Background: Rice (Oryza sativa L.) Chalkiness, the opaque part in the kernel endosperm formed by loosely piled starch and protein bodies. Chalkiness is a complex quantitative trait regulated by multiple genes and various environmental factors. Phytohormones play important roles in the regulation of chalkiness formation but the underlying molecular mechanism is still unclear at present. Results: In this research, Xiangzaoxian24 (X24, pure line of indica rice with high-chalkiness) and its origin parents Xiangzaoxian11 (X11, female parent, pure line of indica rice with high-chalkiness) and Xiangzaoxian7 (X7, male parent, pure line of indica rice with low-chalkiness) were used as materials. The phenotype, physiological and biochemical traits combined with transcriptome analysis were conducted to illustrate the dynamic process and transcriptional regulation of rice chalkiness formation. Impressively, phytohormonal contents and multiple phytohormonal signals were significantly different in chalky caryopsis, suggesting the involvement of phytohormones, particularly ABA and auxin, in the regulation of rice chalkiness formation, through the interaction of multiple transcription factors and their downstream regulators. Conclusion: These results indicated that chalkiness formation is a dynamic process associated with multiple genes, forming a complex regulatory network in which phytohormones play important roles. These results provided informative clues for illustrating the regulatory mechanisms of chalkiness formation in rice.

Potassium is an important essential element for plant growth and development. Long-term potassium deprivation can lead to a severe deficiency phenotype in plants. Interestingly, Phytolacca acinosa is a plant with an unusually high potassium content and can grow well and complete its lifecycle even in severely potassium deficient soil. In this study, we found that its stems and leaves were the main tissues for high potassium accumulation, and P. acinosa showed a strong ability of K⁺ absorption in roots and a large capability of potassium accumulation in shoots. Analysis of plant growth and physiological characteristics indicated that P. acinosa had an adaptability in a wide range of external potassium levels. To reveal the mechanism of K⁺ uptake and transport in the potassium-hyperaccumulator plant P. acinosa, K⁺ uptake-/transport-related genes were screened by transcriptome sequencing, and their expression profiles were compared between K⁺ starved plants and normal cultured plants. Eighteen members of HAK/KT/KUPs, ten members of AKTs, and one member of HKT were identified in P. acinosa. Among them, six HAKs, and two AKTs and PaHKT1 showed significantly different expression. These transporters might be coordinatively involved in K⁺ uptake/transport in P. acinosa and lead to high potassium accumulation in plant tissues. In addition, significantly changed expression of some ABC transporters indicated that ABC transporters might be important for K⁺ uptake and transport in P. acinosa under low K⁺ concentrations.

Cadmium (Cd) is a highly toxic heavy metal that causes serious damage to plant and human health. Phytolacca acinosa Roxb. has a large amount of aboveground biomass and a rapid growth rate, and it has been identified as a novel type of Cd hyperaccumulator that can be harnessed for phytoremediation. However, the molecular mechanisms underlying the response of P. acinosa to Cd²⁺ stress remain largely unclear. In this study, the phenotype, biochemical, and physiological traits of P. acinosa seeds and seedlings were analyzed under different concentrations of Cd²⁺ treatments. The results showed higher Cd²⁺ tolerance of P. acinosa compared to common plants. Meanwhile, the Cd²⁺ content in shoots reached 449 mg/kg under 10 mg/L Cd²⁺ treatment, which was obviously higher than the threshold for Cd hyperaccumulators. To investigate the molecular mechanism underlying the adaptability of P. acinosa to Cd stress, RNA-Seq was used to examine transcriptional responses of P. acinosa to Cd stress. Transcriptome analysis found that 61 genes encoding TFs, 48 cell wall-related genes, 35 secondary metabolism-related genes, 133 membrane proteins and ion transporters, and 96 defense system-related genes were differentially expressed under Cd²⁺ stress, indicating that a series of genes were involved in Cd²⁺ stress, forming a complex signaling regulatory mechanism. These results provide new scientific evidence for elucidating the regulatory mechanisms of P. acinosa response to Cd²⁺ stress and new clues for the molecular breeding of heavy metal phytoremediation.

