The abundant fraction of soil microbiomes regulates the rhizosphere function in crop wild progenitors.

The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome-oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence-a comparison between rhizosphere and bulk soil samples-on bacterial, fungal, protists and invertebrate communities and on soil multifunctionality across nine CWPs at their sites of origin. Overall, rhizosphere influence was higher for abundant taxa across the four microbial groups and had a positive influence on rhizosphere soil organic C and nutrient contents compared to bulk soils. The rhizosphere influence on abundant soil microbiomes was more important for soil multifunctionality than rare taxa and environmental conditions. Our results are a starting point towards the use of CWPs for rhizosphere engineering in modern crops.

A wild rice CSSL population facilitated identification of salt tolerance genes and rice germplasm innovation.

Salt stress is one of the major factors that limits rice production. Therefore, identification of salt-tolerant alleles from wild rice is important for rice breeding. In this study, we constructed a set of chromosome segment substitution lines (CSSLs) using wild rice as the donor parent and cultivated rice Nipponbare (Nip) as the recurrent parent. Salt tolerance germinability (STG) was evaluated, and its association with genotypes was determined using this CSSL population. We identified 17 QTLs related to STG. By integrating the transcriptome and genome data, four candidate genes were identified, including the previously reported AGO2 and WRKY53. Compared with Nip, wild rice AGO2 has a structure variation in its promoter region and the expression levels were upregulated under salt treatments; wild rice WRKY53 also has natural variation in its promoter region, and the expression levels were downregulated under salt treatments. Wild rice AGO2 and WRKY53 alleles have combined effects for improving salt tolerance at the germination stage. One CSSL line, CSSL118 that harbors these two alleles was selected. Compared with the background parent Nip, CSSL118 showed comprehensive salt tolerance and higher yield, with improved transcript levels of reactive oxygen species scavenging genes. Our results provided promising genes and germplasm resources for future rice salt tolerance breeding.

Retinal ganglion cell type-specific expression of synuclein family members revealed by scRNA-sequencing.

Synuclein family members (Snca, Sncb, and Scng) are expressed in the retina, but their precise locations and roles are poorly understood. We performed an extensive analysis of the single-cell transcriptome in healthy and injured retinas to investigate their expression patterns and roles. We observed the expression of all synuclein family members in retinal ganglion cells (RGCs), which remained consistent across species (human, mouse, and chicken). We unveiled differential expression of Snca across distinct clusters (highly expressed in most), while Sncb and Sncg displayed uniform expression across all clusters. Further, we observed a decreased expression in RGCs following traumatic axonal injury. However, the proportion of α-Syn-positive RGCs in all RGCs and α-Syn-positive intrinsically photosensitive retinal ganglion cells (ipRGCs) in all ipRGCs remained unaltered. Lastly, we identified changes in communication patterns preceding cell death, with particular significance in the pleiotrophin-nucleolin (Ptn-Ncl) and neural cell adhesion molecule signaling pathways, where communication differences were pronounced between cells with varying expression levels of Snca. Our study employs an innovative approach using scRNA-seq to characterize synuclein expression in health retinal cells, specifically focusing on RGC subtypes, advances our knowledge of retinal physiology and pathology.

Clinical characteristics and prognosis of laryngeal tuberculosis combined with respiratory tuberculosis.

PURPOSE: To investigate the clinical characteristics, diagnosis and prognosis of patients with laryngeal tuberculosis (LTB) combined with respiratory tuberculosis. MATERIALS AND METHODS: A retrospective analysis was conducted on 134 patients who underwent endoscopy and were eventually diagnosed with LTB. The patients' demographic characteristics, clinical manifestations, endoscopic features, auxiliary examination, imaging examination and prognostic characteristics were analyzed. RESULTS: LTB patients had a median age of 45.5 years (range from 12 to 87 years) and a median course of 3.0 months (range from 0.1 to 72 months). The patients' symptoms mainly presented as hoarseness (97.0 %), abnormal sensation of pharyngeal (49.3 %), cough and sputum (41.0 %), pharyngalgia (39.6 %), dysphagia (10.4 %) and dyspnea (8.2 %). The positive rate of tuberculous symptoms was 25.4 %. Endoscopic features showed that the lesions mainly involved the glottis (87.3 %), presenting as unilateral lesions (66.7 %), near-full-length involvement (88.0 %), with mucosal waves significantly reduced (86.3 %), followed by supraglottis (43.3 %), subglottis (24.6 %) and the pharynx (15.7 %). The lesions may present as granulomatous proliferation (66.4 %), ulceration (65.7 %) or swelling and exudation (51.5 %). A total of 75 patients (56.0 %) were finally diagnosed with combined pulmonary tuberculosis (PTB), with a positive chest X-ray rate of 25.6 % and a positive chest CT rate of 71.2 %. A total of 42 patients who received anti-tuberculosis treatment were followed up, and 73.8 % of patients had significant improvement in symptoms. The morphology of the pharyngeal and laryngeal mucosa returned to basically normal (59.4 %) or scar-like (34.4 %). CONCLUSIONS: LTB is usually found in middle-aged men, and patients' symptoms are mainly hoarseness, abnormal sensation of pharyngeal, pharyngalgia, cough and sputum, and can be combined with tuberculous symptoms. These lesions mainly involve multiple subregions, mainly in the glottis, and can be combined with pharyngeal involvement. There were various types of lesions. Half of the patients were complicated with PTB, and chest CT was superior to X-ray in the detection of pulmonary lesions. After regular anti-tuberculosis treatment, the symptoms and morphology of the pharyngeal and laryngeal mucosa of most patients were significantly improved.

