Metabolic Disturbance Induced by the Embryo Contributes to the Formation of Chalky Endosperm of a Notched-Belly Rice Mutant

Grain chalkiness is a key quality trait of the rice grain, whereas its underlying mechanism is still not thoroughly understood because of the complex genetic and environmental interactions. We identified a notched-belly (NB) mutant that has a notched-line on the belly of grains. The line dissects the endosperm into two distinct parts, the upper translucent part, and the bottom chalky part in the vicinity of the embryo. Using this mutant, our previous studies clued the negative influence of embryo on the biochemical makeup of the endosperm, suggesting the need for the in-depth study of the embryo effect on the metabolome of developing endosperm. This study continued to use the NB mutant to evolve a novel comparison method to clarify the role of embryo in the formation of a chalky endosperm. Grain samples of the wild-type (WT) and NB were harvested at 10, 20, and 30 days after fertilization (DAF), and then divided into subsamples of the embryo, the upper endosperm, and the bottom endosperm. Using non-targeted metabolomics and whole-genome RNA sequencing (RNA-seq), a nearly complete catalog of expressed metabolites and genes was generated. Results showed that the embryo impaired the storage of sucrose, amino acid, starch, and storage proteins in the bottom endosperm of NB by enhancing the expression of sugar, amino acids, and peptide transporters, and declining the expression of starch, prolamin, and glutelin synthesis-related genes. Importantly, the competitive advantage of the developing embryo in extracting the nutrients from the endosperm, transformed the bottom endosperm into an “exhaustive source” by diverting the carbon (C) and nitrogen (N) metabolism from synthetic storage to secondary pathways, resulting in impaired filling of the bottom endosperm and subsequently the formation of chalky tissue. In summary, this study reveals that embryo-induced metabolic shift in the endosperm is associated with the occurrence of grain chalkiness, which is of relevance to the development of high-quality rice by balancing the embryo–endosperm interaction.

Substitution Mapping of Two Closely Linked QTLs on Chromosome 8 Controlling Grain Chalkiness in Rice

Rice varieties are required to have high yield and good grain quality. Grain chalkiness and grain shape are two important traits of rice grain quality. Low chalkiness slender grains are preferred by most rice consumers. Here, we dissected two closely linked quantitative trait loci (QTLs) controlling grain chalkiness and grain shape on rice chromosome 8 by substitution mapping. Two closely linked QTLs controlling grain chalkiness and grain shape were identified using single-segment substitution lines (SSSLs). The two QTLs were then dissected on rice chromosome 8 by secondary substitution mapping. qPGC8.1 was located in an interval of 1382.6 kb and qPGC8.2 was mapped in a 2057.1 kb region. The maximum distance of the two QTLs was 4.37 Mb and the space distance of two QTL intervals was 0.72 Mb. qPGC8.1 controlled grain chalkiness and grain width. qPGC8.2 was responsible for grain chalkiness, grain length and width. The additive effects of qPGC8.1 and qPGC8.2 on grain chalkiness were not affected by higher temperature. Two closely linked QTLs qPGC8.1 and qPGC8.2 were dissected on rice chromosome 8. They controlled the phenotypes of grain chalkiness and grain shape. The two QTLs were insensitive to higher temperature.

The Potential of Silicon in Improving Rice Yield, Grain Quality, and Minimising Chalkiness: A Review

Silicon (Si) is a micronutrient that can increase the resistance of certain plants against multiple biotic or abiotic stresses. It is known that Si has a beneficial effect on plant growth, beginning in the soil, which could lead to a good crop yield. Despite its benefits, Si is not listed among the generally essential elements or nutrients for rice production in many countries such as Malaysia. This review discusses the ability to uptake Si and its benefits on rice. Environmental factors affect rice production, and among the factors, high temperature has been shown to disrupt the physiological development of rice grain, which contributes to chalkiness. Chalkiness is an undesirable trait that decreases grain’s value, milling, cooking, and eating quality. The application of Si could ameliorate rice grain quality, thus providing a valuable reference for Si fertiliser use in high-quality rice production. This review also presents an update on the potentials of Si in improving the rice yield and grain quality, including Si’s ability to minimise grain chalkiness. Therefore, it is anticipated that Si applications will increase rice yield and grain quality and help to reduce chalkiness.

