Enhancing frozen dough quality: Investigating the impact of soy hull polysaccharide (SHP) on rheological properties and microstructure.

The effects of SHP on the texture, rheological properties, starch crystallinity and microstructure of frozen dough were investigated. The efficacy of SHP in enhancing dough quality is concentration-dependent, with frozen dough containing 1.5% SHP exhibiting hardness comparable to fresh dough without SHP (221.31 vs. 221.42 g). Even at 0.5% SHP, there is a noticeable improvement in frozen dough quality. The rheological results showed that the viscoelasticity of dough increased with higher SHP concentration. What's more, XRD and SEM results indicated that the SHP's hydrophilicity reduces the degree of starch hydrolysis, slows down the damage of starch particles during freezing, and consequently lowers the crystallinity of starch. Additionally, CLSM observations revealed that SHP enhances the gluten network structure, diminishing the appearance of holes. Therefore, the physical, chemical properties, and microstructure of frozen dough with SHP demonstrate significant enhancement, suggesting SHP's promising antifreeze properties and potential as a food antifreeze agent.

Characterization of high-internal-phase emulsions based on soy protein isolate with varying concentrations of soy hull polysaccharide and their capabilities for probiotic delivery: In vivo and in vitro release and thermal stability.

In this study, the impact of soy hull polysaccharide (SHP) concentration on high-internal-phase emulsions (HIPEs) formation and the gastrointestinal viability of Lactobacillus plantarum within HIPEs were demonstrated. Following the addition of SHP, competitive adsorption with soy protein isolate (SPI) occurred, leading to increased protein adhesion to the oil-water interface and subsequent coating of oil droplets. This process augmented viscosity and enhanced HIPEs stability. Specifically, 1.8 % SHP had the best encapsulation efficiency and delivery efficiency, reaching 99.3 % and 71.1 %, respectively. After 14 d of continuous zebrafishs feeding, viable counts of Lactobacillus plantarum and complex probiotics in the intestinal tract was 1.1 × 107, 1.3 × 107, respectively. In vitro experiments further proved that HIPEs' ability to significantly enhance probiotics' intestinal colonization and provided targeted release for colon-specific delivery. These results provided a promising strategy for HIPEs-encapsulated probiotic delivery systems in oral food applications.

Analysis of Distribution of Intracranial and Extracranial Atherosclerotic Lesions and Risk Factors for Recurrence in First-Ever and Recurrent Ischemic Stroke Patients in Northeast China.

Objective: The purpose of this study is to analyze the distribution characteristics of atherosclerotic lesions and the risk factors of recurrence in patients with ischemic stroke. Methods: A total of 505 patients diagnosed with ischemic stroke from October 2016 to October 2022 were included. Divide 505 patients with ischemic stroke into old stroke group and new stroke group. Patients without old cerebral infarction were included in the first ischemic stroke group (first group), while patients with old cerebral infarction were included in the recurrent ischemic stroke group (recurrence group).Carotid artery color Doppler ultrasonography and transcranial Doppler ultrasonography were performed on all patients. Results: We compared the distribution and risk factors of atherosclerotic lesions between the first and recurrent groups (378 cases) (127 cases). Mild, moderate, and severe stenosis of the middle cerebral artery (MCA) and occlusion of the intracranial vertebral artery (VA) were the most common in both groups. Intracranial artery stenosis is significantly higher than extracranial artery stenosis, and the anterior circulation artery is more affected than the posterior circulation artery. In the initial and recurrent groups, the proportion of patients with intracranial artery stenosis was significantly higher than that of patients with extracranial artery stenosis (43.4% vs. 22.5% and 53.4% vs. 22.5%), and the number of patients with anterior circulation stenosis was higher than that of other groups. Compared with the first group, the recurrence group had a higher incidence of hypertension, dyslipidemia, and insufficient physical exercise. There is a significant difference in the levels of triglycerides (TG) and platelets (PLT) between the two groups in biochemical indicators. In the first group, infarction was most common in 284 cases (75.1%) of the frontal lobe, followed by 232 cases (61.4%) of the basal ganglia, and 147 cases (38.9%) of the parietal lobe. In the recurrence group, the proportion of frontal lobe infarction [284 (74.0%)], basal ganglia infarction [232 (70.1%)], and parietal lobe infarction [147 (37.0%)] was the highest. It can be observed that the recurrence group had a higher incidence of basal ganglia infarction (70.1% vs. 61.4%), but a lower incidence of occipital lobe infarction (0.8% vs. 4.2%). Conclusions: Our study found no significant difference in the distribution of intracranial and extracranial atherosclerotic lesions between first-ever and recurrent ischemic stroke patients in China. Notably, hypertension, years of dyslipidemia, insufficient physical exercise, elevated triglyceride (TG) levels, and increased platelet (PLT) counts were identified as significant risk factors for stroke recurrence. These findings may have implications for the management and prevention of recurrent ischemic strokes in clinical practice.

