Quality traits analysis of 153 wheat lines derived from CIMMYT and China.

In order to understand the difference of quality for Chinese and CIMMYT wheat varieties (lines), we selected 153 wheat germplasm from both China and CIMMYT to explore the contribution relationship of different allelic variation combinations to wheat quality through genotyping and phenotyping, including grain hardness, polyphenol oxidase (PPO) activity, lipoxygenase (LOX) activity, yellow pigment (YP) content and protein content. In terms of flour milling quality, Chinese wheat varieties were mainly carrying Pina-D1a/Pinb-D1b, accounting for 32.0% of the total tested varieties, while the CIMMYT wheat lines were mainly carrying Pina-D1b/Pinb-D1a with 45.8% of the total collection. The distribution frequencies of subunit 1/2* and 5 + 10 were 47.0% and 42.5%, respectively, in CIMMYT varieties, however they were only 31.4% and 13.7% respectively of the Chinese wheat tested varieties. In addition, the proportion of phytoene synthase (PSY) allele, PPO allele and LOX active allele were roughly the same between Chinese and CIMMYT varieties. Based on the present study, we found that Pina gene had a greater impact on grain hardness value than Pinb gene; The influence of PPO-A1 gene on polyphenol oxidase activity was more significant than PPO-D1 gene. The high protein content of varieties mostly containing hardness genes and 1/2*/5 + 10 subunit combinations. Based on the present study, we found that the quality gene distribution of Chinese and CIMMYT varieties was quite different, for instance, the high-quality HMW-GS subunits of Chinese varieties were lower than CIMMYT lines. It will be much useful for Chinese wheat breeders to develop good quality wheat variety by crossing with 3 good strong gluten CIMMYT wheat lines by molecular marker-assisted selection.

A deep learning-based post-processing method for automated pulmonary lobe and airway trees segmentation using chest CT images in PET/CT.

Background: The proposed algorithm could support accurate localization of lung disease. To develop and validate an automated deep learning model combined with a post-processing algorithm to segment six pulmonary anatomical regions in chest computed tomography (CT) images acquired during positron emission tomography/computed tomography (PET/CT) scans. The pulmonary regions have five pulmonary lobes and airway trees. Methods: Patients who underwent both PET/CT imaging with an extra chest CT scan were retrospectively enrolled. The pulmonary segmentation of six regions in CT was performed via a convolutional neural network (CNN) of DenseVNet architecture with some post-processing algorithms. Three evaluation metrics were used to assess the performance of this method, which combined deep learning and the post-processing method. The agreement between the combined model and ground truth segmentations in the test set was analyzed. Results: A total of 640 cases were enrolled. The combined model, which involved deep learning and post-processing methods, had a higher performance than the single deep learning model. In the test set, the all-lobes overall Dice coefficient, Hausdorff distance, and Jaccard coefficient were 0.972, 12.025 mm, and 0.948, respectively. The airway-tree Dice coefficient, Hausdorff distance, and Jaccard coefficient were 0.849, 32.076 mm, and 0.815, respectively. A good agreement was observed between our segmentation in every plot. Conclusions: The proposed model combining two methods can automatically segment five pulmonary lobes and airway trees on chest CT imaging in PET/CT. The performance of the combined model was higher than the single deep learning model in each region in the test set.

Genome-wide Association Study for Starch Pasting Properties in Chinese Spring Wheat.

In order to understand the genetic basis of starch pasting viscosity characteristics of Chinese spring wheat, we assessed the genetic variation of RVA parameters determined by the Rapid Visco Analyser in a panel of 192 Chinese spring wheat accessions grown in Er'shi, Shihezi and Zhaosu during 2012 and 2013 cropping seasons. A genome-wide association study with 47,362 single nucleotide polymorphism (SNP) markers was conducted to detect marker-trait associations using mixed linear model. Phenotypic variations of RVA parameters ranged from 1.6 to 30.7% and broad-sense heritabilities ranged from 0.62 to 0.91. Forty-one SNP markers at 25 loci were significantly associated with seven RVA traits in at least two environments; among these, 20 SNPs were located in coding sequences (CDS) of 18 annotation genes, which can lead to discovering novel genes underpinning starch gelatinization in spring wheat. Haplotype analysis revealed one block for breakdown (BD) on chromosome 3B and two blocks for pasting temperature (T) on chromosome 7B. Cultivars with superior haplotypes at these loci showed better starch pasting viscosity than the average of all cultivars surveyed. The identified loci and associated markers provide valuable sources for future functional characterization and genetic improvement of starch quality in wheat.

