Work Completed

2025

2024

  • [Outreach] Monthly PCD email with info on PAG presentations (12/17/2024)
  • [Data] 408 markers, 53 QTL, 17 GWAS, 2 maps added from 3 papers (12/17/2024)
  • [Data] 55 markers, 13 QTL, 74 GWAS added from 3 papers (11/26/2024)
  • [Outreach] Monthly PCD email with a video on how to find orthologs and corresponding annotations (11/21/2024)
  • [Outreach] October 2024 PCD Newsletter sent (10/29/2024)
  • [Outreach] Monthly PCD email with a video on cross-searching gene/mRNA names (9/19/2024)
  • [Data] 8 new genomes added to PCD (8/23/2024)
  • [Outreach] Monthly PCD email with a video on search markers by trait and view genome alignment (8/22/2024)
  • [Outreach] July 2024 PCD Newsletter sent (7/30/2024)
  • [Outreach] Monthly PCD email with a video on how to use ortholog/paralog search (6/27/2024)
  • [Data] Updated Vigna angularis cv. Jingnong6 genome v1.7.1 added to PCD (6/26/2024)
  • [Outreach] Monthly PCD email with a video on how to download protein sequences (5/29/2024)
  • [Data] 437 markers, 66 GWAS, 125 QTL, 1 map added from 5 papers (5/24/2024)
  • [Tools] Added ability to search/download polypeptide sequences under Sequence Search (5/22/2024)
  • [Data] JBrowse tracks of aligned markers, GWAS, QTL, SNP added for 15 genomes (5/22/2024)
  • [Data] 2981 markers, 36 QTL, 35 GWAS, 3 maps added from 3 papers (5/10/2024)
  • [Data] SSR and other primer based markers aligned to 15 genomes and loaded to chado (5/3/2024)
  • [Outreach] April 2024 PCD Newsletter sent (4/29/2024)
  • [Data] 590 markers, 11 QTL, 77 GWAS, 2 maps added from 4 papers (4/22/2024)
  • [Data] 13 QTL, 84 GWAS, 192 markers, 1 map added from 7 papers (4/12/2024)
  • [Data] 73 QTL, 3107 markers, 4 maps, 73 GWAS added from 4 papers (3/29/2024)
  • [Outreach] Monthly PCD email with a video on how to download markers from map region (3/28/2024)
  • [Outreach] Monthly PCD email with a video on how to find markers linked to traits (2/26/2024)
  • [Data] CDC Frontier original annotation added to PathwayCyc and NCBI Refseq Cyc was rerun with v26 of ptools and updated (2/9/2024)
  • [Data] NCBI RefSeq annotation of CDC Frontier added (2/6/2024)
  • [Outreach] January 2024 PCD Newsletter sent (1/29/2024)
  • [Outreach] NRSP10 Database Workshop at PAG (1/14/2024)
  • [Data] Aligned SSR markers to P. sativum Cameor genome, added JBrowse tracks for SNPs, SSR, and QTL (1/10/2024)

