Data Collections

Phaseolus data collections

Phaseolus lunatus

Genomes

G27455.gnm1.7NXX
Phaseolus lunatus accession G27455 genome assembly V1

Annotations

G27455.gnm1.ann1.JD7C
Phaseolus lunatus accession G27455 annotation files from genome assembly V1

Phaseolus vulgaris

Genomes

5-593.gnm1.1P7P
Phaseolus vulgaris accession 5-593 (Middle American race), genome assembly v1.
G19833.gnm1.zBnF
Phaseolus vulgaris accession G19833 genome assembly v1.0
G19833.gnm2.fC0g
Phaseolus vulgaris accession G19833 genome assembly v2.1
LaborOvalle.gnm1.VZZS
Phaseolus vulgaris accession Labor Ovalle (race Guatemala) genome assembly v1.
UI111.gnm1.3VTM
Phaseolus vulgaris accession UI111 genome assembly v1

Annotations

5-593.gnm1.ann1.3FBJ
Phaseolus vulgaris accession 5-593 (Middle American race), annotation 1, genome assembly v1.
G19833.gnm1.ann1.pScz
Phaseolus vulgaris accession G19833 annotation files
G19833.gnm2.ann1.PB8d
Phaseolus vulgaris accession G19833 annotation files from genome assembly 2.0
LaborOvalle.gnm1.ann1.L1DY
Phaseolus vulgaris accession Labor Ovalle (race Guatemala), annotation 1, genome assembly v1.
UI111.gnm1.ann1.8L4N
Phaseolus vulgaris accession UI111 annotation files from genome assembly 1.0

Expression

G19833.gnm1.ann1.expr.Negro_jamapa.ORourke_Iniguez_2014
Bean Expression Atlas for common bean cv. Negro jamapa mapped to the G19833 version 1 genome annotation.

GWAS

mixed.gwas.DiVittori_Bitocchi_2021
GWAS of pod dehiscence in Common bean, relative to the G19833 assembly 2.
mixed.gwas.Escobar_Oladzad_2022
GWAS of white mold (Sclerotinia sclerotiorum) resistance for Common bean, relative to the G19833 assembly 2.
mixed.gwas.Jain_Poromarto_2019
GWAS of Soybean cyst nematode (Heterodera glycines) resistance in common bean, relative to G19833 assembly 1.
mixed.gwas.Myers_Wallace_2019
GWAS of total phenolic content of pods, pod color, and flower color in Snap beans, relative to the G19833 assembly 2.
mixed.gwas.Oladzad_Porch_2019
GWAS of production traits under heat and drought stress in Common bean, relative to the the G19833 assembly 2.
mixed.gwas.Parker_BernyMierYTeran_2020
GWAS study of pod dehiscence in Phaseolus vulgaris dry beans, using the Andean and Mesoamerican Diversity Panels.
mixed.gwas.Paulino_Almeida_2021
GWAS of Fusarium wilt resistance for Common bean, relative to the G19833 assembly 2.0.
mixed.gwas.Raggi_Caproni_2019
GWAS study of flowering time control in a panel of homozygous 192 common bean accessions derived from landraces.
mixed.gwas.Shi_Gepts_2021
GWAS of Soybean Cyst Nematode resistance in Common bean, relative to the the G19833 assembly 1.
mixed.gwas.Tigist_Melis_2019
GWAS of Mexican bean weevil (Zabrotes subfasciatus) resistance for Common bean, relative to the G19833 assembly 2.0.
mixed.gwas.Wen_Chang_2019
GWAS assessing soybean cyst nematode (SCN) (Heterodera glycines) resistance, seed coat color, and seed weight in 363 diverse accessions of common bean, P. vulgaris relative to the G19833 assembly 1.0
mixed.gwas.Wu_Wang_2020
GWAS of agronomic, architecture, and biotic stress traits at different locations within China for Common bean, relative to the G19833 assembly 1.0.
mixed.gwas.Zitnick-Anderson_Oladzad_2020
GWAS of Fusarium root rot resistance in Common Bean, relative to the G19833 assembly 2.

QTL Studies

BAT93_x_JALOEEP558.qtl.Caldas_Blair_2009
Three RIL populations were used to find QTLs for seed color.
Cerinza_x_G24404.qtl.Blair_Iriarte_2006
Agronomic performance traits were studied 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.
DOR364_x_BAT477.qtl.Blair_Galeano_2012
A mapping population of 113 RILs in the F5:7 generation was generated using a DOR364 by BAT477 cross.
G2333_x_G19839.qtl.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.
ICABunsi_x_SXB405.qtl.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.
Xana_x_Cornell49242.qtl.Gaitán-Solís_Duque_2002
A map of 175 AFLP, 27 microsatellite, 30 SCAR, 33 ISSR, and 12 RAPD markers, as well as 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).

