Identification of new leaf intrinsic yield genes using cross-species network analysis in plants

Abstract

Plant leaves differ in their size, form and structure, and the processes of cell division and cell expansion contribute to this diversity. Leaf transcriptional networks covering cell division and cell expansion in Arabidopsis thaliana, maize (Zea mays) and aspen (Populus tremula) were compared to identify candidate genes that are conserved in plant growth and ultimately have the potential to increase biomass (intrinsic yield, IY). Our approach revealed that genes showing strongly conserved co-expression were mainly involved in fundamental leaf developmental processes such as photosynthesis, translation, and cell proliferation. Next, known intrinsic yield genes (IYGs) together with cross-species conserved networks were used to predict novel potential Arabidopsis leaf IYGs. Using an in-depth literature screening, 34 out of 100 top predicted IYGs were confirmed to affect leaf phenotype if mutated or overexpressed and thus represent novel potential IYGs. Globally, these new IYGs were involved in processes mostly covering cell cycle, plant defense responses, gibberellin, auxin and brassinosteroid signaling. Application of loss-of-function lines and phenotypic characterization confirmed two newly predicted IYGs to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify new yield genes and to accelerate plant breeding.