Applications and Potential of Genome-Editing Systems in Rice Improvement: Current and Future Perspectives

Abstract

Food crop production and quality are two major attributes that ensure food security. Rice is one of the major sources of food that feeds half of the world’s population. Therefore, to feed about 10 billion people by 2050, there is a need to develop high-yielding grain quality of rice varieties, with greater pace. Although conventional and mutation breeding techniques have played a significant role in the development of desired varieties in the past, due to certain limitations, these techniques cannot fulfill the high demands for food in the present era. However, rice production and grain quality can be improved by employing new breeding techniques, such as genome editing tools (GETs), with high efficiency. These tools, including clustered, regularly interspaced short palindromic repeats (CRISPR) systems, have revolutionized rice breeding. The protocol of CRISPR/Cas9 systems technology, and its variants, are the most reliable and efficient, and have been established in rice crops. New GETs, such as CRISPR/Cas12, and base editors, have also been applied to rice to improve it. Recombinases and prime editing tools have the potential to make edits more precisely and efficiently. Briefly, in this review, we discuss advancements made in CRISPR systems, base and prime editors, and their applications, to improve rice grain yield, abiotic stress tolerance, grain quality, disease and herbicide resistance, in addition to the regulatory aspects and risks associated with genetically modified rice plants. We also focus on the limitations and future prospects of GETs to improve rice grain quality.

Research Trends and Challenges of Using CRISPR/Cas9 for Improving Rice Productivity

“…The advantages of CRISPR/Cas9 technology and its efficiency can be applied as the most dependable and efficient way for new rice breeding [68]. The CRISPR/Cas9 system has been employed to modify the ISA1 gene in rice using Agrobacterium-mediated transformation.…”

“…In comparison to the NHEJ pathway, HDR has a lower efficiency. Another limitation is that some countries are not ready to commercialize genome editing crops [68]. With the increase of gene-editing tools, there exists a need to carefully consider the modern definition of GMOs and the corresponding regulatory frameworks with them [149].…”

Biofortification of Cereals and Pulses Using New Breeding Techniques: Current and Future Perspectives

“…As far as its regulation is considered, the U.S. and Canada have already declared the GE crops free from the GM regulations; however, debate is still ongoing in the E.U. with expected positive outcomes (127,159,160). GE crops are free from transgene, hence these should be regulated like conventional breeding products globally and should reach a maximum consumer for obtaining maximum benefits of technology in a shorter possible time (127).…”

Targeting Cis-Regulatory Elements for Rice Grain Quality Improvement

“…Recently, genome editing technology has been developed and optimized and has been applied successfully to a large number of plants, which has accelerated the identification and application of regulatory elements in gene promoter regions in rice (Huang et al, 2020a;Zeng et al, 2020). Genome editing is a versatile, relevant, and preferred technique for functional genomics, as well as crop improvement, involving introducing DNA mutations in the form of deletions and/or insertions or base substitutions in target gene sequences (Fiaz et al, 2019;Tabassum et al, 2021). The starch synthase gene Wx is very important for rice eating and cooking quality; therefore, it has been a popular target for study.…”