Artificial intelligence model system for bone age assessment of preschool children.

BACKGROUD: Our study aimed to assess the impact of inter- and intra-observer variations when utilizing an artificial intelligence (AI) system for bone age assessment (BAA) of preschool children. METHODS: A retrospective study was conducted involving a total sample of 53 female individuals and 41 male individuals aged 3-6 years in China. Radiographs were assessed by four mid-level radiology reviewers using the TW3 and RUS-CHN methods. Bone age (BA) was analyzed in two separate situations, with/without the assistance of AI. Following a 4-week wash-out period, radiographs were reevaluated in the same manner. Accuracy metrics, the correlation coefficient (ICC)and Bland-Altman plots were employed. RESULTS: The accuracy of BAA by the reviewers was significantly improved with AI. The results of RMSE and MAE decreased in both methods (p < 0.001). When comparing inter-observer agreement in both methods and intra-observer reproducibility in two interpretations, the ICC results were improved with AI. The ICC values increased in both two interpretations for both methods and exceeded 0.99 with AI. CONCLUSION: In the assessment of BA for preschool children, AI was found to be capable of reducing inter-observer variability and enhancing intra-observer reproducibility, which can be considered an important tool for clinical work by radiologists. IMPACT: The RUS-CHN method is a special bone age method devised to be suitable for Chinese children. The preschool stage is a critical phase for children, marked by a high degree of variability that renders BA prediction challenging. The accuracy of BAA by the reviewers can be significantly improved with the aid of an AI model system. This study is the first to assess the impact of inter- and intra-observer variations when utilizing an AI model system for BAA of preschool children using both the TW3 and RUS-CHN methods.

Application of the process-based teaching based on SPARK case database in the practice teaching of radiology in the musculoskeletal system for undergraduate medical students.

BACKGROUND: Process-based teaching is a new education model. SPARK case database is a free medical imaging case database. This manuscript aimed to explore the application of the process-based teaching based on SPARK case database in the practice teaching of radiology in the musculoskeletal system. METHODS: 117 third year medical students were included. They were divided into Group A, B, C and D according to the curriculum arrangement. Group A and B attended the experimental class at the same time, A was the experimental group, B was the control group. Group C and D attended experimental classes at the same time, C was the experimental group, D was the control group. The experimental group used SPARK case database, while the control group used traditional teaching model for learning. The four groups of students were respectively tested after the theoretical class, before the experimental class, after the experimental class, and one week after the experimental class to compare the results. Finally, all students used SPARK case database to study, and were tested one month after the experimental class to compare their differences. RESULTS: The scores after the theoretical class of Group A and B were (100.0 ± 25.4), (101.0 ± 23.8)(t=-0.160, P > 0.05), Group C and D were (94.7 ± 23.7), (92.1 ± 18.6)(t = 0.467, P > 0.05). The scores of Group A and B before and after the experimental class and one week after the experimental class were respectively (84.1 ± 17.4), (72.1 ± 21.3)(t = 2.363, P < 0.05), (107.6 ± 14.3), (102.1 ± 18.0)(t = 1.292, P > 0.05), (89.7 ± 24.3), (66.6 ± 23.2)(t = 3.706, P < 0.05). The scores of Group C and D were (94.0 ± 17.3), (72.8 ± 25.5)(t = 3.755, P < 0.05), (107.3 ± 20.3), (93.1 ± 20.9)(t = 2.652, P < 0.05), (100.3 ± 19.7), (77.2 ± 24.0)(t = 4.039, P < 0.05). The scores of Group A and B for one month after the experimental class were (86.6 ± 28.8), (84.5 ± 24.0)(t = 0.297, P > 0.05), and Group C and D were (95.7 ± 20.3), (91.7 ± 23.0)(t = 0.699, P > 0.05). CONCLUSIONS: The process-based teaching based on SPARK case database could improve the radiology practice ability of the musculoskeletal system of students.

High-resolution bin-based linkage mapping uncovers the genetic architecture and heterosis-related loci of plant height in indica-japonica derived populations.