Pulsed light treatment enhances starch hydrolysis and improves starch physicochemical properties of germinated brown rice.

BACKGROUND: Recently, germinated brown rice (GBR) has gained substantial attention as a functional food because of its nutritional attributes. Notably, pulsed light technology (PLT) has emerged as a promising tool for enhancing rice germination and, consequently, has improved the nutritional and functional qualities of GBR-derived products. However, further research is required to comprehensively understand the impact of PLT on GBR physicochemical properties. The present study aimed to investigate the stimulating effects of PLT on starch hydrolysis, starch structure and functional properties of GBR. RESULTS: The PLT substantially boosted α-amylase activity during brown rice germination, leading to a 10.9% reduction in total starch content and a 17.3% increase in reducing sugar content, accompanied by elevated free water levels. Structural analysis indicated no changes in starch crystalline types, whereas gelatinization temperature slightly increased. Pasting properties exhibited a significant drop in peak viscosity. Scanning electron microscopy showed surface erosion of starch granules with microstructural changes. Furthermore, correlation analysis established positive links between α-amylase activity, reducing sugar accumulation, starch structure and functional properties in GBR. CONCLUSION: The present study demonstrates that PLT enhanced the physicochemical properties of GBR starch, significantly improving the stability of GBR products, thereby contributing to expanded applicability of rice starch in the food industry. © 2023 Society of Chemical Industry.

Analysis of the Diagnostic Value of Transrectal Ultrasonography for Rectal Submucosal Lesions.

Objective: This study aims to investigate the diagnostic value of transrectal ultrasonography for rectal submucosal lesions. Methods: A retrospective analysis was conducted on 132 patients with rectal submucosal lesions admitted to our hospital from June 2018 to May 2022. All patients underwent colonoscopy, miniprobe endoscopic ultrasonography, and transrectal ultrasonography before surgery, obtaining definitive pathological results. The lesions displayed smooth morphological eminence of the mucosa under a colonoscope. Among the patients, there were 76 males and 56 females, with an average age of 50.6 years. Using pathology as the gold standard, the diagnostic accuracy of transrectal ultrasonography and miniprobe endoscopic ultrasonography for rectal submucosal lesions was calculated, and the difference between the two was compared using the chi-square (χ2) test. Results: The overall diagnostic accuracy of transrectal ultrasonography and miniprobe endoscopic ultrasonography for all rectal submucosal lesions was 95.5% and 74.2%, respectively. It was observed that transrectal ultrasonography was superior to miniprobe endoscopic ultrasonography, and the difference was statistically significant (χ2 = 25.48, P < .05). Conclusions: Transrectal ultrasonography demonstrates high diagnostic value for rectal submucosal lesions and may serve as the preferred choice for their examination.

Conformational evolution of soybean protein-polysaccharide at oil-water interface in simulated gastric environment in vitro.

