Large scale dynamic integration of proteomics and genomics to support next-generation rice research

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Rice can be considered the most important worldwide crop for human nutrition, currently providing ~20% of worldwide daily dietary energy. Due to a growing worldwide population, and the effects of climate change, research into improvements in rice yield, resilience to drought and resistance to pathogens is urgently needed. Such research must be underpinned by public databases storing high-quality information about the rice genome, genetic variants carried by varieties with desirable traits, and information about the function of each gene/protein. This project is a collaboration between research teams based at the University of Liverpool, the Beijing Institute of Genomics and the BGI Education Centre. Our teams have considerable track record in the development of methods for studying the abundance of genes (transcriptomics) and proteins (proteomics) on a large scale for rice and other species, as well as computational approaches for interpreting and integrating data from these different techniques. At present, the public databases storing the rice genome and information known about gene/protein function are disconnected from experimental data (transcriptomics/proteomics) being collected in laboratories all over the world. These experimental data can be used directly to improve the annotation of the genome, by showing how strongly particular genes or proteins are expressed under particular growth conditions or for a given rice variety (which gives clues as to functional importance). These data also show how genes or proteins differ in a given variety from the "reference" genome contained in the database. Our groups are developing software tools for integrating and analysing these data in new ways, so that when laboratories submit their data to a public repository, it can be directly integrated and viewed alongside the genome - which at present is not possible. We are also going to generate and analyse new data sets for several important rice varieties, so we can study how these gene and protein sequences differ from the reference genome.Our results will help to improve the sequences and annotation of rice genes and proteins, and will be made easily available to all other rice researchers through the most widely accessed international public databases.