Plant height (PH) is an important trait affecting the plant architecture, seed yield, and harvest index. However, the molecular mechanisms underlying PH heterosis remain unclear. In addition, useful PH-related genes must be urgently identified to facilitate ideal plant architecture breeding in rice (Oryza sativa L.). In the present study, to explore rice quantitative trait loci (QTLs) and heterosis-related loci of PH in rice, we developed a high-generation (>F15 ) population of 272 recombinant inbred lines (RIL) from a cross of two elite varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA [indica] and Z7A [japonica]). Using deep resequencing data, a high-density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM. Finally, 31 PH-related QTLs for different PH component lengths or tiller numbers across five seasons were identified. Two major environment-specific PH QTLs were stably detected in Hainan (qPH-3.1) or Hubei (qPH-5.1), which have undergone significant functional alterations in rice with changes in geographical environment. Based on comparative genomics, gene function annotation, homolog identification, and existing literature (pioneering studies), candidate genes for multiple QTLs were fine-mapped, and the candidate genes qPH-3.1 and qPH-5.1 for PH were further validated using CRISPR-Cas9 gene editing. Specifically, qPH-3.1 was characterized as a pleiotropic gene, and the qPH-3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers. Importantly, 10 PH heterosis-related QTLs were identified in the testcross populations, and a better-parent heterosis locus (qBPH-5.2) completely covered qPH-5.1. Furthermore, the cross results of fixed-genotype RILs verified the dominant effects of qPH-3.1 and qPH-5.1. Together, these findings further our understanding of the genetic mechanisms of PH and offer multiple highly reliable gene targets for breeding rice varieties with ideal architecture and high yield potential in the immediate future.

Chloroplast inner envelope protein FtsH11 is involved in the adjustment of assembly of chloroplast ATP synthase under heat stress.

The maintenance of a proton gradient across the thylakoid membrane is an integral aspect of photosynthesis that is mainly established by the splitting of water molecules in photosystem II and plastoquinol oxidation at the cytochrome complex, and it is necessary for the generation of ATP in the last step of photophosphorylation. Although environmental stresses, such as high temperatures, are known to disrupt this fundamental process, only a few studies have explored the molecular mechanisms underlying proton gradient regulation during stress. The present study identified a heat-sensitive mutant that displays aberrant photosynthesis at high temperatures. This mutation was mapped to AtFtsH11, which encodes an ATP-dependent AAA-family metalloprotease. We showed that AtFtsH11 localizes to the chloroplast inner envelope membrane and is capable of degrading the ATP synthase assembly factor BFA3 under heat stress. We posit that this function limits the amount of ATP synthase integrated into the thylakoid membrane to regulate proton efflux from the lumen to the stroma. Our data also suggest that AtFtsH11 is critical in stabilizing photosystem II and cytochrome complexes at high temperatures, and additional studies can further elucidate the specific molecular functions of this critical regulator of photosynthetic thermotolerance.

Genome-Wide Identification, Evolution, and Expression Analysis of the WD40 Subfamily in Oryza Genus.

The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only OsTTG1 was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula, Oryza nivara, and Oryza longistaminata. In this study, 383 WD40 genes in the Oryza genus were identified, and they were classified into four groups by phylogenetic analysis, with most members in group C and group D. They were found to be unevenly distributed across 12 chromosomes. A total of 39 collinear gene pairs were identified in the Oryza genus, and all were segmental duplications. WD40s had similar expansion patterns in the Oryza genus. Ka/Ks analyses indicated that they had undergone mainly purifying selection during evolution. Furthermore, WD40s in the Oryza genus have similar evolutionary patterns, so Oryza sativa ssp. indica was used as a model species for further analysis. The cis-acting elements analysis showed that many genes were related to jasmonic acid and light response. Among them, OsiWD40-26/37/42 contained elements of flavonoid synthesis, and OsiWD40-15 had MYB binding sites, indicating that they might be related to anthocyanin synthesis. The expression profile analysis at different stages revealed that most OsiWD40s were expressed in leaves, roots, and panicles. The expression of OsiWD40s was further analyzed by qRT-PCR in 9311 (indica) under various hormone treatments and abiotic stresses. OsiWD40-24 was found to be responsive to both phytohormones and abiotic stresses, suggesting that it might play an important role in plant stress resistance. And many OsiWD40s might be more involved in cold stress tolerance. These findings contribute to a better understanding of the evolution of the WD40 subfamily. The analyzed candidate genes can be used for the exploration of practical applications in rice, such as cultivar culture for colored rice, stress tolerance varieties, and morphological marker development.

