Effect of genotyping errors on linkage map construction based on repeated chip analysis of two recombinant inbred line populations in wheat (Triticum aestivum L.).

Linkage maps are essential for genetic mapping of phenotypic traits, gene map-based cloning, and marker-assisted selection in breeding applications. Construction of a high-quality saturated map requires high-quality genotypic data on a large number of molecular markers. Errors in genotyping cannot be completely avoided, no matter what platform is used. When genotyping error reaches a threshold level, it will seriously affect the accuracy of the constructed map and the reliability of consequent genetic studies. In this study, repeated genotyping of two recombinant inbred line (RIL) populations derived from crosses Yangxiaomai × Zhongyou 9507 and Jingshuang 16 × Bainong 64 was used to investigate the effect of genotyping errors on linkage map construction. Inconsistent data points between the two replications were regarded as genotyping errors, which were classified into three types. Genotyping errors were treated as missing values, and therefore the non-erroneous data set was generated. Firstly, linkage maps were constructed using the two replicates as well as the non-erroneous data set. Secondly, error correction methods implemented in software packages QTL IciMapping (EC) and Genotype-Corrector (GC) were applied to the two replicates. Linkage maps were therefore constructed based on the corrected genotypes and then compared with those from the non-erroneous data set. Simulation study was performed by considering different levels of genotyping errors to investigate the impact of errors and the accuracy of error correction methods. Results indicated that map length and marker order differed among the two replicates and the non-erroneous data sets in both RIL populations. For both actual and simulated populations, map length was expanded as the increase in error rate, and the correlation coefficient between linkage and physical maps became lower. Map quality can be improved by repeated genotyping and error correction algorithm. When it is impossible to genotype the whole mapping population repeatedly, 30% would be recommended in repeated genotyping. The EC method had a much lower false positive rate than did the GC method under different error rates. This study systematically expounded the impact of genotyping errors on linkage analysis, providing potential guidelines for improving the accuracy of linkage maps in the presence of genotyping errors.

Knowledge about, attitudes toward and acceptance and predictors of intention to receive the mpox vaccine among cancer patients in China: A cross-sectional survey.

This study aimed to investigate the knowledge about, attitudes toward, and acceptance and predictors of receiving the mpox vaccine among Chinese cancer patients. Patients were selected using a convenience sampling method. A web-based self-report questionnaire was developed to assess cancer patients' knowledge, attitudes, and acceptance regarding the mpox vaccine. Multivariate logistic regression analysis was used to determine predictors of acceptance of the mpox vaccine. A total of 805 cancer patients were included in this study, with a vaccine hesitancy rate of 27.08%. Approximately 66% of the patients' information about mpox and the vaccine came from the mass media, and there was a significant bias in the hesitant group's knowledge about mpox and the vaccine. Multivariable logistic regression analysis suggested that retirement; chemotherapy; the belief that the mpox vaccine could prevent disease, that vaccination should be compulsory when appropriate and that the mpox vaccine prevents mpox and reduces complications; the willingness to pay for the mpox vaccine; the willingness to recommend that friends and family receive the mpox vaccine; and the belief that the mpox vaccine should be distributed fairly and equitably were factors that promoted vaccination. The belief that mpox worsens tumor prognosis was a driving factor for vaccine hesitancy. This study investigated the knowledge of cancer patients about mpox and the vaccine, evaluated the acceptance and hesitancy rates of the mpox vaccine and examined the predictors of vaccination intention. We suggest that the government scientifically promote the vaccine and develop policies such as free vaccination and personalized vaccination to increase the awareness and acceptance rate of the mpox vaccine.

Molecular identification and validation of four stable QTL for adult-plant resistance to powdery mildew in Chinese wheat cultivar Bainong 64.

