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

Project Report

Asian rice, Oryza sativa L., is one of world’s oldest and most important crop species, having been domesticated beginning some ~8,000-9,000 years ago. Asian rice feeds more than half of the global population and has become a key model system for plant biology. Several genetic studies have shown that Oryza rufipogon, which remains extant in South and Southeast Asia, is the wild progenitor of domesticated rice. Our study has focused on understanding molecular variation in the rice genome, studying the origin and spread of rice and the impact of selection on shaping plant genome variation. We re-sequenced portions of 630 genes on rice chromosomes 8, 10 and 12 at ~100 kb intervals in multiple accessions of O. sativa indica and tropical japonica as well as O. rufipogon. Using single nucleotide polymorphism (SNP) data and two different computational techniques to analyze data from molecular variation, we provide new evidence for a single domestication of rice. The approaches we use, one of which was developed by this project, support a single origin for rice, and we are also able to estimate a date for the domestication of rice consistent with the previously-published archaeological studies. How nucleotide variation is distributed across the genome is a central question in molecular population genomics and has been a subject of considerable interest since the earliest surveys of molecular polymorphism. While recombination rate is a major factor that contributes to the genomic distribution of polymorphism, hitchhiking effects may occur in any genomic context where opportunities for recombination between selected mutations and linked neutral sites are limited. In principle, genomic regions with a greater influx of selected mutations have an increased proportion of neutral sites linked to sites under selection and genetic hitchhiking is expected to occur provided that linkage associations are sufficiently strong. Gene-rich regions or other genomic contexts with high densities of functional sites may therefore be subject to the diversity-reducing effects of selection even if crossing-over occurs frequently. In this study we use re-sequencing data from three chromosomes of the perennial common wild rice species Oryza rufipogon and its two derived domesticated subspecies of the Asian cultivated rice O. sativa. We found a strong positive correlation between recombination rate and gene density, which provides an opportunity to examine the roles of these two features when they act antagonistically to shape genome-wide patterns of nucleotide variation. Although we find some evidence of reduced polymorphism in centromeric regions where recombination is suppressed, our analysis suggests that gene density effects outweigh those of recombination in shaping patterns of sequence variability. Our observations suggest that the relationship between nucleotide diversity and gene density in wild and domesticated rice genomes does not arise from mutational effects, but through some form of selection that reduces diversity at neutral sites linked to selected mutations. The negative correlation between nucleotide diversity and gene density in rice indicates that gene effects outweigh those of recombination, and suggests that linkage associations are sufficiently high in gene dense regions to facilitate genetic hitchhiking. Our findings may have widespread implications, as the positive correlation between recombination rate and gene density is found not only in rice but in other grass species as well. In rice, maize and other cereal grass species, recombination has been observed to initiate in gene regions, which explains the strong correlation of recombination rate and gene density in these species. Finally, another major area of study for the project was to identify regions of the genome that show evidence of recent positive selection. Using our SNP data, we identified a total of 20 such regions within the three chromosomes. We found that regions with reduced diversity were widespread in both indica and in particular tropical japonica consistent with the expectation of strong artificial selection during rice domestication. We were also able to find putative selective sweeps that were specific to indica or tropical japonica, as well as regions with sweeps shared by both variety groups. The data from these studies on the origin of rice and selection in the genome can help shape new genetic mapping strategies in rice for future crop improvement. Our work has also contributed to our understanding of a large number of issues in genomic variation of domesticated plant and animal species. The techniques and approaches we developed were also used in analyses of the evolution of soybean, cattle and dogs, as well as microbial species. The outcomes of this project has helped advance both our understanding of population genomics and the tools for further research.

National Science Foundation (NSF)
Division of Integrative Organismal Systems (IOS)
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Diane Jofuku Okamuro
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New York University
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