CottonGen Steering Committee Meeting, Oct 21, 2016

Attending: Don Jones, Dorrie Main, Jing Yu, Sook Jung, Richard Percy, Andy Paterson, Seungho Cho, Peng Wah Chee, Ramesh Buyyarapu

Apologies: Todd Campbell, Josh Udall, Jane Dever,


  • Funding update
    • Cotton Incorporated/USDA-ARS/Cotton industry ~ $190K  per year from 2017 through 2021 
    • NSRP10 - $500K per year from 2015 through 2019 (covers 25 crops including cotton)
    • USDA SCRI GDR - $550K per year from 2014 to 2019 (does not specifically include cotton but development applied in CottonGen)
    • NSF PGRP Tree Databases - $1M per year from 2016 to 2019 (does not include cotton but development applied in CottonGen)
  • Work completed since April 1
    • Covered in detail in the 2016 Q2 and Q3 reports
    • From work completed section on CottonGen
      • [TOOLS] Added 48 maps to CMap (10/18/16)
      • [TOOLS] Additional annotation data added to cotton species JBrowse and made available to download (10/14/16)
      • [DATA] Added CCRI new markers (13,967 SNPs and 126 InDels) to chado (8/30/16)
      • [WEB] 24 SNP VCF files from BYU Udall's Lab downloadable at Data Download/Genome Project SNP Data (8/30/16)
      • [DATA] Added 39,962 BYU SNPs with information from NCBI in chado (8/16/16)
      • [DATA] Added 32,113 new SNPs (UCD_Gh, DOW, TAMU_GH) to chado (8/8/16)
      • [DATA] Added 35,484 new TAMU_GlspSNPs to chado (8/5/16)
      • [DATA] Reloaded 1052 BYU SNPs using the new SNP template (7/29/16)
      • [DATA] Added 171 new TAMU_GH SNP primer and sequences in chado (7/21/16)
      • [DATA] Added 34,550 new TAMU_Gl SNPs in chado (7/21/16)
      • [DATA] Added 6396 new TAMU_tom and 6669 new TAMU_mus SNPs in chado (7/17/16)
      • [DATA] Added 24,829 new TAMU_arm SNPs in CottonGen (7/17/16)
      • [DATA] Added 14,613 new UCD_Gh SNPs in CottonGen (7/17/16)
      • [DATA] Reloaded 35,265 CIR SNPs using the new SNP template (7/7/16)
      • [DATA] Reloaded 66,230 NBRI SNPs using the new SNP template (7/7/16)
      • [DATA] Added TAMU CottonSNP63K AD genome intra species map (7,171 loci) in chado (6/30/16)
      • [DATA] Adde TAMU CottonSNP63K AD genome inter species map (19,191 loci) in chado (6/30/16)
      • [DATA] Added CSIRO MCU-5 × Siokra 1−4, RIL SNP map (1244 loci and 4 QTLs) in chado (6/20/16)
      • [DATA] Reloaded 40,796 CSIRO SNP sequences using the new SNP template (6/20/16)
      • [DATA] Added 974 new CSIRO SNPs that missed from CSIRO 2014 SNP dataset (5/21/16)
      • CottonGen first biannual newsletter released (5/4/16)
      • CottonGen presented at 2016-05 WCRC-6/ICGI 2016 Research Conference, Goiânia - Goiás, Brazil (5/3/16)
      • [DATA] TAMU CottonSNP63K AD genome inter species map (3T-F2, 19,191 loci) available on CottonGen CMap (4/29/16)
      • [DATA] TAMU CottonSNP63K AD genome intra species map (PS-F2, 7,171 loci) available on CottonGen CMap (4/29/16)
      • [TOOL] CottonCyc AD1-BGI pathways available on CottonGen (4/28/16)
      • [TOOL] CottonCyc D5-JGI pathways was updated by using PathwayTools version 19.5 (4/28/16)
      • [TOOL] GBrowse_syn available on CottonGen with data of synteny analysis between D5-JGI and A2-BGI (4/28/16)
      • [DATA] Added 10,521 new TAMU_Gb379 SNPs in chado (4/27/16)
      • [DATA] New cotton trait catergories in chado (4/27/16)
      • [DATA] G.barbadense 3-79 genome sequence and annotation data available in CottonGen JBrowse (4/25/16)
      • [DATA] Fixed problem on JGI-D5 protein homologies and updated links in Data Download (4/23/16)