KEY MESSAGE: Four stable QTL for adult-plant resistance (APR) to powdery mildew were identified on chromosome arms 1DL, 2BS, 2DL, and 6BL in the widely grown Chinese wheat cultivar Bainong 64. These QTL had no effect on response to stripe rust or leaf rust. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating fungal disease. Seedlings of Chinese wheat Bainong 64 are susceptible to Bgt, but adult plants have maintained resistance since it was released in 1996. A population of 171 recombinant inbred lines (RILs) developed from cross Jingshuang 16/Bainong 64 (JS16/BN64) was used to dissect genetic components of powdery mildew resistance. A genetic map comprising 5383 polymorphic markers was constructed using the 15 K SNP chip and kompetitive allele-specific PCR (KASP) markers. Composite interval mapping identified four stable QTL with favorable alleles all from BN64 on chromosome arms 1DL, 2BS, 2DL, and 6BL in at least four environments. They accounted for 8.3%, 13.8%, 14.4%, and 9.0% of the total phenotypic variation explained (PVE) in maximum, respectively. QPmjbr.caas-1DL, situated about 22 Mb from centromere, is probably a new QTL. QPmjbr.caas-2DL located near the end of arm 2DL and explained the largest PVE. Using genetic maps populated with KASP markers, QPmjbr.caas-2BS and QPmjbr.caas-6BL were fine mapped to a 1.8 cM genetic intervals spanning 13.6 Mb (76.0-89.6 Mb) and 1.7 cM and 4.9 Mb (659.9-664.8 Mb), respectively. The four QTL independent of stripe rust and leaf rust resistance were validated for powdery mildew resistance in another RIL population related to BN64 and a cultivar panel using representative KASP markers. Since BN64 has been a leading cultivar and an important breeding parent in China, the QTL and markers reported in this study will be useful for marker-assisted selection of APR.

The influence of virtual environment on thermal perception: physical reaction and subjective thermal perception on outdoor scenarios in virtual reality.

Positive thermal perception can affect users' climate-controlling behavior, indirectly reducing a building's operational carbon emissions. Studies show that some visual elements, such as window sizes and light colors, can influence thermal perception. However, until recently there has been little interest in the interaction of thermal perception and outdoor visual scenarios or natural elements like water or trees, and little quantitative evidence has been found associating visual natural elements and thermal comfort. This experiment explores and quantifies the extent to which visual scenarios outdoors affect thermal perception. The experiment used a double-blind clinical trial. All tests were done in a stable laboratory environment to eliminate temperature changes, and scenarios were shown through a virtual reality (VR) headset. Forty-three participants were divided into three groups randomly, separately watched VR-outdoor scenarios with natural elements, VR-indoor scenarios, and a control scenario of the real laboratory, then finished a subjective questionnaire conducted to evaluate their thermal, environmental, and overall perceptions while their physical data (heart rate, blood pressure, pulse) was real-time recorded. Results show that visual scenarios could significantly influence thermal perception (Cohen's d between groups > 0.8). Significant positive correlations were found between key thermal perception index, thermal comfort, and visual perception indexes including visual comfort, pleasantness, and relaxation (all PCCs ≤ 0.01). Outdoor scenarios, with better visual perception, rank higher average scores (M ± SD = 1.0 ± 0.7) in thermal comfort than indoor groups (average M ± SD = 0.3 ± 1.0) while the physical environment remains unchanged. This connection between thermal and environmental perception can be used in building design. By being visually exposed to pleasing outdoor environments, the positive thermal perception will increase, and thus reduce building energy consumption. Designing positive visual environments with outdoor natural elements is not only a requirement for health but also a feasible path toward a sustainable net-zero future.

Genetic dissection of grain morphology and yield components in a wheat line with defective grain filling.

