, Bindu Ambaru4,5
, Pranjali Thakkar4
, Edward M Marcotte2,3
& Seung Y Rhee4
We introduce a rational approach for associating genes with plant traits by combined use of a genome-scale functional network and targeted reverse genetic screening. We present a probabilistic network (AraNet) of functional associations among 19,647 (73%) genes of the reference flowering plant Arabidopsis thaliana
. AraNet associations are predictive for diverse biological pathways, and outperform predictions derived only from literature-based protein interactions, achieving 21% precision for 55% of genes. AraNet prioritizes genes for limited-scale functional screening, resulting in a hit-rate tenfold greater than screens of random insertional mutants, when applied to early seedling development as a test case. By interrogating network neighborhoods, we identify AT1G80710 (now DROUGHT SENSITIVE 1; DRS1
) and AT3G05090 (now LATERAL ROOT STIMULATOR 1; LRS1
) as regulators of drought sensitivity and lateral root development, respectively. AraNet (http://www.functionalnet.org/aranet/
) provides a resource for plant gene function identification and genetic dissection of plant traits.
1.Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea.
2.Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.
3.Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.
4.Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA.
5.These authors contributed equally to this work.
Correspondence to: Insuk Lee1,2,5
Correspondence to: Edward M Marcotte2,3
Correspondence to: Seung Y Rhee4