Data Sources and their Data Sets

Common Bean Crop Ontology
Common Bean Crop Ontology
A controlled vocabulary to describe crop traits in common bean.
The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
InterMine post-processor
InterMine gene-flanking regions
Gene-flanking regions created by the core InterMine post-processor
InterMine intergenic regions
Intergenic regions created by the InterMine core post-processor
InterPro data set
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
InterPro domain GO annotations
Mapping of GO terms to InterPro entries.
LIS Datastore
LIS gene family phylogenetic tree files
This BAT93 x JALOEEP558 map was constructed using Mapdisto v. 2.0 (Lorieux, 2012), assuming an RI model and using the create groups command both with and without anchor markers.
The objective of this study was to analyze the relationship between quantitative trait loci (QTL) for seed tannin concentration in common bean and Mendelian genes for seed coat color and pattern. Three populations of recombinant inbred lines, derived from crosses between the Andean and Mesoamerican genepools were used for QTL identification and for mapping STS markers associated with seed color loci. This map was created from the BAT93 x JALOEEP558 set.
A 75-member F8 mapping population derived from the cross of BAT93 with JALO EEP558 was used to produce a core linkage map for common bean. The total length of the map is 1226 cM and it is composed of 11 linkage groups. The total of 563 mapped marker loci includes 120 RFLPs, 430 RAPDs, and additional isozyme and phenotypic markers.
In this study, gene-based markers were used for mapping in a recombinant inbred (RI) population of Phaseolus vulgaris L. Gene-based markers were developed that corresponded to genes controlling mutant phenotypes in Arabidopsis thaliana, genes undergoing selection during domestication in maize, and genes that function in a biochemical pathway in A. thaliana. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers.
QTLs for agronomic performance were identified in a population of BC2F(3:5) introgression lines created from the cross of a Colombian large red-seeded commercial cultivar, ICA Cerinza, and a wild common bean accession, G24404. A total of 157 lines were evaluated for phenological traits, plant architecture, seed weight, yield and yield components in replicated trials in three environments in Colombia and genotyped with microsatellite, SCAR, and phaseolin markers that were used to create a genetic map that covered all 11 linkage groups of the common bean genome. The map comprises all 11 common bean linkage groups; the average size of a linkage group is 79.0 cM and the average number of markers per linkage group is 7.6. The map exhibits a total genetic distance of 869.5 cM and an average marker spacing of 10.4 cM. Composite interval mapping analysis identified a total of 41 significant QTLs for the eight traits measured of which five for seed weight, two for days to flowering, and one for yield were consistent across two or more environments.
A mapping population of 113 RILs in the F5:7 generation was generated using a DOR364 by BAT477 cross. The 186 markers comprising the genetic map were amplified fragment length polymorphisms (AFLP: 22 markers), random amplified polymorphic DNA markers (RAPD: 104), and simple sequence repeats (SSR: 60). The map covers all 11 linkage groups of the common bean genome, has a total map length of 1087.5 cM, and shows an average distance between markers of 5.9 cM. Linkage groups were identified by comparisons to the integrated genetic map for common bean based on microsatellites shown in Blair, Pedraza et al. (2003a) (DOR364_x_G19833). Gaps for the genetic map exist on linkage groups b03, b09 and b11 but overall there are only nine gaps larger than 15 cM.
Phaseolus vulgaris cv. Negro jamapa expression profiles in the P. vulgaris reference genome (G 19833) for 24 unique samples from seven distinct tissues; roots, nodules, stems, flowers, leaves, pods, and seeds throughout development.
Genome annotations for the Phaseolus vulgaris G19833 v1 genome assembly.
Synteny between phavu.G19833.gnm1 and other species.
Genetic markers mapped to phavu.G19833.gnm1
Genetic markers mapped to phavu.G19833.gnm1
Genetic markers mapped to phavu.G19833.gnm1
Genetic markers mapped to phavu.G19833.gnm1
Genetic markers mapped to phavu.G19833.gnm1
The G2333_x_G19839_a genetic map contains all 11 common bean linkage groups. It has a total length of 1175 cM and 149 mapped total markers (four of these markers generated two loci each). The map contains 79 microsatellite, 57 RAPD, 8 SCAR, and 3 STS markers; there is also a marker for the seed protein phaseolin (Phs) and a morphological marker for flower color (V). The average length of a linkage group is 106.81 cM and the average number of markers per linkage group is 13.5. The average distance between marker loci across all linkage groups is 7.89 cM. The G2333_x_G19839_a map could be aligned with the common bean integrated map of Freyre, Skroch et al. (1998) based on positions of shared SSR markers (see also Blair, Pedraza et al., 2003). The map description comes from Ochoa, Blair et al. (2006) where this population was originally presented. However, the lengths of individual linkage groups were taken from Figure 2 in Checa and Blair (2008) in which a more complete version of this genetic map was available with reported linkage group sizes.
