Complex Genetic Variation and Physiology of Anaerobic Germination in Rice

Castano-Duque Lina M, Durham NC

Investigators

Abstract

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2017. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The host institutions for the fellowship are Duke University and the International Rice Research Institute (IRRI; Philippines). The sponsoring scientists are Drs. Thomas Mitchell-Olds and Shalabh Dixit. This award is co-funded by the Office of International Science and Engineering. To achieve lower production costs for rice the current agricultural trend is to shift from transplanting seedlings to direct sowing of seeds. Those seeds may have to germinate under anaerobic conditions due to flash flooding. The study of complex genetic variation and physiology in rice under anaerobic germination is necessary to produce seeds with traits that can fulfill societal and agronomical needs. The training objectives in this project are to: 1) learn experimental and analytical approaches for genome association analysis of complex trait variation; 2) learn data analysis approaches that involve genome association and physiology data using machine learning implementation; and, 3) participate and lead outreach activities for minority groups and develop a multi-year curriculum focused on food security with Maureen Joy Charter School in Durham (NC). This project will study complex genetic variation and physiology of anaerobic germination (AG) in rice natural populations, by using new analytical methods to integrate diverse functional information to identify complex trait loci in genome wide association studies (GWAS). These methods can be applied to a range of traits in genetically tractable species. The main research goal is to identify candidate genes that influence quantitative variation for AG in rice, and to determine their mode of action. Specific objectives are to: 1) use GWAS to identify candidate genes associated with AG in sequenced rice genotypes; and, 2) determine the physiological and genetic correlations that contribute towards AG in rice. Data dissemination will be done through CYVERSE-http://www.cyverse.org/, IRIC- http://iric.irri.org/, and GenBank-http://www.ncbi.nlm.nih.gov/sra. Biological materials and seeds will be made available through IRRI-http://irri.org/our-work/seeds.