Functional characterization of DEEPGENES to enhance deeper rooting in cereal crops

Abstract

Global food security and climate change represent major challenges faced by humankind during this century. Developing deeper rooting, more resource efficient crops represents an attractive solution to increase crop production sustainably whilst also enhancing soil carbon (C) sequestration. For example, planting maize varieties with a root system 0.5m deeper than currently sown in USA is predicted to improve foraging for water and nitrogen resources in sub-soil layers whilst burying up to two thirds of carbon related to US transportation emissions. The aim of this PhD project is to identify and characterise key genes that control anatomical and architectural traits contributing to deeper rooting in cereal crops such as maize and barley (as part of the DEEPER project funded by the ARPA-E ROOTS initiative).

A DEEPGENES discovery pipeline was initially developed to pinpoint candidate genes that controlled key traits determining deeper rooting in maize. Root anatomical traits included cortical cell number, cortical cell file number, total cortical area and root cortical aerenchyma plus architectural traits such as crown root angle. Promising DEEPGENE candidates where then shortlisted based on root expression and tissue specificity using maize and cross-species transcriptomic datasets in model plants such as rice and Arabidopsis thaliana. Loss of function mutants in candidate DEEPGENES were designed and/or developed in maize and the cereal model Brachypodium distachyon using CRISPR-Cas9 based approaches, respectively. Phenotypic analysis revealed a candidate regulator for root cortical cell number encoded by the QKY gene.

In parallel with maize studies, a forward genetics approach was used to pinpoint root angle or root length mutants in the barley TILLMore population. Two mutants were characterised which disrupted either: 1) HvPIN1A, encoding an auxin-efflux carrier, which controls root growth and vascular patterning in cereal roots; and 2) A novel Tubby1-like gene called HvEGT1 (Enhancing Gravitropism 1) which regulates root gravitropic set point angle in cereals. Barley and wheat mutant lines disrupting EGT1 function exhibited a deeper rooting phenotype, revealing this sequence as a promising DEEPGENE target to create novel cereal varieties.