The Evolutionary Genomics of Rice Domestication

New York University, New York NY

Investigators

Abstract

PI: Michael Purugganan (New York University) Co-PIs: Carlos Bustamante (Cornell University; subawardee), Scott Jackson (Purdue University; subawardee), Barbara Schaal (Washington University; subawardee), and Scott Williamson (Cornell University; subawardee) Senior Personnel: Dan Fagin (New York University) Key Collaborator: Benjavan Rerkasem (Chiang Mai U, Thailand) Domesticated rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history since its origin in the Neolithic Revolution 10,000-12,000 years ago. Understanding the genomic architecture of domestication and the effects of selection on the structure and variation of crop species genomes remain key areas of interest in plant biology. This project will fine-map domestication genes and examine the role of evolutionary selection in the origin of cultivated rice identifying genomic regions that show signatures of positive selection in approximately 53 Mb of the rice genome associated with 15 quantitative trait loci for six domestication traits. This project will assess the nature of selection under domestication in crop genomes, investigate the evolutionary dynamics of domestication trait genomic regions in rice and its wild ancestor, provide genomic sequence for approximately 5 Mb of O. rufipogon spanning 10 regions that contain domestication loci, create near-isogenic lines to facilitate positional cloning of domestication genes, undertake a comparative genomic analyses of domestication genomic regions between cultivated and wild rice, and develop new statistical methods and models to study crop evolution under domestication. By identifying genomic regions associated with key domestication traits and developing new resources for further characterization of these loci, this project will provide the foundation for new genetic targets towards crop improvement. This project will also collaborate with the New York University Science, Health and Environment Reporting Program to train graduate-level science journalism students in plant genomics, and also work with the Laboratory Investigations with Model Organisms (LIMO) program at Washington University to provide meaningful laboratory internship positions for St. Louis city public school students. Results of this project can be accessed from the project website http://rice-evolution.cornell.edu.