Targeting Cis-Regulatory Elements for Rice Grain Quality Improvement

Abstract

Rice is the most important source of food worldwide, providing energy, and nutrition for more than half of the population worldwide. Rice grain quality is a complex trait that is affected by several factors, such as the genotype and environment, and is a major target for rice breeders. Cis-regulatory elements (CREs) are the regions of non-coding DNA, which play a critical role in gene expression regulation. Compared with gene knockout, CRE modifications can fine-tune the expression levels of target genes. Genome editing has provided opportunities to modify the genomes of organisms in a precise and predictable way. Recently, the promoter modifications of coding genes using genome editing technologies in plant improvement have become popular. In this study, we reviewed the results of recent studies on the identification, characterization, and application of CREs involved in rice grain quality. We proposed CREs as preferred potential targets to create allelic diversity and to improve quality traits via genome editing strategies in rice. We also discussed potential challenges and experimental considerations for the improvement in grain quality in crop plants.

Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L.

“…The mutation in abscisic acid response elements not only lessens the ABA response but also can inhibit the leucine zipper proteins binding that might affect many biological responses [60]. The Ry and gibberellin elements are investigated grain quality in rice [61]. The occurrence of these cis-regulatory elements provided evidence of BnSDGs's role in growth and development.…”

Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century

“…Moreover, to improve crop characteristics, many genes that regulate essential traits must have a high translation rate rather than functional loss or reduction ( Reis et al., 2020 ). Recently, the modification of cis-regulatory elements has been shown to be a practical approach for fine-tuning the expression levels of target genes and is therefore a promising strategy for rice ECQ improvement ( Ding et al., 2021 ).…”

Crop Quality Improvement Through Genome Editing Strategy

“…Although the most frequent application of CRISPR/Cas9 is to create null alleles by targeting the coding sequences, loss-offunction mutations in coding regions may result in pleiotropic or deleterious effects (Li et al, 2020a;Hendelman et al, 2021). Numerous researches in both animals and plants have revealed that many genetic changes driving evolution, domestication, and breeding occurred in cis-regulatory regions, including upstream, introns, and downstream regions of genes (Wang et al, 2014;Ding et al, 2021). Compared with coding region mutations, cis-regulated region editing is more likely to induce small phenotypic changes by modifying the level, timing, or space of gene expression, which benefit crop improvement.…”