KEY MESSAGE: We identified stable QTL for grain morphology and yield component traits in a wheat defective grain filling line and validated genetic effects in a panel of cultivars using breeding-relevant markers. Grain filling capacity is essential for grain yield and appearance quality in cereal crops. Identification of genetic loci for grain filling is important for wheat improvement. However, there are few genetic studies on grain filling in wheat. Here, a defective grain filling (DGF) line wdgf1 characterized by shrunken grains was identified in a population derived from multi-round crosses involving nine parents and a recombinant inbreed line (RIL) population was generated from the cross between wdgf1 and a sister line with normal grains. We constructed a genetic map of the RIL population using the wheat 15K single nucleotide polymorphism chip and detected 25 stable quantitative trait loci (QTL) for grain morphology and yield components, including three for DGF, eleven for grain size, six for thousand grain weight, three for grain number per spike and two for spike number per m2. Among them, QDGF.caas-7A is co-located with QTGW.caas-7A and can explain 39.4-64.6% of the phenotypic variances, indicating that this QTL is a major locus controlling DGF. Sequencing and linkage mapping showed that TaSus2-2B and Rht-B1 were candidate genes for QTGW.caas-2B and the QTL cluster (QTGW.caas-4B, QGNS.caas-4B, and QSN.caas-4B), respectively. We developed kompetitive allele-specific PCR markers tightly linked to the stable QTL without corresponding to known yield-related genes, and validated their genetic effects in a diverse panel of wheat cultivars. These findings not only lay a solid foundation for genetic dissection underlying grain filling and yield formation, but also provide useful tools for marker-assisted breeding.

Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits.

BACKGROUND: Plant architecture associated with increased grain yield and adaptation to the local environments is selected during wheat (Triticum aestivum) breeding. The internode length of individual stems and tiller length of individual plants are important for the determination of plant architecture. However, few studies have explored the genetic basis of these traits. RESULTS: Here, we conduct a genome-wide association study (GWAS) to dissect the genetic basis of geographical differentiation of these traits in 306 worldwide wheat accessions including both landraces and traditional varieties. We determine the changes of haplotypes for the associated genomic regions in frequency in 831 wheat accessions that are either introduced from other countries or developed in China from last two decades. We identify 83 loci that are associated with one trait, while the remaining 247 loci are pleiotropic. We also find 163 associated loci are under strong selective sweep. GWAS results demonstrate independent regulation of internode length of individual stems and consistent regulation of tiller length of individual plants. This makes it possible to obtain ideal haplotype combinations of the length of four internodes. We also find that the geographical distribution of the haplotypes explains the observed differences in internode length among the worldwide wheat accessions. CONCLUSION: This study provides insights into the genetic basis of plant architecture. It will facilitate gene functional analysis and molecular design of plant architecture for breeding.

Molecular characterization and validation of adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895.

KEY MESSAGE: Adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895 was mapped to the physical interval 710.2-713.2 Mb on the long arm of chromosome 2A. Adult-plant resistance to stripe rust is generally more durable than all-stage resistance. Chinese wheat cultivar Zhongmai 895 showed stable stripe rust resistance at the adult-plant stage. To map the genetic loci underlying its resistance, 171 doubled haploid (DH) lines from a Yangmai 16/Zhongmai 895 cross were genotyped with the wheat 660 K SNP chip. Disease severities of the DH population and parents were assessed in four environments. A major QTL designated QYryz.caas-2AL was mapped to interval 703.7-715.3 Mb on the long arm of chromosome 2A using both chip-based and KASP (kompetitive allele-specific PCR) marker-based methods, explaining 31.5 to 54.1% of the phenotypic variances. The QTL was further validated in an F2 population of cross Emai 580/Zhongmai 895 with 459 plants and a panel of 240 wheat cultivars using KASP markers. Three reliable KASP markers predicted a low frequency (7.2-10.5%) of QYryz.caas-2AL in the test panel and remapped the gene to the physical interval 710.2-713.2 Mb. Based on different physical positions or genetic effects from known genes or QTL on chromosome arm 2AL, the gene was predicted to be a new one for adult-plant stripe rust resistance and was named Yr86. Twenty KASP markers linked to Yr86 were developed in this study based on wheat 660 K SNP array and genome re-sequencing. Three of them are significantly associated with stripe rust resistance in natural population. These markers should be useful for marker-assisted selection and also provide a starting point for fine mapping and map-based cloning of the new resistance gene.

