Simultaneous mutation detection of three homoeologous genes in wheat by High Resolution Melting analysis and Mutation Surveyor®

Background: TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful tool for reverse genetics, combining traditional chemical mutagenesis with high-throughput PCR-based mutation detection to discover induced mutations that alter protein function. The most popular mutation detection method for TILLING is a mismatch cleavage assay using the endonuclease CelI. For this method, locus-specific PCR is essential. Most wheat genes are present as three similar sequences with high homology in exons and low homology in introns. Locus-specific primers can usually be designed in introns. However, it is sometimes difficult to design locus-specific PCR primers in a conserved region with high homology among the three homoeologous genes, or in a gene lacking introns, or if information on introns is not available. Here we describe a mutation detection method which combines High Resolution Melting (HRM) analysis of mixed PCR amplicons containing three homoeologous gene fragments and sequence analysis using Mutation Surveyor® software, aimed at simultaneous detection of mutations in three homoeologous genes. Results: We demonstrate that High Resolution Melting (HRM) analysis can be used in mutation scans in mixed PCR amplicons containing three homoeologous gene fragments. Combining HRM scanning with sequence analysis using Mutation Surveyor® is sensitive enough to detect a single nucleotide mutation in the heterozygous state in a mixed PCR amplicon containing three homoeoloci. The method was tested and validated in an EMS (ethylmethane sulfonate)-treated wheat TILLING population, screening mutations in the carboxyl terminal domain of the Starch Synthase II (SSII) gene. Selected identified mutations of interest can be further analysed by cloning to confirm the mutation and determine the genomic origin of the mutation. Conclusion: Polyploidy is common in plants. Conserved regions of a gene often represent functional domains and have high sequence similarity between homoeologous loci. The method described here is a useful alternative to locus-specific based methods for screening mutations in conserved functional domains of homoeologous genes. This method can also be used for SNP (single nucleotide polymorphism) marker development and eco-TILLING in polyploid species.Chongmei Dong, Kate Vincent and Peter Shar

Genes Encoding Structurally Conserved Serpins in the Wheat Genome: Identification and Expression Profiles during Plant Development and Abiotic and Biotic Stress

Serpins constitute a family of proteins with a very wide distribution in nature. Serpins have a well-conserved tertiary structure enabling irreversible protease inhibition or other specific biochemical functions. We examined the 189 putative wheat serpin genes previously identified by Benbow et al. (2019) via analysis of gene annotations (RefSeq v1.0) and combined our previous examinations of wheat ESTs and the 454 genome assembly. We found that 81 of the 189 putative serpin genes, plus two manually annotated genes, encode full-length, structurally conserved serpins. Expression of these serpin genes during wheat development and disease/abiotic stress responses was analysed using a publicly available RNAseq database. Results showed that the wheat LR serpins, homologous to Arabidopsis AtSerpin1 and barley BSZx, are ubiquitously expressed across all tissues throughout the wheat lifecycle, whereas the expression of other wheat serpin genes is tissue-specific, including expression only in the grain, only in the root, and only in the anther and microspore. Nine serpin genes were upregulated in both biotic and abiotic responses. Two genes in particular were highly expressed during disease and abiotic challenges. Our findings provide valuable information for further functional study of the wheat serpins, which in turn may lead to their application as molecular markers in wheat breeding

Genes Encoding Structurally Conserved Serpins in the Wheat Genome: Identification and Expression Profiles during Plant Development and Abiotic and Biotic Stress

Serpins constitute a family of proteins with a very wide distribution in nature. Serpins have a well-conserved tertiary structure enabling irreversible protease inhibition or other specific biochemical functions. We examined the 189 putative wheat serpin genes previously identified by Benbow et al. (2019) via analysis of gene annotations (RefSeq v1.0) and combined our previous examinations of wheat ESTs and the 454 genome assembly. We found that 81 of the 189 putative serpin genes, plus two manually annotated genes, encode full-length, structurally conserved serpins. Expression of these serpin genes during wheat development and disease/abiotic stress responses was analysed using a publicly available RNAseq database. Results showed that the wheat LR serpins, homologous to Arabidopsis AtSerpin1 and barley BSZx, are ubiquitously expressed across all tissues throughout the wheat lifecycle, whereas the expression of other wheat serpin genes is tissue-specific, including expression only in the grain, only in the root, and only in the anther and microspore. Nine serpin genes were upregulated in both biotic and abiotic responses. Two genes in particular were highly expressed during disease and abiotic challenges. Our findings provide valuable information for further functional study of the wheat serpins, which in turn may lead to their application as molecular markers in wheat breeding

Mechanical properties and tribological behavior of Al0.5CoCrFeNb0.5Ni high-entropy alloy at high temperatures

