Steven Cannon

Steven Cannon
United States Department of Agriculture | USDA · Agricultural Research Service (ARS)

About

289
Publications
40,422
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17,911
Citations
Citations since 2017
87 Research Items
9624 Citations
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Introduction
Steven Cannon currently works at the United States Department of Agriculture - Agricultural Research Service (ARS), Ames, IA

Publications

Publications (289)
Article
Full-text available
Introduction Virginia-type peanut, Arachis hypogaea subsp. hypogaea , is the second largest market class of peanut cultivated in the United States. It is mainly used for large-seeded, in-shell products. Historically, Virginia-type peanut cultivars were developed through long-term recurrent phenotypic selection and wild species introgression project...
Article
Full-text available
Motivation Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heter...
Preprint
Full-text available
Motivation Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heter...
Article
Full-text available
Polyploidy and life-strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and the genetic bases of such transitions remain elusive. We assembled chromosome-level genomes of representative perennial species across the genus Glycine including five diploids and a y...
Chapter
Full-text available
In this chapter, we introduce the main components of the Legume Information System (https://legumeinfo.org) and several associated resources. Additionally, we provide an example of their use by exploring a biological question: is there a common molecular basis, across legume species, that underlies the photoperiod-mediated transition from vegetativ...
Article
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 collec...
Article
Full-text available
Significance A great challenge for humanity is feeding its growing population while minimizing ecosystem damage and climate change. Here, we uncover the global benefits arising from the introduction of one wild species accession to peanut-breeding programs decades ago. This work emphasizes the importance of biodiversity to crop improvement: peanut...
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
Although human-imposed selection is known to have altered plant traits during crop domestication, the effect of selection on host susceptibility or resistance is not well understood. Moreover, the domestication of perennial tree fruit crops, unlike annual crops, was driven by hybridization, clonal propagation, and selection of desirable phenotypes,...
Article
Full-text available
We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild ( Glycine soja ) selections and 429 cultivated ( Glycine max ) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to id...
Article
SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensiv...
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
Full-text available
Apios americana an herbaceous perennial legume with climbing, vinous habit, produces underground stem tubers along stolons A americana was wild harvested by Native Americans throughout eastern North America There is also some evidence of cultivation and transport of landraces Early historical records of Apios in North America describe its important...
Article
Full-text available
Over the last 40 years, several researchers have worked to develop improved cultivars of Apios americana. Notable improvements have been made in yield and tuber size. Research over this period has also led to better understanding of genetic and genomic limitations (e.g. sterile triploid populations) and characteristics of floral biology (an unusual...
Article
Full-text available
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
Full-text available
Protein domains can be regarded as sections of protein sequences capable of folding independently and performing specific functions. In addition to amino-acid level changes, protein sequences can also evolve through domain shuffling events such as domain insertion, deletion, or duplication. The evolution of protein domains can be studied by trackin...
Preprint
Full-text available
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...
Preprint
Full-text available
Gene families are groups of genes that have descended from a common ancestral gene present in the species under study. Current, widely used gene family building algorithms can produce family clusters that may be fragmented or missing true family sequences (under-clustering). Here we present a classification method based on sequence pairs that, firs...
Article
Full-text available
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
Full-text available
We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and one of Glycine soja, the closest wild relative of G. max. The G. max assemblies are for widely used U.S. cultivars: the northern line 'Williams 82' (Wm82); and the southern line 'Lee'. The Wm82 assembly improves the prior published assembly...
Article
Full-text available
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
Full-text available
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
Full-text available
Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub‐Saharan Africa, that is resilient to hot and drought‐prone environments. An assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single molecule real‐time sequencing,...
Article
Full-text available
Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples....
Article
Reconstruction of an ancestral genome for a set of plant species has been a challenging task because of complex histories that may include whole genome duplications (WGDs), segmental duplications, independent gene duplications or losses, diploidization, and rearrangement events. Here, we describe the reconstruction a hypothetical ancestral genome f...
Article
Full-text available
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...
Preprint
Full-text available
Cowpea ( Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. A high-quality assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single molecule real-tim...
Article
Full-text available
As sequencing prices drop, genomic data accumulates-seemingly at a steadily increasing pace. Most genomic data potentially have value beyond the initial purpose-but only if shared with the scientific community. This, of course, is often easier said than done. Some of the challenges in sharing genomic data include data volume (raw file sizes and num...
Article
Full-text available
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...
Data
Homology of legume TOG markers mapped in this study. (XLSX)
Data
Genetic map based on BAT93 x JaloEEP558 recombinant inbred line population for all 11 common bean (Pv) chromosomes showing distances (cM) to the left and markers to the right, respectively. (PDF)
Data
SNP marker location comparisons on linkage map distance (cM, y-axis) and physical distance (Mb, x-axis) across each of the eleven chromosomes of common bean (Pv) showing a dashed line at the position of the centromeres according to Schmutz et al. (2014). (PDF)
Data
Intra-chromosal decay of linake disequilibrium (r2) as a function of genetic distance (cM) for pairwise comparisons of the SNP markers on each chromosome (Pv). (PDF)
Data
Intra-chromosal decay of linake disequilibrium (r2) as a function of physical distance (Mb) for pairwise comparisons of the SNP markers at each chromosome (Pv). (PDF)
Data
Per chromosomal (Pv) relationship between D′and r2 for the SNP markers. (PDF)
Data
TOG marker names, map positions, and flanking sequences. (XLSX)
Data
Genotypes in the linkage disequilibrium (LD) germplasm panel including 71 Andean and 115 Mesoamerican genotypes from Blair et al. (2013). (DOCX)
Data
Distribution of minor-allele-frequency (MAF), also known as folded site frequency spectrum, for 768 single nucleotide polymorphism (SNP) markers used in this study (a) across genepools, (b) within the Andean genepool, and (c) within the Mesoamerican genepool. (PDF)
Data
Genome-wide distribution of nucleotide diversity (π) values for 768 single nucleotide polymorphism (SNP) markers used in this study (a) across genepools, (b) within the Andean genepool, and (c) within the Mesoamerican genepool. (PDF)
Article
Full-text available
Recombination (R) rate and linkage disequilibrium (LD) analyses are the basis for plant breeding. These vary by breeding system, by generation of inbreeding or outcrossing and by region in the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome (514 Mb) and n = 11 chromosomes. The goal of this stud...
Article
Full-text available
Key message We report a linkage map for Apios americana and describe synteny with selected warm-season legumes. A translocation event in common bean and soy‑ bean is confrmed against Apios and Vigna species. Abstract Apios (Apios americana; “apios”), a tuberous perennial legume in the Phaseoleae tribe, was widely used as a food by Native Americans....
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
Common bean (Phaseolus vulgaris L.) is the most important food legume crop in Africa and Latin America where rainfall pattern is unpredictable. The objectives were to identify better yielding common bean lines with good canning quality under drought, and to identify traits that could be used as selection criteria for evaluating drought-tolerant gen...
Data
Data S1 Predicted gene family expansions and contractions.
Data
Data S2 Summary of sequence‐based genetic markers and their mapping to assembled scaffold sequences of narrow‐leafed lupin cv. Tanjil.
Data
Data S3 An updated genetic map for narrow‐leafed lupin cv. Tanjil.
Data
Data S6 Dot plot comparisons between narrow‐leafed lupin and other legumes.