2023

  • [Outreach] Monthly PCD email with a summary of new data (12/20/2023)
  • [Outreach] Monthly PCD email with a video on viewing genome and genetic map correspondences (11/27/2023)
  • [Data] PCD traits cleaned-up and updated (11/21/2023)
  • [Outreach] October 2023 PCD Newsletter sent (10/30/2023)
  • [Outreach] Monthly PCD email with a video on how to use the Expression Heatmap tool (9/27/2023) 
  • [Data] 3 more expression datasets added (9/26/2023)
  • [Data] 2 Expression datasets made available (9/14/2023)
  • [Tools] Expression Heatmap tool added (9/14/2023)
  • [Data] Added 2150 markers, 3 maps, 37 QTL from 2 manuscripts (9/5/2023)
  • [Outreach] Monthly PCD email with a video on how to go from trait to GWAS to gene to ortholog (8/29/2023)
  • [Data] Added differentially methylated region track to mung bean genome (8/29/2023)
  • [Data] Added 5134 markers, 38 QTL, 2 genetic maps, 180 GWAS (8/17/2023)
  • [Data] Added 5173 marker, 2 maps, 7 QTL, 7 GWAS (8/10/2023)
  • [Outreach] July 16, 2023 - BIMS and FieldBook at the Breeding Tools Workshop, National Association of Plant Breeding Annual Meeting (7/26/2023)
  • [Outreach] July 2023 PCD Newsletter sent (7/24/2023)
  • [Data] Added 3774 markers, 147 QTL, 5 maps and 7 GWAS (7/21/2023)
  • [Data] Vigna radiata cv. VC1973A, Vigna unguiculata subsp. sesquipedalis and Vicia sativa cv. Studencia genomes added to PathwayCyc (7/19/2023)
  • [Data] Added 84 genetic markers and 34 GWAS (7/12/2023)
  • [Tools] GWAS search added to QTL MegaSearch (7/14/2023)
  • [Outreach] Monthly PCD email with a video on how to search and view traits and associated data (6/29/2023)
  • [Data] Vigna radiata cv. VC1973A (mung bean), Vigna unguiculata subsp. sesquipedalis (cowpea) and Vicia sativa cv. Studencia (vetch) genomes added to PCD (6/26/2023)
  • [Outreach] Monthly PCD email with a video on how to search and view GWAS data (5/30/2023)
  • [Data] Added 64 genetic markers, 65 QTL, 1 map from 2 papers (6/9/2023)
  • [Data] New PathwayCycs for new pea and faba genomes (6/2/2023)
  • [Data] New pea (Zhongwan6) and faba genomes (Hedin/2 and Tiffany) added (5/10/2023)
  • [Outreach] April 2023 PCD Newsletter sent (4/26/2023)
  • [Outreach] Monthly PCD email with Genetic Map and Genome Correspondences video (3/30/2023)
  • [Tools] Ortholog page added to gene/mRNA page (3/2023)
  • [Outreach] Monthly PCD email with New Marker Search video (2/23/2023)
  • [Tools] Toolbar for selecting colors for GWAS display in MapViewer (2/2023)
  • [Tools] MegaSearch updated to allow searching records with empty fields (e.g. for searching genes without any functional annotation) (2/2023)
  • [Outreach] January 2023 PCD Newsletter sent (1/31/2023)
  • [Tools] Gene annotation template and loader created (1/2023)
  • [Tools] MegaSearch updated to query GWAS (1/2023)
  • [Tools] MapViewer updated to display GWAS data (1/2023)
  • [Outreach] PAG NRSP10 Workshop on database usage and tools (1/15/2023)