Lost genome segments associate with trait diversity during rice domestication.

BACKGROUND: DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication. RESULTS: In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length. CONCLUSIONS: We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.

Integrated Metabolomics and Transcriptomics Analysis of Flavonoid Biosynthesis Pathway in Polygonatum cyrtonema Hua.

Flavonoids, a class of phenolic compounds, are one of the main functional components and have a wide range of molecular structures and biological activities in Polygonatum. A few of them, including homoisoflavonoids, chalcones, isoflavones, and flavones, were identified in Polygonatum and displayed a wide range of powerful biological activities, such as anti-cancer, anti-viral, and blood sugar regulation. However, few studies have systematically been published on the flavonoid biosynthesis pathway in Polygonatum cyrtonema Hua. Therefore, in the present study, a combined transcriptome and metabolome analysis was performed on the leaf, stem, rhizome, and root tissues of P. cyrtonema to uncover the synthesis pathway of flavonoids and to identify key regulatory genes. Flavonoid-targeted metabolomics detected a total of 65 active substances from four different tissues, among which 49 substances were first study to identify in Polygonatum, and 38 substances were flavonoids. A total of 19 differentially accumulated metabolites (DAMs) (five flavonols, three flavones, two dihydrochalcones, two flavanones, one flavanol, five phenylpropanoids, and one coumarin) were finally screened by KEGG enrichment analysis. Transcriptome analysis indicated that a total of 222 unigenes encoding 28 enzymes were annotated into three flavonoid biosynthesis pathways, which were "phenylpropanoid biosynthesis", "flavonoid biosynthesis", and "flavone and flavonol biosynthesis". The combined analysis of the metabolome and transcriptome revealed that 37 differentially expressed genes (DEGs) encoding 11 enzymes (C4H, PAL, 4CL, CHS, CHI, F3H, DFR, LAR, ANR, FNS, FLS) and 19 DAMs were more likely to be regulated in the flavonoid biosynthesis pathway. The expression of 11 DEGs was validated by qRT-PCR, resulting in good agreement with the RNA-Seq. Our studies provide a theoretical basis for further elucidating the flavonoid biosynthesis pathway in Polygonatum.

Image-based vegetation analysis of desertified area by using a combination of ImageJ and Photoshop software.

Fractional vegetation cover (FVC) is a crucial indicator to estimate degradation and desertification for grasslands. However, traditional small-scale FVC analysis methods, such as visual estimation and point-sampling, are cumbersome and imprecise. Innovative methods like image-based FVC analysis methods, while accurate, face challenges such as complex analytical procedures and the necessary training for operations. Therefore, in this study, a combined application of ImageJ and Photoshop was employed to achieve a more effective analysis of FVC values in desertification areas. Our results showed that the FVC results obtained by combination of Photoshop and ImageJ were dependable and precise (R2 > 0.98), demonstrating equivalency to results obtained through either visual estimation or Photoshop-based methods. Furthermore, even in the face of background interference and varied shooting angles, the combination of ImageJ and Photoshop software was still able to maintain a low error rate when analyzing FVC values (average error rate = - 2.6%). In conclusion, the imaged-based combined FVC analysis method employed in our research was an effective, precise, and efficient technique for analyzing small-scale FVC, promising substantial improvement over conventional methods.

Capsule-epithelium-fibre unit ultrastructure in the human lens.