The conformation and characteristics of soybean hull polysaccharide (SHP)/soy bean protein isolate (SPI) complex at oil-water interface in simulated gastric environment in vitro were discussed. Isothermal titration calorimetry (ITC) thermodynamic results illustrated that SPI formed a complex with SHP. ζ-potential and microstructure showed a flocculation phenomenon after SPI/SHP emulsion droplet treatment (especially at 60 min), which indicated that the inter droplet steric hindrance and repulsion were reduced after the emulsion was treated. Additionally, at 60 min, in FT-IR spectrum fitting results, the contents of ß-sheet and ß-turn structure were the lowest, which might be that the polar group residues exposed in the SPI/SHP complex at the interface interacted with Na+ by ion-dipole interaction or protonated with H+. The blue shift of maximum absorption intensity also indicated that the tryptophan residues moved to the hydrophobic environment, which made the treated droplets flocculate without obvious aggregation.

Application of soy protein isolate fiber and soy soluble polysaccharide non-covalent complex: A potential way for pH-triggered release.

The non-covalent interactions between protein and polysaccharide have the potential to design responsive materials. In this study, soy protein isolate fiber/soy soluble polysaccharide (SPIF/SSPS) non-covalent complex was used to create an emulsion, and the pH-response performance was evaluated by investigating their microstructure, interfacial properties, and stability at pH values of 2.0-10.0. The SPIF/SSPS complex was relatively stable at pH 2.0 and 4.0, and the corresponding emulsions had uniform droplets that showed outstanding storage stability after 21 days. However, the SPIF/SSPS complex was dissociated gradually with the elevation of pH, especially under alkaline condition, that caused the flocculation and coalescence in emulsion. This phenomenon not only relate to electrostatic repulsion, but also relate to the disintegration of SPIF. Furthermore, the encapsulated curcumin is released rapidly from emulsion when the pH increased above 6.0. This research may provide an outstanding pH-response strategy that have the potential for pH-triggered release.

Combined transcriptome and metabolome analyses reveal the mechanisms of ultrasonication improvement of brown rice germination.

This study investigated the effects of ultrasonication treatment on the germination rate of brown rice. Brown rice grains were subjected to ultrasound (40 kHz/30 min) and then incubated for 36 h at 37 °C to germinate the seeds. Ultrasonic treatment increased the germination rate of brown rice by up to ∼28 % at 30 h. Transcriptomic and metabolomic analyses were performed to explore the mechanisms underlying the effect of ultrasonic treatment on the brown rice germination rate. Comparing the treated and control check samples, 867 differentially expressed genes (DEGs) were identified, including 638 upregulated and 229 downregulated), as well as 498 differentially accumulated metabolites (DAMs), including 422 up accumulated and 76 down accumulated. Multi-omics analysis revealed that the germination rate of brown rice was promoted by increased concentrations of low-molecular metabolites (carbohydrates and carbohydrate conjugates, fatty acids, amino acids, peptides, and analogues), and transcription factors (ARR-B, NAC, bHLH and AP2/EREBP families) as well as increased carbon metabolism. These findings provide new insights into the mechanisms of action of ultrasound in improving the brown rice germination rate and candidate DEGs and DAMs responsible for germination have been identified.

A systematic review on the safety of Psoraleae Fructus: potential risks, toxic characteristics, underlying mechanisms and detoxification methods.

Psoraleae Fructus (PF) is an important traditional herbal medicine with a long history of clinical application. It is widely used to treat various diseases, such as osteoporosis, leucoderma and diarrhea. As a traditional nontoxic herb, it has aroused worldwide concern about the potential risks due to increasing adverse reaction events. This article reviews the botany, ancient records of medical uses, adverse reactions, toxicological research advance and detoxification methods of PF. According to clinical studies, liver injury is the most predominant in PF-related adverse reactions. The underlying mechanisms include bile acid metabolism and transport disorders, oxidative stress, mitochondrial damage, inhibition of liver cell regeneration and inflammatory reactions. Furthermore, the potential toxins of PF are summarized. Traditional methods of processing and compatibility will provide reference for reducing the toxicity of PF, which requires further research. In sum, this work systematically summarizes the reserach progress on the safety of PF, which will provide comprehensive insights into the toxicity of PF and facilitate its safe use and future development.

