Data Sources and their Data Sets

CATHGENE3D
CDD
Common Bean Crop Ontology
Common Bean Crop Ontology
A controlled vocabulary to describe crop traits in common bean.
GO
GO
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.
HAMAP
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
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
/data/v2/LEGUMES/Fabaceae/genefamilies/legume.genefam.fam1.M65K/legume.genefam.fam1.M65K.trees_ML_rooted
LIS gene family phylogenetic tree files
5-593.gnm1.1P7P
[description from Dr. Phil McClean] Accession 5-593 was developed by Dr. Mark Bassett at the University of Florida. 5-593 traces back to B-351, a black-seeded variety developed by Dr. Jim Beaver, University of Puerto Rico from the cross of the Middle American varieties Bonita (white-seeded) and Jamapa (black-seeded). Dr. Bassett irradiated B-351, selected a line with determinate growth habit, back-crossed the selected line to B-351, and selected the plant with best determinate growth habit in the F2 and F3 generations. The best segregant in the F3 generation was designated 5-593. 5-593 was initially obtained from the USDA National Plant Germplasm System (NPGS; aka GRIN) as PI 608674. Dr. Bassett used 5-593 as the recipient parent to introgress many genes for seed coat color and pattern, flower color, and other morphological traits typically to the backcross three generation. These introgression lines are also available from the USDA NPGS.
5-593.gnm1.ann1.3FBJ
[description from Dr. Phil McClean] Accession 5-593 was developed by Dr. Mark Bassett at the University of Florida. 5-593 traces back to B-351, a black-seeded variety developed by Dr. Jim Beaver, University of Puerto Rico from the cross of the Middle American varieties Bonita (white-seeded) and Jamapa (black-seeded). Dr. Bassett irradiated B-351, selected a line with determinate growth habit, back-crossed the selected line to B-351, and selected the plant with best determinate growth habit in the F2 and F3 generations. The best segregant in the F3 generation was designated 5-593. 5-593 was initially obtained from the USDA National Plant Germplasm System (NPGS; aka GRIN) as PI 608674. Dr. Bassett used 5-593 as the recipient parent to introgress many genes for seed coat color and pattern, flower color, and other morphological traits typically to the backcross three generation. These introgression lines are also available from the USDA NPGS.
BAT93_x_JALOEEP558.gen.Blair_Cortés_2018
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.
BAT93_x_JALOEEP558.gen.Caldas_Blair_2009
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.
BAT93_x_JALOEEP558.gen.Freyre_Skroch_1998
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.
BAT93_x_JALOEEP558.gen.McConnell_Mamidi_2010
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.
Cerinza_x_G24404.gen.Blair_Iriarte_2006
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.
DOR364_x_BAT477.gen.Blair_Galeano_2012
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.
Frijol_Bayo.gnm1.QH8L
[Description by Dr. Phil McClean] The cultivated landrace, Frijol Bayo, was collected in a market in Cordoba, Veracruz, Mexico in 1951 by Howard Scott Gentry. Frijol Bayo is white-seeded, photoperiod insensitive with indeterminate growth habit, and has a hundred seed weight of 12.3 g. It exhibits broad adaptation and is drought (Beebe et al., 2011) and heat (Rodriguez, 2018) tolerant. With respect to biotic stress, it is resistant to common bacterial blight (Rodriguez, 2018), Uromyces appendiculatus, and two leaf hoppers, Empoasca krameri and Phaeoisariopsis griseola (Porch, T., unpublished data). DNA for the Frijol Bayo genome assembly was isolated from leaves from single seed descent; seeds for Frijol Bayo are available from USDA GRIN (G40001-Seq; PI 692269).
Frijol_Bayo.gnm1.ann1.ML22
[Description by Dr. Phil McClean] The cultivated landrace, Frijol Bayo, was collected in a market in Cordoba, Veracruz, Mexico in 1951 by Howard Scott Gentry. Frijol Bayo is white-seeded, photoperiod insensitive with indeterminate growth habit, and has a hundred seed weight of 12.3 g. It exhibits broad adaptation and is drought (Beebe et al., 2011) and heat (Rodriguez, 2018) tolerant. With respect to biotic stress, it is resistant to common bacterial blight (Rodriguez, 2018), Uromyces appendiculatus, and two leaf hoppers, Empoasca krameri and Phaeoisariopsis griseola (Porch, T., unpublished data). DNA for the Frijol Bayo genome assembly was isolated from leaves from single seed descent; seeds for Frijol Bayo are available from USDA GRIN (G40001-Seq; PI 692269).
