Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations

F2 and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F2 and RIL populations

An anoikis-related gene signature for prediction of the prognosis in prostate cancer

PurposeThis study presents a novel approach to predict postoperative biochemical recurrence (BCR) in prostate cancer (PCa) patients which involves constructing a signature based on anoikis-related genes (ARGs).MethodsIn this study, we utilised data from TCGA-PARD and GEO databases to identify specific ARGs in prostate cancer. We established a signature of these ARGs using Cox regression analysis and evaluated their clinical predictive efficacy and immune-related status through various methods such as Kaplan-Meier survival analysis, subject work characteristics analysis, and CIBERSORT method. Our findings suggest that these ARGs may have potential as biomarkers for prostate cancer prognosis and treatment. To investigate the biological pathways of genes associated with anoikis, we utilised GSVA, GO, and KEGG. The expression of ARGs was confirmed by the HPA database. Furthermore, we conducted PPI analysis to identify the core network of ARGs in PCa.ResultsBased on analysis of the TCGA database, a set of eight ARGs were identified as prognostic signature genes for prostate cancer. The reliability and validity of this signature were well verified in both the TCGA and GEO codifications. Using this signature, patients were classified into two groups based on their risk for developing BCR. There was a significant difference in BCR-free time between the high and low risk groups (P < 0.05).This signature serves as a dependable and unbiased prognostic factor for predicting biochemical recurrence (BCR) in prostate cancer (PCa) patients. It outperforms clinicopathological characteristics in terms of accuracy and reliability. PLK1 may play a potential regulatory role as a core gene in the development of prostate cancer.ConclusionThis signature suggests the potential role of ARGs in the development and progression of PCa and can effectively predict the risk of BCR in PCa patients after surgery. It also provides a basis for further research into the mechanism of ARGs in PCa and for the clinical management of patients with PCa

Early Non-Response as a Predictor of Later Non-Response to Antipsychotics in Schizophrenia: A Randomized Trial

BACKGROUND: It remains a challenge to predict the long-term response to antipsychotics in patients with schizophrenia who do not respond at an early stage. This study aimed to investigate the optimal predictive cut-off value for early non-response that would better predict later non-response to antipsychotics in patients with schizophrenia. METHODS: This multicenter, 8-week, open-label, randomized trial was conducted at 19 psychiatric centers throughout China. All enrolled participants were assigned to olanzapine, risperidone, amisulpride, or aripiprazole monotherapy for 8 weeks. The positive and negative syndrome scale (PANSS) was evaluated at baseline, week 2, week 4, and week 8. The main outcome was the prediction of nonresponse. Nonresponse is defined as a \u3c 20% reduction in the total scores of PANSS from baseline to endpoint. Severity ratings of mild, moderate, and severe illness corresponded to baseline PANSS total scores of 58, 75, and 95, respectively. RESULTS: At week 2, a reduction of \u3c 5% in the PANSS total score showed the highest total accuracy in the severe and mild schizophrenia patients (total accuracy, 75.0% and 80.8%, respectively), and patients who were treated with the risperidone and amisulpride groups (total accuracy, 82.4%, and 78.2%, respectively). A 10% decrease exhibited the best overall accuracy in the moderate schizophrenia patients (total accuracy, 84.0%), olanzapine (total accuracy, 79.2%), and aripiprazole group (total accuracy, 77.4%). At week 4, the best predictive cut-off value was \u3c 20%, regardless of the antipsychotic or severity of illness (total accuracy ranging from 89.8 to 92.1%). CONCLUSIONS: Symptom reduction at week 2 has acceptable discrimination in predicting later non-response to antipsychotics in schizophrenia, and a more accurate predictive cut-off value should be determined according to the medication regimen and baseline illness severity. The response to treatment during the next 2 weeks after week 2 could be further assessed to determine whether there is a need to change antipsychotic medication during the first four weeks. TRIAL REGISTRATION: This study was registered on Clinicaltrials.gov (NCT03451734)

The international competitiveness research of china’s agricultural products

Since ancient times, China is a country with a large population and abundant agriculture. With the reform of China’s market economy and entered WTO, it has improved the international participation degree of agricultural products in China. Especially in recent years, in the highly open international markets and countries have pledged to weaken their agricultural support, China’s agricultural products in the international market ushered in a broader space for development, but due to various reasons, China’s agricultural products trade has formed a huge deficit in recent years. To reduce the trade deficit, continue to expand exports of agricultural products, create income for China’s foreign exchange and increase farmers’ income, we need to continue improving the international competitiveness of China’s agricultural products

jcvi: jcvi v0.6.6

What's new Wrappers for DNA aligners available: NUCMER, LAST Batch Ks calculations Misc bug fixes for ALLMAPS Calculate DUST and TRF bed Imputation, liftover and STR predictio

Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations

F2 and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F2 and RIL populations

Fertilization Practices: Optimization in Greenhouse Vegetable Cultivation with Different Planting Years

Cucumber plant growth and the fate of N in the plant-soil system are influenced by fertilization practices, the strengths of which may vary among soils. Three soils with different years of greenhouse vegetable cultivation (0, 2, and 18 years) were fertilized differently (CK, no N fertilizer applied; CF, chemical NPK fertilizers applied; RCF, reduced chemical NPK fertilizers applied, with N, P, and K reduced by 46.5%, 68.6%, and 54.7%; RCF+CM, 75% of the total N derived from chemical fertilizer and the rest from chicken manure in the case of reduced fertilization) in a pot experiment to study the changes in cucumber (Cucumis sativus L.) growth, N uptake, residue, and losses. The original N in soil was insufficient to maintain leaf growth and chlorophyll synthesis at later growth stages, even in soil with 18 years of greenhouse vegetable cultivation, where the original N content was the highest (total N 1.73 g kg−1). However, the CF treatment with excessive N fertilization inhibited leaf growth at the early growing stage and accelerated leaf senescence later, especially in soil with longer years of greenhouse vegetable cultivation. Therefore, reduced fertilizer application (RCF and RCF+CM) is appropriate to improve cucumber growth and productivity in greenhouse cultivation with different planting years. Although the same amount of N was applied, the RCF+CM treatment performed better than the RCF treatment in terms of increasing plant N uptake (by 30.5%) and soil N pool storage (by 25.0%) while decreasing N losses (by 16.6%) in soil with 0 years of greenhouse vegetable cultivation. In soil with 2 and 18 years of greenhouse vegetable cultivation, the soil itself functions much better in exogenous N retention and supply, with the N storage and losses not significantly different between the RCF and RCF+CM treatments. We conclude that reduced fertilization with the co-application of chicken manure is optimal for plant growth promotion, output-input ratio increase, soil N fertility improvement, and environmental risk mitigation