Integrated transcriptomic and metabolomic analysis of chili pepper fruits provides new insight into the regulation of the branched chain esters and capsaicin biosynthesis.

Chili pepper (Capsicum spp.) is one of the world's most popular vegetables and spices. Aroma is an important quality indicator of pepper, but the nature of the related volatiles is still not clear. In this study, we investigated the fruit of two pepper varieties, one with strong fruity aroma 'CC' Capsicum chinense and one without 'TJ' Capsicum annuum at four different developmental stages using transcriptomic and metabolomic analysis. The results showed that the content of green leaf volatiles (GLVs) was higher in TJ than in CC and was higher in the young fruit stage in both varieties. GLVs content was positively correlated with the expression of 13-LOX1, 2, 5 and HPL. But the levels of branched-chain (BC) esters and capsaicin were higher in CC, and were positively correlated with the expression of IMPS4 and DADH1. Our findings shed light on the molecular mechanism of aroma biosynthesis in pepper and provide a theoretical basis for the molecular breeding of high-quality pepper fruits.

QTL Mapping Reveals Both All-Stage and Adult-Plant Resistance to Powdery Mildew in Chinese Elite Wheat Cultivars.

Powdery mildew caused by Blumeria graminis f. sp. tritici is a threat to wheat production in China. Mapping quantitative trait loci (QTL) for resistance to powdery mildew and developing breeder-friendly markers are important initial steps in breeding resistant cultivars. An all-stage resistance gene and several QTL were identified using a population of 254 recombinant inbred lines developed from a Jingdong 8/Aikang 58 cross. The population was evaluated for powdery mildew resistance across six field environments over three consecutive growing seasons utilizing two different mixtures of B. graminis f. sp. tritici isolates, named #Bgt-HB and #Bgt-BJ. Using genotypic data obtained from the Wheat TraitBreed 50K single-nucleotide polymorphism array, seven stable QTL were identified on chromosome arms 1DL, 2AL, 2DS, 4DL, 5AL, 6BL.1, and 6BL.2. The QTL on 2AL conferred all-stage resistance to B. graminis f. sp. tritici race E20 in greenhouse tests and explained up to 52% of the phenotypic variance in field trials but was resistant only against #Bgt-HB. The gene involved in this QTL was predicted to be Pm4a based on genome location and gene sequence. QPmja.caas-1DL, QPmja.caas-4DL, and QPmja.caas-6BL.1 were identified as potentially new QTL for powdery mildew resistance. QPmja.caas-2DS and QPmja.caas-6BL.1 were effective against both B. graminis f. sp. tritici mixtures, indicating their probable broad-spectrum resistance. A Kompetitive allele-specific PCR marker closely linked to QPmja.caas-2DS was developed and validated in a panel of 286 wheat cultivars. Because both Jingdong 8 and Aikang 58 have been leading cultivars and breeding parents, the QTL and marker reported represent valuable resources for wheat researchers and breeders.

The willingness of Chinese healthcare workers to receive monkeypox vaccine and its independent predictors: A cross-sectional survey.

