In rice production, pre-harvest sprouting (PHS) of late ripening seeds is one of the most serious quality defects in rice grain quality. In the present study, PHS impact was investigated by examining the physicochemical properties, eating and cooking quality (ECQ) of rice grain. Four rice cultivars suffering from PHS had impaired ECQ, reduced apparent amylose content, and decreased total starch content, with an increase in total protein content. The viscosity of flours and starches prepared from the PHS grains was significantly reduced. Starch molecular structure analysis also showed remarkable decreases in the short chains of amylopectin, long amylose chains and reduced starch crystallinity of the PHS grains. Moreover, the PHS native starch tended to have low starch digestibility. This provides useful information for understanding the effects of PHS on white rice grain quality as well as on starch fine structure and its physicochemical properties.

Amylose content (AC) is a critical factor for the quality of rice. It is determined by the biosynthesis gene Waxy (Wx) and a variety of quantitative trait loci (QTLs). Although many QTLs have been reported to affect rice AC, few of them have been investigated under varying growth conditions, especially various temperatures, which are known to greatly influence the AC. We analyzed the AC at different temperatures and planting seasons in a set of chromosome segment substitution lines (CSSLs) which were derived from a cross between the indica variety 9311 and the japonica variety Nipponbare carrying the same Wxb allele. A joint analysis detected a single locus, qSAC3, with a high logarithm of odds (LOD) score in four different conditions. The qSAC3 from indica 9311 (qSAC3ind) substantially increased the AC in japonica Nipponbare under all tested growth conditions. Furthermore, introducing the qSAC3ind into the soft rice variety Nangeng9108 with Wxmq, a mutant allele of Wxb, also moderately increased its AC and improved its appearance quality significantly by reducing the chalkiness of the polished rice. Our results indicate that the qSAC3ind could increase the AC of japonica rice in different environments as well as in the background of different Wx alleles and that qSAC3 is a valuable locus for fine-tuning the rice AC and ameliorating the dull endosperm in rice varieties with the Wxmq allele.

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 Wx^mp allele derived from the ancestral Wx^mq 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 Wx^mp, Wx^mq, or Wx^b−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.

High quality stands as a pivotal competitive edge in the rice industry. Optimizing amylose content (AC) and the physicochemical properties of endosperm starch by regulating the Wx gene is crucial for enhancing rice grain quality. In this study, we created a novel Wx^b-d25 allele by deleting a 25 bp segment (−26 to −2) within the Wx core promoter using CRISPR/Cas9. Compared with the wild type and the previously reported Wx^b-i1, Wx^b-d25 exhibited no significant changes in agronomic traits. However, its grains displayed temperature-dependent variations in AC and altered transparency and viscosity characteristics, holding the potential to synergistically improve both the eating and cooking quality (ECQ) and appearance quality (AQ) of rice. Further studies demonstrated that this promoter modification, by partially disrupting the transcription initiator, significantly downregulated the original Wx-01 transcript and generated a novel Wx transcript (ONT.7395.1) in Wx^b-d25 grains. Despite its low expression abundance, the ONT.7395.1 transcript could be completely processed into mature Wx mRNA. The combined effects of the dual transcripts resulted in significantly increased Wx gene expression and AC in Wx^b-d25 grains under conventional cultivation conditions. These findings provide a genetic resource and a theoretical foundation for utilizing the Wx^b-d25 allele to improve rice grain quality.

Nanjing series japonica rice varieties developed by the Institute of Food Crops, Jiangsu Academy of Agricultural Sciences in China have the characteristics of an excellent taste quality, high yield, and good resistance. They are widely promoted and applied in the lower reaches of the Yangtze River in China’s japonica rice planting areas. In response to the problem of the lack of coordination between nitrogen fertilizer management measures and variety characteristics in production, which makes it difficult to synergistically improve yield and quality, this study adopted a split-plot experimental design to study the effect of nitrogen fertilizer application on yield and rice quality of Nanjing series japonica rice varieties. In 2021, four nitrogen application rates of 0 (N₁), 150 (N₂), 300 (N₃), and 450 (N₄) kg hm⁻² (all pure nitrogen) were set up, and in 2022, four treatments of 120 (N₁), 180 (N₂), 240 (N₃), and 300 (N₄) kg hm⁻² were set up, all with nitrogen application rate as the main plot factor and variety as the sub-plot factor. The results showed that the differences between the different nitrogen fertilizer treatments were significant at the 5% or 1% level, except for the milled rice rate, head rice rate, peak viscosity, setback viscosity, and paste temperature in 2021 and panicle number, grain number per panicle, all Rapid Visco-analyzer (RVA) characteristic values, and amylose content in 2022. With an increase in the nitrogen application rate, the number of panicles, grain number per panicle, and yield increased. Either the rates of brown rice, milled rice, or head rice and chalky grains or chalkiness showed an increase trend. The peak viscosity, hot viscosity, final viscosity, and breakdown viscosity decreased, while the setback viscosity increased. For the quality of cooked rice, the hardness increased, appearance, viscosity, and balance decreased, protein content increased, and taste value decreased. The interaction between nitrogen application rate and variety was significant at p < 0.05 or p < 0.01 only for yield components, processing quality, and rice protein content in 2021 and for eating and cooking quality, appearance quality, and peak viscosity in 2022. Other traits were not significant. The comprehensive results from two years of experiments showed that, under the conditions of this experiment, a nitrogen application rate of 240–300 kg hm⁻² could improve the quality of rice in the Nanjing series varieties while maintaining a high yield. The results of this experiment have a guiding significance for the high-yield and high-quality cultivation of excellent-tasting Nanjing series japonica rice.

Grain size in rice (Oryza sativa L.) shapes yield and quality, but the underlying molecular mechanism is not fully understood. We functionally characterized GRAIN NUMBER AND LARGE GRAIN SIZE 44 (GNL44), encoding a RING-type protein that localizes to the cytoplasm. The gnl44 mutant has fewer but enlarged grains compared to the wild type. GNL44 is mainly expressed in panicles and developing grains. Grain chalkiness was higher in the gnl44 mutant than in the wild type, short-chain amylopectin content was lower, middle-chain amylopectin content was higher, and appearance quality was worse. The amylose content and gel consistency of gnl44 were lower, and protein content was higher compared to the wild type. Rapid Visco Analyzer results showed that the texture of cooked gnl44 rice changed, and that the taste value of gnl44 was lower, making the eating and cooking quality of gnl44 worse than that of the wild type. We used gnl44, qgl3, and gs3 monogenic and two-gene near-isogenic lines to study the effects of different combinations of genes affecting grain size on rice quality-related traits. Our results revealed additive effects for these three genes on grain quality. These findings enrich the genetic resources available for rice breeders.