This study aimed to investigate the capsule-epithelium-fibre unit ultrastructure of the human lens, particularly the interfaces of the epithelium with the capsule and the epithelium with the fibre cell. A total of 12 lenses from donor humans who died of trauma without systemic and ocular diseases were investigated by transmission electron microscopy (TEM), combined with immunofluorescence staining for localising certain specific proteins. Some of the results were further studied in the anterior lens capsules of cataract patients. Our results revealed capsule protrusion into the epithelium in some areas and potential processing of capsule components. The young elongating fibre cells directly adjacent to the epithelium with a high stain density strongly expressed CD24. Numerous extracellular vesicles could be seen in the space between human lens epithelial cells (HLECs) and between HLECs and the capsule. Mitophagy and autophagy were also observed in the HLECs. Our research may be beneficial in better understanding the function of the human lens.

Autophagy-prominent cell clusters among human lens epithelial cells: integrated single-cell RNA-sequencing analysis.

BACKGROUND: Autophagy is an important process that maintains the quality of intracellular proteins and organelles. There is extensive evidence that autophagy has an important role in the lens. Human lens epithelial cells (HLECs) play a key role in the internal homeostasis of the lens. HLEC subtypes have been identified, but autophagy-prominent cell clusters among HLECs have not been characterized. PURPOSE: To explore the existence of autophagy-prominent cell clusters in HLECs. METHODS: Three donated lenses (HLECs from two whole lenses and HLECs from one lens without the anterior central 6-mm zone) were used for single-cell RNA sequencing (scRNA-seq). AUCell and AddModuleScore analysis were used to identify potential autophagy-prominent cell clusters. Transmission electron microscopy (TEM) was used to confirm the results. RESULTS: High-quality transcripts from 18,120 cells were acquired by scRNA-seq of the two intact lenses. Unsupervised clustering classified the cells into four clusters. AUCell and AddModuleScore analysis revealed cluster 1 is autophagy-prominent. scRNA-seq analysis of HLECs from the lens capsule lacking the central zone confirmed the cluster 1 HLECs was located in the central capsule zone. The TEM result showed that greater autophagy activity was observed in the HLECs in central capsule zone, which further supported the above conclusions based on scRNA-seq analysis that autophagy was prominent in the central zone where the cluster 1 HLECs located. CONCLUSIONS: We identified an autophagy-prominent cell cluster among HLECs and revealed that it was localized in the central zone of the lens capsule. Our findings will aid investigations of autophagy in HLECs and provide insights to guide related research.

Terbuthylazine exposure induces innate immune response and inflammation through activating cGAS-STING/NF-κB pathway in myocardium of broiler chicken (Gallus gallus).

Terbuthylazine (TBA), a triazine herbicide, is extensively employed in agriculture for its wide range of effectiveness. However, prolonged utilization of TBA can pose a potential hazard to animals and human health. Here, a total of 180 broiler chickens (Gallus gallus) were stochastically assigned to three groups (control group, 0.4 mg/kg TBA group, and 4 mg/kg TBA group) for investigating the impact of TBA on cardiotoxicity. The results revealed that TBA exposure resulted in pathological alterations in the myocardium. Moreover, TBA exposure activated cGAS-STING pathway and markedly elevated the mRNA and protein expression levels of innate immune response (cGAS, STING, TBK1, and IRF3) in myocardium. Additionally, NF-κB signal was also activated under TBA exposure, which was characterized by the increasing mRNA expression levels of NF-κB, IKKα and the protein expression levels of p-NF-κB/NF-κB, IKKα, p-IκBα/IκBα in the TBA treatment groups. Meanwhile, the expression of pro-inflammatory cytokines (TNF-α and IL-1ß) were also significantly increased. In summary, our findings suggested that cGAS-STING/NF-κB pathway functionated in the innate immune response and inflammation in myocardium brought on by TBA exposure, which provided new insights into the TBA toxicology.

Detection and Recognition Algorithm of Arbitrary-Oriented Oil Replenishment Target in Remote Sensing Image.