G19833.gnm1.ann1.expr.4ZDQ
LIS expression dataset phavu1 (An RNA-Seq based gene expression atlas of the common bean cv. Negro jamapa).
G19833.gnm1.ann1.pScz
Genome annotations for the Phaseolus vulgaris G19833 v1 genome assembly.
G19833.gnm1.ann1.syn.xQ7F
Synteny calculations involves identification of orthologous genes by selecting reciprocal top hits between chromosome pairs from an all-against-all blastp search of genes between two species (evalue threshold of 1e-10), followed by DAGchainer to predict chains of syntenic genes in complete genomes. Proportions of synonymous-site changes (Ks) between orthologs are calculated, and synteny blocks are filtered for block-wise median Ks values. Synteny blocks have also been calculated to show these paralogous WGD-derived duplications.
G19833.gnm1.mrk.BARCBean6K
A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two 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. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.
G19833.gnm1.mrk.Benchimol_deCampos_2007
A common bean genomic library was constructed using the ‘IAC-UNA’ variety enriched for (CT) and (GT) for microsatellite motifs. From 1,209 sequenced clones, 714 showed microsatellites distributed over 471 simple and 243 compound motifs. GA/CT and GT/CA were the most frequent motifs found among these sequences. A total of 123 microsatellites has been characterized. Out of these, 87 were polymorphic (73.7%), 33 monomorphic (26.8%), and 3 (2.4%) did not amplify at all. In a sample of 20 common bean materials selected from the Agronomic Institute Germplasm Bank, the number of alleles per locus varied 2–9, with an average of 2.82. The polymorphic information content (PIC) of each marker varied from 0.05 to 0.83, with a 0.45 average value. Cluster and principal coordinate analysis of the microsatellite data were consistent with the original assignment of the germplasm accessions into the Andean and Mesoamerican gene pools of common bean. Low polymorphism levels detected could be associated with the domestication process. These microsatellites could be a valuable resource for the bean community because of their use as new markers for genetic studies.
G19833.gnm1.mrk.Blair_Pedraza_2003
A total of 150 microsatellite markers developed for common bean (Phaseolus vulgaris L.) were tested for parental polymorphism and used to determine the positions of 100 genetic loci on an integrated genetic map of the species. The value of these single-copy markers was evident in their ability to link two existing RFLP-based genetic maps with a base map developed for the Mesoamerican Andean population, DOR364 G19833. Two types of microsatellites were mapped, based respectively on gene-coding and anonymous genomic-sequences. Gene-based microsatellites proved to be less polymorphic (46.3%) than anonymous genomic microsatellites (64.3%) between the parents of two intergenepool crosses. The majority of the microsatellites produced single bands and detected single loci, however four of the gene-based and three of the genomic microsatellites produced consistent double or multiple banding patterns and detected more than one locus. Microsatellite loci were found on each of the 11 chromosomes of common bean, the number per chromosome ranging from 5 to 17 with an average of ten microsatellites each. Total map length for the base map was 1,720 cM and the average chromosome length was 156.4 cM, with an average distance between microsatellite loci of 19.5 cM. The development of new microsatellites from sequences in the Genbank database and the implication of these results for genetic mapping, quantitative trait locus analysis and marker-assisted selection in common bean are described.
G19833.gnm1.mrk.Cardoso_Oblessuc_2008
The objective of this work was to develop new microsatellite markers in common bean. Ninety-nine new microsatelitte loci were developed from a microsatellite-enriched library for (CT)8 and (GT)8 motifs, from CAL-143 line. The majority of microsatellite sequences (51%) was related to cellular metabolism. The remaining sequences were associated to transcription functions. Only 17.2% of the sequences presented some level of similarity with other plant species genes.