The Pyramiding of Elite Allelic Genes Related to Grain Number Increases Grain Number per Panicle Using the Recombinant Lines Derived from Indica-japonica Cross in Rice.

Indica(xian)-japonica(geng) hybrid rice has many heterosis traits that can improve rice yield. However, the traditional hybrid technology will struggle to meet future needs for the development of higher-yield rice. Available genomics resources can be used to efficiently understand the gene-trait association trait for rice breeding. Based on the previously constructed high-density genetic map of 272 high-generation recombinant inbred lines (RILs) originating from the cross of Luohui 9 (indica, as female) and RPY geng (japonica, as male) and high-quality genomes of parents, here, we further explore the genetic basis for an important complex trait: possible causes of grain number per panicle (GNPP). A total of 20 genes related to grains number per panicle (GNPP) with the differences of protein amino acid between LH9 and RPY were used to analyze genotype combinations, and PCA results showed a combination of PLY1, LAX1, DTH8 and OSH1 from the RPY geng with PYL4, SP1, DST and GNP1 from Luohui 9 increases GNPP. In addition, we also found that the combination of LAX1-T2 and GNP1-T3 had the most significant increase in GNPP. Notably, Molecular Breeding Knowledgebase (MBK) showed a few aggregated rice cultivars, LAX1-T2 and GNP1-T3, which may be a result of the natural geographic isolation between the two gene haplotypes. Therefore, we speculate that the pyramiding of japonica-type LAX-T2 with indica-type GNP1-T3 via hybridization can significantly improve rice yield by increasing GNPP.

Integrated Transcriptomic and Metabolomic Analyses Uncover the Differential Mechanism in Saline-Alkaline Tolerance between Indica and Japonica Rice at the Seedling Stage.

Saline-alkaline stress is one of the major damages that severely affects rice (Oryza sativa L.) growth and grain yield; however, the mechanism of the tolerance remains largely unknown in rice. Herein, we comparatively investigated the transcriptome and metabolome of two contrasting rice subspecies genotypes, Luohui 9 (abbreviation for Chao2R under study, O. sativa ssp. indica, saline-alkaline-sensitive) and RPY geng (O. sativa ssp. japonica, saline-alkaline-tolerant), to identify the main pathways and important factors related to saline-alkaline tolerance. Transcriptome analysis showed that 68 genes involved in fatty acid, amino acid (such as phenylalanine and tryptophan), phenylpropanoid biosynthesis, energy metabolism (such as Glycolysis and TCA cycle), as well as signal transduction (such as hormone and MAPK signaling) were identified to be specifically upregulated in RPY geng under saline-alkaline conditions, implying that a series of cascade changes from these genes promotes saline-alkaline stress tolerance. The transcriptome changes observed in RPY geng were in high accordance with the specifically accumulation of metabolites, consisting mainly of 14 phenolic acids, 8 alkaloids, and 19 lipids based on the combination analysis of transcriptome and metabolome. Moreover, some genes involved in signal transduction as hub genes, such as PR5, FLS2, BRI1, and NAC, may participate in the saline-alkaline stress response of RPY geng by modulating key genes involved in fatty acid, phenylpropanoid biosynthesis, amino acid metabolism, and glycolysis metabolic pathways based on the gene co-expression network analysis. The present research results not only provide important insights for understanding the mechanism underlying of rice saline-alkaline tolerance at the transcriptome and metabolome levels but also provide key candidate target genes for further enhancing rice saline-alkaline stress tolerance.

Genome-Wide Identification and Evolution Analysis of the CYP76 Subfamily in Rice (Oryza sativa).