The global monkeypox outbreak in 2022 has severely affected the life and health of people. Currently, partial smallpox vaccines have been approved for monkeypox prevention. Considering the potential occupational health risks of monkeypox infection among healthcare workers (HCWs), this study explored the willingness of Chinese HCWs to receive the monkeypox vaccine and analyzed the factors influencing their decision. We conducted an online cross-sectional survey among HCWs of 10 Chinese hospitals from May 30th, 2022 to August 1st, 2022. Specifically, a self-report questionnaire was administered to evaluate the attitude and acceptance of HCWs toward the monkeypox vaccine, followed by a multivariate logistic regression analysis to determine the independent predictors of vaccination. The survey included 1032 participants, of whom 90.12% expressed their willingness for vaccination (vaccine hesitancy rate = 9.88%). Univariate analysis showed that 11 variables differed significantly between the vaccine acceptance and vaccine hesitancy groups. Multivariate logistic regression analysis demonstrated that the age of 30-40 years (odds ratio [OR] = 0.504, 95% confidence interval [CI]: 0.284-0.893, p = 0.019 vs. age of <30 years old), working in a secondary hospital (OR = 0.449, 95% CI: 0.249-0.808, p = 0.019 vs. working in a tertiary hospital), considering vaccination necessary for controlling monkeypox infection (OR = 4.135, 95% CI: 2.109-8.106, p < 0.001 vs. not considering it necessary), willingness to pay for the monkeypox vaccine (OR = 2.125, 95% CI: 1.206-3.745, p = 0.009 vs. no willingness to pay), considering implementation of mandatory vaccination necessary (OR = 1.990, 95% CI: 1.023-3.869, p = 0.043 vs. not considering it necessary), and recommending family members and friends to take the vaccine (OR = 13.847, 95% CI: 7.487-25.609, p < 0.001 vs. not recommending) were crucial independent predictors of the willingness to receive monkeypox-related vaccination. This study evaluated the acceptance and hesitancy rates of Chinese HCWs toward the monkeypox vaccine and found that the willingness to receive vaccination was mainly correlated to age, hospital level, and attitude toward vaccination. Therefore, to promote vaccine absorption, we recommend expanding publicity, formulating reasonable policies, and improving the recognition of vaccines.

Identifying the Mechanism of Polygoni Cuspidati Rhizoma et Radix in Treating Acute Liver Failure Based on Network Pharmacology and Molecular Docking.

Materials and Methods: The potential bioactive compounds of PCRR and their targets were collected from TCMSP, TCMID, and BATMAN-TCM databases with absorption, distribution, metabolism, and excretion protocols (oral bioavailability ≥30% and drug-likeness ≥0.18). The ALF-related target genes were identified using the GeneCards and OMIM databases. A protein-protein interaction (PPI) network among these targets was constructed using the Cytoscape software to obtain the core targets. The genes associated with ALF were analyzed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to identify the signaling pathways related to the therapeutic effect of PCRR in ALF. Results: In total, 10 bioactive compounds of PCRR and 200 targets related to them were obtained, and 2913 ALF-related target genes were identified. PPI network analysis pinpointed 15 core targets, namely, TP53, AKT1, JUN, HSP90AA1, MAPK1, RELA, TNF, ESR1, IL6, MYC, MAPK14, FOS, RB1, CDKN1A, and EGFR. GO enrichment and KEGG pathway analyses revealed that the therapeutic mechanisms of PCRR in ALF are related to cell metabolism, oxidative stress, inflammation, and hepatocyte apoptosis. Conclusion: This is the first study to explore the therapeutic mechanisms of PCRR in ALF via network pharmacology and molecular docking. This study provides a research platform with candidate ALF-related targets of PRCC for the development of therapeutics against ALF.

Fine mapping of QPm.caas-3BS, a stable QTL for adult-plant resistance to powdery mildew in wheat (Triticum aestivum L.).

KEY MESSAGE: A stable QTL QPm.caas-3BS for adult-plant resistance to powdery mildew was mapped in an interval of 431 kb, and candidate genes were predicted based on gene sequences and expression profiles. Powdery mildew is a devastating foliar disease occurring in most wheat-growing areas. Characterization and fine mapping of genes for powdery mildew resistance can benefit marker-assisted breeding. We previously identified a stable quantitative trait locus (QTL) QPm.caas-3BS for adult-plant resistance to powdery mildew in a recombinant inbred line population of Zhou8425B/Chinese Spring by phenotyping across four environments. Using 11 heterozygous recombinants and high-density molecular markers, QPm.caas-3BS was delimited in a physical interval of approximately 3.91 Mb. Based on re-sequenced data and expression profiles, three genes TraesCS3B02G014800, TraesCS3B02G016800 and TraesCS3B02G019900 were associated with the powdery mildew resistance locus. Three gene-specific kompetitive allele-specific PCR (KASP) markers were developed from these genes and validated in the Zhou8425B derivatives and Zhou8425B/Chinese Spring population in which the resistance gene was mapped to a 0.3 cM interval flanked by KASP14800 and snp_50465, corresponding to a 431 kb region at the distal end of chromosome 3BS. Within the interval, TraesCS3B02G014800 was the most likely candidate gene for QPm.caas-3BS, but TraesCS3B02G016300 and TraesCS3B02G016400 were less likely candidates based on gene annotations and sequence variation between the parents. These results not only offer high-throughput KASP markers for improvement of powdery mildew resistance but also pave the way to map-based cloning of the resistance gene.