Regain flood adaptation in rice through a 14-3-3 protein OsGF14h.

Contemporary climatic stress seriously affects rice production. Unfortunately, long-term domestication and improvement modified the phytohormones network to achieve the production needs of cultivated rice, thus leading to a decrease in adaptation. Here, we identify a 14-3-3 protein-coding gene OsGF14h in weedy rice that confers anaerobic germination and anaerobic seedling development tolerance. OsGF14h acts as a signal switch to balance ABA signaling and GA biosynthesis by interacting with the transcription factors OsHOX3 and OsVP1, thereby boosting the seeding rate from 13.5% to 60.5% for anaerobic sensitive variety under flooded direct-seeded conditions. Meanwhile, OsGF14h co-inheritance with the Rc (red pericarp gene) promotes divergence between temperate japonica cultivated rice and temperate japonica weedy rice through artificial and natural selection. Our study retrieves a superior allele that has been lost during modern japonica rice improvement and provides a fine-tuning tool to improve flood adaptation for elite rice varieties.

Emodin-induced hepatotoxicity is enhanced by 3-methylcholanthrene through activating aryl hydrocarbon receptor and inducing CYP1A1 in vitro and in vivo.

BACKGROUND & AIMS: Polygonum multiflorum Thunb. (PMT) is the most common traditional Chinese medicine used to treat multiple diseases, and the hepatotoxicity caused by PMT has made great concern around world. Recent results showed that emodin is the potential toxic components of PMT, but the molecular mechanisms of emodin on liver toxicity remain to be elucidated. METHODS: Evaluation of parent- and metabolite-induced cytotoxicity in emodin were compared in L02 cells and mouse model from the perspective of drug metabolizing enzymes. The effect and mechanism of emodin-induced hepatotoxicity were analyzed using electrophoretic mobility shift, promoter reporter, and high content screening. RESULTS: We showed that emodin treatment (360 mg/kg in mice, 50 µM in L02 cells) induced hepatotoxicity and enhanced reactive oxidative stress (ROS) level. Importantly, emodin-induced ROS accumulation and hepatotoxicity were attenuated in the condition of CH223191, a selective inhibitor of aryl hydrocarbon receptor (AhR), and aggravated by 3-methylcholanthrene, a selective activator of AhR. Interestingly, we performed the study on ROS mediated ER stress and mitochondrial dysfunction in emodin-induced hepatotoxicity, the results showed that emodin can decrease MMP and trigger ER stress with Ca2+ overloading and the expression of ATF4 increasing, further resulted with increased apoptosis in L02 cells and mice mortality rate, while the changes were alleviated by CH223191. Furthermore, the 5-hydroxyemodin, a metabolite by emodin through CYP1A2 enzyme, showed more severe hepatotoxicity compared to emodin. CONCLUSIONS: Our results validated that the metabolism of emodin to 5-hydroxyemodin by CYP1A played an important role in the hepatocellular toxicity of emodin and provided evidence that CYP1A1 and AhR could be used to predict and validate patient-specific liver injury of PMT or other herbs containing emodin.

[Protective effect of ophiopogonin D against isoproterenol-induced cardiomyocyte injury and targets].

