Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities

Abstract

Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.

The 21st Century Agriculture: When Rice Research Draws Attention to Climate Variability and How Weedy Rice and Underutilized Grains Come in Handy

“…The 21st century witnessed increasing attention among researchers in laying a strong foundation for a greener revolution, where improved crop varieties require less inputs, especially water and fertilizer, to feed the estimated 9.8 billion people by the mid-century [69,70]. Cantrell and Hettel [71] highlighted that rice research in the 21st century should emphasize how to reduce both the production and the research gaps, along with strategic research plans to develop and utilize new technologies and tools.…”

Synthetic Apomixis an Old Enigma to Preserve Hybrid Vigor

“…In modern time, CRISPR technology is widely utilized with tremendous success in agriculture especially for crops essential for food security perspectives i.e., rice, wheat, maize, Arabidopsis, cotton, tomato and potato. The user friendly and low budget requirement of genome editing has spurred the research for crop-trait development not only in academia but also with private companies dealing in agriculture products [57]. Moreover, the genome editing technology has not only speed up the breeding effort to improve yield, grain quality, resistance against a/biotic stresses and domestication in plants, but also withstand in diverse environment with high value traits such as hybrid vigour or heterosis, which has proved to be a major challenge for researchers and farmers.…”

Base Editing: The Ever Expanding Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Tool Kit for Precise Genome Editing in Plants

“…Various tools have been widely used for precise genome editing in plants, including clustered regularly interspaced short palindromic repeats (CRISPR) based gene editing techniques, such as CRISPR/CRISPR associated protein 9 (Cas9), CRISPR/Cas12a (Cpf1), and CRISPR/Cas13 [6][7][8][9], owing to their reliability. All these techniques have certain advantages and disadvantages and have become more precise, efficient, and robust in recent years [1,[10][11][12][13]. The formation of DNA double-strand breaks (DSBs) at target loci is one of the primary features of CRISPR/Cas genome editing.…”