2022

  • [Outreach] Monthly PCD email sent (12/22/2022)
  • [Tools]Template/loader for GWAS data created (12/2022)
  • [Outreach] Monthly PCD email with Overlay Omics Data in PathwayCyc video (11/28/2022)
  • [Tools] BIMS/MCL made compatible with PHP8 (11/2022)
  • [Outreach] October 2022 PCD Newsletter sent (10/31/2022)
  • [Tools] MegaSearch Ortholog/paralog search added (10/28/2022)
  • [Tools] TripalMap 2.0 released (10/2022)
  • [Tools] ChadoSearch v2.7 for Drupal 7 released (10/2022)
  • [Tools] Tripal MegaSearch v1.4 for Drupal 7 released (10/2022)
  • [Outreach] Monthly PCD email with BLAST to mRNA details to JBrowse video (9/27/2022)
  • [Outreach] Monthly PCD email with MegaSearch for Genetic Maps video (8/30/2022)
  • [Tools] Data templates - ORCID/DOI enabled in data loading templates (8/2022)
  • [Tools] BIMS - Trait descriptor export (BIMS-Field Book) through BrAPI enabled (8/2022)
  • [Tools] MegaSearch - Accordion style form added in query section (8/2022)
  • [Tools] MapViewer - Resolution of the map comparison view improved (8/2022)
  • [Tools] New search pages available for Trait and Trait Descriptor (8/2022)
  • [Tools] Trait and dataset pages updated with more hyperlinks (8/2022)
  • [Outreach] CGD presentation at 2022 ASHS Conference (8/1/2022)
  • [Outreach] July 2022 PCD Newsletter sent (7/26/2022)
  • [Tools] Mapviewer - layout of the landing page improved (7/2022)
  • [Outreach] Monthly PCD email with MegaSearch for QTL video (6/27/2022)
  • [Tools] New corresponding matrices in MapViewer (6/2022)
  • [Tools] MapViewer and map page updated to display details of bin map (6/2022)
  • [Tools] Created ‘bin’ pages with Map/LG/marker/QTL information (6/2022)
  • [Outreach] Monthly PCD email with BLAST tool video (5/31/2022)
  • [Data] The P. acutifolius acc. W6 15578 and P. lunatus cv. G27455 genomes now available in PathwayCyc.  PathwayCyc updated to v26.0 (5/4/2022)
  • [Outreach] April 2022 PCD Newsletter sent (4/28/2022)
  • [Data] P. lunatus cv. G27455 added to Chado, Blast, JBrowse (4/14/2022)
  • [Data] P. acutifolius acc. W6 15578 v2.0 added to Chado, Blast, JBrowse (4/6/2022)
  • [Outreach] Ortholog/paralog search added (4/5/2022)
  • [Outreach] Monthly PCD email with Marker Search video (3/24/2022)
  • [Data] Lentil genomes and Tepary Bean (P. acutifolius Frijol Bayo) added to PathwayCyc (3/16/2022)
  • [Data] P. acutifolius Frijol Bayo v1 genome added to chado, Blast, JBrowse (3/16/2022)
  • [Outreach] Monthly PCD email with MapViewer video (2/24/2022)
  • [Data] Lentil genomes (L. culinaris CDC Redberry v2.0 and L. ervoides IG 72815 v1.0) added to chado, Blast, JBrowse (2/11/2022)
  • [Outreach] 2nd PCD Newsletter  published (1/28/2022)

