Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines

Mapping chromosome regions responsible for quantitative phenotypic variation in recombinant populations provides an effective means to characterize the genetic basis of complex traits. We conducted a quantitative trait loci (QTL) analysis of 150 rice recombinant inbred lines (RILs) derived from a cross between two cultivars, Oryza sativa ssp. indica cv. 93-11 and Oryza sativa ssp. japonica cv. Nipponbare. The RILs were genotyped through next-generation sequencing, which accurately determined the recombination breakpoints and provided a new type of genetic markers, recombination bins, for QTL analysis. We detected 49 QTL with phenotypic effect ranging from 3.2 to 46.0% for 14 agronomics traits. Five QTL of relatively large effect (14.6–46.0%) were located on small genomic regions, where strong candidate genes were found. The analysis using sequencing-based genotyping thus offers a powerful solution to map QTL with high resolution. Moreover, the RILs developed in this study serve as an excellent system for mapping and studying genetic basis of agricultural and biological traits of rice. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-010-1449-8) contains supplementary material, which is available to authorized users

Health outcomes among patients diagnosed with schizophrenia in the US veterans health administration population who transitioned from once-monthly to once-every-3-month Paliperidone Palmitate: an observational retrospective analysis

There is limited literature on treatment patterns, healthcare resource utilization (HRU), and costs among patients who transition from once-monthly paliperidone palmitate (PP1M) to once-every-3-month paliperidone palmitate (PP3M) in a real-world setting. Hence, this study compared treatment patterns, HRU, and costs 12-month pre- and post-PP3M transition among Veteran’s Health Administration (VHA) patients with schizophrenia.WOS:000488950000028Scopus - Affiliation ID: 60105072PMID: 31396809Science Citation Index Expanded - Social Sciences Citation IndexQ1 - Q2ArticleUluslararası işbirliği ile yapılan - EVETEkim2019YÖK - 2019-2

Economic outcomes in patients with chemotherapy-naive metastatic castration-resistant prostate cancer treated with enzalutamide or abiraterone acetate plus prednisone

Introduction: Prostate cancer (PC) is the second leading cause of cancer death among US men and accounts for considerable healthcare expenditures. We evaluated economic outcomes in men with chemotherapy-naı¨ve metastatic castration-resistant PC (mCRPC) treated with enzalutamide or abiraterone acetate plus prednisone (abiraterone). Methods: We performed a retrospective analysis on 3174 men (18 years or older) utilizing the Veterans Health Administration (VHA) database from 1 April 2014 to 31 March 2018. Men with mCRPC were included if they had at least one pharmacy claim for enzalutamide or abiraterone (first claim date = index date) following surgical or medical castration, had no chemotherapy treatment within 12 months prior to the index date, and had continuous VHA enrollment for at least 12 months pre- and post-index date. Men were followed until death, disenrollment, or end of study and were 1:1 propensity score matched (PSM). All-cause and PC-related resource use and costs per patient per month (PPPM) in the 12 months post index were compared between matched cohorts. Results: We identified 1229 men with mCRPC prescribed enzalutamide and 1945 prescribed abiraterone with mean ages of 74 and 73 years, respectively. After PSM, each cohort had 1160 patients. The enzalutamide cohort had fewer all-cause (2.51 vs 2.86; p\0.0001) and PC-related outpatient visits (0.86 vs 1.03; p\0.0001), with corresponding lower all-cause ($2588 vs$3115; p\0.0001) and PC-related ($1356 vs$1775; p\0.0001) PPPM outpatient costs compared with the abiraterone cohort. Allcause total costs (medical and pharmacy) PPPM ($8085 vs$9092; p = 0.0002) and PC-related total costs PPPM ($6321 vs$7280; p\0.0001) were significantly lower in the enzalutamide cohort compared with the abiraterone cohort. Conclusions: Enzalutamide-treated men with chemotherapy-naı ¨ve mCRPC had significantly lower resource utilization and healthcare costs compared with abiraterone-treated men. Plain Language Summary: Plain language summary available for this article.WOS:000516999800002Scopus - Affiliation ID: 60105072PMID: 32112280Science Citation Index ExpandedQ1 - Q2ArticleUluslararası işbirliği ile yapılan - EVETMayıs2020YÖK - 2019-2