G19833.gnm1.mrk.Gaitan-Solis_Duque_2002
We constructed a microsatellite-enriched genomic library for Bactris gasipaes, an economically important, domesticated palm. We developed 18 polymorphic microsatellite markers, and found an average of seven alleles per locus in a sample of 14 individuals selected from a germplasm bank. Cross-species amplification was evaluated in six other Bactris species. The loci detected will permit population studies and germplasm characterization, and can be used for genetic analyses in related species.
G19833.gnm1.mrk.Galeano_Cortes_2012
In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings.
G19833.gnm1.mrk.Galeano_Fernandez_2011
In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 x BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR3646G19833 (DG) and BAT936JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudochromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.
G19833.gnm1.mrk.Grisi_Blair_2007
The present study describes a new set of 61 polymorphic microsatellite markers for beans and the construction of a genetic map using the BAT93 x Jalo EEP558 (BJ) population for the purpose of developing a reference linkage map for common bean (Phaseolus vulgaris). The main objectives were to integrate new microsatellites on the existing framework map of the BJ population, and to develop the first linkage map for the BJ population based exclusively on microsatellites. Of the total of 264 microsatellites evaluated for polymorphism, 42.8% showed polymorphism between the genitors. An integrated map was created totaling 199 mapped markers in 13 linkage groups, with an observed length of 1358 cM and a mean distance between markers of 7.23 cM. For the map constructed exclusively with microsatellites, 106 markers were placed in 12 groups with a total length of 606.8 cM and average distance of 6.8 cM. Linkage group designation and marker order for BM microsatellites generally agreed with previous mapping, while the new microsatellites were well distributed across the genome, corroborating the utility of the BJ population for a reference map. The extensive use of the microsatellites and the availability of a reference map can help in the development of other genetic maps for common bean through the transfer of information of marker order and linkage, which will allow comparative analysis and map integration, especially for future quantitative trait loci and association mapping studies.
G19833.gnm1.mrk.Hanai_deCampos_2007
3 cDNA libraries generated by the Bean EST project (http://lgm.esalq.usp.br/BEST/), comprising a unigene collection of 3126 sequences and a genomic microsatellite-enriched library, were analyzed for the presence of SSRs. A total of 219 expressed sequence tags (ESTs) were found to carry 240 SSRs (named EST-SSR), whereas 714 genomic sequences contained 471 SSRs (named genomic-SSR). A subset of 80 SSRs, 40 EST-SSRs, and 40 genomic-SSRs were evaluated for molecular polymorphism in 23 genotypes of cultivated beans from the Mesoamerican and Andean genetic pools, including Brazilian cultivars and 2 related species. Of the common bean genotypes, 31 EST-SSR loci were polymorphic, yielding 2–12 alleles as compared with 26 polymorphic genomic-SSRs, accounting for 2–7 alleles. Cluster analysis from data using both genic and genomic-SSR revealed a clear separation between Andean and Mesoamerican beans. The usefulness of these loci for distinguishing bean genotypes and genetic mapping is discussed.
G19833.gnm1.mrk.Hougaard_Madsen_2008
Here we validate our global approach in the common bean and in the AA genome complement of the allotetraploid peanut. We present the successful conversion of 50% of the bioinformatics-defined primers into legume anchor markers in bean and diploid Arachis species. One hundred and four new loci representing single-copy genes were added to the existing bean map. These new legume anchor-marker loci enabled the alignment of genetic linkage maps through corresponding genes and provided an estimate of the extent of synteny and collinearity. Extensive macrosynteny between Lotus and bean was uncovered on 8 of the 11 bean chromosomes and large blocks of macrosynteny were also found between bean and Medicago. This suggests that anchor markers can facilitate a better understanding of the genes and genetics of important traits in crops with largely uncharacterized genomes using genetic and genome information from related model plants.
G19833.gnm1.mrk.McClean_Mamidi_2010
Genetically-positioned transcript loci of common bean were mapped relative to the recent soybean 1.01 pseudochromosome assembly. In nearly every case, each common bean locus mapped to two loci in soybean, a result consistent with the duplicate polyploidy history of soybean. Blocks of synteny averaging 32 cM in common bean and 4.9 Mb in soybean were observed for all 11 common bean linkage groups, and these blocks mapped to all 20 soybean pseudochromosomes. The median physical-to-genetic distance ratio in common bean (based on soybean physical distances) was ~120 kb/cM. ~15,000 common bean sequences (primarily EST contigs and EST singletons) were electronically positioned onto the common bean map using the shared syntentic blocks as references points.
