Plant Genome Engineering for Targeted Improvement of Crop Traits

Abstract

To improve food security, plant biology research aims to improve crop yield and tolerance to biotic and abiotic stress, as well as increasing the nutrient contents of food. Conventional breeding systems have allowed breeders to produce improved varieties of many crops; for example, hybrid grain crops show dramatic improvements in yield. However, many challenges remain and emerging technologies have the potential to address many of these challenges. For example, site-specific nucleases such as TALENs and CRISPR/Cas systems, which enable high-efficiency genome engineering across eukaryotic species, have revolutionized biological research and its applications in crop plants. These nucleases have been used in diverse plant species to generate a wide variety of site-specific genome modifications through strategies that include targeted mutagenesis and editing for various agricultural biotechnology applications. Moreover, CRISPR/Cas genome-wide screens make it possible to discover novel traits, expand the range of traits, and accelerate trait development in target crops that are key for food security. Here, we discuss the development and use of various site-specific nuclease systems for different plant genome-engineering applications. We highlight the existing opportunities to harness these technologies for targeted improvement of traits to enhance crop productivity and resilience to climate change. These cutting-edge genome-editing technologies are thus poised to reshape the future of agriculture and food security.

Keywords: CRISPR/Cas systems; climate change; crop improvement; food security; genome editing; genome engineering; synthetic biology.

FIGURE 1

Site-specific nuclease-induced genome editing. The double-stranded breaks (DSBs) introduced by CRISPR/Cas or TALEN complexes stimulates the endogenous DNA repair machineries, non-homologous end joining (NHEJ) or homology-directed repair (HDR). The NHEJ machinery repairs the DNA imperfectly and introduces frameshifts by insertion or deletion leading to loss-of-function mutations. However, the HDR pathway precisely inserts a piece of DNA (from an exogenous template DNA with enough similarity to the DSB flanking sequence) by homologous recombination, which is useful for the introduction of specific point mutations or a new gene sequence.

FIGURE 2

Simplified workflow for CRISPR/Cas9-mediated plant genome editing. The production of edited plants with a desired phenotype starts from the design of a sgRNA for a specific target sequence and cloning of the sequence to express the sgRNA into a binary vector containing the Cas DNA sequence. Then the delivery of CRISPR/Cas materials into the plant cell, followed by assays to confirm the presence of the edited events, and regeneration of whole plants.

FIGURE 3

CRISPR-mediated genome-wide screening. Schematic illustration of the procedure for generating a wide variety of new plant traits by targeting one or several genes using a pool of sgRNAs. After generation of edited plants, deep phenotyping and genotyping screening are required to discover the interesting traits and their genetic background. LOF, loss of function.

FIGURE 4

Application of plant genome editing for targeted trait improvement.