The CYP76 subfamily, a member of the CYP superfamily, plays crucial roles in the biosynthesis of phytohormones in plants, involving biosynthesis of secondary metabolites, hormone signaling, and response to environmental stresses. Here, we conducted a genome-wide analysis of the CYP76 subfamily in seven AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, and Oryza glumaepatula. These were identified and classified into three groups, and it was found that Group 1 contained the largest number of members. Analysis of cis-acting elements revealed a large number of elements related to jasmonic acid and light response. The gene duplication analysis revealed that the CYP76 subfamily expanded mainly in SD/WGD and tandem forms and underwent strong purifying selection during evolution. Expression pattern analysis of OsCYP76s in various developmental stages revealed that the majority of OsCYP76s exhibit relatively restricted expression patterns in leaves and roots. We further analyzed the expression of CYP76s in O. sativa, japonica, and O. sativa, indica under cold, flooding, drought, and salt abiotic stresses by qRT-PCR. We found that OsCYP76-11 showed a huge increase in relative expression after drought and salt stresses. After flooding stress, OsiCYP76-4 showed a greater increase in expression compared to other genes. CYP76 in japonica and indica showed different response patterns to the same abiotic stresses, revealing functional divergence in the gene family during evolution; these may be the key genes responsible for the differences in tolerance to indica japonica. Our results provide valuable insights into the functional diversity and evolutionary history of the CYP76 subfamily and pave the way for the development of new strategies for improving stress tolerance and agronomic traits in rice.

Epstein-Barr virus infection-associated cholangiocarcinoma: a report of one case and the review of literature.

The clinical data of a patient with Epstein-barr virus (EBV) associated with cholangiocarcinoma was reported in this paper: a case of a 36-year-old female presented with abdominal pain and systemic skin yellowing combined with skin itching. Laboratory studies showed increase in alanine aminotransferase 242 U/L, aspartate aminotransferase 404 U/L, r-glutamyltransferase 1516 U/L, total bilirubin 308.2 µmol/L and CA199 (101.0 U/ml). AFP (4.5 ng/ml) was normal. CT revealed multiple space-occupying lesions in the liver. PET-CT revealed liver malignant tumor and lymph node metastasis. Liver puncture pathology revealed infiltrative growth of significant heterocyst nests in the liver tissue, which was morphologically consistent with malignant tumors, considering poorly differentiated carcinoma. Pathology suggestion: combining liver puncture with morphology, immunohistochemistry, and EBV in situ hybridization results, it was consistent with EB virus-associated poorly differentiated carcinoma, therefore, consider EBV infection-associated poorly differentiated cholangiocarcinoma (CCA) (LELC morphology). The patient underwent liver transplantation in Hangzhou Shulan Hospital on June 8, 2021 successfully. After surgery, the patient orally took tacrolimus for anti-rejection, entecavir for antiviral therapy, gemcitabine 1.2 g + cis-platinum 30 mg for chemotherapy. After following up for more than 5 months post liver transplantation, the condition of the patient deteriorated. The patient subsequently died. Based on the case of our patient and the review of existing literature, when the patient's serum CA199 increased, AFP did not change significantly, and there was no previous history of hepatitis B. CT revealed a low-density mass in the liver, ring enhancement in the arterial phase, and heterogeneous enhancement of the tumor in the delayed phase. Ring enhancement of the liver lesion mass was observed on MRI. Consider the might possibility of hepatic CCA. When patients showed recurrent tonsillitis at an early age, EBV virus infection should be vigilant and oropharyngeal tissue should persist, diagnosis of EBV-associated liver cancer should be considered. In particular, EBV infection-related liver cancer is relatively rare, the clinician should improve the recognition of the disease to strive for early diagnosis and therapy.

Application of SPARK teaching in acute abdomen radiography teaching for undergraduate medical students.

