Search

Fungal effectors of wheat stem rust The fungal pathogen Ug99 (named for its identification in Uganda in 1999) threatens wheat crops worldwide. Ug99 can kill entire fields of wheat and is undeterred by many of the disease-resistance genes that otherwise protect wheat crops. Two papers describe two peptides secreted by the fungus as it attacks the wheat (see the Perspective by Moscou and van Esse). Chen et al. show that fungal AvrSr50 binds to the plant's immune receptor Sr50, and Salcedo et al. show that fungal AvrSr35 binds to Sr35. Successful binding activates the plant's immune defenses. Removing or inactivating these Avr effectors leaves the plant defenseless and susceptible to disease. Science , this issue p. 1607 , p. 1604 ; see also p. 1541

To investigate the clinical efficacy of continuous irrigation combined with closed thoracic drainage for esophagojejunal anastomotic fistula (EJAF) complicated with mediastinal, thoracic and abdominal infection after total gastrectomy.Clinical data of 22 EJAF patients complicated with mediastinal, thoracic and abdominal infection after radical gastrectomy at Department of General Surgery of the 901th Hospital of PLA from June 2012 to May 2018 were retrospectively analyzed. Case inclusion criteria:(1) gastric adenocarcinoma confirmed by preoperative endoscopic pathology undergoing radical total gastrectomy without severe organ dysfunction;(2)EJAF complicated with mediastinal, thoracic and abdominal infections diagnosed by postoperative radiography, the presence of pleural effusion confirmed by CT and ultrasound. Among them, 10 cases were treated with simple thoracic closed drainage (single drainage group); 12 cases received same closed thoracic drainage, and a rubber catheter was placed next to the closed thoracic drainage tube in the same sinus. A 0.9% sodium chloride solution was applied in continuous drip irrigation with drip velocity at 50 to 100 ml/h(continuous flushing plus drainage group). Infection indicators, anastomotic fistula healing time and related clinical indicators were compared between the two groups.In the simple drainage group, 5 cases were males, age was (61.9±10.7) years old, 4 cases received laparoscopic surgery, 6 cases received open surgery, 6 cases were EJAF grade III, 4 cases were EJAF IV. In continuous flushing and drainage group, 6 cases were males, age was (61.7±11.0) years old, 7 cases received laparoscopic surgery, 5 cases received open surgery, 6 cases were EJAF grade III, and 6 cases were EJAF grade IV. Baseline data including gender, age, underlying diseases, preoperative hematological examination indexes, surgical methods, tumor TNM stage and EJAF grade were not significantly different between the two groups (all P0.05). When postoperative EJAF was complicated with mediastinal, thoracic and abdominal infection, biochemical parameters including white blood cell, procalcitonin, C-reactive protein were not significantly different between two groups (all P0.05). All patients of both groups achieved clinical cure without death. Compared with the simple drainage group after closed thoracic drainage, the continuous irrigation plus drainage group had significantly shorter duration of infection parameters returning to normal levels [white blood cell count: (6.8 ± 2.0) days vs.(10.5±3.0) days, t=4.062, P0.001; procalcitonin: (7.5±1.0) days vs. (9.2±1.9) days, t=3.236, P=0.040; C-reactive protein: (8.8±1.0) days vs. (11.2±1.5) days, t=5.177, P0.001], meanwhile time in surgical ICU [(4.9±2.5) days vs. (9.9±6.7) days, t=2.935, P=0.006], healing time of fistula [(42.9±12.5) days vs. (101.8±53.2) days, t=4.187, P=0.001] and total postoperative hospital stay [(62.3±15.8) days vs. (119.7 ±59.4) days, t=3.634, P=0.002] were significantly shorter, and total hospitalization cost was significantly lower (median 86 000 yuan vs. 124 000 yuan, Z=2.063, P=0.040) in the continuous irrigation plus drainage group.The continuous closed thoracic drainage with 0.9% sodium chloride solution can accelerate infection control and remission of EJAF patients complicated with mediastinal, thoracic and abdominal infections, and shorten the healing time of anastomotic fistula.