G19833.gnm1.mrk.Murray_Larsen_2002
A set of 79 previously mapped bean (Phaseolus vulgaris) genomic (Bng) clones were partially sequenced. BLAST database searches detected homologies between 59 of these clones and genes from a variety of plants, especially Arabidopsis thaliana. Some matches in the database to the Bng clones included a putative P-glycoprotein-ABC transporter from Arabidopsis, an early nodulin-binding protein (ENBPI) from Medicago truncatula, a lon-protease protein from spinach, a branched-chain amino-acid aminotransferase from Arabidopsis, and a vacuolar sorting receptor (BP-80) from Pisum sativum. Additional matches were found for genes involved in isoprenoid biosynthesis, sulfur metabolism, proline biosynthesis, and floral development. Sequence tagged site (STSs) were produced for 16 of the clones, 2 of which contain simple sequence repeats (SSRs). Polymorphisms were detected for six of the STSs.
G19833.gnm1.mrk.Parker_BernyMierYTeran_2020
Genetic markers for the GWAS dataset provided with Parker, Berny Mier y Teran (2020).
G19833.gnm1.mrk.PvCookUCDavis2009
PvCookUCDavis2009 is a 768-marker array of single nucleotide polymorphisms (SNP) based on Trans-legume Orthologous Group (TOG) genes. A total of 91.4% of TOG markers had singleton hits with annotated Pv genes and all mapped outside of regions of resistance gene clusters.
G19833.gnm1.mrk.Raggi_Caproni_2019
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 50 k Single Nucleotide Polymorphisms (SNPs). The Genome-Wide Association Study 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.
G19833.gnm1.mrk.Yu_Park_2000
Here we report the first successful assignment of 15 SSR markers to the Phaseolus vulgaris molecular linkage map. A total of 37 SSR primer pairs were developed and tested for amplification and product-length polymorphism with BAT93 and Jalo EEP558, the parental lines of an F7 recombinant inbred (RI) population previously used for the construction of a common bean molecular linkage map. Sixteen of the SSRs polymorphic to the parental lines were analyzed for segregation and 15 of them were assigned to seven different linkage groups, indicating a widespread distribution throughout the bean genome. Map positions for genes coding for DNAJ-like protein, pathogenesis-related protein 3, plastid-located glutamine synthetase, endochitinase, sn-glycerol-3 phosphate acyltransferase, NADP-dependent malic enzyme, and protein kinase were determined for the first time. Addition of three SSR loci to linkage group B4 brought two separated smaller linkage groups together to form a larger linkage group. Analysis of allele segregation in the F7 RI population revealed that all 16 SSRs segregated in the expected 1:1 ratio. These SSR markers were stable and easy to assay by polymerase chain reaction (PCR). They should be useful markers for genetic mapping, genotype identification, and marker-assisted selection of common beans.
G19833.gnm1.zBnF
Files in this directory include the scaffold assemblies for Phaseolus vulgaris, version 1.0 for the genome.
G19833.gnm2.ann1.PB8d
Genome annotations for the Phaseolus vulgaris G19833 v2 genome assembly.
G19833.gnm2.ann1.syn.DVDW.yml
Synteny calculations involves identification of orthologous genes by selecting reciprocal top hits between chromosome pairs from an all-against-all blastp search of genes between two species (evalue threshold of 1e-10), followed by DAGchainer to predict chains of syntenic genes in complete genomes. Proportions of synonymous-site changes (Ks) between orthologs are calculated, and synteny blocks are filtered for block-wise median Ks values. Synteny blocks have also been calculated to show these paralogous WGD-derived duplications.
G19833.gnm2.fC0g
Files in this directory include the scaffold assemblies for Phaseolus vulgaris, version 2.0 for the genome.
G19833.gnm2.mrk.DiVittori_Bitocchi_2021
In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5 kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated with the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci.
