From September 26-29th 2016, rice researchers from around the globe gathered in Montpellier, France to participate in the 14th International Symposium on Rice Functional Genomics (ISRFG) to discuss recent advances and exciting breakthroughs in rice genome biology and how this knowledge is being applied to improve the yield, and quality of rice, a major cereal crop.
Dr. Sushma Naithani and Dr. Joshua Stein from Gramene database shared information about the tools, data and genomics resources available in Gramene database and how they can assist the community of rice researchers to advance in their respective research goals.
The researchers from the various CGIAR centers, such as IRRI, AfricaRice, CIAT, CIRAD, IRD and JIRCAS involved in the global Rice science partnership (GRiSP), reported progress in the development of Green Super Rice (GSR) varieties. One of the remarkable achievement in rice research has been the recent sequencing of the 3010 rice accessions of the rice germplasm core collection (with an average sequencing depth of 14x). This sequence data (raw) is freely available to the scientific community worldwide (from EBI, NCBI and DDBJ). The SNP genotyping data (29 million SNPs) derived from this project (using rice reference genome Nipponbare) now being hosted at IRIC, a Rice SNP-Seek Database together with phenotype and variety information / passport data (from IRIS: The International Rice Information System). Rice SNP-Seek Database also hosts 14 million SNPs that were derived from AfricaRice project. Gramene database also hosts the genotype data from 3000 rice genome project.
The 3,000 rice genome sequence data are also being utilized for developing a new Affymatrix chip consisting of 55,000 SNP will become available to rice community that includes about 25000 SNP discovered from the 3K rice genomes sequencing project. Another SNP chip for studying African rice varieties and interspecific rice hybrids is being developed by AfricaRice and Cornell University based on the core collection of O. glaberrima and O. barthii.
Dr. Khady Nani Drame from AfricaRice gave a plenary talk on “Molecular Breeding to boost rice production in Africa” and spoke about the ongoing testing of various rice varieties in different locations and under different climatic conditions in Africa. These studies aim to explore natural variations in the rice varieties of Asian (O. sativa) and African (O. glaberrima) origins for their ability to tolerate various abiotic stresses and to identify associated genes and QTLs. The candidate genes from these varieties are being integrated in the African rice breeding program.
Currently, a few advanced GSRs are under field trial in various Asian and African countries, which produce higher yields compared to sensitive varieties when grown in the environment posing challenges, e.g. drought, submergence, salinity and iron toxicity.
After the conference, the participants toured the Camargue, a natural wetland area on Rhône river delta where rice is being grown for centuries and the Centre Français du Riz (CFR), the experimental rice breeding station. Sushma Naithani enjoyed the company of old and new friends and learned about their interesting research projects and offer updates on the Gramene.
At Gramene database, we look forward to learn about the advancement in the area of rice research and aim to integrate the data, tools and resources that can help the community to analyze and visualize the genomic data in the broader context of genome and the cellular-level pathway network. Thus help mine the genomic data in more meaningful ways, and discover candidate genes, QTLs, pathways etc. for supporting the molecular breeding of climate smart, high yielding rice varieties.