Maize 2016 Workshop

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Gramene - Comparative Plant Genomics Database Workshop
Event Info
Maize Genetics Conference 2016
Thursday, 17 March 2016, 3:30 - 4:30 PM EST
Hyatt Regency Jacksonville Riverfront, Daytona Room
Doreen Ware & Yinping Jiao
Marcela Karey Tello-Ruiz & Sushma Naitani
Bo Wang & Lifang Zhang

About the workshop

The Gramene database is an integrated resource for comparative genome and functional analysis in plants. The database provides agricultural researchers and plant breeders with valuable biological information on genomes and plant pathways of numerous crops and model species - including maize - thus enabling powerful comparisons across species. During this workshop, we will demonstrate how to navigate the website and review the available resources at Gramene, including the newly curated pathways and orthologous pathway projections in the Plant Reactome, and the capabilities of the independent Expression Atlas resource for gene expression. In addition, we will introduce a new search tool and web interface that helps users search, interpret and explore our data. Besides maize, the current data release of Gramene contains an additional 38 reference genomes including sorghum, rice, wheat, barley, soybean, Arabidopsis, Brassicas, poplar, medicago, tomato, potato, banana, cocoa, peach, grapevine, Amborella, spikemoss, and algae. In recent years, Gramene has positioned itself as a resource for genome variation data, with focus on maize, rice, and Arabidopsis. The current release includes the maize HapMap2 (~55 million SNPs in 104 lines) and Panzea's 2.7 GBS (~720K SNPs in 16,718 lines) variation data sets. In the last year, we added new variation in barley, wheat, a wild species of rice, and EMS-induced mutations in sorghum. Also, maize specific annotation tracks include MAKER-P gene models, methylome signatures, genomewide long non-coding RNAs, and nascent transcriptomes. Besides curated rice pathways, the Plant Reactome incorporates pathway projections to 58 plant species, including maize, peanut ancestors, and the common bean. This workshop is open to the community of plant researchers and breeders; beginners, as well as frequent users of the Gramene database alike are welcome and encouraged to join. Attendees may bring their own data to work with during the workshop. Gramene is supported by an NSF grant IOS-1127112, and partially from USDA-ARS (1907-21000-030-00D).

During the workshop, the new maize B73 V4 genome browser will be introduced. This constitutes an early release of the Zea mays B73 RefGen_v4 assembly and gene annotation.

Following the Gramene workshop and during the Zea mays genome assemblies session at 4:30 pm, Dr. Yinping Jiao will be presenting a short talk on "A dramatically improved maize B73 reference genome constructed using single-molecule technologies".

Dr. Bo Wang of the Cold Spring Harbor Laboratory will also be giving a talk on "Unveiling the complexity of maize transcriptome by single-molecule long-read sequencing during the Maize Conference" on Friday March 18, 2016 at 9:15 AM.

Workshop material

  • Exercises

File:MGC Exercises 2016.doc

  • Test data sets & URLs:
Upload your own data & create custom browser tracks
Test files at
Genome assembly conversion. Test file with RefGen_v2 coordinates
File:Test qtls v2.txt
BLAST exercise
Sorghum variegatum Sh1 CDS in fasta: File:SvSh1 CDS.txt
  • Slides

Other resources

Upcoming webinars

  • Genetic variation data on the genome browser (29 March 2016). By Dr. Marcela Karey Tello-Ruiz
  • New Gramene search (26 April 2016). By Joseph Mulvaney & Andrew Olsen


  • Please provide feedback for the workshop. We look forward to serve you better!

Internet Access

There will be free wireless internet access in the conference room.


For more information for the workshop, please e-mail Marcela Karey Tello-Ruiz:


The Gramene Project is a collaboration between Cold Spring Harbor Laboratory (CSHL), Oregon State University (OSU), the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL - EBI), the Ontario Cancer Research Institute (OCIR), and the American Society of Plant Biologists (ASPB).

The Gramene Project is funded by the NSF award IOS:1127112 (IPGA: Gramene - Exploring Function through Comparative Genomics and Network Analysis).

Partial support comes from the USDA and USDA-ARS.