In view of the fact that the aerial images of UAVs are usually taken from a top-down perspective, there are large changes in spatial resolution and small targets to be detected, and the detection method of natural scenes is not effective in detecting under the arbitrary arrangement of remote sensing image direction, which is difficult to apply to the detection demand scenario of road technology status assessment, this paper proposes a lightweight network architecture algorithm based on MobileNetv3-YOLOv5s (MR-YOLO). First, the MobileNetv3 structure is introduced to replace part of the backbone network of YOLOv5s for feature extraction so as to reduce the network model size and computation and improve the detection speed of the target; meanwhile, the CSPNet cross-stage local network is introduced to ensure the accuracy while reducing the computation. The focal loss function is improved to improve the localization accuracy while increasing the speed of the bounding box regression. Finally, by improving the YOLOv5 target detection network from the prior frame design and the bounding box regression formula, the rotation angle method is added to make it suitable for the detection demand scenario of road technology status assessment. After a large number of algorithm comparisons and data ablation experiments, the feasibility of the algorithm was verified on the Xinjiang Altay highway dataset, and the accuracy of the MR-YOLO algorithm was as high as 91.1%, the average accuracy was as high as 92.4%, and the detection speed reached 96.8 FPS. Compared with YOLOv5s, the p-value and mAP values of the proposed algorithm were effectively improved. It can be seen that the proposed algorithm improves the detection accuracy and detection speed while greatly reducing the number of model parameters and computation.

Structure characterization and bioactivity of neutral polysaccharides from different sources of Polygonatum Mill.

Polygonati rhizoma (PR), a traditional medical and edible product, is rich in polysaccharides and exhibits physiological activity, including antioxidant, hypoglycemic and hypolipidemic properties. Neutral polysaccharides have been reported to be one of the main active ingredients of Polygonatum, with many of these fractions being responsible for the biological activity. This behavior was shown to be closely connected to the chemical structure, monosaccharide composition, and glycosidic bond type. There are few reports on the chemical constituents of the neutral polysaccharides from different sources of PR. In this study, neutral polysaccharides of PR from four different regions of China (Chun'an (Zhejiang), Xixia (Henan), Danfeng (Shanxi), and Pan'an (Zhejiang)), named CAZJ, XXHN, DFSX, and PAZJ, respectively, were isolated by anion-exchange and gel-permeation chromatography. Structures of the four polysaccharides were investigated. The results showed that all of them were mainly glucose and mannose, while the monosaccharide composition and content of polysaccharides from different sources varied. The molecular weights of CAZJ, XXHN, DFSX, and PAZJ were 14.119, 22.352, 18.127, and 15.699 kDa, respectively. Infrared spectra illustrated the existence of α-glycosidic bond and ß-glycosidic bond in the polysaccharides. CAZJ, XXHN, and DFSX possessed a pyranose ring structure, whereas PAZJ had a furanose ring structure. Congo red test indicated that XXHN, DFSX, and PAZJ had a triple-helix structure. X-ray diffraction showed that the polysaccharides consisted of crystalline and amorphous regions. All four polysaccharides exhibited different degrees of antioxidant and hypoglycemic activities with a dose-dependent manner in the 1.0-10.0 mg/mL concentration range. Correlation analysis revealed that the bioactivities of polysaccharides was significantly related to monosaccharide composition, uronic acid, and protein content. The results suggested that neutral polysaccharides could be used as potential natural antioxidants and hypoglycemic agents for functional and nutraceutical applications.

Exposure to zinc induces lysosomal-mitochondrial axis-mediated apoptosis in PK-15 cells.

Zinc (Zn), a kind of metallic element, can cause poisonous effects on host physiology when its excess exposure. Lysosomes and mitochondria are the toxic targets of heavy metals, and the lysosomal-mitochondrial axis is also verified to take part in apoptosis, but the related underlying mechanisms in Zn-induced cytotoxicity remain undefined. Here, we identified that excess Zn could cause cell damage in PK-15 cells accompanied by the lysosomal and mitochondrial dysfunction, with the evidence by the elevated levels of cathepsin B/D (CTSB/CTSD) in cytoplasm and decrease of Lyso-Tracker Red signal, red fluorescence intensity of AO staining, mitochondrial complex enzyme activities and ATP production. Additionally, the number of Annexin V+/PI--stained cells, apoptosis-related genes (Bax, Bid, Bak1, Caspase-9, and Caspase-3) and proteins levels of Bax, Bak1, Caspase-9, cleaved Caspase-3 and cytoplasmic Cyt C were signally elevated under Zn exposure, while the protein levels of Bcl2 and mitochondrial Cyt C were observably decreased. Importantly, Pepstatin A (the activity inhibitor of CTSD) and RNA interference of CTSD (si-CTSD) was used to reduce the release of lysosomal CTSD to the cytoplasm, which could signally alleviated Zn-induced mitochondrial damage and apoptosis. In summary, these results suggested that Zn could induced lysosomal and mitochondrial dysfunction in PK-15 cells, and the CTSD played an important role in Zn-induced lysosomal-mitochondrial axis-mediated apoptosis. Our results provided a new insight in Zn-induced toxicology, which for protecting the ecological environment and public health.

