Report from maize meeting in Italy

By Doreen Ware

Last week I had the pleasure of attending the 52nd Maize Genetics meeting that took place from March 18-21, 2010, in Riva del Garda, Italy. This is the first time the meeting has taken place in Italy. The science and venue set a very high bar for the future maize genetics meetings. The meetings was organized into a series of 10 sessions over the course of 4 days, intermingled with poster viewing sessions in the afternoon and evening, a community discussion led by the maize genetics executive committee (MGEC) and a dedication of a special Maydica issue to Ron Phillips.

The sessions fell in 2 two categories, Plenary (3) and topic areas (7). The Plenary sessions consisted of 5 talks, Marianne Banzinger (CIMMYT) P1, Ann Sylvester (University of Wyoming) P2, Michele Morgante (Univ. Undine) P3, Enrico Coen (John Innes Center) P4, Alain Charcosset (INRA Paris) P5 which spanned several broad domain areas, accessing natural diversity and adaption for crop improvement (P1, P5), paradigms in development (P2, P4), hyper-variability in plant genomes (P4). The remaining 7 sessions were divided into 7 topic areas S2 Functional and Quantitative Genomics, S3 Development and Cell Biology, S4 Genome Updates, S6 biochemical genetics, S7 Quantitative Genetics and Breeding, S9 Transposons and Epigenetics, and S10 Epigenetics and development. A complete meeting agenda and posters abstracts are available at the meeting website.

While at the meeting I had the opportunity to present an update from the Maize Genome Sequencing Consortium (MGSC) as part of Genome updates. My 10-minute talk consisted of a progress update from the MGSC in the last year, review of the current content, views and functionality of the project web portal, and the roadmap for the 2010. One of many actions includes the integration of the Maize B73 reference genome in the 2010 fall release of Gramene and the future release of the MaizeCyc, which will be curated in collaboration with Gramene, MaizeGDB and community members.

In the last year the MGSC hit several milestones, including the publication of the genome in Science, release of new and updated BAC sequence, release of 8.7X 454-titanium sequence, a second improved assembly, and improvements to the project portal. The publication of the genome sequence was coordinated with the release of more than 10 related publications in Science, PLOS Genetics, and PNAS by the maize community.

Sequence updates from the projects included the addition of 20 new BACs and updates to more than 2000 existing BACs. An updated reference assembly was released March 5, 2010. The RefGen_V2 B73 included updates to the sequence and scaffold improvements that have improved anchoring to the maize chromosomes and improved order and orientation of the contigs within the BAC sequences. Sequence improvements included the addition of several new BACs, as well as improvement to existing BACs present in the RefGen_V1. Order and orientation was improved at two levels, the physical map, and within the BACs. At the physical map level the improvements included anchoring of Chr. 0 contigs (previously unanchored FPC contigs in the maize physical map), minor position shifts of existing anchored FPC contigs within a chromosome, and identification and re-anchoring of a chimera contig on Chr. X. These higher-level scaffold improvements were guided by the maize optical map (Optical Map project led by David Schwartz) and NAM genetic map (Maize Diversity Project led by Ed Buckler). In addition to the higher-level scaffold improvements within the BACs, order and orientation was improved guided by newly anchored fosmid sequence and synteny to sorghum. Overall the RefGen_V2 B73 shows significant improvements over the previous assembly with 99.7% of the FPC contigs anchored to chromosomes, and 80% of the BACs sequences are ordered and oriented.

In the past year improvements to the project website includes the addition of new data, enhancements in performance and visualization, new and updated analysis, and additional integration with other plant projects. The genome browser display has been transitioned from a Fingerprint Assembly where views of the sequence were guided through BAC entries on the physical map, to a sequence assembly display based on the RefGen_V1. To assist the community in the transition in the new display, the previously available views are archived and available for use by the community through the end of the funded project. Previously available analysis have been updated with the new releases, and new data sets have been added including diversity data and links to functional genomics data sets, including Affy Array probes and maize insertion tag lines. A list of available data sets that have been integrated in the project portal can be viewed in the release notes. In the last year the software supporting the site has been updated from Ensembl V53, which included major changes in the browser entry points and displays. These updates have improved the overall look and feel of the sites as well as performance.

The last 30 seconds of my 10-minute talk contained the roadmap for the future, which includes the release of new gene annotations, based on the RefGen_V2. The improvements to the models will be supported by additional evidence data sets, the improved order and orientation of the contigs sequences within the BACs which will allow the building of gene models across the BACs, which was not possible in the first round of annotations. We anticipate the next release of the website with the RefGen_V2 and the new annotations will be available in May 2010. In the next months we will be making additional improvements based on RNAseq data that will be added as evidence to the models. At the maize meeting during the talk, we are soliciting the community for any RNAseq data sets that they would be willing to contribute by April 20, 2010. The contact for submission of the data sets can be made to Andrew Olson who is working on the gene annotations. In addition to updates to the gene annotations, addition of community data sets to the project website, CSHL will also be performing additional analysis on the 8.7 X 454 B73 genomic sequence; to identify unique space not currently accounted for in the current BAC based assembly. The main objective of this work will be to identify gene space, and where possible anchor sequence contigs to a chromosome using existing genetic resources that will become available in the next 8 months.

While at the meeting I had the opportunity to interact with several maize community members who use or contribute to the Gramene and the Maize sequencing projects. Overall most people were very pleased with the improvements to the site, and found the improvements led to overall improvements in usability. Several users did express concerns about the lack of ease in moving between the new site and the archival site and had several concrete suggestions on how this could be improved. Many members had concern with regard to the next release of gene annotations that will be coming out in May 2010 and the ability to find their gene of interest. The specific concerns had to do with mapping of the names between assemblies. In these discussions, I communicated that where possible, we would be mapping the names of the existing models to the new models.

When listening to presentations and viewing posters I observed many examples where the sequence, assembly and existing annotation have been useful for the community. There were several examples where the genes associated with a specific mutant phenotype cloning was accelerated based on the available maize sequence. There were also examples where the near complete genome facilitated the identification of complete gene families filling in gaps in emerging genetic, biochemical or signaling networks. The assembly of the sequence facilitated whole genome views, supporting previous work about the hyper-variability in the maize genome as well as support work on some new thoughts of the origin of maize. I noticed a perceived trend away from technology driven/genomics style talks, to ones that focused on the biology of the maize.