High-throughput UAV-based rice panicle detection and genetic mapping of heading-date-related traits

IntroductionRice (Oryza sativa) serves as a vital staple crop that feeds over half the world's population. Optimizing rice breeding for increasing grain yield is critical for global food security. Heading-date-related or Flowering-time-related traits, is a key factor determining yield potential. However, traditional manual phenotyping methods for these traits are time-consuming and labor-intensive.MethodHere we show that aerial imagery from unmanned aerial vehicles (UAVs), when combined with deep learning-based panicle detection, enables high-throughput phenotyping of heading-date-related traits. We systematically evaluated various state-of-the-art object detectors on rice panicle counting and identified YOLOv8-X as the optimal detector.ResultsApplying YOLOv8-X to UAV time-series images of 294 rice recombinant inbred lines (RILs) allowed accurate quantification of six heading-date-related traits. Utilizing these phenotypes, we identified quantitative trait loci (QTL), including verified loci and novel loci, associated with heading date.DiscussionOur optimized UAV phenotyping and computer vision pipeline may facilitate scalable molecular identification of heading-date-related genes and guide enhancements in rice yield and adaptation

AirMeasurer: open-source software to quantify static and dynamic traits derived from multiseason aerial phenotyping to empower genetic mapping studies in rice

Low-altitude aerial imaging, an approach that can collect large-scale plant imagery, has grown in popularity recently. Amongst many phenotyping approaches, unmanned aerial vehicles (UAVs) possess unique advantages as a consequence of their mobility, flexibility and affordability. Nevertheless, how to extract biologically relevant information effectively has remained challenging. Here, we present AirMeasurer, an open-source and expandable platform that combines automated image analysis, machine learning and original algorithms to perform trait analysis using 2D/3D aerial imagery acquired by low-cost UAVs in rice (Oryza sativa) trials. We applied the platform to study hundreds of rice landraces and recombinant inbred lines at two sites, from 2019 to 2021. A range of static and dynamic traits were quantified, including crop height, canopy coverage, vegetative indices and their growth rates. After verifying the reliability of AirMeasurer-derived traits, we identified genetic variants associated with selected growth-related traits using genome-wide association study and quantitative trait loci mapping. We found that the AirMeasurer-derived traits had led to reliable loci, some matched with published work, and others helped us to explore new candidate genes. Hence, we believe that our work demonstrates valuable advances in aerial phenotyping and automated 2D/3D trait analysis, providing high-quality phenotypic information to empower genetic mapping for crop improvement

The feasibility study of non-invasive fetal trisomy 18 and 21 detection with semiconductor sequencing platform

Objective: Recent non-invasive prenatal testing (NIPT) technologies are based on next-generation sequencing (NGS). NGS allows rapid and effective clinical diagnoses to be determined with two common sequencing systems: Illumina and Ion Torrent platforms. The majority of NIPT technology is associated with Illumina platform. We investigated whether fetal trisomy 18 and 21 were sensitively and specifically detectable by semiconductor sequencer: Ion Proton. Methods: From March 2012 to October 2013, we enrolled 155 pregnant women with fetuses who were diagnosed as high risk of fetal defects at Xiamen Maternal & Child Health Care Hospital (Xiamen, Fujian, China). Adapter-ligated DNA libraries were analyzed by the Ion Proton??? System (Life Technologies, Grand Island, NY, USA) with an average 0.3 ?? sequencing coverage per nucleotide. Average total raw reads per sample was 6.5 million and mean rate of uniquely mapped reads was 59.0%. The results of this study were derived from BWA mapping. Z-score was used for fetal trisomy 18 and 21 detection. Results: Interactive dot diagrams showed the minimal z-score values to discriminate negative versus positive cases of fetal trisomy 18 and 21. For fetal trisomy 18, the minimal z-score value of 2.459 showed 100% positive predictive and negative predictive values. The minimal z-score of 2.566 was used to classify negative versus positive cases of fetal trisomy 21. Conclusion: These results provide the evidence that fetal trisomy 18 and 21 detection can be performed with semiconductor sequencer. Our data also suggest that a prospective study should be performed with a larger cohort of clinically diverse obstetrics patients.open2

Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages

Germplasm resource innovation is a crucial factor for cultivar development, particularly within the context of hybrid rice breeding based on the three-line system. Quan 9311A, a cytoplasmic male sterile (CMS) line, has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China. This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11, with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A. Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines. In this study, the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing. The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A, providing exceptional agronomic traits that are unavailable in earlier CMS lines. Despite the removal of the fertility restorer gene Rf3 from 93-11, numerous chromosomal segments from 93-11 persist in the Quan 9311A genome. Furthermore, the hybrid rice Quanyousimiao (QYSM) and the restorer line Wushansimiao (WSSM) were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis. It was found that QYSM carries a great number of superior alleles, which accounts for its high grain yield and wide adaptability. These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors. The study introduced innovative concepts to further integrate genomics with traditional breeding techniques. Ultimately, Quan 9311A signified a significant milestone in rice breeding technology, opening up novel avenues for hybrid rice development

Development of the fundamental power coupler for 324 MHz superconducting cavities

The China Spallation Neutron Source upgrade project (CSNS-II) has completed the preliminary design report and is expected to start in the fall of 2023. It plans to add two types of superconducting cavities: the 324-MHz double spoke superconducting cavity and the 648-MHz elliptical superconducting cavity in the linac section of the accelerator to upgrade the beam power from 100 to 500 kW, requiring more than 40 new fundamental power couplers (FPCs). These couplers will operate at pulse mode with a peak power ranging from 100 to 380 kW. To master the entire R&D process of the FPC for superconducting cavities, meanwhile, provide the horizontal test condition for various superconducting cavities research, a pair of 324-MHz power couplers for the double spoke superconducting cavity are developed. This coupler is a coaxial structure with a disk-warm ceramic window, and its characteristic impedance is 50  Ω. Multiphysics design is performed to ensure that the coupler meets the actual requirements. Structures of the coupler are optimized to realize a clean assembly with the cavity in Class 10 clean room and avoid window failure due to the bombardment of electrons generated by possible cavity field emission. We have successfully fabricated two FPCs and high power conditioned them on the test bench at room temperature. The test results show that FPCs can transmit a peak radio frequency (rf) power of 2 MW with a duty factor of 1.625% in traveling wave mode and an rf power of 500 kW with a duty factor of 3% in standing wave mode with arbitrary reflection wave phase. It meets the requirement of spoke cavities for CSNS-II—200 kW maximum power with a duty factor of 3%. Multipacting (MP) zones found during the high-power conditioning agree reasonably well with those predicted by simulations

Real-world utilization patterns of systemic immunosuppressants among US adult patients with atopic dermatitis.

At the time of this study, prior to the introduction of biologics in the US, systemic therapies used for the treatment of moderate-to-severe atopic dermatitis included off-label immunosuppressants and corticosteroids. Immunosuppressant therapy is associated with a substantial risk of side-effects, therefore needing clinical monitoring, and is likely to incur a significant healthcare burden for patients and payers. This retrospective cohort study based on claims data measured immunosuppressant use and its associated burden among US adult patients with atopic dermatitis covered under commercial or Medicare Supplemental insurance from January 01, 2010, to September 30, 2015. Overall, based on age, gender, region, and index year, 4201 control patients with atopic dermatitis without immunosuppressant use were matched with 4204 patients treated with immunosuppressants. The majority (68.5%) of patients using immunosuppressants were non-persistent with immunosuppressant treatment during the 12-month follow-up period after a mean (standard deviation) of 88.1 (70.7) days of immunosuppressant use; 72.3% required systemic steroid rescue treatment. Immunosuppressant users had higher incidence of immunosuppressant-related clinical events than controls; in addition, a larger proportion of immunosuppressant users versus controls developed cancer (0.28% vs 0.14%, respectively; P < 0.0001). Healthcare utilization and costs associated with clinical events and monitoring were also higher for immunosuppressant users compared with controls (total costs, $9516 vs$1630, respectively; P < 0.0001; monitoring costs, $363 vs$54, respectively; P < 0.0001). This study revealed that patients treated with systemic immunosuppressants often require systemic steroids or changes to treatment. The increase in immunosuppressant-related clinical events, including the need for increased monitoring with immunosuppressant treatment, compared with controls demonstrates a substantial treatment burden and highlights the unmet need for more effective long-term therapies for atopic dermatitis with improved safety profiles and reduced monitoring requirements