The high-temperature mechanical properties and tribological behavior of the Al0.5CoCrFeNb0.5Ni high-entropy alloy (HEA) were investigated. The results show that Al0.5CoCrFeNb0.5Ni HEA consists of FCC, BCC and (Cr–Co–Fe)2Nb-type Laves phases. The hardness is about 572 HV at room temperature and decreases slightly at high temperatures, still maintaining a high value (>350 HV) at 900 °C. The yield strength is nearly 2000 MPa at room temperature and tends to decrease with rising temperature (800–1200 °C). The observation of the microstructure after the hot compression tests and the evaluation of the true stress-strain curves illustrate that the softening mechanism is primarily dynamic recrystallization, which occurs mainly in the FCC and BCC phases. The degree of wear increases and then decreases from 200 °C to 800 °C. The best wear resistance was observed at 800 °C, showing the maximum friction coefficient and the minimum wear rate, which was attributed to the increased oxidation that formed oxide layers mainly consisting of Cr2O3 to protect the wear surfaces. The wear mechanism of alloys is affected by temperature. Below 400 °C the wear is mainly abrasive and adhesive wear, at temperatures above 600 °C, the wear transitions from abrasive to oxidative wear, and at 800 °C the wear changes to oxidative wear

De Novo Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen Puccinia hordei Identifies Candidates for Three Avirulence Genes

Puccinia hordei (Ph) is a damaging pathogen of barley throughout the world. Despite its importance, almost nothing is known about the genomics of this pathogen, and a reference genome is lacking. In this study, the first reference genome was assembled for an Australian isolate of Ph (“Ph560”) using long-read SMRT sequencing. A total of 838 contigs were assembled, with a total size of 207 Mbp. This included both haplotype collapsed and separated regions, consistent with an estimated haploid genome size of about 150Mbp. An annotation pipeline that combined RNA-Seq of Ph-infected host tissues and homology to proteins from four other Puccinia species predicted 25,543 gene models of which 1,450 genes were classified as encoding secreted proteins based on the prediction of a signal peptide and no transmembrane domain. Genome resequencing using short-read technology was conducted for four additional Australian strains, Ph612, Ph626, Ph608 and Ph584, which are considered to be simple mutational derivatives of Ph560 with added virulence to one or two of three barley leaf rust resistance genes (viz. Rph3, Rph13 and Rph19). To identify candidate genes for the corresponding avirulence genes AvrRph3, AvrRph13 and AvrRph19, genetic variation in predicted secreted protein genes between the strains was correlated to the virulence profiles of each, identifying 35, 29 and 46 candidates for AvrRph13, AvrRph3 and AvrRph19, respectively. The identification of these candidate genes provides a strong foundation for future efforts to isolate these three avirulence genes, investigate their biological properties, and develop new diagnostic tests for monitoring pathogen virulence

Generation and molecular marker and cytological characterization of wheat – Secale strictum subsp. anatolicum derivatives

Cereal rye and its wild forms are important sources of genetic diversity for wheat breeding due to their resistances to biotic and abiotic stresses. Secale strictum subsp. anatolicum (Boiss.) K. Hammer (SSA) is a weedy relative of cultivated rye, S. cereale. Meiotic chromosome pairing in F1 hybrids of SSA and S. cereale reveals strong genomic affinity between the two genomes. A study of the transferability of S. cereale sequence-based markers to SSA and hexaploid triticale demonstrated their applicability for tracing SSA chromatin in wheat. The transferability of the markers was over 80% from homoeologous groups 1, 2, and 3, and greater than 70% from groups 4 to 7. This study focused on the generation and molecular and cytogenetic characterization of wheat–SSA alien derivatives. Twelve were identified using combinations of non-denaturing fluorescence in situ hybridization (ND-FISH), genomic in situ hybridization (GISH), and molecular marker analysis. All SSA chromosomes, except 3Ra and 6Ra, were transferred to wheat either in the form of monosomic additions (MA), mono-telosomic additions (MtA), double-mono-telosomic additions (dMtA), or double-monosomic additions (dMA). The germplasm developed in this study will help to enhance the genetic base of wheat and facilitate molecular breeding of wheat and triticale.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

A Novel JAK1 Inhibitor SHR0302 Combined With Prednisone for First-Line Treatment of Chronic Graft-Versus-Host Disease: A Phase I Clinical Trial

Chronic graft-versus-host disease (cGVHD) is a potentially life-threatening complication after allogeneic hematopoietic stem cell transplantation. Standard steroid first-line treatment could not satisfy therapeutic needs due to limited efficacy. As a highly selective Janus kinase (JAK) 1 inhibitor, SHR0302 exhibits a reduced inhibition effect on JAK2 and might have less effect on hematopoiesis. This phase I clinical trial investigated the tolerability and safety of SHR0302 in combination with prednisone, and its early efficacy evidence as a potential first-line treatment to moderate/severe cGVHD. The standard 3 + 3 dose escalation was implemented to find the optimal dose of SHR0302. And prednisone was concurrently administrated with a dose of 1 mg/kg/d and then gradually tapered after 2 weeks. Eighteen patients were enrolled into the study. Grade ≥ 3 treatment-related adverse events were observed in 38.9% of patients. Only one patient developed DLT (grade ≥ 3 hypercholesterolemia) in the highest dose-level group who had pre-existing hypercholesterolemia. The maximum tolerated dose was not reached. No patient discontinued treatment due to AEs. Sixteen out of 18 patients were evaluable for responses, the ORR at week 4 and week 24 were 94.4 and 87.5%, respectively. Overall, the treatment of SHR0302 combined with prednisone was safe and well-tolerated, preliminary clinical results presented a high response for previously untreated cGVHD and a significant reduction in prednisone use in this study. A phase II trial will be conducted to further investigate its therapeutic effects clinically