      • [WEB] Added a new project page for TAMU Cotton63KSNP Array (4/22/16)
      • [DATA] G.barbadense 3-79 genome sequence with protein alignments and homologies available on Data Download (4/20/16)
      • [DATA] Fixed the problem on UCD SNP/InDel data caused by the system upgrade (4/20/16)
      • [DATA] Fixed the problem on USDA CFB SNP data caused by the system upgrade (4/18/16)
      • [DATA] UCD SNP/InDel and TM-1x3-79 map genotype data on Data Download (4/16/16)
      • [TOOL] A new AND/OR option in CottonGen Trait Search (4/11/16)
      • [DATA] Added ARS-CS NCGC SSR genotypic data, contains 204,776 genotypic scores from 104 SSRs screened on 1969 germplasm (4/8/16)
  • Proposed work for next six months
    • 2016 - Q4 (Oct - Dec)
      • Complete Cotton Trait Ontology (Jing)
      • Add map/marker/qtl data for 100 publications (Deah/Morgan/Jing/Jodi)
      • Complete v1 of the reference transcriptomes (RefTrans) for GH, GB, GHi, GHe (Ping)
      • Send out biannual newsletter (Dorrie)
      • Create project pages and populate with information and data (Chun-Huai/Jing/Dorrie)
      • Develop a SNP genotyping search function similar to <add link>(Chun-Huai/Jing/Sook)
      • Update CottonCycs to v20 of PathwayTools
      • Complete CottonGen BIMS v0.5 (Taein/Sook/Sushan/Todd)
      • Contribute to cotton community PGRP proposals (Dorrie)
      • Prepare materials for (Jing, Sook, Taein,  Dorrie)
        • 2 hr breeders workshop at beltwide
        • CottonGen presentation at beltwide (hopefully)
        • CottonGen brochure for Beltwide and PAG
        • CottonGen demo for PAG
        • CottonGen poster for PAG
      • Hold a FieldBook App webinar for NRSP10 breeders in November (Sook, Dorrie)
      • Advertise for new CottonGen postdoc (Dorrie)
      • Add short audio-visual and text tutorials in CottonGen similar to those in GDR (Jodi/Jing/Sook) - may need to be pushed back into 2017, Q1
    • 2017 - Q1 (Jan - Mar)
      • Breeders workshop at Beltwide (Dorrie/Jing)
      • CottonGen presentation at Beltwide (Dorrie)
      • CottonGen activites at PAG (Jing/Dorrie)
      • Hold  in-person CottonGen steering commitee meetings at both Beltwide and PAG - yes
      • Complete cotton community project pages (Jing)
      • Host 1-2 CottonGen webinars (Dorrie/Jing/Sook/Jodi)
      • Survey CottonGen users (might use independent consultant Michael Coe)
      • Add genotype data for 400 lines from the 63K array (Jing)
      • Continue work on BIMS
      • Implement Josh Udall PolyCat tool in CottonGen: 
        PolyCat  - A Resource for Genome Categorization of Sequencing Reads From Allopolyploid Organisms
        "I'd like to provide a web interface to a sequence search so that users can get the genomic positions and the matching homoeologs in a single search. BLAST might do it, I guess for a search. But often users have the sequence on one genome for a region, but they'd like to pull up the homoeolog quickly. Alternatively, if they have a sequence, they want to know if it is the A- or D- version of it"
    • Add other data as needed

      (1) Seungho - where are the plant ontology descriptors, particularly useful for transcriptome research, we are working on the trait ontology, will be posted on CottonGen when ready
      (2) Dorrie - Update SRA Sequence tables in CottonGen on a monthly basis
      (3) Go to a biannual meeting schedule - email committee and ask them to provide feedback, ask questions about reports