G19833.gnm2.mrk.Zitnick-Anderson_Oladzad_2020
The Andean (ADP; n = 270) and Middle American (MDP; n = 280) Diversity Panels were screened in the greenhouse to identify genetic factors associated with FRR resistance. Forty-seven MDP and 34 ADP lines from multiple market classes were identified as resistant to FRR. Greenhouse phenotyping repeatability was confirmed via five control lines. Genome-wide association mapping using ∼200k SNPs was performed on standard phenotyping score 1-9, as well as binary and polynomial transformation of score data. Sixteen and seven significant genomic regions were identified for ADP and MDP, respectively, using all three classes of phenotypic data. Most candidate genes were associated with plant immune/defense mechanisms. For the ADP population, ortholog of glucan synthase-like enzyme, senescence-associated genes, and NAC domain protein, associated with peak genomic region Pv08:0.04-0.18 Mbp, were the most significant candidate genes. For the MDP population, the peak SNPs Pv07:15.29 Mbp and Pv01:51 Mbp mapped within gene models associated with ethylene response factor 1 and MAC/Perforin domain-containing gene respectively. The research provides a basis for bean improvement through the use of resistant genotypes and genomic regions for more durable root rot resistance.
G2333_x_G19839.gen.Checa_Blair_2008
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.
G27455.gnm1.7NXX.yml
Files in this directory include the genome assembly for Phaseolus lunatus accession G27455
G27455.gnm1.ann1.JD7C
Genome annotations for the Phaseolus lunatus G27455 V1 genome assembly.
ICABunsi_x_SXB405.gen.Parker_BernyMierYTeran_2020
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.
LaborOvalle.gnm1.VZZS
Genome assembly for Phaseolus vulgaris accession Labor Ovalle. Labor Ovalle is a race Guatemala common bean variety released by the Institute of Agricultural Science and Technology (ICTA). Labor Ovalle was a landrace native to the highlands that was improved by selection efforts of the ICTA breeding program led by Dr. Fernando Aldana. Labor Ovalle is a round-seeded Bolonilio market class bean. The project was a joint effort of North Dakota State University and Hudson/Alpha Institute for Biotechnology. Funding for the project was provided by the United States Agency for International Development through the Feed the Future Legume Innovation Laboratory.
LaborOvalle.gnm1.ann1.L1DY
Genome annotation files for Phaseolus vulgaris accession Labor Ovalle, assembly 1. Labor Ovalle is a race Guatemala common bean variety released by the Institute of Agricultural Science and Technology (ICTA). Labor Ovalle was a landrace native to the highlands that was improved by selection efforts of the ICTA breeding program led by Dr. Fernando Aldana. Labor Ovalle is a round-seeded Bolonilio market class bean. The project was a joint effort of North Dakota State University and Hudson/Alpha Institute for Biotechnology. Funding for the project was provided by the United States Agency for International Development through the Feed the Future Legume Innovation Laboratory.
Stampede_x_RedHawk.gen.Song_Jia_2015
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.
UI111.gnm1.3VTM
Files in this directory include the genome assembly for Phaseolus vulgaris accession UI111
UI111.gnm1.ann1.8L4N
Genome annotations for the Phaseolus vulgaris UI111 v1 genome assembly.
W6_15578.gnm2.L2V4
[Description by Dr. Kirstin Bett] W6 15578 is a wild P. acutifolius accession obtained from the Western Regional Plant Introduction Station of the USDA. Originally collected by O.W. Norvell in Mexico in 1955, it now has the Plant Introduction number PI 638833. It is photoperiod sensitive, has an indeterminate growth habit, small, mottled seeds, and the pods shatter at maturity. It was used as a donor parent in the development of an interspecific hybrid population to improve abiotic stress tolerance in common bean (Souter et al. 2017(1)). W6 15578 was one of the parents, along with PI 430219, of the tepary bean mapping population, BR-06, developed and genotyped at the University of Saskatchewan (Gujaria-Verma et al. 2016(2)).
