Fine-tuning grain amylose contents by genome editing of Waxy cis-regulatory region in rice

Deciphering the Role of Waxy Gene Mutations in Enhancing Rice Grain Quality

Amylose content (AC) stands as a pivotal determinant of rice grain quality, primarily governed by the Waxy gene (Wx). The allelic variation within this gene, particularly the presence of the Wxmp allele derived from the ancestral Wxmq allele, significantly influences AC and is prevalent among soft japonica rice varieties in southern China. Although both alleles are associated with lower AC, there remains a paucity of detailed understanding regarding the interplay between specific functional single nucleotide polymorphisms (SNPs) within these alleles and the overarching rice grain quality. To investigate this, we engineered three distinct transgenic rice lines, each harboring the Wxmp, Wxmq, or Wxb-5c alleles in the background of the glutinous rice cultivar Nip(wx). This suite of transgenic rice lines showcased varying degrees of grain transparency inversely correlated to AC, which in turn influenced other physicochemical properties of the rice grains, such as taste value of cooked rice, gel consistency, and starch pasting properties. Additionally, analyses of gene expression and enzyme activity revealed that the functional SNPs, Ex4-53G to A and Ex5-53T to C, lead to a decline in the activity of granule-bound starch synthase I (GBSSI) without altering expression levels.

Editing Silicon Transporter Genes to Reduce Arsenic Accumulation in Rice

Rice is a dominant source of inorganic arsenic (As) exposure for populations consuming rice as a staple food. Decreasing As accumulation in rice grain is important for improving food safety. Arsenite [As(III)], the main form of As in paddy soil porewater, is taken up inadvertently by OsLsi1 and OsLsi2, the two key transporters for silicon (Si) uptake in rice roots. Here, we investigated whether editing OsLsi1 or OsLsi2 can decrease As accumulation in rice grain without compromising grain yield. We used the CRISPR-Cas9 technology to edit the promoter region of OsLsi1 and the C-terminal coding sequence of OsLsi1 and OsLsi2, and we generated a total of 27 mutants. Uptake and accumulation of Si and As were evaluated in both short-term hydroponic experiments and in a paddy field. Deletion of 1.2-2 kb of the OsLsi1 promoter suppressed OsLsi1 expression in roots and Si uptake markedly and did not affect As(III) uptake or grain As concentration. Some of the OsLsi1 and OsLsi2 coding sequence mutants showed large decreases in the uptake of Si and As(III) as well as large decreases in Si accumulation in rice husks. However, only OsLsi2 mutants showed significant decreases (by up to 63%) in the grain total As concentration. Editing OsLsi2 mainly affected the accumulation of inorganic As in rice grain with little effect on the accumulation of dimethylarsenate (DMA). Grain yields of the OsLsi2 mutants were comparable to those of the wild type. Editing OsLsi2 provides a promising way to reduce As accumulation in rice grain without compromising the grain yield.

Impacts of Inherent Components and Nitrogen Fertilizer on Eating and Cooking Quality of Rice: A Review

With the continuous improvement of living standards, the preferences of consumers are shifting to rice varieties with high eating and cooking quality (ECQ). Milled rice is mainly composed of starch, protein, and oil, which constitute the physicochemical basis of rice taste quality. This review summarizes the relationship between rice ECQ and its intrinsic ingredients, and also briefly introduces the effects of nitrogen fertilizer management on rice ECQ. Rice varieties with higher AC usually have more long branches of amylopectin, which leach less when cooking, leading to higher hardness, lower stickinesss, and less panelist preference. High PC impedes starch pasting, and it may be hard for heat and moisture to enter the rice interior, ultimately resulting in worse rice eating quality. Rice with higher lipid content had a brighter luster and better eating quality, and starch lipids in rice have a greater impact on rice eating quality than non-starch lipids. The application of nitrogen fertilizer can enhance rice yield, but it also decreases the ECQ of rice. CRNF has been widely used in cereal crops such as maize, wheat, and rice as a novel, environmentally friendly, and effective fertilizer, and could increase rice quality to a certain extent compared with conventional urea. This review shows a benefit to finding more reasonable nitrogen fertilizer management that can be used to regulate the physical and chemical indicators of rice grains in production and to improve the taste quality of rice without affecting yield.