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.

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.

Pentatricopeptide repeats (PPR) proteins function in organellar RNA metabolism and plant development constitute one of the largest protein families in land plants. Besides the organelle localization, some of this family members localized in nuclear, indicating mysterious and wider roles of PPR proteins. Oryza sativa L. nuclear-localized PPR protein 1 (OsNPPR1), a member of the PPR family in rice, is a novel nuclear RNA-binding protein, which plays a pivotal role in mitochondria. However, there is scarce knowledge about its protein partners and RNA-related roles in mitochondria function. Here, using yeast two-hybrid assay, RIP-seq and IP-MS, we uncover OsNPPR1's interacting endogenous RNA targets and protein binding partners. OsNPPR1 potentially interacts with many nuclear factors including splicing factors, transcription and post-transcription factors to perform its function in nuclear, and controls mitochondria metabolism through binding nuclear encoded mitochondria genes. Together, our data reveal new insights into the molecular roles and characteristics of nuclear PPR proteins and provide new ways to further research.