Cadmium (Cd) is an extremely toxic heavy metal that can move from the soil to plants and enter the human body via the food chain, causing severe health issues for humans. Phytoremediation uses hyperaccumulators to extract heavy metals from polluted soil. Phytohormones, wildly used plant growth regulators, have been explored to improve phytoremediation efficiency. Abscisic acid (ABA) is also an essential regulator of plant tolerance to biotic and abiotic stresses, including heavy metal-induced toxicity. Previous research has revealed that Phytolacca acinosa Roxb. (P. acinosa) has a strong ability to enrich Cd and can be used as a Cd hyperaccumulator. In this study, physiological and biochemical analysis revealed that under Cd stress, exogenous ABA application alleviated oxidative stress, increased the Cd²⁺ concentration in P. acinosa, especially in the roots, and changed the phytohormone concentration in P. acinosa. Transcriptome analysis was conducted to explore the molecular mechanisms by which ABA regulates Cd uptake and accumulation in P. acinosa, and to further understand the regulatory role of ABA. The results show that ABA treatment affected gene expression in P. acinosa roots under Cd stress. This study identified 5788 differentially expressed genes (DEGs) (2541 up-regulated and 3247 down-regulated). Moreover, 96 metal transport-related DEGs, 54 phytohormone-related DEGs, 89 cell wall-related DEGs, 113 metal chelation-related DEGs, and 102 defense system-related DEGs cooperated more closely under exogenous ABA application to regulate Cd uptake and accumulation in P. acinosa under Cd stress. These results may help to elucidate the mechanisms by which ABA regulates Cd uptake and accumulation in plants, and provide a reference for developing a phytohormone-based strengthening strategy to improve the phytoremediation ability of other hyperaccumulators or accumulator species. The key genes involved in ABA’s regulation of Cd uptake and accumulation in P. acinosa need to be further analyzed and functionally verified. This may expand our understanding of the molecular regulatory mechanisms underlying heavy metal uptake and accumulation in hyperaccumulators.

Plants frequently encounter relatively low and fluctuating potassium (K⁺) concentrations in soil, with roots serving as primary responders to this stress. Histone modifications, such as de-/acetylation, can function as epigenetic markers of stress-inducible genes. However, the signaling network between histone modifications and low-K⁺ (LK) response pathways remains unclear. This study investigated the regulatory role of Histone Deacetylase Complex 1 (HDC1) in primary root growth of Arabidopsis thaliana under K⁺ deficiency stress. Using a hdc1-2 mutant line, we observed that HDC1 positively regulated root growth under LK conditions. Compared to wild-type (WT) plants, the hdc1-2 mutant exhibited significantly inhibited primary root growth under LK conditions, whereas HDC1-overexpression lines displayed opposite phenotypes. No significant differences were observed under HK conditions. Further analysis revealed that the inhibition of hdc1-2 on root growth was due to reduced apical meristem cell proliferation rather than cell elongation. Notably, the root growth of hdc1-2 showed reduced sensitivity compared to WT after auxin treatment under LK conditions. HDC1 may regulate root growth by affecting auxin polar transport and subsequent auxin signaling, as evidenced by the altered expression of auxin transport genes. Moreover, the organ-specific RT-qPCR analyses unraveled that HDC1 negatively regulates the expression of CBL-CIPK-K⁺ channel-related genes such as CBL1, CBL2, CBL3, AKT1, and TPK1, thereby establishing a molecular link between histone deacetylation, auxin signaling, and CBLs-CIPKs pathway in response to K⁺ deficiency.

Chalkiness, as a major undesired-index for rice quality evaluation, is the opaque/white structure in rice endosperm, and determines the rice grade and price to a large extent. Reducing chalkiness remains one of the most important goals for breeders and producers. In this study, we identified a rice chalkiness formation-related gene (OsCFF1) that encodes a glycosyltransferase (GT). Through screening of OsCFF1 alleles in 60 rice cultivars, four genotypes were identified, including WT and three natural variations. Cultivars with natural variations that cause the function loss of OsCFF1 usually produce fewer chalky grains. Higher OsCFF1 expression during the grain-filling period is usually associated with a higher degree of chalkiness. Notably, the chalkiness in gene-edited rice kernels was decreased by more than 90% after knocking out OsCFF1 through CRISPR/Cas9, indicating a quality reversal from inferior rice with high chalkiness to superior rice with very little chalkiness. We also found that OsCFF1 might catalyze the glycosylation of GA_4, and the corresponding mechanism requires in-depth exploration. In summary, OsCFF1 is a key factor controlling the formation of rice chalkiness and demonstrates enormous potential for application in high-quality rice breeding.