Knowledge about, attitude and acceptance towards, and predictors of intention to receive the COVID-19 vaccine among cancer patients in Eastern China: A cross-sectional survey.

OBJECTIVE: The coronavirus disease 2019 (COVID-19) pandemic has had a serious impact on health all over the world. Cancer patient, whose immunity is often compromised, faces a huge challenge. Currently, some COVID-19 vaccines are being developed and applied on general population; however, whether cancer patients should take COVID-19 vaccine remains unknown. Our study aimed to explore the knowledge, attitude, acceptance, and predictors of intention to receive the COVID-19 vaccine among cancer patients in Eastern China. METHODS: A cross-sectional study was conducted in Eastern China from June 17th to September 3rd, 2021. Patients were selected using a convenience sampling method. A self-report questionnaire was developed to assess knowledge about the COVID-19 vaccine, attitude towards the vaccine and acceptance of the vaccine; following a review of similar studies previously published in the scientific literature, multivariate logistic regression analysis was used to determine the predictors associated with COVID-19 vaccine acceptance. RESULTS: A total of 2158 cancer patients were enrolled in this study. The rate of vaccine hesitancy was 24.05% (519/2158); further, among the participants of vaccine acceptance, 767 had taken COVID-19 vaccine (35.54%), and 872 were willing to get vaccinated (40.01%). A total of 24 variables including demographic characteristics, clinical status of cancer, impact of COVID-19 pandemic on study participants, patients' knowledge about the COVID-19 vaccine, and attitude towards the vaccine, had significant differences between the "vaccine hesitancy" population and "vaccine acceptance" population. Multivariate logistic regression analysis indicated that parameters including alcohol consumption (odds ratio [OR] = 1.849; 95% confidence interval [CI]: 1.375-2.488; P-reference [P-Ref] < 0.001 vs non-drinkers), income impacted by COVID-19 pandemic (OR = 1.930, 2.037 and 2.688 for mild, moderate, and severe impact, respectively; all P-Ref < 0.01 vs no impact), knowledge of how the vaccine was developed (OR = 1.616; 95% CI: 1.126-2.318; P-Ref = 0.009 vs unknown), believing in the safety of the vaccine (OR = 1.502; 95% CI: 1.024-2.203; P-Ref = 0.038 vs denying the safety of vaccine), willingness to pay for the vaccine (OR = 3.042; 95% CI: 2.376-3.894; P-Ref < 0.001 vs unwilling), and willingness to recommend families and friends to get vaccinated (OR = 2.744; 95% CI: 1.759-4.280; P-Ref < 0.001 vs do not recommend) were contributors to vaccine acceptance. While such as being retired (OR = 0.586; 95% CI: 0.438-0.784; P-Ref < 0.001 vs unemployed), undergoing multiple therapies of cancer (OR = 0.408; 95% CI: 0.221-0.753; P-Ref = 0.004 vs no ongoing treatment), and worrying that the vaccine might deteriorate the prognosis of cancer (OR = 0.393; 95% CI: 0.307-0.504; P-Ref < 0.001 vs might not) were contributors to vaccine hesitancy. CONCLUSION: This study provided preliminary estimates of the rates of vaccine acceptance and vaccine hesitancy among cancer patients in Eastern China. The intention to receive the COVID-19 vaccine was impacted by factors such as patient occupation, alcohol consumption, and some parts of knowledge about and attitude towards COVID-19 vaccine. It is recommended to develop individualized vaccination plans that meet the healthcare needs of cancer patients.