BACKGROUND: Acute abdomen is a series of acute and severe abdominal diseases commonly encountered in clinic. It is important to strengthen the image teaching of acute abdomen for undergraduates. AIM: This study aimed to explore the application effect of SPARK[sub-speciality (S), problem-based learning (P), assessment (A), report (R) and reading skill (K)] teaching mode in the experimental teaching of acute abdomen for undergraduate medical students. METHODS: We selected a total of 58 third year medical students for observation. The students were divided into experimental group and control group. Among them, 29 students in the experimental group studied in SPARK teaching mode, 29 students in the control group studied in traditional teaching mode. The two groups of students were tested after the theory class, before and after the experimental class, and one week after the experimental class, to compare the application effects of the two teaching modes. After the test one week after the experimental class, the two groups of students jointly adopted SPARK mode to learn, and were tested again one month after the experimental class to compare whether the two groups of students achieved the same results. The total score of all tests was 150. RESULTS: The average scores of the experimental group and the control group after theory class were (69.0 ± 26.4) and (72.1 ± 24.1) respectively, with no statistical difference (t = 0.468, P = 0.642). The average scores of the experimental group before, after and one week after the experimental class were higher than those of the control group. The experimental group was (84.5 ± 23.1), (109.7 ± 23.8), (105.5 ± 31.0) respectively, and the control group was (52.8 ± 15.1), (93.8 ± 17.0), (80.0 ± 22.8) respectively. The differences were statistically significant (t = -6.195, P = 0.00; t = -2.919, P = 0.05; t = -3.569, P = 0.01). The average scores of the experimental group and the control group after one month were (99.0 ± 31.0) and (95.5 ± 25.6) respectively, and there was no significant difference between the two groups (t = -0.462, P = 0.646). CONCLUSIONS: The SPARK teaching mode was helpful for undergraduate medical students to consolidate image foundation, improve image reading skills.

Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa).

The cAMP-dependent protein kinase A, cGMP-dependent protein kinase G and phospholipid-dependent protein kinase C (AGC) perform various functions in plants, involving growth, immunity, apoptosis and stress response. AGC gene family is well described in Arabidopsis, however, limited information is provided about AGC genes in rice, an important cereal crop. This research studied the AGC gene family in the AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza nivara, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula and Oryza longistaminata were searched and classified into six subfamilies, and it was found that these species have similar numbers of members. The analysis of gene duplication and selection pressure indicated that the AGC gene family expanded mainly by segmental or whole genome duplication (WGD), with purifying selection during the long evolutionary period. RNA-seq analysis revealed that OsAGCs of subfamily V were specifically highly expressed in leaves, and the expression patterns of these genes were compared with that of photosynthesis-related genes using qRT-PCR, discovered that OsAGC9, OsAGC20, and OsAGC22 might participate in photosynthesis. These results provide an informative perspective for exploring the evolutionary of AGC gene family and its practical application in rice.

Uncovering the genetic mechanisms regulating panicle architecture in rice with GPWAS and GWAS.

BACKGROUND: The number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total of 421 purified, homozygous rice accessions representing diverse genetic variations within O. sativa. The release of High-Density Rice Array (HDRA, 700 k SNPs) dataset provides a new opportunity to discover the genetic variants of panicle architectures in rice. RESULTS: In this report, a new method genome-phenome wide association study (GPWAS) was performed with 391 individuals and 27 traits derived from RDP1 to scan the relationship between the genes and multi-traits. A total of 1985 gene models were linked to phenomic variation with a p-value cutoff of 4.49E-18. Besides, 406 accessions derived from RDP1 with 411,066 SNPs were used to identify QTLs associated with the total spikelets number per panicle (TSNP), grain number per panicle (GNP), empty grain number per panicle (EGNP), primary branch number (PBN), panicle length (PL), and panicle number per plant (PN) by GLM, MLM, FarmCPU, and BLINK models for genome-wide association study (GWAS) analyses. A total of 18, 21, 18, 17, 15, and 17 QTLs were identified tightly linked with TSNP, GNP, EGNP, PBN, PL, and PN, respectively. Then, a total of 23 candidate genes were mapped simultaneously using both GWAS and GPWAS methods, composed of 6, 4, 5, 4, and 4 for TSNP, GNP, EGNP, PBN, and PL. Notably, one overlapped gene (Os01g0140100) were further investigated based on the haplotype and gene expression profile, indicating this gene might regulate the TSNP or panicle architecture in rice. CONCLUSIONS: Nearly 30 % (30/106) QTLs co-located with the previous published genes or QTLs, indicating the power of GWAS. Besides, GPWAS is a new method to discover the relationship between genes and traits, especially the pleiotropy genes. Through comparing the results from GWAS and GPWAS, we identified 23 candidate genes related to panicle architectures in rice. This comprehensive study provides new insights into the genetic basis controlling panicle architectures in rice, which lays a foundation in rice improvement.