Combined Transcriptome and Proteome Analysis of Anthers of AL-type Cytoplasmic Male Sterile Line and Its Maintainer Line Reveals New Insights into Mechanism of Male Sterility in Common Wheat.

Cytoplasmic male sterility (CMS) plays an essential role in hybrid seeds production. In wheat, orf279 was reported as a CMS gene of AL-type male sterile line (AL18A), but its sterility mechanism is still unclear. Therefore, transcriptomic and proteomic analyses of the anthers of AL18A and its maintainer line (AL18B) were performed to interpret the sterility mechanism. Results showed that the electron transport chain and ROS scavenging enzyme expression levels changed in the early stages of the anther development. Biological processes, i.e., fatty acid synthesis, lipid transport, and polysaccharide metabolism, were abnormal, resulting in pollen abortion in AL18A. In addition, we identified several critical regulatory genes related to anther development through combined analysis of transcriptome and proteome. Most of the genes were enzymes or transcription factors, and 63 were partially homologous to the reported genic male sterile (GMS) genes. This study provides a new perspective of the sterility mechanism of AL18A and lays a foundation to study the functional genes of anther development.

Large-scale transcriptome comparison reveals distinct gene activations in wheat responding to stripe rust and powdery mildew.

BACKGROUND: Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Similar mechanisms and gene transcripts are assumed to be involved in the host defense response because both pathogens are biotrophic fungi. The main objective of our study was to identify co-regulated mRNAs that show a change in expression pattern after inoculation with Pst or Bgt, and to identify mRNAs specific to the fungal stress response. RESULTS: The transcriptome of the hexaploid wheat line N9134 inoculated with the Chinese Pst race CYR 31 was compared with that of the same line inoculated with Bgt race E09 at 1, 2, and 3 days post-inoculation. Infection by Pst and Bgt affected transcription of 23.8% of all T. aestivum genes. Infection by Bgt triggered a more robust alteration in gene expression in N9134 compared with the response to Pst infection. An array of overlapping gene clusters with distinctive expression patterns provided insight into the regulatory differences in the responses to Bgt and Pst infection. The differentially expressed genes were grouped into seven enriched Kyoto Encyclopedia of Genes and Genomes pathways in Bgt-infected leaves and four pathways in Pst-infected leaves, while only two pathways overlapped. In the plant-pathogen interaction pathway, N9134 activated a higher number of genes and pathways in response to Bgt infection than in response to Pst invasion. Genomic analysis revealed that the wheat genome shared some microbial genetic fragments, which were specifically induced in response to Bgt and Pst infection. CONCLUSIONS: Taken together, our findings indicate that the responses of wheat N9134 to infection by Bgt and Pst shows differences in the pathways and genes activated. The mass sequence data for wheat-fungus interaction generated in this study provides a powerful platform for future functional and molecular research on wheat-fungus interactions.

Pattern recognition of multiple excitation autofluorescence spectra for colon tissue classification.

OBJECTIVES: The aim of this study was to explore the usefulness of multiple excitation autofluorescence (AF) and a spectral feature-based pattern recognition in classification of colon tissues. MATERIALS AND METHODS: Under four different excitation wavelengths (337, 375, 405 and 460 nm), AF spectra of freshly excised normal and adenocarcinoma colon tissues were measured. Pattern recognition method including features extraction, data reduction using principal component analysis (PCA) and Fisher's discriminant analysis (FDA) were performed for classification. RESULTS: There was a significantly difference between spectral patterns of normal and adenocarcinoma tissues. Compared with the other three excitation wavelengths, the AF spectra obtained under 337 nm excitation provided more diagnostic information, but also more sensitive to the trivial change resulted from neoplastic transformation. For discriminating normal from adenocarcinoma tissues, the sensitivity, specificity and accuracy using 337 nm excitation in the present study were 88.9%, 80.0% and 83.9%, respectively. Compared these values with those determined from multispectral data analysis, our findings indicate that the latter has higher specificity while maintaining the same sensitivity (sensitivity 88.9% vs. 88.9%, specificity 91.4% vs. 80.0%, and accuracy 90.3% vs. 83.9%). CONCLUSION: This study suggests that the pattern recognition of the multiple excitation AF spectra is an effective algorithm for improving the diagnostic accuracy of adenocarcinoma.