A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica.

KEY MESSAGE: we identified a functional chromogen gene C from wild rice, providing a new insight of anthocyanin biosynthesis pathway in indica and japonica. Accumulation of anthocyanin is a desirable trait to be selected in rice domestication, but the molecular mechanism of anthocyanin biosynthesis in rice remains largely unknown. In this study, a novel allele of chromogen gene C, OrC1, from Oryza rufipongon was cloned and identified as a determinant regulator of anthocyanin biosynthesis. Although OrC1 functions in purple apiculus, leaf sheath and stigma in indica background, it only promotes purple apiculus in japonica. Transcriptome analysis revealed that OrC1 regulates flavonoid biosynthesis pathway and activates a few bHLH and WD40 genes of ternary MYB-bHLH-WD40 complex in indica. Differentially expressed genes and metabolites were found in the indica and japonica backgrounds, indicating that OrC1 activated the anthocyanin biosynthetic genes OsCHI, OsF3H and OsANS and produced six metabolites independently. Artificial selection and domestication of C1 gene in rice occurred on the coding region in the two subspecies independently. Our results reveal the regulatory system and domestication of C1, provide new insights into MYB transcript factor involved in anthocyanin biosynthesis, and show the potential of engineering anthocyanin biosynthesis in rice.

Pharmacokinetics and pharmacodynamics of enrofloxacin treatment of Escherichia coli in a murine thigh infection modeling.

BACKGROUND: Enrofloxacin is an antibacterial drug with broad-spectrum activity that is widely indicated for veterinary use. We aim to develop the clinical applications of Enrofloxacin against colibacillosis by using the neutropenic mice thigh infection model. RESULTS: The minimum inhibitory concentration (MIC) distribution of 67 isolated E. coli strains to ENR was calculated using CLSI guidelines. Whereas, the MIC50 value calculation was considered as the population PD parameter for ENR against E. coli strains. The MIC values of 15 E. coli strains were found to be nearest to the MIC50 i.e., 0.25 µg/mL. Of all the tested strains, the PK-PD and E. coli disease model was established via selected E. coli strain i.e., Heilong 15. We analyzed the PK characteristics of ENR and its metabolite ciprofloxacin (CIP) following a single subcutaneous (s.c.) injection of ENR (1.25, 2.5, 5, 10 mg/kg). The concentration-time profiling of ENR within the plasma specimens was determined by considering the non-compartmental analysis (NCA). The basic PK parameters of ENR for the peak drug concentration (Cmax) and the area under the concentration-time curve (AUC) values were found to be in the range of 0.27-1.97 µg/mL and 0.62-3.14 µg.h/mL, respectively. Multiple s.c. injection over 24 h (1.25, 2.5, 5, 10 mg/kg at various time points i.e., 6, 8, 12, and 24 h respectively) were administered to assess the targeted PD values. The Akaike Information Criterion (AIC) was used to choose PD models, and the model with the lowest AIC was chosen. The inhibitory Emax model was employed to calculate the related PK-PD parameters. The results of our study indicated that there was a strong correlation between the AUC/MIC and various antibacterial activities (R2 = 0.9928). The target values of dividing AUC/MIC by 24 h for bacteriostatic action were 1-log10 reduction, 2-log10 reduction, and 3-log10 reduction 0.325, 0.4375, 0.63, and 0.95 accordingly. CONCLUSION: The identified pharmacodynamics targets for various antibacterial effects will be crucial in enhancing ENR clinical applications and serving as a key step in reducing bacterial resistance.

Bridge mechanical thrombectomy may be a better choice for acute large vessel occlusions.