W6_15578.gnm2.ann1.LVZ1
[Description by Dr. Kirstin Bett] W6 15578 is a wild P. acutifolius accession obtained from the Western Regional Plant Introduction Station of the USDA. Originally collected by O.W. Norvell in Mexico in 1955, it now has the Plant Introduction number PI 638833. It is photoperiod sensitive, has an indeterminate growth habit, small, mottled seeds, and the pods shatter at maturity. It was used as a donor parent in the development of an interspecific hybrid population to improve abiotic stress tolerance in common bean (Souter et al. 2017(1)). W6 15578 was one of the parents, along with PI 430219, of the tepary bean mapping population, BR-06, developed and genotyped at the University of Saskatchewan (Gujaria-Verma et al. 2016(2)).
Xana_x_Cornell49242.gen.Gaitán-Solís_Duque_2002
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.
mixed.gen.Blair_Cortés_2018
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)
mixed.gen.Galeano_Fernandez_2011
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.
mixed.gwas.DiVittori_Bitocchi_2021
In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5 kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated with the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci.
mixed.gwas.Jain_Poromarto_2019
Common bean (Phaseolus vulgaris L.) is an important high protein crop grown worldwide. North Dakota and Minnesota are the largest producers of common beans in the USA, but crop production is threatened by soybean cyst nematode (SCN; Heterodera glycines Ichinohe) because most current cultivars are susceptible. Greenhouse screening data using SCN HG type 0 from 317 plant introductions (PI's) from the USDA core collection was used to conduct a genome wide association study (GWAS). These lines were divided into two subpopulations based on principal component analysis (Middle American vs. Andean). Phenotypic results based on the female index showed that accessions could be classified as highly resistant (21% and 27%), moderately resistant (51% and 48%), moderately susceptible (27% and 22%) and highly susceptible (1% and 3%) for Middle American and Andean gene pools, respectively. Mixed models with two principal components (PCs) and kinship matrix for Middle American genotypes and Andean genotypes were used in the GWAS analysis using 3,985 and 4,811 single nucleotide polymorphic (SNP) markers, respectively which were evenly distributed across all 11 chromosomes. Significant peaks on Pv07, and Pv11 in Middle American and on Pv07, Pv08, Pv09 and Pv11 in Andean group were found to be associated with SCN resistance. Homologs of soybean rhg1, a locus which confers resistance to SCN in soybean, were identified on chromosomes Pv01 and Pv08 in the Middle American and Andean gene pools, respectively. These genomic regions may be the key to develop SCN-resistant common bean cultivars.
mixed.gwas.Myers_Wallace_2019
Snap beans are a significant source of micronutrients in the human diet. Among the micronutrients present in snap beans are phenolic compounds with known beneficial effects on human health, potentially via their metabolism by the gut-associated microbiome. The genetic pathways leading to the production of phenolics in snap bean pods remain uncertain. In this study, we quantified the level of total phenolic content (TPC) in the Bean Coordinated Agriculture Program (CAP) snap bean diversity panel of 149 accessions. The panel was characterized spectrophotometrically for phenolic content with a Folin-Ciocalteu colorimetric assay. Flower, seed and pod color were also quantified, as red, purple, yellow and brown colors are associated with anthocyanins and flavonols in common bean. Genotyping was performed through an Illumina Infinium Genechip BARCBEAN6K_3 single nucleotide polymorphism (SNP) array. Genome-Wide Association Studies (GWAS) analysis identified 11 quantitative trait nucleotides (QTN) associated with TPC. An SNP was identified for TPC on Pv07 located near the P gene, which is a major switch in the flavonoid biosynthetic pathway. Candidate genes were identified for seven of the 11 TPC QTN. Five regulatory genes were identified and represent novel sources of variation for exploitation in developing snap beans with higher phenolic levels for greater health benefits to the consumer.
mixed.gwas.Parker_BernyMierYTeran_2020
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.
mixed.gwas.Raggi_Caproni_2019
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.
