QTLs controlling high oil content, high oleic content, and low linoleic content have been characterized in several seed oil crop species. Here we employ genome-wide association approaches on a recently genotyped collect...
Article
Full-text available
Background Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to thousands of accessions. There is a need for tools to help rapidly explore such datasets, to assess characteristics such as overa...
Article
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MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org). It enables researchers to create and export customized annotation datasets that can be merged with their own research data for use in downstream analyses. MaizeMine uses the InterMine data warehousing system to integrate genomi...
Article
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Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core...
Article
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Legumes, comprising one of the largest, most diverse, and most economically important plant families, are the subject of vibrant research and development worldwide. Continued improvement of legume crops will benefit from the recent proliferation of genetic (including genomic) resources; but the diversity, scale, and complexity of these resources pr...
Article
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Background Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources o...
Article
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Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions...
Article
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Common bean (Phaseolus vulgaris L.), one of the most important grain legume crops for direct human consumption, faces many challenges as a crop. Domesticated from wild relatives that inhabit a relatively narrow ecological niche, common bean faces a wide range of biotic and abiotic constraints within its diverse agroecological settings. Biotic stres...
Article
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The factors behind genome size evolution have been of great interest, considering that eukaryotic genomes vary in size by more than three orders of magnitude. Using a model of two wild peanut relatives, Arachis duranensis and Arachis ipaensis, in which one genome experienced large rearrangements, we find that the main determinant in genome size red...
Article
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The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple...
Article
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The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are pr...
Chapter
Peanut or groundnut (Arachis hypogaea), an allotetraploid species, recently became the focus of a global genomics initiative with the goal of developing genome-wide molecular resources to facilitate breeding. Publicly available reference genome sequence of peanut’s diploid progenitors (peanutbase.org) is enabling expansion of genotyping tools for g...
Article
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Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaen...
Chapter
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Large-scale genomic data for peanut have only become available in the last few years, with the advent of low-cost sequencing technologies. To make the data accessible to researchers and to integrate across diverse types of data, the International Peanut Genomics Consortium funded the development of PeanutBase, at http://peanutbase.org. This website...
Article
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Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these...
Article
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A framework for understanding the synthesis and catalysis of metabolites and other biochemicals by proteins is crucial for unraveling the physiology of cells. To create such a framework for Zea mays L. subsp. mays (maize), we developed MaizeCyc, a metabolic network of enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary plant p...
Article
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Knobs are conspicuous heterochromatic regions found on the chromosomes of maize and its relatives. The number, locations, and sizes of knobs vary dramatically, with most lines containing between four and eight knobs in mid-arm positions. Prior data suggest that some knobs may reduce recombination. However, comprehensive tests have not been carried...
Article
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First released in 1991 with the name MaizeDB, the Maize Genetics and Genomics Database, now MaizeGDB, celebrates its 20th anniversary this year. MaizeGDB has transitioned from a focus on comprehensive curation of the literature, genetic maps and stocks to a paradigm that accommodates the recent release of a reference maize genome sequence, multiple...
Article
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Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popula...
Article
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The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time-sometimes disappearing en...
Article
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CViT (chromosome visualization tool) is a Perl utility for quickly generating images of features on a whole genome at once. It reads GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features on those chromosomes. It can display features on any chromosomal unit system, including genetic (centimorgan), cytol...
Article
Full-text available
An international consortium is sequencing the euchromatic genespace of Medicago truncatula. Extensive bioinformatic and database resources support the marker-anchored bacterial artificial chromosome (BAC) sequencing strategy. Existing physical and genetic maps and deep BAC-end sequencing help to guide the sequencing effort, while EST databases prov...

Citations

... The HO trait is considered pleiotropic on levels of other fatty acids in the seed (Isleib et al. 1996(Isleib et al. , 2006bBarkley et al. 2011Barkley et al. , 2013 and does not affect flavor in fresh samples (Pattee et al. 2002a, b;Talcott et al. 2005;Isleib et al. 2006aIsleib et al. , 2015. As a simply inherited trait, environment plays little to no role (Andersen and Gorbet 2002;Mozingo et al. 2004;Tonnis et al. 2020) and minor modifiers are thought to exist but have yet to be identified (Isleib et al. 2006b;Barkley et al. 2013;Tonnis et al. 2020;Otyama et al. 2022). ...
... However, a single reference genome-based approach to gene family identification cannot identify the gene family members that are missing from the reference genome but are present in other genomes. Hufford et al. published a maize pan-genome based on 26 high-quality genomes containing a large amount of presence-absence variation (PAV) and SV information, thus laying the foundation for gene family and functional studies [14]. ...
... From a technical perspective, the BGH core has been developed with the Tripal toolkit (i.e. Drupal v7, Tripal v3), an open-source project supporting the development of biological databases [8,35,36] complemented by the development of additional modules [37]. All these elements are further described below. ...
... C above ambient) around pods and late season flower termination resulted in elevated oleate in Spanish market type and runner market type. A recent genome-wide association study (GWAS) (Otyama et al., 2021) identified several candidate genes related to oleic, linoleic and palmitic acid contents, which was a big step towards the elucidation of molecular basis underlying fatty acid phenotype in peanut. ...
... Plant species include Arabidopsis (6), Medicago (12), wheat (https://urgi.versailles.inra.fr/WheatMine), maize (11,13), and several from the legume family (14) (see registry.intermine.org). InterMine is also used for drug development (TargetMine (15)) and by large-scale projects and consortia (PhytoMine (16), modMine (17), AllianceMine (https://www.alliancegenome.org/alliancemine)). ...
... via genotyping-by-sequencing (GBS) that can then facilitate peanut molecular breeding. The 58 K SNP array 'Axiom_Arachis' , developed by resequencing 41 peanut accessions, was used to identify genetic diversity across 384 Arachis genotypes including USDA Mini Core Collection and wild species 15,16 , while 787 accessions from the U.S. Peanut core collection were genotyped by the 14 K 'Arachis_Axiom2' SNP array to reveal their genetic diversity 17 . Compared to SNP arrays, GBS is a more cost-effective technique based on sequencing of the reduced genome associated with restriction sites using NGS 18,19 . ...
... In legumes, where there is substantial genome synteny across the entire family [e.g., (Ren et al., 2019)], the potential for comparative genomics to speed up research in understudied species is particularly high. With improving databases for mining genomic information from more widespread cultivated legumes [e.g., (Bauchet et al., 2019;Berendzen et al., 2021)], this task has become easier than in the past. ...
... The power of GWAS is dependent on genetic diversity 29 . The magnitude of LD and its decrease with genetic distance plays a crucial role in determining the mapping resolution 30 . The recombination rate influences the rate of LD decay in a population over time 31 . ...
... Cultivated peanut (Arachis hypogaea) is an important oil and protein crop from South America [10,11]. It is an allotetraploid plant that resulted from a cross between A. duranensis and A. ipaensis [11][12][13]. A. monticola is a wild allotetraploid plant known to be the direct progenitor of A. hypogaea [14]. To date, genome sequencing of at least six Arachis species has been completed, including A. duranensis, A. ipaensis, A. monticola, A. hypogaea cv. ...