Direct mechanical thrombectomy (DMT) was confirmed non-inferior to bridge mechanical thrombectomy (BMT, MT preceded by intravenous alteplase within 4.5 h after symptom onset) for acute ischemic stroke with large vessel occlusions (AIS-LVO) in mothership patients. However, the noninferiority of DMT in the general population (including drip and ship mode) is controversial, and the impact of thrombolysis on retrieval attempts remains uncertain. This was a post-hoc analysis of a multi-center, prospective enrolled study. Patients were divided into the BMT group and the DMT group. Baseline characteristics and clinical outcomes were compared by using univariate analysis, multivariable analysis, and propensity score matching analysis, respectively. Of all 245 patients enrolled in this study, 79 (32.2%) patients underwent BMT. In the multivariable analysis, the ratio of excellent prognosis (defined as modified Rankin Scale [mRS] score 0-1 at 90 days) was significantly higher in the BMT group compared with the DMT group (odds ratio, 2.731; 95% confidence interval, 1.238-6.023; P = 0.013). The ratio of good prognosis (mRS score 0-2 at 90 days), successful recanalization rate [modified Thrombolysis In Cerebral Ischemia (mTICI) score 2b-3] and mortality rate were similar between the two groups. The excellent prognosis rate was significantly higher in the BMT group after propensity score matching (P = 0.023). BMT was associated with a higher ratio of excellent prognosis (mRS 0-1) and a similar successful recanalization rate without increasing peri-operation complications compared with DMT in AIS-LVO patients. It is prudent to continue BMT until further data is available.

Identification and genetic analysis of qCL1.2, a novel allele of the "green revolution" gene SD1 from wild rice (Oryza rufipogon) that enhances plant height.

BACKGROUND: The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The "green revolution" gene semi-dwarf 1 (SD1) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene. RESULTS: We identified a PH-related quantitative trait locus, qCL1.2,from wild riceusing a set of chromosome segment substitution lines. qCL1.2encodesa novel allele of SD1 gene. The wild allele of SD1 is a dominant locus that can significantly promote rice internode length by regulating the expression levels of genes involved in gibberellin biosynthesis and signal transduction. Nucleotide diversity and haplotype network analyses of the SD1 gene were performed using 2822 rice landraces. Two previously reported functional nucleotide polymorphisms clearly differentiated japonica and indica rice; however, they were not associated with PH selection. Other new functional nucleotide polymorphisms in the coding, but not promoter, regions were involved in PH selection during rice domestication. Our study increasesunderstanding of the rice SD1 gene and provides additional evidence of this gene's selection during rice domestication. CONCLUSIONS: Our findings provide evidence thatSD1 gene from wild rice enhances plant height and new functional nucleotide polymorphisms of this gene were artificially selected during cultivated rice differentiation.

The C-S-A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice.

Floral organs in rice (Oryza sativa) can be purple, brown, or red in color due to the accumulation of flavonoids, but the molecular mechanism underlying specific organ pigmentation is not clear. Here, we propose a C-S-A gene model for rice hull pigmentation and characterize it through genetic, molecular, and metabolomic approaches. Furthermore, we conducted phylogenetic studies to reveal the evolution of rice color. In this gene system, C1 encodes a R2R3-MYB transcription factor and acts as a color-producing gene, and S1 encodes a bHLH protein that functions in a tissue-specific manner. C1 interacts with S1 and activates expression of A1, which encodes a dihydroflavonol reductase. As a consequence, the hull is purple where functional A1 participation leads to high accumulation of cyanidin 3-O-glucoside. Loss of function of A1 leads to a brown hull color due to accumulation of flavonoids such as hesperetin 5-O-glucoside, rutin, and delphinidin 3-O-rutinoside. This shows a different evolutionary pathway of rice color in japonica and indica, supporting independent origin of cultivars in each subspecies. Our findings provide a complete perspective on the gene regulation network of rice color formation and supply the theoretical basis for extended application of this beneficial trait.

Fine mapping and identification of a novel locus qGL12.2 control grain length in wild rice (Oryza rufipogon Griff.).

KEY MESSAGE: A wild rice QTL qGL12.2 for grain length was fine mapped to an 82-kb interval in chromosome 12 containing six candidate genes and none was reported previously. Grain length is an important trait for yield and commercial value in rice. Wild rice seeds have a very slender shape and have many desirable genes that have been lost in cultivated rice during domestication. In this study, we identified a quantitative trait locus, qGL12.2, which controls grain length in wild rice. First, a wild rice chromosome segment substitution line, CSSL41, was selected that has longer glume and grains than does the Oryza sativa indica cultivar, 9311. Next, an F2 population was constructed from a cross between CSSL41 and 9311. Using the next-generation sequencing combined with bulked-segregant analysis and F3 recombinants analysis, qGL12.2 was finally fine mapped to an 82-kb interval in chromosome 12. Six candidate genes were found, and no reported grain length genes were found in this interval. Using scanning electron microscopy, we found that CSSL41 cells are significantly longer than those of 9311, but there is no difference in cell widths. These data suggest that qGL12.2 is a novel gene that controls grain cell length in wild rice. Our study provides a new genetic resource for rice breeding and a starting point for functional characterization of the wild rice GL gene.