한빛사 논문
Insuk Leea,1,2, Young-Su Seob,1,3, Dusica Coltraneb, Sohyun Hwanga, Taeyun Oha, Edward M. Marcottec,d,2, and Pamela C. Ronaldb,e,f,2
aDepartment of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea;
bDepartment of Plant Pathology, University of California, Davis, CA 95616;
cCenter for Systems and Synthetic Biology, and
dDepartment of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712-1064;
eJoint Bioenergy Institute, Emeryville, CA 94608; and
fThe Genome Center, University of California, Davis, California 95616
Footnotes
1 I.L. and Y.-S.S. contributed equally to this work.
2 To whom correspondence may be addressed.
3 Present address: Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea.
Author contributions: I.L., Y.-S.S., E.M.M., and P.C.R. designed research; I.L., Y.-S.S., D.C., E.M.M., and P.C.R. performed research; I.L., Y.-S.S., S.H., T.O., E.M.M., and P.C.R. analyzed data; and I.L., E.M.M., and P.C.R. wrote the paper.
Abstract
Rice is a staple food for one-half the world's population and a model for other monocotyledonous species. Thus, efficient approaches for identifying key genes controlling simple or complex traits in rice have important biological, agricultural, and economic consequences. Here, we report on the construction of RiceNet, an experimentally tested genome-scale gene network for a monocotyledonous species. Many different datasets, derived from five different organisms including plants, animals, yeast, and humans, were evaluated, and 24 of the most useful were integrated into a statistical framework that allowed for the prediction of functional linkages between pairs of genes. Genes could be linked to traits by using guilt-by-association, predicting gene attributes on the basis of network neighbors. We applied RiceNet to an important agronomic trait, the biotic stress response. Using network guilt-by-association followed by focused protein?protein interaction assays, we identified and validated, in planta, two positive regulators, LOC_Os01g70580 (now Regulator of XA21; ROX1) and LOC_Os02g21510 (ROX2), and one negative regulator, LOC_Os06g12530 (ROX3). These proteins control resistance mediated by rice XA21, a pattern recognition receptor. We also showed that RiceNet can accurately predict gene function in another major monocotyledonous crop species, maize. RiceNet thus enables the identification of genes regulating important crop traits, facilitating engineering of pathways critical to crop productivity.
systems biology, plant genetics, gene-trait associations
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