Yale researchers have published a cellular atlas of genetic activity in
rice, documenting with unprecedented detail how and when genes are turned
off and on within cells of a living organism.

The staggering amount of data collected during the five-year project,
published online in the journal Nature Genetics, chronicles the molecular
differences and similarities among 40 cell types essential to the life cycle
of one of the world?s most important crops.

?All crops will benefit from knowledge and tools derived from the rice
atlas,?? said Timothy Nelson, professor of molecular, cellular &
developmental biology and senior author of the study. For instance,
scientists hope to find networks of genes responsible for photosynthesis and
those that could lead to production of food and biomass for uses such as
alternate energy, he said.

The atlas is composed of cell-specific transcriptomes?huge datasets that
document the relative activity of each of rice?s 30,000 genes for a
particular cell type. The collection of 40 transcriptomes released in this
study permit the comparison of any gene?s activity among each of 40 cell
types, including different stages of the development of roots, shoots and
embryos. Eventually, the Yale team hopes to add another 40 different cell
types to the data, which are available on the web to researchers around the
world.

?The atlas provides a unique resource to the research
community?comprehensive data on the gene-by-gene contribution of the cell
types that cooperate to make tissues, organs, and the entire body function,?
Nelson said. ?The comprehensiveness of the atlas is a technical
achievement?some important cell types were extremely difficult to sample in
sufficient quantity.?

Among its immediate applications, the data allow researchers to distinguish
which genes are activated in key cell types at certain stages of
development, providing clues to their roles in building the body. Also,
scientists were able to identify genes with critical ?housekeeping?
functions that are essential at all times in all cell types.

?This cellular atlas is a deep resource that can be mined for cellular
information on any gene or biological process,? Nelson said. The Plant
Genome Research Program of the National Science Foundation funded the work.
Other members of the Yale team were: Yuling Jiao, S. Lori Tausta, Neeru
Gandotra, Ning Sun, Tie Liu, Nicole K. Clay, Teresa Ceserani, Meiqin Chen,
Ligeng Ma, Matthew Holford, Huiyong Zhang, Hongyu Zhao and Xing-Wang Deng.
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