Unknown

Dataset Information

0

Genetic dissection of the biotic stress response using a genome-scale gene network for rice.


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.

SUBMITTER: Lee I 

PROVIDER: S-EPMC3215029 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

altmetric image

Publications

Genetic dissection of the biotic stress response using a genome-scale gene network for rice.

Lee Insuk I   Seo Young-Su YS   Coltrane Dusica D   Hwang Sohyun S   Oh Taeyun T   Marcotte Edward M EM   Ronald Pamela C PC  

Proceedings of the National Academy of Sciences of the United States of America 20111031 45


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,  ...[more]

Similar Datasets

| S-EPMC4883713 | biostudies-literature
| S-EPMC6586736 | biostudies-literature
| S-EPMC8421479 | biostudies-literature
| S-EPMC10507716 | biostudies-literature
| S-EPMC10671030 | biostudies-literature
| S-EPMC6379984 | biostudies-other
| S-EPMC4964798 | biostudies-literature
| S-EPMC8019945 | biostudies-literature
| S-EPMC5429764 | biostudies-literature
| S-EPMC6423299 | biostudies-other