The Rice Atlas

These different varieties of rice may hold the key to more efficient food production.

Basmati, jasmine, red, brown, white. Its colors and flavors lend themselves well to different types of cuisine and in many cultures it is considered a staple food.

Oryza sativa, more commonly known as rice, has recently served as a model organism for biological research regarding molecular genetics.

A team of Yale scientists headed by MCDB professor Timothy Nelson created a database of the gene activity for 60 different types of cells in rice. This Rice Atlas can be used as a resource for scientists who want to understand the genes or gene products of specific cell types, and therefore the functions of cell types. As professor Nelson explains, “it is a resource like an encyclopedia that you can consult for lots of different reasons depending on what your biological interest is”.

Nelson’s paper, which was recently published in Nature Genetics, details the unique workflow that he used to isolate and analyze the rice genes. To look at the RNA that was unique in each particular cell type, Nelson’s lab used laser microdissection to isolate specific cells from thin tissue slices of the rice plants. In this method, selected cells are tacked with a near-infrared laser to a plastic film to harvest them away from their neighbors. The isolated RNA from the pure population of cells was profiled using microarrays- arrays of thousands of microscopic spots, each con­taining a DNA sequence probe for a particular rice gene. Finally statistics and informatics were employed to characterize the cell’s “transcriptome”— how much RNA was present from each of the ~30,000 rice genes. The project, which began five years ago, has already characterized 60 cell type transcriptomes and Nelson sees his team continuing until they reach 100 cell types.

This resource project has many practical applications such as increasing the productivity of food crops and biofuels feedstocks. The need for food is increasing exponentially but the amount of agricultural land on earth is fixed. Nelson recognizes this problem and is going to use cell-specific information from the rice atlas to better understand the basis of C4 photosynthesis in plants such as corn and maize. C4 photosynthesis is the cooperation of two different photosynthetic cell types to carry out an efficient form of carbon fixation that leads to greater yields of the crop under particular conditions of temperature, illumination and other resources. Nelson hopes to turn C3 photosynthesizing plants such as rice and wheat into C4 photosynthesizers with the hope of making them more efficient crops.

From RNA transcriptomes to a Rice Atlas of gene function, Nelson’s lab is solving the world’s problems one grain at a time.