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

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Applications and Potential of Genome-Editing Systems in Rice Improvement: Current and Future Perspectives agronomy Review Applications and Potential of Genome-Editing Systems in Rice Improvement: Current and Future Perspectives Javaria Tabassum 1 , Shakeel Ahmad 1,2 , Babar Hussain 3 , Amos Musyoki Mawia 1, Aqib Zeb 1 and Luo Ju 1,* 1 State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; [email protected] (J.T.); [email protected] (S.A.); [email protected] (A.M.M.); [email protected] (A.Z.) 2 Maize Research Station, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan 3 Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +86-135-7570-6965 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 Citation: Tabassum, J.; Ahmad, S.; its variants, are the most reliable and efficient, and have been established in rice crops. New GETs, Hussain, B.; Mawia, A.M.; Zeb, A.; Ju, such as CRISPR/Cas12, and base editors, have also been applied to rice to improve it. Recombinases L. Applications and Potential of Genome-Editing Systems in Rice and prime editing tools have the potential to make edits more precisely and efficiently. Briefly, in Improvement: Current and Future this review, we discuss advancements made in CRISPR systems, base and prime editors, and their Perspectives. Agronomy 2021, 11, 1359. applications, to improve rice grain yield, abiotic stress tolerance, grain quality, disease and herbicide https://doi.org/10.3390/ resistance, in addition to the regulatory aspects and risks associated with genetically modified rice agronomy11071359 plants. We also focus on the limitations and future prospects of GETs to improve rice grain quality. Academic Editors: V. Mohan Murali Keywords: rice; grain yield; abiotic stress; biotic stress; grain quality; food security; CRISPR/Cas Achary and Malireddy K. Reddy systems; base editing; prime editing Received: 3 June 2021 Accepted: 29 June 2021 Published: 2 July 2021 1. Introduction Rice (Oryza sativa L.) is grown across the globe and consumed by approximately Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in 3 billion people or around 50% of the world population [1,2]. Rice was grown on 162 million published maps and institutional affil- hectares and its global production was 755 million tons in 2019 (http://www.fao.org/ iations. faostat/en, accessed on 29 June 2021). The world population may rise anywhere from 9.7 to 11 billion in 2050 (https://population.un.org/wpp/, accessed on 29 June 2021); thus, a significant increase in rice yield will be required to feed the growing population. The global demand for rice is estimated to increase by 50% by 2050 [3]. However, climate change is a major limiting factor for crop production and increases in temperature are leading to more Copyright: © 2021 by the authors. frequent and severe drought spells and soil salinization [4]. Rice faces several biotic and Licensee MDPI, Basel, Switzerland. This article is an open access article abiotic stresses that significantly lower its production. Approximately 3000 L of water is distributed under the terms and needed to produce 1 kg of rice, while it is a drought susceptible species due to the thin conditions of the Creative Commons cuticle wax and small root systems, drought can cause up to 100% yield losses [5]. Similarly, Attribution (CC BY) license (https:// soil salinity could reduce 50% of global rice production [6] and cold stress also threatens rice creativecommons.org/licenses/by/ production and quality [1]. Therefore, an increase in rice production and improvement of 4.0/). its grain quality are essential for healthy and sustainable life in the future [2]. An increase in Agronomy 2021, 11, 1359. https://doi.org/10.3390/agronomy11071359 https://www.mdpi.com/journal/agronomy Agronomy 2021, 11, 1359 2 of 24 rice yield and development of stress resilient rice plants are essential for global food security. Moreover, the improvement in grain quality parameters enhances consumer demand and commercial value of rice varieties [7]. Earlier, rice grain quality, climate resilience, disease Agronomy 2021, 11, x FOR PEER REVIEWresistance, and yield have improved via conventional breeding approaches (mutagenesis3 of 24 and hybridization). However, these techniques are time-consuming, tedious, require