Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings.

KEY MESSAGE: Ten stable loci for freezing tolerance (FT) in wheat were detected by genome-wide association analysis. The putative candidate gene TaRPM1-7BL underlying the major locus QFT.ahau-7B.2 was identified and validated. Frost damage restricts wheat growth, development, and geographical distribution. However, the genetic mechanism of freezing tolerance (FT) remains unclear. Here, we evaluated FT phenotypes of 245 wheat varieties and lines, and genotyped them using a Wheat 90 K array. The association analysis showed that ten stable loci were significantly associated with FT (P < 1 × 10-4), and explained 6.45-26.33% of the phenotypic variation. In particular, the major locus QFT.ahau-7B.2 was consistently related to all nine sets of FT phenotypic data. Based on five cleaved amplified polymorphic sequence (CAPS) markers closely linked to QFT.ahau-7B.2, we narrowed down the target region to the 570.67-571.16 Mb interval (0.49 Mb) on chromosome 7B, in which four candidate genes were annotated. Of these, only TaRPM1-7BL exhibited consistent differential expression after low temperature treatment between freezing-tolerant and freezing-sensitive varieties. The results of cloning and whole-exome capture sequencing indicated that there were two main haplotypes for TaRPM1-7BL, including freezing-tolerant Hap1 and freezing-sensitive Hap2. Based on the representative SNP (+1956, A/G), leading to an amino acid change in the NBS domain, a CAPS marker (CAPS-TaRPM1-7BL) was developed and validated in 431 wheat varieties (including the above 245 materials) and 318 F2 lines derived from the cross of 'Annong 9267' (freezing-tolerant) × 'Yumai 9' (freezing-sensitive). Subsequently, the TaRPM1-7BL gene was silenced in 'Yumai 9' by virus-induced gene silencing (VIGS), and these silenced wheat seedlings exhibited enhanced FT phenotypes, suggesting that TaRPM1-7BL negatively regulates FT. These findings are valuable for understanding the complex genetic basis of FT in wheat.

[A Real-time Reconstruction Method of CBCT Short Scan Based on Attenuation Compensation].

Aiming at the problem of timeliness of CBCT reconstruction, a CBCT fast short scan reconstruction method is proposed. At the same time, the image reconstruction process in which a new attenuation compensation algorithm is applied to improve image quality. When performing FDK three-dimensional reconstruction of a single-frame acquisition image, the Parker-weighted image is calculated in real time, and a new attenuation compensation algorithm is applied in the back projection process to complete the short scan Parker-weighted reconstruction. This method simulates the CBCT synchronous acquisition and reconstruction process by establishing collection and reconstruction threads. Under the premise of satisfying the reconstruction quality, the reconstruction can be completed within 1 to 2 seconds after the patient collection is completed, which achieves the purpose of real-time.

A supervised network for fast image-guided radiotherapy (IGRT) registration.

3D/3D image registration in IGRT, which aligns planning Computed Tomography (CT) image set with on board Cone Beam CT (CBCT) image set in a short time with high accuracy, is still a challenge due to its high computational cost and complex anatomical structure of medical image. In order to overcome these difficulties, a new method is proposed which contains a coarse registration and a fine registration. For the coarse registration, a supervised regression convolutional neural networks (CNNs) is used to optimize the spatial variation by minimizing the loss when combine the CT images with the CBCT images. For the fine registration, intensity-based image registration is used to calculate the accurate spatial difference of the input image pairs. A coarse registration can get a rough result with a wide capture range in less than 0.5 s. Sequentially a fine registration can get accurate results in a reasonable short time. RSD-111 T chest phantom was used to test our new method. The set-up error was calculated in less than 10s in time scale, and was reduced to sub-millimeter level in spatial scale. The average residual errors in translation and rotation are within ±0.5 mm and ± 0.2°.

[Design and Implementation of Automated QA Software for Cone Beam CT Image].

In order to improve the speed and accuracy of cone beam CT image quality assurance, an automatic image quality assurance software based on feature extraction is designed and implemented. This paper introduces how the software can realize the positioning of Catphan500 phantoms and the selection of ROI in each module through Canny algorithm and Hough transform circle detection. For the different modules in the Catphan500 phantom, this paper describes the calculation methods of HU accuracy, spatial linearity, HU uniformity and spatial linearity in the software. Finally, the article verifies the feasibility of the software through experiments.

Fast MCsquare-Based Independent Dose Verification Platform for Pencil Beam Scanning Proton Therapy.

PURPOSE: To commission MCsquare (a multi-cores CPU-based dose calculation engine) for pencil beam scanning (PBS) proton therapy, integrate it into RayStation treatment plan system (TPS) to create a dedicated platform for fast independent dose verification. METHOD: A MCsquare-based independent dose verification platform (MC2InRS) was developed to realize automatic dose re-calculation for clinical use, including data preparation, dose calculation, 2D/3D gamma analysis. MCsquare was commissioned based on in-air lateral dose profiles, integrated depth dose, and the absolute dose of different beam energies for Proteus®ONE. MC2InRS was validated with measurement data using various targets and depths in a water phantom. This study also investigated 15 clinical cases to demonstrate the feasibility and effectiveness of MC2InRS platform in clinic practice. RESULTS: Between simulation and measurement, the distal range differences at 80% (R80) and 20% (R20) dose levels for each energy were below 0.05 mm, and 0.1 mm, respectively, and the absolute dose differences were below 0.5%. 29 out of 36 QA planes reached a 100% gamma passing rate (GPR) for 2%/2mm criteria, and a minimum of 98.3% gamma was obtained in water phantom between simulation and measurement. For the 15 clinical cases investigated, the average 2D GPR (2%/2mm) was 95.4%, 99.3% for MCsquare vs. measurement, MCsquare vs. TPS, respectively. The average 3D GPR (2%/2mm) was 98.9%, 95.3% for MCsquare vs. TPS in water, and computed tomography (CT), respectively. CONCLUSION: MC2InRS, a fast, independent dose verification platform, has been developed to perform dose verification with high accuracy and efficiency for Pencil Bream Scanning (PBS). Its potential to be applied in routine clinical practice has also been discussed.