To determine the incidence of surgical site infection (SSI) after abdominal surgery and to further evaluate the related risk factors of SSI in China.The multicenter cross-sectional study collected clinical data of all adult patients who underwent abdominal surgery from May 1, 2018 to May 31, 2018 in 30 domestic hospitals, including basic information, perioperative parameters, and incisional microbial culture results. The primary outcome was the incidence of SSI within postoperative 30 days. SSI was classified into superficial incision infection, deep incision infection, and organ/gap infection according to the US Centers for Disease Control and Prevention (CDC) criteria. The secondary outcome variables were ICU stay, postoperative hospital stay, total hospital stay, 30-day mortality and treatment costs. Multivariate logistic regression was used to analyze the risk factors of SSI.A total of 1666 patients were enrolled in the study, including 263 cases of East War Zone Hospital of PLA, 140 cases of Affiliated Hospital of Qingdao University, 108 cases of The First Affiliated Hospital of Nanchang University, 87 cases of Central War Zone Hospital of PLA, 77 cases of West China Hospital, 74 cases of Guangdong General Hospital, 71 cases of Chenzhou First People's Hospital, 71 cases of Zigong First People's Hospital, 64 cases of Zhangjiagang First People's Hospital, 56 cases of Nanyang City Central Hospital, 56 cases of Lanzhou General Hospital of Lanzhou Military Command, 56 cases of Shandong Provincial Hospital, 52 cases of Shangqiu First People's Hospital, 52 cases of People's Hospital of Xinjiang Uygur Autonomous Region, 48 cases of The Second Xiangya Hospital of Central South University, 48 cases of Chinese PLA General Hospital, 44 cases of Affiliated Hospital of Xuzhou Medical University, 38 cases of Hunan Province People's Hospital, 36 cases of Dongguan Kanghua Hospital, 30 cases of Shaoxing Central Hospital, 30 cases of Northern Jiangsu People's Hospital, 29 vases of The First Affiliated Hospital of Zhengzhou University, 27 cases of General Hospital of Tianjin Medical University, 22 cases of Zigong Fourth People's Hospital, 21 cases of The Second Hospital of University of South China, 18 cases of Tongji Hospital, 15 cases of Nanchong Central Hospital, 12 cases of The 901th Hospital of PLA, 11 cases of Hunan Cancer Hospital, 10 cases of Lanzhou University Second Hospital. There were 1019 males and 647 females with mean age of (56.5±15.3) years old. SSI occurred in 80 patients (4.8%) after operation, including 39 cases of superficial incision infection, 16 cases of deep incision infection, and 25 cases of organ/interstitial infection. Escherichia coli was the main pathogen of SSI, and the positive rate was 32.5% (26/80). Compared with patients without SSI, those with SSI had significantly higher ICU occupancy rate [38.8%(31/80) vs. 13.9%(220/1586), P0.001], postoperative hospital stay (median 17 days vs. 7 days, P0.001) and total hospital stay (median 22 days vs. 13 days, P0.001), and significantly higher cost of treatment (median 75 000 yuan vs. 44 000 yuan, P0.001). Multivariate analysis showed that male rise(OR=2.110, 95%CI:1.175-3.791, P=0.012), preoperative blood glucose level rise(OR=1.100, 95%CI: 1.012-1.197, P=0.026), operative time (OR=1.006, 95%CI:1.003-1.009, P0.001) and surgical incision grade (clean-contaminated incision:OR=10.207, 95%CI:1.369-76.120, P=0.023; contaminated incision: OR=10.617, 95%CI:1.298-86.865, P=0.028; infection incision: OR=20.173, 95%CI:1.768-230.121, P=0.016) were risk factors for SSI; and laparoscopic surgery (OR=0.348, 95%CI:0.192-0.631, P=0.001) and mechanical bowel preparation(OR=0.441,95%CI:0.221-0.879, P=0.020) were protective factors for SSI.The incidence of postoperative SSI in patients with abdominal surgery in China is 4.8%. SSI can significantly increase the medical burden of patients. Preoperative control of blood glucose and mechanical bowel preparation are important measures to prevent SSI.

Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. With the vast amount of SNP variation data accumulated for wheat in recent years, the presented imputation framework will greatly improve prediction accuracy in breeding populations and increase resolution of trait mapping hence, facilitate cross-referencing of genotype datasets available across different wheat populations.

Gene expression has been widely used in functional genomics research; however, the gene expressions quantified with different methods have been frequently inconsistent, thus challenging the conclusions from such research. Here we have addressed this issue, while taking into account RNA alternative splicing. We found that when a gene was subjected to RNA alternative splicing, it was impossible or difficult to properly quantify the expression of a transcript of the gene or its overall expression using quantitative real-time PCR (qPCR), Northern hybridization, microarray, or serial analysis of gene expression. Shot-gun RNA-seq was the most proper to quantify the expression of a transcript or a gene in such cases. Moreover, the expressions of individual transcripts quantified by shot-gun RNA-seq were highly reproducible (r = 0.90–0.98) between individuals. Therefore, shot-gun or full-length RNA-seq should be the method of choice to properly quantify the expression of a transcript or a gene.

Summary Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence‐based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome‐wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans‐acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low‐recombining pericentromeric regions of chromosomes., Significance Statement This study offers insights into the genetic basis of recombination rate variation in allopolyploid wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive recombination rate QTL can be utilized to manipulate crossover frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low recombining pericentromeric regions of chromosomes.

In order to adapt to the application requirements of GNSS receivers in different scenarios, study the method of the performance of dynamic measurement accuracy for GNSS receiver and improve the performance of accuracy for GNSS receiver, a polynomial curve fitting algorithm is proposed in this paper for the application in dynamic and high-dynamic scenarios. In addition, taking the velocity measurement accuracy as an example, we compared the actual output data of the GNSS simulator and the navigation receiver to analyze the influence of various error sources on the velocity measurement accuracy of the navigation receiver and reduce the accidental error. The experimental results show that the performance of measurement accuracy for GNSS receiver has been improved by more than 25%, which provides a basis for the selection of velocity measurement algorithm models for various types of carriers in different scenarios.

The GPS L1C signals are the new civil signals transmitted in the L1 band during the course of GPS modernization. The double-channel structure of the data channel and pilot channel is used in the L1C signals. The pilot channel has higher transmission power, facilitate capturing and tracking of signals. The MBOC modulation method is used to broaden transmission bandwidth of signals and make receiving and processing of signals more flexible. Higher precision and better multi-path resistance can be achieved in case of matched receiving. The satellite transmitting GPS L1C signals is not formally launched, so research on capturing, tracking and telegram parsing of L1C signals is less. This paper deeply studies receiving and processing method of GPS L1C signals, validates correctness of capturing, tracking and telegram decoding algorithm by using the L1C signals transmitted by Japan QZSS satellite, and provides references for receiving, processing and large-scale application of GPS L1C signals and signals of navigation systems such as Beidou system.

Wheat (Triticum aestivum L.) is a primary staple cereal and significant source of mineral nutrients in human diets. Therefore, increasing concen - tration of the essential mineral, Zn, and decreas - ing concentration of the toxic mineral, Cd, could significantly improve human health. Because plant mechanisms for uptake and translocation of Cd and Zn are related, we assessed both Cd and Zn concentration to evaluate their indepen - dence in hard winter wheat germplasm. Grain Cd concentrations of some genotypes grown in Nebraska trials were above the Codex guidance level (0.2 mg kg -1 ), and highly repeatable dif - ferences in grain Cd were found between pairs of low and moderate-Cd commercial cultivars. Grain Cd concentration was predicted by Cd concentration in aboveground plant tissues at anthesis. However, grain Zn concentration was not predicted by Zn concentration in aboveg - round plant tissues. Genome-wide associa- tion scans using high-density single nucleotide polymorphism (SNp) markers identified Cd- associated SNps on 5AL in a region homoeolo - gous to the Cdu1 locus on 5BL in durum wheat (Triticum turgidum L. var. durum Desf.). Genetic regulation of grain cadmium concentration in bread wheat may be more complex than in durum wheat because epistatic interactions between SNp markers were identified, and SN p marker haplotypes were imperfect predictors of grain Cd phenotype. The SN p marker asso - ciations with Zn concentration were weak and inconsistent across trials, and Zn concentration was independent of 5AL markers. The inde - pendent genetic regulation of grain Cd and Zn concentrations indicates that breeding low Cd hard winter wheat genotypes without reducing Zn concentration has high potential for success.

