To use the chip, researchers purify total RNA (which reflects the genes expressed in the tissue) from plant tissue, make a copy of these molecules with a chemical tag added, and then "wash" the chip with the RNA sample. If a gene is being expressed in the tissue, its corresponding RNA will be present and bind to the complementary DNA sequences on the chip. The locations of the bound RNA have a visible signal because of the tag, rather like bright and dim pixels on a computer screen. Analysis of which pieces of DNA on the chip have signals indicates which genes are expressed in the tissue.
The chip is the first commercial citrus microarray and allows analysis of expression of more than 20,000 different genes. The array will also be used to develop a detailed genetic map of citrus that will help researchers locate many genes. The map location information will be used to make the development of new varieties more efficient.
"This industry-supported effort both added to and made use of publicly available citrus sequences to develop an entirely new tool that will benefit all citrus researchers and help sustain the citrus industry locally and worldwide," said Timothy Close, a professor of genetics at UCR and a co-leader of the project. "We owe a special thanks to colleagues in the citrus community: Abhaya Dandekar at UC Davis, Bob Shatters, Jose Chaparro and Greg McCollum at the USDA Horticultural Research Lab, and Avi Sadka at Volcani Institute in Israel for sharing the full content of their citrus sequence data.
"Other colleagues in the United States, Japan and Spain who deposited sequences to the public repository maintained by the National Center for Biotechnology Information also made valuable contributions. The use of all available public data resulted in very nice coverage of the citrus genome. We are pleased
Source:University of California - Riverside