This study aims to unveil the effect of ophiopogonin D(OPD) on isoproterenol(ISO)-induced apoptosis of rat cardiomyocytes and the possible targets, which is expected to provide clues for further research on the myocardial protection of ophiopogonins. Cell count kit-8(CCK-8) assay was used to detect viability of cells treated with OPD and ISO, Western blot to examine the effect of OPD and ISO on the expression of endoplasmic reticulum stress-related Bip, Bax, Perk, ATF4, caspase-12, and CHOP, flow cytometry to determine cell apoptosis rate, and Hoechst 33258 and Tunel staining to observe cell apoptosis and morphological changes. In addition, the probe for calcium ion-specific detection was employed to investigate calcium ion release from the endoplasmic reticulum, and OPD-bond epoxy-activated agarose solid-phase microspheres were prepared and used as affinity matrix to capture OPD-binding target proteins in H9 c2 cell lysate. For the target proteins of OPD identified by high-resolution mass spectrometry, the related signal pathways were enriched and the potential targets of OPD against cardiomyocyte injury were discussed. The experimental result showed that 10 µmol·L~(-1) ISO can significantly induce the expression of endoplasmic reticulum stress-related proteins and promote cell apoptosis. Different concentration of OPD can prevent the damage of myocardial cells caused by ISO. According to mass spectrometry results, 19 proteins, including Fam129 a and Pdia6, were involved in multiple signaling pathways such as the unfolded protein reaction bound by the ERN1 sensor, tricarboxylic acid cycle, and Nrf2 signal transduction pathway. The above results indicate that OPD protects cardiomyocytes by regulating multiple signaling pathways of target proteins and affecting cell cycle progression.

Comparative multi-omics analysis of hypoxic germination tolerance in weedy rice embryos and coleoptiles.

Hypoxic germination tolerance is an important trait for seedling establishment of direct-seeded rice. Our comparative metabolomics analysis revealed that weedy rice accumulated more sugar and amino acids than cultivated rice accumulated in the embryo and coleoptile tissues under hypoxic stress. At the transcriptional level, oxidative phosphorylation activity in weedy rice was higher than in cultivated rice that likely led to more efficient energy metabolism during hypoxic stress. Based on our comparative proteomics analysis, enriched proteins related to cell wall implied that the advantages in energy metabolism of weedy rice were ultimately reflected in the formation of tissue structures. In this study, we found that most of key hypoxic germination tolerance (HGT) genes shared the same genetic backgrounds with Oryza japonica, however, several of them genetically similar to other Oryza plant also play important roles. Our findings suggest weedy rice can serve as genetic resources for the improvement of direct-seeding rice.

Long noncoding RNA LINC00184 facilitates the proliferation, metastasis, and adenine metabolism of cholangiocarcinoma via modulating hsa-miR-23b-3p/ANXA2 axis.

The purpose of this article was to probe the mechanism underlying long noncoding RNA (lncRNA)-LINC00184 in cholangiocarcinoma development and to investigate the effects of LINC00184 on cholangiocarcinoma. We used bioinformatics to analyze the expression of LINC00184, microRNA (miR)-23b-3p and ANXA2 in cholangiocarcinoma tissues. The levels of LINC00184, miR-23b-3p, and ANXA2 were detected by qRT-PCR. Cell proliferation was tested by CCK8. Transwell assay was used to detect cell invasion and migration. The target connection between LINC00184, miR-23b-3p, or ANXA2 was probed by luciferase reporter assay. RNA pull-down method was employed to test the relationship among LINC00184/miR-23b-3p/ANXA2 in cholangiocarcinoma cells. The Pearson correlation coefficient analyzed was applied to analyze the correlation among LINC00184, miR-23b-3p, and ANXA2. LC-MS/M analysis was used to explore whether the changes of adenine metabolism was affected by LINC00184 in cholangiocarcinoma cells. We discovered that LINC00184 expression was heightened in cholangiocarcinoma patients and cells. Knockdown of LINC00184 repressed cell proliferation, invasion, migration and adenine metabolism in cholangiocarcinoma cells. miR-23b-3p was regarded as a target of LINC00184 and its depletion perversed the inhibitive influence of LINC00184 silencing on cholangiocarcinoma cells. ANXA2 was a target of miR-23b-3p and was negatively modulated by miR-23b-3p. Moreover, ANXA2 was positively modulated by LINC00184 via sponging miR-23b-3p. In short, silencing of LINC00184 suppressed cell proliferation, invasion and migration through over-expression of miR-23b-3p and reducing of ANXA2 in cholangiocarcinoma cells. These findings contribute to understanding the influences of LINC00184, miR-23b-3p, and ANXA2 on cholangiocarcinoma and provide basis for cholangiocarcinoma treatment.