Multi-locus genome-wide association studies for five yield-related traits in rice.

BACKGROUND: Improving the overall production of rice with high quality is a major target of breeders. Mining potential yield-related loci have been geared towards developing efficient rice breeding strategies. In this study, one single-locus genome-wide association studies (SL-GWAS) method (MLM) in conjunction with five multi-locus genome-wide association studies (ML-GWAS) approaches (mrMLM, FASTmrMLM, pLARmEB, pKWmEB, and ISIS EM-BLASSO) were conducted in a panel consisting of 529 rice core varieties with 607,201 SNPs. RESULTS: A total of 152, 106, 12, 111, and 64 SNPs were detected by the MLM model associated with the five yield-related traits, namely grain length (GL), grain width (GW), grain thickness (GT), thousand-grain weight (TGW), and yield per plant (YPP), respectively. Furthermore, 74 significant quantitative trait nucleotides (QTNs) were presented across at least two ML-GWAS methods to be associated with the above five traits successively. Finally, 20 common QTNs were simultaneously discovered by both SL-GWAS and ML-GWAS methods. Based on genome annotation, gene expression analysis, and previous studies, two candidate key genes (LOC_Os09g02830 and LOC_Os07g31450) were characterized to affect GW and TGW, separately. CONCLUSIONS: These outcomes will provide an indication for breeding high-yielding rice varieties in the immediate future.

Genome-wide association studies of ionomic and agronomic traits in USDA mini core collection of rice and comparative analyses of different mapping methods.

BACKGROUND: Rice is an important human staple food vulnerable to heavy metal contamination leading to serious concerns. High yield with low heavy metal contamination is a common but highly challenging goal for rice breeders worldwide due to lack of genetic knowledge and markers. RESULTS: To identify candidate QTLs and develop molecular markers for rice yield and heavy metal content, a total of 191 accessions from the USDA Rice mini-core collection with over 3.2 million SNPs were employed to investigate the QTLs. Sixteen ionomic and thirteen agronomic traits were analyzed utilizing two univariate (GLM and MLM) and two multivariate (MLMM and FarmCPU) GWAS methods. 106, 47, and 97 QTLs were identified for ionomics flooded, ionomics unflooded, and agronomic traits, respectively, with the criterium of p-value < 1.53 × 10- 8, which was determined by the Bonferroni correction for p-value of 0.05. While 49 (~ 20%) of the 250 QTLs were coinciding with previously reported QTLs/genes, about 201 (~ 80%) were new. In addition, several new candidate genes involved in ionomic and agronomic traits control were identified by analyzing the DNA sequence, gene expression, and the homologs of the QTL regions. Our results further showed that each of the four GWAS methods can identify unique as well as common QTLs, suggesting that using multiple GWAS methods can complement each other in QTL identification, especially by combining univariate and multivariate methods. CONCLUSIONS: While 49 previously reported QTLs/genes were rediscovered, over 200 new QTLs for ionomic and agronomic traits were found in the rice genome. Moreover, multiple new candidate genes for agronomic and ionomic traits were identified. This research provides novel insights into the genetic basis of both ionomic and agronomic variations in rice, establishing the foundation for marker development in breeding and further investigation on reducing heavy-metal contamination and improving crop yields. Finally, the comparative analysis of the GWAS methods showed that each method has unique features and different methods can complement each other.

Effect of multi-allele combination on rice grain size based on prediction of regression equation model.

Rice yield potential is partially affected by grain size and weight, which associates with a great number of genes and QTLs. However, it is still unclear that how multiple alleles in different genes take a combined effect on grain shape/size. Here, we investigated seven core grain size-related functional genes (GL7, GS3, GW8, GS5, TGW6, WTG1, and An-1) and observed a wide phenotypic variation for five agronomic traits (grain length, grain width, grain length-width ratio, grain thickness and thousand-grain weight) in 521 rice germplasm. The correlation analysis showed a strong association among these grain traits which have distinct impacts on determining the final rice grain size. Genotyping analysis demonstrated that a relatively small number of allele combinations were preserved in the diverse population and these allele combinations were significantly associated with differences in grain size. Furthermore, alleles were regarded as individual variables to develop the multiple regression equation. We found that B and C allelic types of GS3 and conventional type of WTG1 played relevant roles in grain size and thousand-grain weight, separately. The models would conduce to devise instructive approaches by selecting appropriate candidate alleles, which could fuel further research for breeding preferred grain shape and high-yielding crop.