Genome annotations for the Phaseolus lunatus G27455 V1 genome assembly.
Pod Dehiscence QTLs were identified using three phenotyping methods and an ICA Bunsi (PD-susceptible) x SXB 405 (PD-resistant) recombinant inbred mapping population. An unreplicated spring planting of 238 RIL field plots were visually evaluated for dehiscence. A replicated summer planting produced mature, non-dehiscing pods from 191 RILs that were phenotyped in two ways: the proportion of pods dehiscing after 7 days in a 65 C dessicator and 7 subsequent days at room temperature, and peak force required to induce pod fracture at the apical end of the pod beak measured with an Imada force measurement guage. Composite interval mapping was completed with the R package R/qtl.
Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the BARCBean6K_1 and BARCBean6K_2 BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly.
Genome annotations for the Phaseolus vulgaris UI111 v1 genome assembly.
This genetic linkage map includes 175 AFLP, 27 microsatellite, 30 SCAR, 33 ISSR, and 12 RAPD markers. The map also contains 13 loci coding for seed proteins, and four traditional genes (Fin/fin for growth habit, Asp/asp for seed coat shininess, P/p for seed color, and I/i for resistance to bean common mosaic virus). Therefore the map comprises a total of 294 markers, its total length is 1042 cM, and the average marker distance is 3.53 cM. The map consists of 14 linkage groups that were correlated with the 11 linkage groups of the integrated linkage map of Freyre, Skroch et al. (1998) by using anchor markers included in previously published bean maps. The linkage groups B02, B03, and B04 of the Freyre, Skroch et al. (1998) consensus map each correspond to a pair of linkage groups in the Perez-Vega, Paneda et al. (2010) map.
LIS gene families
Files in this directory include sequences, markers, and map files related to the markers described in Blair, Cortes et al. (2013) and Blair, Cortes et al. (2018)
This common bean consensus map was created using the DB (DOR364_x_BAT477, Mesoamerican intra-gene pool cross), DG (DOR364_x_G19833, inter-gene pool cross), and BJ (BAT93_x_JALOEEP558, inter-gene pool cross) mapping populations. The consensus map contains a total of 1010 markers; these include 446 SNP, 392 SSR, 99 RAPD, 45 RFLP, 22 AFLP, 5 STS, and one phenotypic marker. The total size of the map is 2041 cM, there are 11 linkage groups, and the average size of a linkage group is 185 cM (range is between 131 cM for Pv10 to 276 cM for Pv02). There is an average of 91 markers per linkage group (range is between 151 on Pv02 to 67 on Pv09), 83% of which markers appear as single copies, and the average inter-marker distance is 2 cM. The numbers of anchor markers shared between the component populations are 98, 87, 14, and 4 markers for the DG-DB, DG-BJ, DB-BJ, and DG-BJ-DB population sets, respectively.
GWAS study of pod dehiscence in Phaseolus vulgaris dry beans, using the Andean and Mesoamerican Diversity Panels. Association mapping was carried out with generalized linear models and results were visualized with the QQMAN package in R. Regions of significance were delimited as the areas between the first and last significant SNPs on a chromosome. A Bonferroni-corrected alpha of 0.05 was used to determine the significance of SNPs after they met the threshold established as a minor allele frequency (MAF) of 0.1.
The aim of this study was to investigate the genetic control of days to flowering using a whole genome association approach on a panel of 192 highly homozygous common bean genotypes purposely developed from landraces using single-seed descent. The phenotypic characterization was carried out at two experimental sites throughout two growing seasons, using a randomized partially replicated experimental design. The same plant material was genotyped using double digest restriction-site-associated DNA sequencing, producing, after a strict quality control, a dataset of about 50k SNPs after filtering against: loci with >10% missing values; individuals with >10% missing loci; markers with MAF<5%; and heterozygosity>=2%. The GWAS revealed significant and meaningful associations between days to flowering and several SNP markers; seven genes are proposed as the best candidates to explain the detected associations.
phalu.G27455.gnm1.ann1 genome annotation
Plant Ontology
Plant Ontology
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies.
Plant Trait Ontology
Plant Trait Ontology
A controlled vocabulary of describe phenotypic traits in plants.
Sequence Ontology
Sequence Ontology
The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence.
Legume Federation
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The Legume Information System (LIS) is a research project of the USDA-ARS:Corn Insects and Crop Genetics Research in Ames, IA.
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