2021

2020

  • [Data] New Lupinus data: maps (2), markers (888), QTL (17) (11/20/2020)
  • [Data] New Vigna data: maps (1), markers (1946), QTL (12) (11/13/2020)
  • [Data] New Chickpea data: maps (1), markers (839), QTL (19) (11/13/2020)
  • [Data] New Cowpea data: maps (2), markers (405), QTL (8), traits (2) (11/06/2020)
  • [Data] New Chickpea data: maps (1), markers (8210) (11/06/2020)
  • [Data] New Bean data: maps (3), markers (80), QTL (66), traits (5) (10/30/2020)
  • [Data] New Bean data: maps (1), QTL (29) (10/23/2020)
  • [Data] New Bean data: maps (2), traits (3), QTL (13) (10/16/2020)
  • [Data] New Bean data: markers (112) (10/12/2020)
  • [Data] New Chickpea data: markers (2083), maps (3), QTL (18), traits (4) (10/5/2020)
  • [Data] New Bambara data: markers (238), map (1), QTL (37), trait (3) (10/5/2020)
  • [Data] New Cowpea data: markers (17994), map (2), QTL (12) (9/25/2020)
  • [Data] New Pea data: map (1) (8/12/2020)
  • [Data] New Pea data: markers (1374), map (1) (8/6/2020)
  • [Data] New Cowpea data: markers (376), map (1), QTL (34), phenotype (90) (8/6/2020)
  • [Data] New Black Gram data: markers (6), QTL (10) (8/6/2020)
  • [Data] New Lupin data: QTL (1) (8/6/2020)
  • [Data] New Bean data: markers (116) (8/6/2020)
  • [Data] New Pea data: markers (157), maps (1), QTL (13) (7/17/2020)
  • [Data] New Faba data: markers (663), maps (4), QTL (26) (7/17/2020) 
  • [Data] New Cowpea data: markers (708) (7/17/2020)
  • [Data] Adzuki bean (Jingnong 6) synteny added (7/9/2020)
  • [Data] Adzuki bean (Jingnong 6) PathwayCyc added (6/26/2020)
  • [Data] New Chickpea data: traits (1), QTL (11) (6/10/2020)
  • [Data] New Lentil data: markers (6143), QTL (1), maps (1) (6/10/2020)
  • [Data] New Bean data: traits (2), QTL (53), markers (2628), maps (1) (6/10/2020)
  • [Data] New Pea data: markers (11) (6/10/2020)
  • [Data] New Faba Bean data: markers (2356), maps (5) (6/10/2020)
  • [Data] New Cowpea data: markers (10) (6/10/2020)
  • [Data] New Lentil data: markers (889), maps (2), traits (2), QTL (15) (5/22/2020)
  • [Data] New Adzuki genome (Jingnong6) added to PCD, Blast, JBrowse (5/21/20)
  • [Data] New PathwayCycs for ICC4958 (v3) and PI489777 (v2) added (5/1/2020)
  • [Data] Updated versions of ICC4958 (v3) and PI489777 (v2) genomes added to database, JBrowse, and BLAST (4/17/2020)
  • [Data] New Lentil data: markers (2,865), QTL(19), map (1) (4/16/2020)
  • [Data] New Pigeon pea data: markers (55,882), QTL (11), map (1) (4/10/2020)
  • [Data] New Bean data: marker sequences (12) (4/7/2020)
  • [Data] New Vetch data: markers (5) (3/26/2020)
  • [Data] New Cowpea data: markers (109) (3/10/2020)
  • [Data] New Bean data: markers (23) (3/10/2020)
  • [Data] New Vicia data: markers (8) (3/3/2020)
  • [Data] Lupin genome added to Synteny Viewer (2/18/20)
  • [Data] Lupin PathwayCyc added (2/6/2020)
  • [Data] New Vigna data: markers (14) (2/6/2020)
  • [Data] New Chickpea data: markers (7523) (2/3/2020)
  • [Data] Lupinus angustifolius cv. Tanjil v1.0 genome added to PCD, and corrected in BLAST and JBrowse (1/28/2020)
  • [Data] New Pea data: genetic map (1), QTL (12), markers (6453), phenotype measurements (66), trait (1) (1/28/2020)
  • [Data] New Vigna data: genetic map (1), QTL (4), markers (100) (1/27/2020)
  • [Data] New Bean data: genetic map (1), QTL (29), phenotype measurements (96), traits (6) (1/27/2020)
  • [Data] New Cowpea data: genetic map (1), markers (32125), QTL (17) (1/27/2020)
  • [Data] New Faba data: genetic map (1), markers (17), QTL (12), phenotype measurements (228) (1/27/2020)
  • [Data] New Vigna data: genetic map (4), markers (149), QTL (124), MTL (2), phenotype measurements (227), traits (2) (1/17/2020)
  • [Data] New Vigna data: genetic map (1), markers (1503), QTL (13) (1/13/2020)
  • [Data] New Pea data: markers(54) (1/13/2020)
  • [Data] New Lentil data: genetic map (1), markers (543), QTL (14) (1/13/2020)
  • [Data] New Lentil data: genetic map (1), QTL (39), phenotype measurements (72), traits (3) (1/7/2020)
  • [Data] New Pea data: genetic map (1), markers (12033), QTL (9) (1/7/2020)
  • [Data] New Chickpea data: genetic maps (9), markers (9212), QTL (134), phenotype measurements (105), trait (1) (1/7/2020)

