Genome Engineering and Agriculture: Opportunities and Challenges

Abstract

In recent years, plant biotechnology has witnessed unprecedented technological change. Advances in high-throughput sequencing technologies have provided insight into the location and structure of functional elements within plant DNA. At the same time, improvements in genome engineering tools have enabled unprecedented control over genetic material. These technologies, combined with a growing understanding of plant systems biology, will irrevocably alter the way we create new crop varieties. As the first wave of genome-edited products emerge, we are just getting a glimpse of the immense opportunities the technology provides. We are also seeing its challenges and limitations. It is clear that genome editing will play an increased role in crop improvement and will help us to achieve food security in the coming decades; however, certain challenges and limitations must be overcome to realize the technology's full potential.

Keywords: Agriculture; CRISPR; Food production; Genome editing; Genome engineering; Meganuclease; Quality traits; TALEN; Transformation; Zinc-finger nuclease.

Fig. 1

Examples of genome edits that can alter gene or protein activity. (A) Illustration of transcription and translation of a “normal” gene. (B) Illustration of a single-nucleotide polymorphism leading to an early stop codon. (C) Illustration of a single-nucleotide polymorphism within the conserved 5′ splice site that can result in missplicing and inclusion of an intron. Within this example, the intron is shown to comprise an early stop codon. (D) Illustration of a single-nucleotide polymorphism within the conserved 3′ splice site that can result in missplicing and exclusion of a downstream exon. (E) Illustration of a single-nucleotide deletion that can result in a frameshift and early stop codon. (F) Illustration an inframe deletion within a site that encodes an amino acid critical for protein function. Gray boxes, 5′ and 3′ untranslated regions; white boxes, exons; blue rectangle, DNA region encoding amino acids critical for protein function; red lines, mRNA; white circles, amino acids; blue circles, amino acids critical for protein function; red circles, amino acids not normally encoded by the wild-type gene; NMD, nonsense-mediated decay; forward slash, intron–exon or exon–intron junction; dash, deleted nucleotide.