Impact of treatment-duration-ratio of traditional Chinese medicine on survival period of primary liver cancer -A real-world study.

Introduction: In China, traditional Chinese medicine (TCM) is regarded as an effective treatment for primary liver cancer (PLC). The present study analyzed the effect of TCM on the survival period of patients with PLC by analyzing the relationship between the treatment-duration-ratio of traditional Chinese medicine (C-TDR, (traditional Chinese medicine treatment duration)/(Overall treatment duration) × 100%) and the survival time of 1002 patients with PLC. Methods: In this study, 1002 patients with PLC admitted to TCM Oncology Department of Changhai Hospital from January, 2015 to December, 2019 were enrolled. The univariate and multivariate Cox regression equation, propensity score matching (PSM) were performed to identify independent prognostic factors for survival outcomes of PLC patients at different stages and estimate the influence of C-TDR on survival time. Results: Cox regression analysis indicated that C-TDR was an independent prognostic factor for survival outcome (P＜0.05) and a corresponding reduction of relative risk of death of 75.67% (relative risk (RR) = 0.2433; 95%Confedential Interval (CI) = 0.1747-0.3388). Similarly, it is also an independent prognostic factor for patients outcome of each stage (P＜0.05). The 251 patients of BCLC-A reduced 96.09% risk of mortality (RR = 0.0391; 95%CI = 0.0151-0.1012). The 396 BCLC-B patients decreased risk of death of 81.24% (RR = 0.1876, 95%CI = 0.1112-0.3163). Moreover, 355 patients of stage C demonstrated a 51.36% lower risk of death (RR = 1.0016, 95%CI = 0.9885-1.0149). Significant differences were found in the median overall survival (OS) both higher and lower C-TDR of all patients. Even after PSM, the overall survival of two groups were significantly improved following each stage. Conclusion: Earlier administration of traditional Chinese medicine can reduce the risk of mortality and prolong survival in patients with liver cancer.

The SnRK2 family in pepper (Capsicum annuum L.): genome-wide identification and expression analyses during fruit development and under abiotic stress.

Plant-specific SnRK2 (sucrose nonfermenting-1-related protein kinase 2) genes play crucial roles in the coordination of plant growth and development and responses to stress. However, comprehensive studies have not been performed for this gene family in pepper (Capsicum annuum), a very important Solanaceous vegetable worldwide. To fully understand the status of SnRK2s in chili pepper, a total of 9 putative SnRK2 genes (named CaSnRK2.1-2.9) were identified in pepper in the present study. These genes were located on 7 different chromosomes and classified into three subfamilies based on the phylogenetic tree. Their conserved motif compositions and exon-intron structures were systematically analyzed, and the results strongly supported the classification. Furthermore, a total of 81 putative cis-elements were found in the promoter regions, and the cis-elements related to hormone and stress signaling were abundant. Finally, the CaSnRK2 gene expression profiles among different tissues, especially developing fruit tissue, and under various abiotic stresses were investigated to identify tissue-specific or stress-responsive candidates. This study was the first to comprehensively investigate the SnRK2 family in pepper, and the results provide important clues for further functional analyses of fruit development and abiotic stress responses.

The dynamic transcriptome of pepper (Capsicum annuum) whole roots reveals an important role for the phenylpropanoid biosynthesis pathway in root resistance to Phytophthora capsici.

