Besides increasing grain yield, improving rice (Oryza sativa L.) quality has been paid more and more attention recently. Cooking and eating quality (CEQ) is an important indicator of rice quality. Since CEQs are quantitative traits and challenging for measurement, efforts have mainly focused on two major genes, Wx and SSIIa. Chalkiness and floury endosperm significantly affect the eating quality of rice, leading to noticeable changes in CEQ. Due to the easily observable phenotype of floury endosperm, cloning single gene mutations that cause floury endosperm and evaluating changes in CEQs indirectly facilitate the exploration of the minor genes controlling CEQ. In this study, eight mutants with different degrees of floury endosperm, generated through ethylmethane sulfonate (EMS) mutagenesis, were analyzed. These mutants exhibited wide variation in starch morphology and CEQs. Particularly, the z2 mutant showed spherical starch granules significantly increased rapid visco analyzer (RVA) indexes and urea swelling, while the z4 mutant displayed extremely sharp starch granules and significantly decreased RVA indexes and urea swelling compared to the wild type. Additionally, these mutants still maintained correlations with certain RVA profiles, suggesting that the genes PUL, which affect these indexes, may not undergo mutation. Cloning these mutated genes in the future, especially in z2 and z4, will enhance the genetic network of rice eating quality and hold significant importance for molecular marker-assisted breeding to improve rice quality.

Starch biosynthesis is crucial in determining rice quality during rice endosperm development. This study obtained a stable inheritable white-core endosperm mutant, h5, by treating the japonica rice variety Nipponbare with MNU (N-methyl-N-nitro-sourea). The mutated gene is an allele of OsAGPL2, which encodes the large subunit of ADP-glucose pyrophosphorylase (AGPase), a key and rate-limiting enzyme in the rice starch biosynthesis pathway. A G-C mutation in the third exon of OsAGPL2 led to impaired starch synthesis, significantly reduced amylose content (AC) and gel consistency (GC), and a marked decrease in AGPase activity. The haplotype analysis revealed that an SNP in the 3′UTR and two SNPs in the 5′UTR of OsAGPL2 were associated with significant differences in AC and GC among rice resources. These SNPs can be utilized to design molecular markers for breeding programs to improve rice quality. This study elucidates the impact of OsAGPL2 on the eating and cooking quality of rice. It identifies superior haplotypes, providing a theoretical foundation and molecular markers for accumulating minor-effect genes to enhance rice quality.

In addition to increasing grain yield, improving rice (Oryza sativa L.) quality has received increasing attention recently. The cooking and eating quality (CEQ) is an important indicator of rice quality. Chalkiness and floury endosperm have a significant impact on the CEQ of rice, resulting in noticeable changes. Due to the easily observable phenotype of floury endosperm, cloning single gene mutations that cause floury endosperm and indirectly evaluating changes in CEQs facilitates the exploration of minor genes controlling CEQ. In this study, a stable genetic allele variant of flo4, named flo4-7, was obtained through EMS mutagenesis. The flo4-7 allele variant carries the cyOsPPDKB mutation. flo4-7 showed a significant reduction in compound starch granules and a significant increase in single starch granules in endosperm cells, indicating the involvement of cyOsPPDKB in the synthesis of endosperm starch. Additionally, flo4-7 exhibited a significant decrease in gel consistency (GC) compared to the wild type. Through the analysis of GC data from 166 rice germplasm resources, a C-T variation in the 18th exon of cyOsPPDKB was found to be a crucial site, causing a significant difference in GC between indica and japonica rice. This locus can be used in the future to develop molecular markers for molecular marker-assisted breeding. This study provides a good research foundation for improving the CEQ of rice.

Pyruvate kinase (PK) is the terminal rate-limiting enzyme of glycolysis and occupies a central position in plant energy metabolism and carbon skeleton allocation. Plant PK isoenzymes comprise the cytosolic pyruvate kinase (PKc) and the plastidic pyruvate kinase (PKp), which differ markedly in gene origin, protein structure, subcellular localization, and physiological function, exhibiting independent evolutionary histories and functional diversification. Recent studies have revealed that PKc possesses dynamic subcellular distribution, allowing it to shuttle among the cytosol, mitochondria, and nucleus, where it participates in stress responses and epigenetic regulation through protein–protein interactions. PKp is localized to plastids and connects carbon metabolism with lipid biosynthesis and the methylerythritol phosphate (MEP) pathway by supplying pyruvate, thereby playing critical roles in seed development and oil accumulation. This review comprehensively summarizes recent advances in plant PKc and PKp concerning protein structure and subunit composition, tissue-specific expression, subcellular localization, protein interaction networks, activity regulation, and their effects on plant growth, development, and stress responses. In addition, phylogenetic tree, motif, and domain analyses of pyruvate kinase genes from Oryza sativa (rice), Glycine max (soybean), Gossypium hirsutum (cotton), Solanum tuberosum (potato), Arachis hypogaea (peanut), and Arabidopsis thaliana, as well as promoter cis-element analyses, are performed. This review aims to provide theoretical references for crop quality improvement and stress-resilient breeding.

As living standards rise, there has been a growing emphasis on quality traits related to rice’s taste potential. Recent studies explored correlations among quality traits, but the influence of major genes governing a specific quality trait on other quality traits remains elusive. Here, we report on the application of grain quality genes, two of Waxy (Wx) and Starch synthase II-a (SSIIa), which dominates in rice cooking and eating quality, and two grain length/width-related genes, grain size 3 (GS3) and grain width 7 (GW7), on appearance quality traits. Five allele-specific markers for these genes were developed, and used to stack the desirable alleles at these loci. The effects of individual or combined alleles at the loci were evaluated using a set of 156 rice germplasm. We found that the Wx-In1 (Intron 1) locus exerts a major effect in controlling both amylose content and gel consistency, while the SSIIa-Ex8 (Exon 8) locus primarily governs alkali spreading value. The impact on chalkiness-related traits follows the hierarchy of Wx-In1 > SSIIa-Ex8 > Wx-Ex10 (Exon 10). GS3-Ex2 (Exon 2) has a highly significant impact on chalkiness-related traits, and the GW7-Pro (Promoter) locus exerts a synergistic effect. The GS3-Ex2 locus exerts an effect in controlling both gel consistency and alkali spreading value, while the GW7-Pro locus governs amylose content. The data for newly developed allele-specific markers will facilitate the improvement of rice quality in rice.