Leaf senescence is the final stage of plant development. Many internal and external factors affect the senescence process in rice (Oryza sativa L.). In this study, we identified qCC2, a major quantitative trait locus (QTL) for chlorophyll content using a population derived from an interspecific cross between O. sativa (cv. Hwaseong) and Oryza grandiglumis. The O. grandiglumis allele at qCC2 increased chlorophyll content and delayed senescence. GW2 encoding E3 ubiquitin ligase in the qCC2 region was selected as a candidate for qCC2. To determine if GW2 is allelic to qCC2, a gw2-knockout mutant (gw2-ko) was examined using a dark-induced senescence assay. gw2-ko showed delayed leaf senescence in the dark with down-regulated expression of senescence-associated genes (SAGs) and chlorophyll degradation genes (CDGs). The association of the GW2 genotype with the delayed senescence phenotype was confirmed in an F₂ population. RNA-seq analysis was conducted to investigate 30-day-old leaf transcriptome dynamics in Hwaseong and a backcross inbred line—CR2002—under dark treatment. This resulted in the identification of genes involved in phytohormone signaling and associated with senescence. These results suggested that transcriptional regulation was associated with delayed senescence in CR2002, and RING-type E3 ubiquitin ligase GW2 was a positive regulator of leaf senescence in rice.

Chlorophyll biosynthesis is a crucial biological process in plants, and chlorophyll content is one of the most important traits in rice breeding programs. In this study, we identified a lethal, chlorophyll-deficient, yellow seedling (YS) phenotype segregating in progeny of CR5055-21, an F₂ plant derived from a backcross between Korean japonica variety ‘Hwaseong’ (Oryza sativa) and CR5029, which is mostly Hwaseong with a small amount of Oryza grandiglumis chromosome segments. The segregation of the mutant phenotype was consistent with a single gene recessive mutation. Light microscopy of YS leaf cross-sections revealed loosely arranged mesophyll cells and sparse parenchyma in contrast to wildtype. In addition, transmission electron microscopy showed that chloroplasts did not develop in the mesophyll cells of the YS mutant. Quantitative trait loci (QTL)-seq analysis did not detect any significant QTL, however, examination of the individual delta-SNP index identified a 2-bp deletion (AG) in the OsCHLI gene, a magnesium (Mg)-chelatase subunit. A dCAPs marker was designed and genotyping of a segregating population (n = 275) showed that the mutant phenotype co-segregated with the marker. The 2-bp deletion was predicted to result in a frameshift mutation generating a premature termination. The truncated protein likely affects formation and function of Mg-chelatase, which consists of three different subunits that together catalyze the first committed step of chlorophyll biosynthesis. Transcriptome analysis showed that photosynthesis and carbohydrate metabolism pathways were significantly altered although expression of OsCHLI was not. Chlorophyll- and carotenoid-related genes were also differentially expressed in the YS mutant. Our findings demonstrated that OsCHLI plays an important role in leaf pigment biosynthesis and leaf structure development in rice.

Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index F_ST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.

Developing rice varieties with increased mineral element content is the most cost-effective and efficient approach for alleviating human malnutrition and nutrient deficiencies. In this study, quantitative trait loci (QTLs) were mapped for mineral element content in 96 introgression lines derived from a cross between the elite Korean Oryza sativa japonica cultivar “Hwaseong” and the wild rice Oryza rufipogon (IRGC105491). The population was grown in two locations, and Fe, Zn, Mn, and Ca contents of the brown rice were measured. Six QTLs were identified on chromosomes 6, 8, and 10, and all O. rufipogon alleles increased trait values. The positions of qFe10 and qZn10 were further defined; higher Fe and Zn contents are related to the 375-kb O. rufipogon segment between the markers RM1873 and RM25612. The combined analysis of the whole-genome sequencing data, spatiotemporal expression profile, and gene expression suggested that a transcription factor gene, namely the rice homeobox gene 9 (LOC_Os10g33960) marks as the high potential candidate associated with Fe and/or Zn regulation. This study provides valuable information on candidate genes qFe10 and qZn10 from O. rufipogon, which may be vital in developing rice varieties with increased Fe and/or Zn content without any penalty in traits of agronomic importance.

Previously, five putative quantitative trait loci (QTLs) for low-temperature germination (LTG) have been detected using 96 BC₃F₈ lines derived from an interspecific cross between the Korean japonica cultivar “Hwaseong” and Oryza rufipogon. In the present study, two introgression lines, CR1517 and CR1518, were used as parents to detect additional QTLs and analyze interactions among QTLs for LTG. The F₂ population (154 plants) along with parental lines, Hwaseong and O. rufipogon, were evaluated for LTG and coleoptile length under low-temperature conditions (13 °C). Among five QTLs for LTG, two major QTLs, qLTG1 and qLTG3, were consistently detected at 6 and 7 days after incubation. Three minor QTLs were detected on chromosomes 8 and 10. Two QTLs, qLTG10.1 and qLTG10.2, showing linkage on chromosome 10, exerted opposite effects with the Hwaseong allele at qLTG10.2 and the O. rufipogon allele at qLTG10.1 respectively, in turn, increasing LTG. Interactions among QTLs were not significant, implying that the QTLs act in an additive manner. Near-isogenic line plants with the combination of favorable alleles from O. rufipogon and Hwaseong exhibited higher LTG than two introgression lines. With regard to coleoptile length, three QTLs observed on chromosomes 1, 3, and 8 were colocalized with QTLs for LTG, suggesting the pleiotropy of the single gene at each locus. According to the results, the introgression of favorable O. rufipogon alleles could hasten the development of rice with high LTG and high coleoptile elongation in japonica cultivars.

Starch characteristics are of paramount importance for the eating and cooking quality of rice (Oryza sativa L.), and many genes act in concert to regulate starch biosynthesis. In this study, we investigated the seed morphology, starch structure, and genetic basis of the endosperm cavity mutant “KDS-1830C.” The “KDS-1830C” mutant displayed an opaque endosperm with a central cavity, in contrast to the normal translucent endosperm of the wild-type “Kitaake.” Scanning electron microscopy analysis revealed distinct starch granule morphologies with “Kitaake” grains exhibiting polygonal granules and “KDS-1830C” showing irregularly shaped, rounded granules. Comparison of yield-related and starch physico-chemical traits revealed significant differences in grain width, thickness, weight, and protein content, with “KDS-1830C” having lower seed hardness. QTL-seq analysis identified a significant locus on chromosome 11 associated with the cavity phenotype. A non-synonymous SNP in the LOC_Os11g37560 gene was detected as the candidate causal mutation and is predicted to generate a premature stop codon. This gene's ortholog in Arabidopsis, LESV, is known to influence starch granule structure. Protein structure prediction suggests that the nonsense mutation in “KDS-1830C” results in a truncated β sheet structure, potentially impairing amylopectin binding and granule crystallization. These findings enhance our understanding of the genetic and structural factors influencing rice endosperm development and starch biosynthesis, which are of critical importance to maintaining and improving rice grain quality.