Genome editing for healthy crops: traits, tools and impacts

Many plant-associated microbes are pathogens that impair plant growth and reproduction. Plants respond to infection using a two-branched innate immune system. The first branch recognizes and responds to molecules common to many classes of microbes, including non-pathogens. The second responds to pathogen virulence factors, either directly or through their effects on host targets. These plant immune systems, and the pathogen molecules to which they respond, provide extraordinary insights into molecular recognition, cell biology and evolution across biological kingdoms. A detailed understanding of plant immune function will underpin crop improvement for food, fibre and biofuels production.

Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a method for controlling gene expression based on Cas9, an RNA-guided DNA endonuclease from a type II CRISPR system. We show that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This system, which we call CRISPR interference (CRISPRi), can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects. CRISPRi can be used to repress multiple target genes simultaneously, and its effects are reversible. We also show evidence that the system can be adapted for gene repression in mammalian cells. This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale. Copyright © 2013 Elsevier Inc. All rights reserved.

Crop pathogens and pests reduce the yield and quality of agricultural production. They cause substantial economic losses and reduce food security at household, national and global levels. Quantitative, standardized information on crop losses is difficult to compile and compare across crops, agroecosystems and regions. Here, we report on an expert-based assessment of crop health, and provide numerical estimates of yield losses on an individual pathogen and pest basis for five major crops globally and in food security hotspots. Our results document losses associated with 137 pathogens and pests associated with wheat, rice, maize, potato and soybean worldwide. Our yield loss (range) estimates at a global level and per hotspot for wheat (21.5% (10.1-28.1%)), rice (30.0% (24.6-40.9%)), maize (22.5% (19.5-41.1%)), potato (17.2% (8.1-21.0%)) and soybean (21.4% (11.0-32.4%)) suggest that the highest losses are associated with food-deficit regions with fast-growing populations, and frequently with emerging or re-emerging pests and diseases. Our assessment highlights differences in impacts among crop pathogens and pests and among food security hotspots. This analysis contributes critical information to prioritize crop health management to improve the sustainability of agroecosystems in delivering services to societies.