Integrated RNA-Seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots.

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice's cold-stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold-stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold-stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

Oxygen Evolution Reaction over the Au/YSZ Interface at High Temperature.

The oxygen evolution reaction (OER) is a sluggish electrocatalytic reaction in solid oxide electrolysis cells (SOECs) at high temperatures (600-850 °C). Perovskite oxide has been widely investigated for catalyzing the OER; however, the formation of cation-enriched secondary phases at the oxide/oxide interface blocks the active sites and decreases OER performance. Herein, we show that the Au/yttria-stabilized zirconia (YSZ) interface possesses much higher OER activity than the lanthanum strontium manganite/YSZ anode. Electrochemical characterization and density functional theory calculations suggest that the Au/YSZ interface provides a favorable path for OER by triggering interfacial oxygen spillover from the YSZ to the Au surface. In situ X-ray photoelectron spectroscopy results confirm the existence of spillover oxygen on the Au surface. This study demonstrates that the Au/YSZ interface possesses excellent catalytic activity for OER at high temperatures in SOECs.

Enhancing CO2 Electroreduction with the Metal-Oxide Interface.

The electrochemical CO2 reduction reaction (CO2RR) typically uses transition metals as the catalysts. To improve the efficiency, tremendous efforts have been dedicated to tuning the morphology, size, and structure of metal catalysts and employing electrolytes that enhance the adsorption of CO2. We report here a strategy to enhance CO2RR by constructing the metal-oxide interface. We demonstrate that Au-CeOx shows much higher activity and Faradaic efficiency than Au or CeOx alone for CO2RR. In situ scanning tunneling microscopy and synchrotron-radiation photoemission spectroscopy show that the Au-CeOx interface is dominant in enhancing CO2 adsorption and activation, which can be further promoted by the presence of hydroxyl groups. Density functional theory calculations indicate that the Au-CeOx interface is the active site for CO2 activation and the reduction to CO, where the synergy between Au and CeOx promotes the stability of key carboxyl intermediate (*COOH) and thus facilitates CO2RR. Similar interface-enhanced CO2RR is further observed on Ag-CeOx, demonstrating the generality of the strategy for enhancing CO2RR.

Functional inactivation of UDP-N-acetylglucosamine pyrophosphorylase 1 (UAP1) induces early leaf senescence and defence responses in rice.

Plant leaf senescence and defence responses are important biological processes, but the molecular mechanisms involved are not well understood. This study identified a new rice mutant, spotted leaf 29 (spl29). The SPL29 gene was identified by map-based cloning, and SPL29 was confirmed as UDP-N-acetylglucosamine pyrophosphorylase 1 (UAP1) by enzymatic analysis. The mutant spl29 lacks UAP activity. The biological phenotypes for which UAP is responsible have not previously been reported in plants. The spl29 mutant displayed early leaf senescence, confirmed by chlorophyll loss and photosystem II decline as physiological indicators, chloroplast degradation as a cellular characteristic, and both upregulation of senescence transcription factors and senescence-associated genes, and downregulation of photosynthesis-related genes, as molecular evidence. Defence responses were induced in the spl29 mutant, shown by enhanced resistance to bacterial blight inoculation and upregulation of defence response genes. Reactive oxygen species, including O2 (-) and H2O2, accumulated in spl29 plants; there was also increased malondialdehyde content. Enhanced superoxide dismutase activity combined with normal catalase activity in spl29 could be responsible for H2O2 accumulation. The plant hormones jasmonic acid and abscisic acid also accumulated in spl29 plants. ROS and plant hormones probably play important roles in early leaf senescence and defence responses in the spl29 mutant. Based on these findings, it is suggested that UAP1 is involved in regulating leaf senescence and defence responses in rice.