PAG 2014: Some Highlights

22nd Plant and Animal Genome conference was held from Jan 11 to 16 2014, in San Diego CA.
As at previous PAG meetings Gramene team presented a workshop introducing the latest developments and additions to the Gramene database. This year’s workshop highlights included the new Drupal based content management and web interface for Gramene and developments and advances made on the Plant Reactome database, a new platform for plant biochemical and signaling pathways. There was a full house indicating an increased interest and usage of Gramene and the team was thrilled to hear EBI-Gramene collaborative efforts being talked of at the first plenary talk by Ewan Birney.
As usual PAG was an information overload, but here are few highlights from PAG 2014:
Allele mining:
Many aspects of Genetic Diversity within crop species, including, analysis methods, population structure, and how diversity connects genotype to the phenotype was discussed. Research addressed included: Validity of using neutral markers as a guideline for selecting core germplasm collections for mining allelic diversity of agronomic traits (C. Richards), Evaluating rice germplasm core collections by deconstructing genomes to understand the subpopulation structure and naturally occurring admixture (M.Wright), Discovering cell wall chemistry and fungal symbiosis associated allele variants through whole genome re-sequencing in Populus (W. Muchero). Extensive rice re-sequencing and allelic variant calling project encompassing over 3000 rice accessions in the International Rice Gene Bank at IRRI and development of a rice information portal under the International Rice Informatics Consortium (Kenneth McNelly).
Harnessing the Genetic Diversity to Advance Food Security:
This workshop explored the strategies to utilize genetic diversity in crops and livestock in ensuring global food security. The presentation included: Mining wild crop resources of chick pea for climate resilience (D.Cook); Introducing perennial traits of wild relatives to cultivated Sorghum varieties (A. Patterson); The importance of Gene Banks in harnessing plant and animal genetic resources for ensuring food security (Harvey Blackburn)
iPlant Collaborative - Unified Cyber infrastructure for All Life Sciences:
iPlant collaborative updated their progress in empowering discovery through enabling the bench scientists in analysis and creating new knowledge in the age of big-data. The presentations highlighted the use of iPlant Cyber infrastructure in a variety of research projects including, genome sequence and assembly of polyploidy weeds (David Hovarth), transcrptomics of virus pathogenesis in Brachypodium (K.K. Mandadi) and leveraging iPlant resources to build a iMicrobe, a resource for rapidly expanding research on the Microbiome (B. Hurwitz)
Forest Trees:
As in previous years Forest Tree community came together at PAG 2014 to present and discuss Tree Research topics from evolutionary genomics to networks and regulation. Topics presented included; Disentangling the genetic diversity in Populus trichocarpa of Pacific Northwest into subcomponents of introgression, isolation and natural selection, and a significant finding was the Fst outliers within subpopulations which show overrepresentation of environmental responsive genes, indicating allelic variants underlying adaptation (Q. Cronk); Investigating the “defensome” of Eucalyptus (defense transcriptome) revealing shared gene sets upregulated in response to different pathogen challenges as well as pathogen specific gene upregulation providing opportunities to address pathogen challenges through tree breeding (S.Naidoo); Comparative analysis of gene regulatory networks in Arabidopsis, rice and Poplar using co-expression networks, resulting in an an intriguing outcome where it was shown that in orthology predictions, half of the time, the functional ortholog is different from the ortholog predicted from the protein sequence, and tools for this analysis is available from http://plantgenie.org (T.Hvidsten).