Application and future perspective of CRISPR/Cas9 genome editing in fruit crops

Abstract

Fruit crops, including apple, orange, grape, banana, strawberry, watermelon, kiwifruit and tomato, not only provide essential nutrients for human life but also contribute to the major agricultural output and economic growth of many countries and regions in the world. Recent advancements in genome editing provides an unprecedented opportunity for the genetic improvement of these agronomically important fruit crops. Here, we summarize recent reports of applying CRISPR/Cas9 to fruit crops, including efforts to reduce disease susceptibility, change plant architecture or flower morphology, improve fruit quality traits, and increase fruit yield. We discuss challenges facing fruit crops as well as new improvements and platforms that could be used to facilitate genome editing in fruit crops, including dCas9‐base‐editing to introduce desirable alleles and heat treatment to increase editing efficiency. In addition, we highlight what we see as potentially revolutionary development ranging from transgene‐free genome editing to de novo domestication of wild relatives. Without doubt, we now see only the beginning of what will eventually be possible with the use of the CRISPR/Cas9 toolkit. Efforts to communicate with the public and an emphasis on the manipulation of consumer‐friendly traits will be critical to facilitate public acceptance of genetically engineered fruits with this new technology.

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

“…We need to continuously improve horticultural commodities to meet the rising demand for food and ornamental production. The widespread applications of CRISPR/Cas technologies in horticultural crops open the possibility for accelerating new variety development [12][13][14][15][16][17] . Engineering cis-regulatory regions using CRISPR/Cas allows the creation of novel variants, resulting in quantitative variation, and thus holds great potential for creating phenotypic diversity.…”

“…Despite the importance of regulatory changes in genes, the application of CRISPR/ Cas-mediated cis-engineering has only been explored sporadically. The genome sequence for at least 181 horticultural species is available 11 and genome editing has been used to generate primarily knockout mutations in at least 25 of them [12][13][14][15][16][17] . These achievements demonstrate the feasibility of applying CRISPR/Cas-mediated cisengineering to expand the phenotypic diversity of many horticultural crops.…”

A Revolution toward Gene-Editing Technology and Its Application to Crop Improvement

“…The MADS-box transcription factor-encoding RIPENING INHIBITOR (RIN) gene was found to regulate fruit ripening in tomato. This technique was modulated to engineer three target regions within the gene; RIN mutant (homozygous) tomato plants displayed incomplete ripening with a low pigmentation (red) rate compared with wild-type plants, which demonstrated the crucial role of RIN in the ripening process [100,118]. Furthermore, orthologs of GA4 in B. oleracea, BolC.GA4.a, were used to induce 10% targeted mutations by Cas9 and led to a dwarf phenotype that was linked with GA4 knockout [71,100,119,120].…”

“…Genome editing may be the only way to improve this important staple food and fruit. To date, only a small number of fruit-producing species (citrus, tomatoes, watermelons, grapes, or strawberries) with traits inherited from CRISPR/Cas9 via the germline have been recorded [118]. Genome editing of gibberellin biosynthesis has allowed the generation of dwarf fruit trees [124], with the capacity for a high productivity rate through dense planting and decreased usage of water and fertilizers and lower land and labor costs.…”

Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners

“…The use of modern genomic tools is not limited to population genetics, as other interesting approaches can reveal important aspects of the domestication process. For instance, one can analyze changes in the transcriptional activity of genes related to domestication (Hekman et al, 2015), demonstrate the phenotypic effects of certain alleles through the use of genomic editing tools (Zhou J. et al, 2019), search for epigenetic patterns that changed between domesticated and wild taxa (Janowitz Koch et al, 2016) or analyze the genetic makeup of archeological samples (Irving-Pease et al, 2019).…”