Up-regulation of phenylpropanoid biosynthesis system in peach species by peach aphids produces anthocyanins that protect the aphids against UVB and UVC radiation.

Conspicuous color is a common trait of foliar galls, but their relationship with gall-inducing insects is unknown. Red and green galls were taken from sunny or shady parts of peach species Prunus persica (L.) Batsch. f. rubro-plena Schneid with peach aphid Tuberocephalus momonis (Matsumura) infestation. We found that the loss of photosynthetic pigments was associated with the conspicuous coloration of green gall tissues. The concentrations of anthocyanins significantly increased following ultraviolet (UV) irradiation of green gall tissues, suggesting that accumulation of anthocyanins in red galls is related to ultraviolet B and C (UVB and UVC) radiation. The expression of structural genes related to the biosynthesis of chlorogenic acid and malic acid benzoate was increased in all gall tissues and negatively correlated with the expression profiles of certain genes associated with photosynthetic biosynthesis, indicating that the increased transcript levels of the phenylpropanoid pathway might cause loss of photosynthetic efficiency in the gall tissues. Transcriptome and quantitative reverse transcription PCR analyses revealed that MYB transcription factors that up-regulate the biosynthesis of anthocyanins in red gall tissues might be activated by both UVB and UVC exposure. Comet assays suggest that green and red gall tissues have similar DNA damage following UV irradiation. No obvious effect of the up-regulated compounds on the growth of the peach aphid was observed. Interestingly, peach aphids under leaves painted with anthocyanins had lower mortality following UV irradiation than those in controls. These results suggest that the anthocyanins in red gall tissues have a defensive function for the peach aphid, protecting it against UV radiation.

CD52 Is a Prognostic Biomarker and Associated With Tumor Microenvironment in Breast Cancer.

Tumor microenvironment (TME) plays an essential role in the development and metastasis of breast cancer (BC). More studies are needed on the differences and functions of immune components and matrix components. In this study, we calculated the proportion of tumor-infiltrating immune cells (TICs) and the proportion of immune and matrix components of BC patients from The Cancer Genome Atlas (TCGA). We performed Cox regression analysis and constructed protein-protein interaction (PPI) network based on the differentially expressed genes (DEGs) and obtained the most crucial gene CD52. CD52 significantly upregulated and affected the prognosis of BC patients. Gene set enrichment analysis (GSEA) suggested that the genes in the CD52 high-expression group were mainly enriched in immune-related pathways, while those in the CD52 low-expression group were mainly enriched in metabolic pathways. TICs analyses showed that there should be a positive correlation between CD52 expression and CD8+ T cells, activated memory CD4+ T cells, macrophage M1, and Gamma Delta T cells. It indicated that CD52 might be an essential factor in maintaining the immune-dominant position of TME. These results suggest that CD52 might be a potential biomarker for prognosis and provide a new therapeutic target for BC patients.

The Electric Field Responses of Inorganic Ionogels and Poly(ionic liquid)s.

Ionic liquids (ILs) are a class of pure ions with melting points lower than 100 °C. They are getting more and more attention because of their high thermal stability, high ionic conductivity and dielectric properties. The unique dielectric properties aroused by the ion motion of ILs makes ILs-contained inorganics or organics responsive to electric field and have great application potential in smart electrorheological (ER) fluids which can be used as the electro-mechanical interface in engineering devices. In this review, we summarized the recent work of various kinds of ILs-contained inorganic ionogels and poly(ionic liquid)s (PILs) as ER materials including their synthesis methods, ER responses and dielectric analysis. The aim of this work is to highlight the advantage of ILs in the synthesis of dielectric materials and their effects in improving ER responses of the materials in a wide temperature range. It is expected to provide valuable suggestions for the development of ILs-contained inorganics and PILs as electric field responsive materials.