Phytophthora root rot, caused by the soilborne oomycete pathogen Phytophthora capsici (Leon.), is a devastating disease causing significant losses in pepper production worldwide. To uncover the mechanism of root-mediated resistance to P. capsici we elucidated the dynamic transcriptome of whole pepper roots of the resistant accession CM334 and the susceptible accession NMCA10399 after P. capsici infection at 0, 12 and 36 hpi using RNA-Seq method. We detected that the roots of the resistant CM334 and the susceptible NMCA10399 had different transcriptional responses to P. capsici, suggesting the former activated a response to P. capsici earlier than the latter. KEGG enrichment analysis showed the pathways involved in the synthesis of secondary metabolites were those in which the most DEGs were enriched. Focusing on the gene regulation of phenylpropanoid biosynthesis-related genes, we found genes related to the key enzyme phenylalanine ammonia-lyase (PAL) were activated earlier with greater changes in the resistant accession than in the susceptible one. Moreover, genes related to cinnamoyl-CoA reductase (CCR1) were also upregulated in resistant roots but downregulated with great folder changes in susceptible roots. Briefly, we inferred that the phenylpropanoid biosynthesis pathway, especially cinnamaldehyde and lignin derived from its branches, played significant roles in pepper root resistance to P. capsici. These results provide new insight into root-mediated resistance to P. capsici in pepper.

Genome-Wide Identification and Expression Profile of Dof Transcription Factor Gene Family in Pepper (Capsicum annuum L.).

Dof (DNA-binding One Zinc Finger) transcription factor family is unique to plants and has diverse roles associated with plant-specific phenomena, such as light, phytohormone and defense responses as well as seed development and germination. Although, genome-wide analysis of this family has been performed in many species, information regarding Dof genes in the pepper, Capsicum annuum L., is extremely limited. In this study, exhaustive searches of pepper genome revealed 33 potential CaDofs that were phylogenetically clustered into four subgroups. Twenty-nine of the 33 Dof genes could be mapped on 11 chromosomes, except for chromosome 7. The intron/exon organizations and conserved motif compositions of these genes were also analyzed. Additionally, phylogenetic analysis and classification of the Dof transcription factor family in eight plant species revealed that S. lycopersicum and C. annuum as well as O. sativa and S. bicolor Dof proteins may have evolved conservatively. Moreover, comprehensive expression analysis of CaDofs using a RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that these genes exhibit a variety of expression patterns. Most of the CaDofs were expressed in at least one of the tissues tested, whereas several genes were identified as being highly responsive to heat and salt stresses. Overall, this study describes the first genome-wide analysis of the pepper Dof family, whose genes exhibited different expression patterns in all primary fruit developmental stages and tissue types, as in response to abiotic stress. In particular, some Dof genes might be used as biomarkers for heat and salt stress. The results could expand our understanding of the roles of Dof genes in pepper.

Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy.

Phytophthora root rot caused by Phytophthora capsici (P. capsici) is a serious limitation to pepper production in Southern China, with high temperature and humidity. Mapping PRR resistance genes can provide linked DNA markers for breeding PRR resistant varieties by molecular marker-assisted selection (MAS). Two BC1 populations and an F2 population derived from a cross between P. capsici-resistant accession, Criollo de Morelos 334 (CM334) and P. capsici-susceptible accession, New Mexico Capsicum Accession 10399 (NMCA10399) were used to investigate the genetic characteristics of PRR resistance. PRR resistance to isolate Byl4 (race 3) was controlled by a single dominant gene, PhR10, that was mapped to an interval of 16.39Mb at the end of the long arm of chromosome 10. Integration of bulked segregant analysis (BSA) and Specific Length Amplified Fragment sequencing (SLAF-seq) provided an efficient genetic mapping strategy. Ten polymorphic Simple Sequence Repeat (SSR) markers were found within this region and used to screen the genotypes of 636 BC1 plants, delimiting PhR10 to a 2.57 Mb interval between markers P52-11-21 (1.5 cM away) and P52-11-41 (1.1 cM). A total of 163 genes were annotated within this region and 31 were predicted to be associated with disease resistance. PhR10 is a novel race specific gene for PRR, and this paper describes linked SSR markers suitable for marker-assisted selection of PRR resistant varieties, also laying a foundation for cloning the resistance gene.