2019

  • [Data] New Pea data: genetic maps (13), markers (15000) (12/17/2019)
  • [Data] New Pea data: genetic map (1), marker loci (64038) (12/13/2019)
  • [Data] New genetic markers: common bean (29), pea (3), faba (3), vetch (16)
  • [Data] New Pigeonpea data: genetic markers (56070) (12/5/2019)
  • [Data] New Chickpea data: genetic markers (1153) (12/5/2019)
  • [Data] New Lentil data: genetic markers (5090) (12/5/2019)
  • [Data] New Bean data: genetic markers (237), MTL (1), genetic map (1) (12/5/2019)
  • [Data] New Cowpea data: genetic markers (14972) (11/22/2019)
  • [Data] New Bambara data: genetic markers (293), genetic map (1), QTL (67), traits (5) (11/21/2019)
  • [Data] Pigeon Pea PathwayCyc added (11/19/19)
  • [Data] New Lupin data: genetic map (1) (11/14/2019)
  • [Data] Bean PathwayCyc added (11/14/19)
  • [Data] Cowpea PathwayCyc added (11/4/19)
  • [Data] New Lupin data: genetic markers (2875), genetic map (2), QTL (18), MTL (5), traits (3) (11/5/2019)
  • [Data] New Lupin data: genetic markers (355), genetic map (1) (11/4/2019)
  • [Data] New Lupin data: genetic markers (52) (10/31/19)
  • [Data] New Lupin data: genetic markers (9412), genetic map (1) (10/30/19)
  • [Data] New Lupin data: genetic markers (17 new, 114 additional info) (10/29/19)
  • [Data] Pea PathwayCyc added (10/24/19)
  • [Data] Cowpea, Pigeon Pea, and Bean added to Synteny Viewer (10/23/19)
  • [Data] Pea added to Synteny Viewer (10/21/19)
  • [Data] Vigna unguiculata IT97K-499-35 v1.1, Phaseolus vulgaris v2.1, and Cajanus cajan v1.0 genomes loaded into chado (10/18/19)
  • [Data] New Lupin data added: genetic markers (4722), genetic maps (2), QTL (33), MTL (8), traits (3) (10/17/2019)
  • [Data] New Lupin data added: genetic markers (1579) (10/11/2019)
  • [Data] New Vetch data added: genetic markers (39) (10/10/2019)
  • [Data] New Pigeon pea data added: genetic markers (33162), genetic maps (9), QTL (19), MTL (1), traits (7) (10/10/2019)
  • [Data] BIMS: Bambara GRIN data uploaded, accessions (42), descriptors (2), phenotype measurements (43) (9/12/2019)
  • [Data] BIMS: Lupin GRIN data uploaded, accessions (1159), descriptors (46), phenotype measurements (6040) (9/12/2019)
  • [Data] BIMS: Phaseolus GRIN data uploaded, accessions (17802), descriptors (80), phenotype measurements (277484) (9/9/2019)
  • [Data] BIMS: Pigeon pea GRIN data uploaded, accessions (3994), descriptors (10), phenotype measurements (39548) (9/11/2019)
  • [Data] BIMS: Vetch GRIN data uploaded, accessions (1476), descriptors (35), phenotype measurements (6371) (9/12/2019)
  • [Data] BIMS: Cowpea GRIN data uploaded, accessions (11499), descriptors (32), phenotype measurements (103969) (9/10/2019)
  • [Data] New Cowpea data added: genetic markers (92741), genetic maps (12), QTL (363), traits (13) (9/24/2019)
  • [Data] Pea genome loaded into chado (9/16/19)
  • [Data] Cowpea, Pigeon Pea, Lupin, Bean genomes added to JBrowse and BLAST (9/5/19)
  • [Data] Pea genome added to JBrowse and BLAST (9/4/19)
  • [Data] New Common Bean data added: genetic markers (12350), genetic maps (4), QTL (326), MTL (1), traits (10) (9/12/2019)
  • [Data] New Common Bean data added: genetic markers (13923), genetic maps (12), QTL (181), traits (14) (8/29/2019)
  • [Tools] Converted site from CSFL to PCD and upgraded to Tripal 3 (08/30/2019)
  • [Data] New data added: genetic map (1), genetic markers (3625) (7/10/2019)
  • [Data] New data added: germplasm (17), genetic maps (8), genetic markers(1557), QTL (91), traits(6) (7/1/2019)
  • [Data] New data added: genetic maps (2), genetic markers (63378) (6/26/2019)
  • [Tools] MegaSearch added (6/4/2019)
  • [Data] New InterProScan analysis added: InterProScan: C. reticulatum PI489777 genome v1 (5/28/2019)
  • [Data] New InterProScan analysis added: InterProScan: C. arietinum ICC 4958, v2.0 (desi) (5/21/2019)
  • [Data] New BLAST analysis added: BLAST: C. reticulatum PI489777 genome v1 Swissprot (5/21/2019)
  • [Data] New BLAST analysis added: BLAST: C. arietinum ICC 4958 v2.0 (desi) Swissprot (5/21/2019)
  • [Data] New BLAST analysis added: BLAST: C. arietinum CDC Frontier (kabuli), Swissprot (5/21/2019)
  • [Data] New data added: germplasm (2), genetic map (1), genetic markers (6154), QTL (10), traits (2) (4/24/2019)
  • [Data] New data added: germplasm (11), genetic maps (5), genetic markers (5695), QTL (128), traits (4) (Q1 2019)