Genetic Maps

BAT93_x_JALOEEP558.map.Blair_Cortés_2018_c
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.map.Blair_Cortés_2018_d
Genetic map of markers to Phaseolus vulgaris accession G19833 genome assembly v1.0
BAT93_x_JALOEEP558.map.Caldas_Blair_2009
Three RIL populations were used to find QTLs for seed color.
BAT93_x_JALOEEP558.map.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.
Cerinza_x_G24404.map.Blair_Iriarte_2006
Agronomic performance traits were studied 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.
DOR364_x_BAT477.map.Blair_Galeano_2012
A mapping population of 113 RILs in the F5:7 generation was generated using a DOR364 by BAT477 cross.
G2333_x_G19839.map.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.
Stampede_x_RedHawk.map.Song_Jia_2015
A mapping population of 267 F2 plants from the cross of common bean varieties Stampede and Red Hawk developed by Dr. Phil McClean at North Dakota State University.
Xana_x_Cornell49242.map.Gaitán-Solís_Duque_2002
A map of 175 AFLP, 27 microsatellite, 30 SCAR, 33 ISSR, and 12 RAPD markers, as well as 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).
mixed.map.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.
mixed.map.PvMcCleanNDSU2007
Gene-based markers were used for mapping a RIL population of P. vulgaris. Over 1,800 SNPs and indels were found, 300 of which were screened in the RIL population. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers.

Markers

G19833.gnm1.mrk.BARCBean6K
A core set of 6000 SNPs based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips.
G19833.gnm1.mrk.Bean683WGRS_5M
Approximately 5 million SNP markers reported by Wu, Wang et al. 2020, identified from whole genome resequencing (WGRS) of 683 common bean genotypes, relative to the Phaseolus vulgaris assembly G19833.gnm1.
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.
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.
G19833.gnm1.mrk.Cardoso_Oblessuc_2008
Ninety-nine new microsatelitte loci were developed from a microsatellite-enriched library for (CT)8 and (GT)8 motifs, from CAL-143 line.
G19833.gnm1.mrk.Gaitan-Solis_Duque_2002
18 polymorphic microsatellite markers from Bactris gasipaes.
G19833.gnm1.mrk.Galeano_Cortes_2012
In this study, a total of 313 new gene-based markers were developed at target genes.
G19833.gnm1.mrk.Galeano_Fernandez_2011
The DOR364 x BAT477 linkage map consisted of 291 markers with a total map length of 1,788 cM.
G19833.gnm1.mrk.Grisi_Blair_2007
61 polymorphic microsatellite markers for beans and the construction of a genetic map using the BAT93 x Jalo EEP558 (BJ) population.
G19833.gnm1.mrk.Hanai_deCampos_2007
Three cDNA libraries generated by the Bean EST project 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).
G19833.gnm1.mrk.Hougaard_Madsen_2008
One hundred and four new loci representing single-copy genes were added to the existing bean map.
G19833.gnm1.mrk.Kim_Kaur_2006
Genetic markers from Kim, Kaur, et al. (2006) mapped to G19833.gnm1.
G19833.gnm1.mrk.McClean_Mamidi_2010
Around 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. Sequence tagged site (STSs) were produced for 16 of the clones, 2 of which contain simple sequence repeats (SSRs).
G19833.gnm1.mrk.Parker_BernyMierYTeran_2020
Genetic markers for the GWAS dataset provided with Parker, Berny Mier y Teran (2020).
G19833.gnm1.mrk.PvCookUCDavis2009
A 768-marker array of single nucleotide polymorphisms (SNP) based on Trans-legume Orthologous Group (TOG) genes.
G19833.gnm1.mrk.Raggi_Caproni_2019
Plant material was genotyped using double digest Restriction-site Associated DNA sequencing, producing about 50,000 SNPs.
G19833.gnm1.mrk.Wen_Chang_2019
GWAS assessing soybean cyst nematode (SCN) (Heterodera glycines) resistance, seed coat color, and seed weight in 363 diverse accessions of common bean, P. vulgaris relative to the G19833 assembly 1.0
G19833.gnm1.mrk.Yu_Park_2000
15 SSR markers assigned to the Phaseolus vulgaris molecular linkage map.
G19833.gnm2.mrk.Andean_MidAmer_GBS
Marker SNPs developed by GBS on Andean and Middle American gene pools, with reads mapped to the Phaseolus vulgaris G19833 gnm2 assembly.
G19833.gnm2.mrk.DiVittori_Bitocchi_2021
We developed a BC4/F4 introgression line population and narrowed the major locus for pod shattering down to a 22.5 kb region.
G19833.gnm2.mrk.Escobar_Oladzad_2022
A set of 52,201 SNPs reported by Escobar, Oladzad et al. (2022) based on genotyping-by-sequencing (GBS) of a multiparent advanced generation inter-cross (MAGIC) dry bean population of 1,050 F5:7 RILs. Reads were mapped and sorted against the G19833.gnm2 reference assembly for common bean.

Diversity

G19833.gnm1.div.Moghaddam_Mamidi_2016
Genotyping (variant) data for two diverse collections of Phaseolus vulgaris accessions: the Mesoamerican Diversity Panel (MDP) and the Andean Diversity Panel (ADP).

Phaseolus acutifolius

Genomes

Frijol_Bayo.gnm1.QH8L
Phaseolus acutifolius accession Frijol Bayo, genome assembly v1.
W6_15578.gnm2.L2V4
Phaseolus acutifolius accession W6_15578, genome assembly v2.

Annotations

Frijol_Bayo.gnm1.ann1.ML22
Genome annotation files for Phaseolus acutifolius accession Frijol Bayo; JGI annotation version 1 on assembly 1
W6_15578.gnm2.ann1.LVZ1
Phaseolus acutifolius accession W6_15578, annotations on genome assembly v2.