Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana.
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.
Lee
Insuk
I
Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea. insuklee@yonsei.ac.kr
Ambaru
Bindu
B
Thakkar
Pranjali
P
Marcotte
Edward M
EM
Rhee
Seung Y
SY
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D002874:Chromosome Mapping; D018745:Genome, Plant / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*
D029681:Arabidopsis Proteins