Evolutionary biologist Carlos Machado will contribute his expertise to help understand the evolution of wild rice species and how this can be applied to maximize the genes that enable the grain to best survive extreme environments.

Evolutionary biologist Carlos Machado will help understand the evolution of wild rice species and how this can be applied to maximize the genes that enable the grain to best survive extreme environments.

A multi-institutional research consortium, that includes the University of Maryland, has been awarded $9.9 million from the National Science Foundation to develop a deeper understanding of the wild relatives of cultivated rice with the ultimate goal of creating next-generation varieties that are better capable of withstanding drought and poorer soils and produce higher yields than current forms of domesticated rice. The main goals are to conduct comparative genomic studies of wild rice species and identify genes that could be used to improve the crop.

University of Maryland evolutionary biologist Carlos A. Machado studies the processes and mechanisms of species divergence and will contribute his expertise in genomic, population genetic, and phylogenetic approaches to help understand the evolution of wild rice species and varieties and how this can be applied to maximize the genes that enable the grain to best survive extreme environments.

“This is a very exciting opportunity because the data we are collecting will give us the opportunity to address basic questions in evolutionary genetics and genome biology, and to use the results to identify genes or gene variants in wild rice species that can be used for the improvement of cultivated rice. It will be the most comprehensive within-genus comparative genomics platform for any plant system,” said Machado.

Machado, who was assistant professor in the University of Arizona’s Department of Ecology and Evolutionary Biology before joining the University of Maryland Department of Biology two years ago, has been a long-time collaborator of the project’s principal investigator Rod Wing, a plant scientist who directs the Arizona Genomics Institute at the University of Arizona. Asian cultivated rice (Oryza sativa) feeds more people worldwide than any other crop. As the rice-dependent population is expected to double in ~25 years, breeders are faced with the enormous task of doubling rice yields with less land, water, and fertilizers, and on poorer soils.
Oryza sativaAsian cultivated rice (Oryza sativa) feeds more people worldwide than any other crop. As the rice-dependent population is expected to double in ~25 years, breeders are faced with the enormous task of doubling rice yields with less land, water, and fertilizers, and on poorer soils.

“We need to figure out a way to come up with a rice variety with increased yield and capable of growing on less land, on poorer soil, with less water, and with less fertilizer.” says Wing.
"What this project will achieve is to identify and catalog all the genes found in the wild relatives of rice and analyze their functions," Wing says. "The idea is to identify genes that confer adaptations helping wild varieties cope with extreme environments and breed them into cultivated rice." 

The data could be used immediately to enhance food security, Wing pointed out, by providing a "toolkit of genes" that can be used to improve crop rice. In addition, the project has important implications for evolutionary studies.

"We will be able to reconstruct the evolution of the rice genus Oryza in great detail, more detail than for any other plant group. With that information on hand we can ask if particular genes or genomic regions have been more prone to be exchanged among species during rice evolution, and which genes or gene variants account for differences between species. Those unique genes or gene variants will become targets for genetic and functional studies to determine their involvement in traits that differentiate species in their capacity to deal with stressful environments" Machado said.

The project will generate a set of publicly available genomics resources for the genus Oryza including physical maps for three wild relatives of cultivated rice and one closely related outgoup species (Leersia perrieri), complete reference genome sequences for O. barthii (wild progenitor of West African cultivated rice) and O. punctata (a wild Oryza species that will serve as the evolutionary outgroup species for all eight AA genome species), gene and small RNA expression data sets for 11 Oryza species and L. perrieri, and DNA polymorphism data sets across the AA genome phylogeny. The project will integrate these new resources with 5 to 8 forthcoming new Oryza reference genome sequences. Specific research areas that will be addressed include: analyses of structural variation, phylogenomics, population genomics, genome evolution and the origin of new genes, and the role of transposable elements in genome evolution. In addition to Machado and Wing, the team also includes Michael Sanderson (University of Arizona), Manyuan Long (University of Chicago), Scott Jackson (Purdue University) and Doreen Ware (Cold Spring Harbor). 
