Past year’s accomplishments: overview

1. Past year’s accomplishments: overview

2. Major Endeavors Interface redesign ARS Project Plan

3. Data Updates • Sequence-indexed mutations – UniformMu • Gene expression – updates to eFP, MapMan, etc. • Metabolism – Updates to MaizeCyc, release CornCyc • Protein classifications, gene homologs, and syntelogs on gene model pages • Diversity – Genotype search tool, HapMapv1, HapMapv2, raw NAM SNPs (1,144 markers), 282 inbred panel on 55K SNP Array, SNP data and sort tool for Ames Panel • Phenotypes – NSF Phenotype RCN collaboration to enable phenotype searches across multiple plant databases • Literature curation – Prepared datasets for automated gene function extraction

4. New Genome Browser Tracks • Assembly/Genome Features (5) knobs, foreign contamination, organellar genomes, nucleosome occupancy, B73/Mo17 methylation • Diversity (4) Hapmap1 and 2, ISU SNPs on 291 IBM RILs, Illumina SMP50 • Expression and Transcripts (5) IBM SAM eQTL, 5’ Methylcytosine methylation, miRNA, KNOTTED binding regions, Agilent microarray annotations • Gene Models (2) Sorghum syntelogs, Split gene annotation artifacts, • Repetitive Elements (3) Sirevirus LTRs, Ac/Ds, and UniformMu

5. Outreach & Training National Corn Grower Association (NCGA) 3 Podcasts (Gardiner) Plant Genomes Resources Exhibit at PAG and ASPB (Schaeffer, Gardiner, Harper) MaizeGDB Redesign Seminar at Maize Meeting (Andorf) MaizeGDB Seminar, 2012 International Sorghum Genomics Workshop (Lawrence) Corn Insects and Crop Genetics Research Unit Brown Bag Research Seminar Series (Lawrence and Andorf) MaizeGDB Tutorials at Maize Meeting, Genetics of Maize-Microbe Interactions Conference, and the University of Missouri at Columbia (Harper) MaizeGDB Seminar, Corn Breeding Research Meeting (formerly NCCC167; Lawrence) MaizeGDB Seminar at the PAG XXI PIR Workshop: Knowledge Mining Tools for Proteins, Complexes and PTMs (Schaeffer) MaizeGDB Seminar at the Crop Plant Trait Ontology Workshop (Schaeffer)

6. Peer-Reviewed Publications Maize Metabolic Network Construction and TranscriptomeAnalysis Monaco MK, Sen TZ, Dharmawardhana PD, Ren L, Schaeffer M, Naithani S, Amarasinghe V,Thomason J, Harper L,Gardiner J,Cannon EKS,Lawrence CJ,Ware D,JaiswalP.The Plant Genome 2013 Mar 6(1):1-12. Maize chromosomal knobs are located in gene-dense areas and suppress local recombination.GhaffariR, Cannon EK, Kanizay LB, Lawrence CJ, DaweRK. Chromosoma. 2013 Mar;122(1-2):67-75. The plant ontology as a tool for comparative plant anatomy and genomic analyses.Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, JaiswalP. Plant Cell Physiol. 2013 Feb;54(2):e1. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.ArighiCN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C. Database (Oxford). 2013 Jan 17;2013:bas056. Maize multiple archesporial cells 1 (mac1), an ortholog of rice TDL1A, modulates cell proliferation and identity in early anther development.Wang CJ, Nan GL, Kelliher T, Timofejeva L, Vernoud V, Golubovskaya IN, Harper L, Egger R, Walbot V, CandeWZ. Development. 2012 Jul;139(14):2594-603. RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.Robbins RJ, Amaral-Zettler L, Bik H, Blum S, Edwards J, Field D, Garrity G, Gilbert JA, Kottmann R, Krishtalka L, Lapp H, Lawrence C, Morrison N, Tuama EÓ, Parr C, San Gil I, Schindel D, Schriml L, Vieglas D, WooleyJ. Stand Genomic Sci. 2012 Oct 10;7(1):159-65. Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks.Andorf CM, Honavar V, Sen TZ. PLoS One. 2013;8(2):e56833. Molecular simulation of fibronectin adsorption onto polyurethane surfaces.PanosM, Sen TZ, AhunbayMG. Langmuir. 2012 Aug 28;28(34):12619-28. A rigid network of long-range contacts increases thermostability in a mutant endoglucanase.Rader AJ, Yennamalli RM, Harter AK, SenTZ. J BiomolStructDyn. 2012;30(6):628-37.

7. Proposals Submitted NSF Plant Genome Research Program • Detection of Structural Variation and Epistasis via NGS-Enabled BAC-by-BAC Genome Sequencing of Maize • Pat Schnable, PI, Carolyn Lawrence and Brent Buckner, coPIs • $4,044,713 total over 3 years, ~$275,000 to coPI Lawrence. United Sorghum CheckoffProgram • Coordination to Support Sorghum Genomics: Developing Community Resources with Emphasis on Informatics Systems • Carolyn Lawrence, PI, Maria Salas-Fernandez, coPI • $552,938 over 3 years

8. Collaborators are key! • Interface redesign: WG and testers • Project plan: community survey, WG, ARS administration, and reviewers • New data: contributors, other repositories, and researchers using the data • New tools: their creators and our various collaborators (e.g., Gramene, PMN, NCBI, Phytozome, etc.)