large mutant screens, and are prone to human biases [4]. Therefore, more powerful, precise, fast, and robust crop improvement approaches, such as genome editing, will be required to discussed. We also focus on the limitations and future prospects of GETs to improve rice meet the rice demand by the ever-growing world population (Figure1). for the above-mentioned traits. Figure 1. Overview of plant breeding approaches for developing rice varieties with improved yield, stress tolerance and Figure 1. Overview of plant breeding approaches for developing rice varieties with improved yield, stress tolerance and grain quality. (A) Conventional breeding for crop improvement, e.g., rice grain quality improvement. (B) Mutational grainbreeding quality. approach (A) Conventional for rice grain breeding quality improvement. for crop improvement, (C) Genetic engineering e.g., rice grain for incorporating quality improvement. the desired (geneB) Mutational in pop- breedingular rice approach variety. for(D) riceApplication grain quality of gene improvement. editing tools (forC) rice Genetic plant engineering improvement, for e.g., incorporating targeting rice the grain desired quality gene sensitive in popular ricegenes variety. via ( DCRISPR/Cas) Application systems. of gene Upward editing green tools forarrow rice shows plant improvement, improved or high e.g., targetinggrain quality/yield/disease rice grain quality resistance sensitive genesin viathe CRISPR/Cas plant. Downward systems. red Upward arrow shows green deprived arrow shows or low improved grain quality/yield/disease or high grain quality/yield/disease resistance in the plant. resistance Q-gene, in Quality the plant. Downwardgene; Cas9, red CRISPR-associated arrow shows deprived protein or9; lowCas12a, grain CRISPR-asso quality/yield/diseaseciated protein resistance12a; Cas12b, in CRISPR-associated the plant. Q-gene, protein Quality 12b; gene; Cas13a, CRISPR-associated protein 13a; Cas13b, CRISPR-associated protein 13b; BE, Base Editors; Trans/Recom, Trans- Cas9, CRISPR-associated protein 9; Cas12a, CRISPR-associated protein 12a; Cas12b, CRISPR-associated protein 12b; Cas13a, posases or Recombinases; PE, Prime Editors. CRISPR-associated protein 13a; Cas13b, CRISPR-associated protein 13b; BE, Base Editors; Trans/Recom, Transposases or Recombinases; PE, Prime Editors.2. CRISPR/Cas9 Based Rice Crop Improvement In the CRISPR/Cas9 genome editing system, Cas9 nuclease introduces double strand breaks (DSBs) in DNA at the sgRNA target site. These DSBs are repaired by the non-ho- mologous end joining (NHEJ) pathway that results in insertion or deletions (indels) at the target site, thus knocking out the targeted gene [12] (Figure 2). The CRISPR/Cas9 system is the most prevalent GET that has been used to improve several agronomic traits of rice, such as grain yield, abiotic stress tolerance, disease resistance, herbicide resistance, in ad- dition to rice grain quality (Figure 3). Classical breeding requires selection of progenies for 6–7 years to obtain the desired level of homozygosity, while the CRISPR/Cas9 system delivers it within a year, making it a powerful plant breeding tool [12]. Herein, we dis- cussed the applications of CRISPR/Cas9 for rice crop improvement. Agronomy 2021, 11, 1359 3 of 24 Conventional breeding and mutagenesis techniques drag undesirable genes along with the targeted genes, and take a long time; henceforth, they do not fit the requirements (i.e., of rapidly increasing the production and quality parameters to cope with world hunger and malnutrition challenges). Additionally, hybridization is possible between two plants of the same species, limiting the introduction of new genes and traits. Powerful genome editing technologies (GETs) tackle these limitations of conventional mutational breeding and are capable of transferring a desired trait in any plant species in a short time (Figure1) and, thus, have great potential for speeding up the breeding programs. However, detailed information about the gene sequence, structure, gene function, novel genes and quantitative trait loci (QTL) responsible for traits of interest is vital for application of GETs [8]. GETs modify a specific gene of the desired trait by cutting DNA via target-specific nucleases; thus, the breeding processes are swift. Site-specific endonucleases
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