Substitution Mapping of Two Closely Linked QTLs Controlling Grain Chalkiness and Grain Shape on Rice Chromosome 8

Background: Rice varieties are required to have high yield and good grain quality. Grain chalkiness and grain shape are two important traits of rice grain quality. Low chalkiness slender grains are preferred by most rice consumers. Here, we dissected two closely linked quantitative trait loci (QTLs) controlling grain chalkiness and grain shape on rice chromosome 8 by substitution mapping. Results: Two closely linked QTLs controlling grain chalkiness and grain shape were identified using single-segment substitution lines (SSSLs). The two QTLs were then dissected on rice chromosome 8 by secondary substitution mapping. qPGC8.1 was located in an interval of 1382.6 kb and qPGC8.2 was mapped in a 2057.1 kb region. The maximum distance of the two QTLs was 4.37 Mb and the space distance of two QTL intervals was 0.72 Mb. qPGC8.1 controlled grain chalkiness and grain width. qPGC8.2 was responsible for grain chalkiness and for grain length and grain width. The additive effects of qPGC8.1 and qPGC8.2 on grain chalkiness were not affected by heat stress. Conclusions: Two closely linked QTLs qPGC8.1 and qPGC8.2 were dissected on rice chromosome 8. They controlled the phenotypes of grain chalkiness and grain shape. The two QTLs were insensitive to high temperature.

Fine mapping of two grain chalkiness QTLs sensitive to high temperature in rice

Background Grain chalkiness is one of important factors affected rice grain quality. It is known that chalkiness is affected by the high temperature during the seed filling period. Although a larger of QTLs for chalkiness were reported across all 12 chromosomes, only a few of the QTLs were fine mapped or cloned up to now. Here, we fine map two QTLs for chalkiness in two single-segment substitution lines (SSSLs), 11–09 with substitution segment from O. sativa and HP67–11 with substitution segment from O. glaberrima. Results The grain chalkiness of SSSLs 11–09 and HP67–11 was significantly lower than that in the recipient Huajingxian 74 (HJX74) in consecutive 8 cropping seasons. The regression correlation analysis showed that percentage of chalky grain (PCG) and percentage of chalky area (PCA) were significantly and positively correlated with percentage of grain chalkiness (PGC). Two QTLs for grain chalkiness were located on two chromosomes by substitution mapping. qPGC9 was mapped on chromosome 9 with an estimated interval of 345.6 kb. qPGC11 was located on chromosome 11 and delimited to a 432.1 kb interval in the O. sativa genome and a 332.9 kb interval in the O. glaberrima genome. qPGC11 is a QTL for grain chalkiness from O. glaberrima and was mapped in a new region of chromosome 11. The effect of two QTLs was incomplete dominance. The additive effects of two QTLs on chalkiness in second cropping season (SCS) were significantly greater than that in first cropping season (FCS). Conclusions qPGC11 is a new QTL for grain chalkiness. The two QTLs were fine mapped. The donor alleles of qPGC9 and qPGC11 were sensitive to the high temperature of FCS.

Embryo-Endosperm Interaction and Its Agronomic Relevance to Rice Quality

Embryo-endosperm interaction is the dominant process controlling grain filling, thus being crucial for yield and quality formation of the three most important cereals worldwide, rice, wheat, and maize. Fundamental science of functional genomics has uncovered several key genetic programs for embryo and endosperm development, but the interaction or communication between the two tissues is largely elusive. Further, the significance of this interaction for grain filling remains open. This review starts with the morphological and developmental aspects of rice grain, providing a spatial and temporal context. Then, it offers a comprehensive and integrative view of this intercompartmental interaction, focusing on (i) apoplastic nutrient flow from endosperm to the developing embryo, (ii) dependence of embryo development on endosperm, (iii) regulation of endosperm development by embryo, and (iv) bidirectional dialogues between embryo and endosperm. From perspective of embryo-endosperm interaction, the mechanisms underlying the complex quality traits are explored, with grain chalkiness as an example. The review ends with three open questions with scientific and agronomic importance that should be addressed in the future. Notably, current knowledge and future prospects of this hot research topic are reviewed from a viewpoint of crop physiology, which should be helpful for bridging the knowledge gap between the fundamental plant sciences and the practical technologies.