mixed.gwas.Shi_Gepts_2021
Soybean cyst nematode (SCN, Heterodera glycines) has become the major yield-limiting biological factor in soybean production. Common bean is also a good host of SCN, and its production is challenged by this emerging pest in many regions such as the upper Midwest USA. The use of host genetic resistance has been the most effective and environmentally friendly method to manage SCN. The objectives of this study were to evaluate the SCN resistance in the USDA common bean core collection and conduct a genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN HG Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips, consisting of 4,654 SNPs. Results showed that 15 accessions were resistant to SCN with a Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. The association study showed that 11 SNP markers, located on chromosomes Pv04, 07, 09, and 11, were strongly associated with resistance to HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type 1.2.3.5.6.7 based on the public dataset (N = 276), consisting of a diverse set of common bean accessions genotyped with the BARCBean6K_3 chip. Six SNPs associated with HG Type 2.5.7 resistance on Pv 01, 02, 03, and 07, and 12 SNPs with HG Type 1.2.3.5.6.7 resistance on Pv 01, 03, 06, 07, 09, 10, and 11 were detected. The accuracy of genomic prediction (GP) was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that genomic selection (GS) of SCN resistance is feasible. This study provides basic information for developing SCN-resistant common bean cultivars, using the USDA core germ plasm accessions. The SNP markers can be used in molecular breeding in common beans through marker-assisted selection (MAS) and GS.
mixed.gwas.Zitnick-Anderson_Oladzad_2020
Common bean (Phaseolus vulgaris L.) production worldwide is hampered by Fusarium root rot (FRR), which is caused by Fusarium solani. Screening for FRR resistance on a large scale is notoriously difficult and often yields inconsistent results due to variability within the environment and pathogen biology. A greenhouse screening assay was developed incorporating multiple isolates of F. solani to improve assay reproducibility. The Andean (ADP; n = 270) and Middle American (MDP; n = 280) Diversity Panels were screened in the greenhouse to identify genetic factors associated with FRR resistance. Forty-seven MDP and 34 ADP lines from multiple market classes were identified as resistant to FRR. Greenhouse phenotyping repeatability was confirmed via five control lines. Genome-wide association mapping using ∼200k SNPs was performed on standard phenotyping score 1-9, as well as binary and polynomial transformation of score data. Sixteen and seven significant genomic regions were identified for ADP and MDP, respectively, using all three classes of phenotypic data. Most candidate genes were associated with plant immune/defense mechanisms. For the ADP population, ortholog of glucan synthase-like enzyme, senescence-associated genes, and NAC domain protein, associated with peak genomic region Pv08:0.04-0.18 Mbp, were the most significant candidate genes. For the MDP population, the peak SNPs Pv07:15.29 Mbp and Pv01:51 Mbp mapped within gene models associated with ethylene response factor 1 and MAC/Perforin domain-containing gene respectively. The research provides a basis for bean improvement through the use of resistant genotypes and genomic regions for more durable root rot resistance.
mixed.gwas.Zitnick_Anderson_Oladzad_2020
Common bean (Phaseolus vulgaris L.) production worldwide is hampered by Fusarium root rot (FRR), which is caused by Fusarium solani. Screening for FRR resistance on a large scale is notoriously difficult and often yields inconsistent results due to variability within the environment and pathogen biology. A greenhouse screening assay was developed incorporating multiple isolates of F. solani to improve assay reproducibility. The Andean (ADP; n = 270) and Middle American (MDP; n = 280) Diversity Panels were screened in the greenhouse to identify genetic factors associated with FRR resistance. Forty-seven MDP and 34 ADP lines from multiple market classes were identified as resistant to FRR. Greenhouse phenotyping repeatability was confirmed via five control lines. Genome-wide association mapping using ∼200k SNPs was performed on standard phenotyping score 1-9, as well as binary and polynomial transformation of score data. Sixteen and seven significant genomic regions were identified for ADP and MDP, respectively, using all three classes of phenotypic data. Most candidate genes were associated with plant immune/defense mechanisms. For the ADP population, ortholog of glucan synthase-like enzyme, senescence-associated genes, and NAC domain protein, associated with peak genomic region Pv08:0.04-0.18 Mbp, were the most significant candidate genes. For the MDP population, the peak SNPs Pv07:15.29 Mbp and Pv01:51 Mbp mapped within gene models associated with ethylene response factor 1 and MAC/Perforin domain-containing gene respectively. The research provides a basis for bean improvement through the use of resistant genotypes and genomic regions for more durable root rot resistance.
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