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Article
Open AccessCombining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean
Mung bean (Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous traits for adaptation to northern and southern latitudes. This study investi...
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Article
Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition
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 remai...
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Protocol
Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources
In this chapter, we introduce the main components of the Legume Information System (https://legumeinfo.org) and several associated resources. Additionally, we provide an...
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Article
An accumulation of genetic variation and selection across the disease-related genes during apple domestication
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 domesticatio...
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Article
Open AccessGenetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing
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) varietie...
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Article
Open AccessGCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data
Large genoty** datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genoty** datasets may have thousands to millions of data points per accession, across tens to...
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Article
Evaluating two different models of peanut’s origin
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Chapter
Chromosomal Structure, History, and Genomic Synteny Relationships in Lupinus
The genome assembly of narrow-leafed lupin (NLL, Lupinus angustifolius) provides critical information for inferring the evolutionary history of NLL relative to other species in the large genistoid clade and to ot...
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Article
Open AccessGenome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean
Breeding programs benefit from information about marker-trait associations for many traits, whether the goal is to place those traits under active selection or to maintain them through background selection. As...
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Article
Open AccessEvaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection
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 ...
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Article
Open AccessThe genome sequence of segmental allotetraploid peanut Arachis hypogaea
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 ...
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Article
Open AccessA reference-grade wild soybean genome
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 fin...
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Article
Open AccessA review of breeding objectives, genomic resources, and marker-assisted methods in common bean (Phaseolus vulgaris L.)
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 e...
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Article
Open AccessA transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes
We report a linkage map for Apios americana and describe synteny with selected warm-season legumes. A translocation event in common bean and soybean is con...
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Chapter
Genomics Resources for Peanut Improvement
Peanut or groundnut (Arachis hypogaea), an allotetraploid species, recently became the focus of a global genomics initiative with the goal of develo** genome-wide molecular resources to facilitate breeding. Pub...
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Article
Open AccessGenomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume
For species with potential as new crops, rapid improvement may be facilitated by new genomic methods. Apios (Apios americana Medik.), once a staple food source of Native American Indians, produces protein-rich tu...
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Article
Open AccessDynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.)
Bean common mosaic virus (BCMV) is widespread, with Phaseolus species as the primary host plants. Numerous BCMV strains have been identified on the basis of a panel of bean varieties t...
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Article
Open AccessThe genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut
David Bertioli and colleagues report the genomes of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut, Arachis hypogaea. Their analyses are a first step in understanding the evol...
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Article
Open AccessAn ontology approach to comparative phenomics in plants
Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language a...
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Article
Open AccessComprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress
The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental...