2018

  • [Data] GRIN data added to BIMS (12/5/18)
  • [Tools] Dot plot, Correspondence matrix and PNG export functionality added for MapViewer, available (08/2018)
  • [Tools] MapViewer updated with dynamic drawing element positioning for QTLs and Correspondences (06/2018)
  • [Tools] New Synteny Viewer for Cicer genomes added (7/2018)

2017

  • [Tools] MapViewer map visualization tool added (01/2017) 
  • [Data] C. arietinum ICC 4958 PathwayCyc added to CSFL (11/7/17)
  • [Data] RefTrans v2 completed for all 4 crops and available in CSFL (11/7/17)
  • [Tools] Tripal BLAST module replaces BLAST and batch BLAST, NCBI ESTs updated for all crops (6/14/17)
  • [Data] C. reticulatum PI489777 PathwayCyc added (2/1/17)
  • [Outreach] CSFL Video Tutorials added (1/7/17)
  • [Data] C. reticulatum PI489777 gene models and scaffolds added to database (1/5/17)

2016

  • [Data] Alignment of CSFL Chickpea RefTrans v1 added as JBrowse track for C. reticulatum genome (12/15/16)
  • [Data] C. arietinum ICC 4958 gene models and scaffolds added to database (11/30/16)
  • [Data] More faba bean and chickpea publication data added to database (11/30/16)
  • [Data] C. reticulatum PI489777 genome added to BLAST and Batch BLAST tools (11/28/16)
  • [Outreach] CSFL User Manual added under Help menu (11/21/16)
  • [Data] Homology Analysis of C. reticulatum PI489777 v1 genome CDS vs. Swissprot and TrEMBL added to PI489777 genome download page (11/18/16)
  • [Data] DNA and RNA SRA dataset tables under "Data Download" updated (11/16/16)
  • [Data] Cicer genome assemblies and related model genomes (Medicago truncatula, Lotus japonicus, Glycine max) added to BLAST and Batch BLAST (11/10/16)
  • [Data] C. reticulatum PI489777 genome added to JBrowse and genome page for chickpea (11/3/16)
  • [Data] Alignment of CSFL Chickpea RefTrans v1 added as JBrowse track for C. arietinum genomes (10/18/16)
  • [Data] Homology Analysis of C. arietinum ICC 4958 v2.0 genome CDS vs. Swissprot and TrEMBL added to ICC 4958 genome download page (9/8/16)
  • [Data] Addition of P. sativum Reference Transcriptome (4/20/16)
  • [Data] A list of marker types and links to information about each added under "Data" menu (4/14/16) 
  • [Data] ChickpeaCyc updated (4/8/16)
  • [Data] Table with CSFL QTL trait abbreviations added (3/7/16)
  • [Data] Addition of links to DNA and RNA NCBI SRA database datasets under "Data Download" (1/26/16)

2015

  • [Data] Addition of L. culinaris and V. faba Reference Transcriptomes (RefTrans)  (12/23/15)
  • [Data] Current marker (50,526), map (18), and QTL (150) data added for lentil (12/1/15)
  • [Data] Current marker (31,069), map (40), and QTL (505) data added for chickpea (11/2/15)
  • [Data] Current marker (7,064), map (28), and QTL (775) data added for pea  (11/2/15)
  • [Data] Current marker (2,329), map (11), and QTL (105) data added for faba bean  (11/2/15)
  • [Data] C. arietinum ICC 4958 genome added to JBrowse and BLAST  (11/2/15)
  • [Data] Addition of C. arietinum Reference Transcriptome (RefTrans)  (11/2/15)
  • [Tools] Major website redesign for more efficient usability  (11/2/15)
  • [Tools] Replacement of GBrowse with JBrowse  (11/2/15)
  • [Tools] Improved the data overview page to dynamically update as data is added to the database  (11/2/15)

Archive of work completed before redesign