Overview

Domestication is a complex evolutionary process in which human use of plant and animal species leads to morphological and/or physiological changes that distinguish domesticated species from their wild ancestors. It is a process of recent, rapid species evolution, and studies on the dynamics of domestication, beginning with Charles Darwin, inform our understanding of the origins and diversification of new taxa. Moreover, domestication is arguably the single most important technological innovation in human history, and was the linchpin of the Neolithic Revolution 10,000-12,000 years ago, in which hunter-gatherer groups transitioned into sedentary agricultural societies that ultimately gave rise to current human cultures.

Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, and has fed more people throughout human history than any other food plant. Rice is also widely recognized as a model system for the study of cereal crop genomes, yet despite its position as the world's predominant cereal food crop and as a model for grass genomics research, relatively little is known about the evolutionary forces that shape genomic diversity in rice.

The long-term objective of this research is to study the genetic architecture of rice domestication and to examine the role of selection on genome variation and the origin of cultivated rice. We will integrate two methods to pursue these major goals: (i) quantitative trait locus (QTL) mapping, which identifies specific genomic regions that harbor genes associated specific domestication traits, and (ii) selective sweep mapping, which searches the genome for signatures of positive selection referred to as selective sweeps. We will use this integrated genome-scale approach on previously identified QTLs underlying several traits associated with domestication in rice. Combining the genome scanning ability of QTL mapping with the higher resolution of adaptive trait locus mapping will allow us to fine-map domestication QTLs from 3.5-7.0 Mb to 0.3-0.6 Mb.

Our research will address several key issues in plant evolution and crop domestication. We will be able to fine-map domestication trait QTLs, assess the nature of selection under domestication in crop genomes, and investigate the evolutionary dynamics of domestication trait genomic regions in rice and its wild ancestor O. rufipogon. We will also analyze near-isogenic lines to facilitate molecular studies of domestication genes, undertake a comparative genomic analyses between cultivated and wild rice, and develop new statistical models and methods to detect and study selection in mixed mating crop species. Our work will also include outreach programs to NYU science journalism students and high school students from the St. Louis, Missouri city public schools as well as a Developing Country Collaboration with Thailand.

Supported by the National Science Foundation Plant Genome Research Program

Note: This is a continuation of NSF Plant Genome Research Program project 03-19553