A four-gene signature in the tumor microenvironment that significantly associates with the prognosis of patients with breast cancer.

Breast cancer (BRCA) is a highly heterogeneous disease due to the complicated microenvironment in the tumor, making the treatment benefits varied. Therefore, this study aims to identify a gene signature in the tumor microenvironment (TME) associated with the prognosis of BRCA patients. We downloaded the immune, stromal, and proliferation (ISP)-associated genes from the literature on BRCA. mRNA expression and clinical information obtained from The Cancer Genome Atlas (TCGA) were performed to identify the initial biomarker. Furthermore, we validated the robustness of the gene signature in the independent validation data set GSE20685. A four-gene signature in TME, including CD74, MMP9, RPA3, and SHCBP1, was constructed to predict the overall survival of BRCA. The survival time of the high-risk group was significantly worse than that of the low-risk group. Univariate and multivariate Cox regression analysis showed that our four-gene ISP signature was an independent prognostic factor in TCGA and GSE20685 data sets. The AUC suggested that our four-gene ISP signature was comparable to TNM classification at predicting the overall survival of BRCA patients. Interestingly, BRCA patients with high-risk scores were more likely to be associated with stromal and proliferation of cancer. In contrast, those with high-risk scores were more likely to be associated with tumor immunity-related pathway. We found an innovative biomarker in TME to predict the prognosis of BRCA. This signal might reflect the imbalance of TME and provide potential biomarkers for the individualized and precise treatment of BRCA.

Weedy Rice as a Novel Gene Resource: A Genome-Wide Association Study of Anthocyanin Biosynthesis and an Evaluation of Nutritional Quality.

The pericarp color of rice grains is an important agronomic trait affected by domestication, and the color pigment, anthocyanin, is one of the key determinants of rice nutritional quality. Weedy rice, also called red rice because its pericarp is often red, may be a novel gene resource for the development of new rice. However, the genetic basis and nutritional quality of anthocyanin are poorly known. In this study, we used a genome-wide association study (GWAS) to find novel and specific QTLs of red pericarp in weedy rice. The known key gene site of red pericarp Rc was detected as the common genetic basis of both weedy and cultivated rice, and another 13 associated signals of pericarp color that were identified may contribute specifically to weedy rice pericarp color. We then nominated three pericarp color genes that may contribute to weedy rice divergence from cultivated rice based on selection sweep analysis. After clarifying the distribution and growth dynamics of pigment in weedy rice caryopsis, we compared its nutritional quality with cultivated rice. We found that sampled weedy rice pericarps had much greater quantities of anthocyanin, beneficial trace elements, free amino acids, and unsaturated fatty acids than the cultivated rice. In conclusion, the gene resources and novel genetic systems of rice anthocyanin biosynthesis explored in this study are of great value for the development of nutritious, high anthocyanin content rice.

Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game.

Crop weediness, especially that of weedy rice (Oryza sativa f. spontanea), remains mysterious. Weedy rice possesses robust ecological adaptability; however, how this strain originated and gradually formed proprietary genetic features remains unclear. Here, we demonstrate that weedy rice at Asian high latitudes (WRAH) is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice. We also identified novel quantitative trait loci underlying weedy-specific traits, and revealed that a genome block on the end of chromosome 1 is associated with rice weediness. To identify the genomic modifications underlying weedy rice evolution, we generated the first de novo assembly of a high-quality weedy rice genome (WR04-6), and conducted a comparative genomics study between WR04-6 with other rice reference genomes. Multiple lines of evidence, including the results of demographic scenario comparisons, suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication. A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.