Background The soybean cyst nematode (SCN), Heterodera glycines, is one of the most devastating diseases limiting soybean production worldwide. It is known that small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play important roles in regulating plant growth and development, defense against pathogens, and responses to environmental changes. Results In order to understand the role of soybean miRNAs during SCN infection, we analyzed 24 small RNA libraries including three biological replicates from two soybean cultivars (SCN susceptible KS4607, and SCN HG Type 7 resistant KS4313N) that were grown under SCN-infested and -noninfested soil at two different time points (SCN feeding establishment and egg production). In total, 537 known and 70 putative novel miRNAs in soybean were identified from a total of 0.3 billion reads (average about 13.5 million reads for each sample) with the programs of Bowtie and miRDeep2 mapper. Differential expression analyses were carried out using edgeR to identify miRNAs involved in the soybean-SCN interaction. Comparative analysis of miRNA profiling indicated a total of 60 miRNAs belonging to 25 families that might be specifically related to cultivar responses to SCN. Quantitative RT-PCR validated similar miRNA interaction patterns as sequencing results. Conclusion These findings suggest that miRNAs are likely to play key roles in soybean response to SCN. The present work could provide a framework for miRNA functional identification and the development of novel approaches for improving soybean SCN resistance in future studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3963-4) contains supplementary material, which is available to authorized users.

In the past three years, a trend towards the centralisation of decision-making power in Chinese foreign policy instituted by Xi Jinping has become more and more apparent. The driver of the shift in Chinese foreign policy is the reform of its decision-making system. The ‘reform’ not only refers to institution building but also includes change of the former procedures of foreign policy decisionmaking to create a more efficient decision-making system.

File contains 2 supplementary figures and 4 supplementary tables. Figure S1. The effects of different TopHap alignment parameters on the proportion of RNA-seq reads misaligned to single copy homoeologous genes in the wheat genome. Figure S2. Distribution of log10 FPKM values for all genes in each biological replicate. Figure S3. Proportion of RNA-seq reads for RKQQC (orange) and MCCFC (blue) datasets mapped to the public SCCL reference genome. Standard error for each time-point is shown. Figure S4. Distribution of Pearson correlation coefficient (PCC) values estimated for the same gene pairs by comparing the expression values from the MCCFC dataset with those in the RKQQC dataset. The PCC value for wheat and Pgt genes are shown in grey and red, respectively. Table S1. Summary of next-generation sequence data generated for this study. Data is available from the NCBI SRA BioProject PRJNA347320. Table S3. Summary of genomic assemblies, genome annotations using the PASA pipeline and BUSCO assembly quality assessments for each P. graminis isolate. Table S20. Summary of BLAST2GO enrichment analysis of over represented wheat gene ontology terms in the three network edge conservation groups: MCCFC-specific, RKQQC-specific and conserved. Table S21. Summary of metadata for the combined GO sub-networks. (DOCX 960Â kb)

After signing a bilateral free trade agreement with China and joining in the China-led Asian Infrastructure Investment Bank (AIIB), Switzerland has become one of China’s best partners in Europe. The bilateral relationship has been upgraded from “strategic partnership” to “innovative strategic partnership,” and is regarded by the Chinese as “a model relationship for China-European countries.” Two fundamental reasons explain why Switzerland has achieved such harmonious relations with the world’s second largest economy: first, there is no historical conflict between the two countries; second, Switzerland is more pragmatic than other European countries in strengthening bilateral cooperation with China. So far, the two countries have institutionalized dialogues and other exchanges involving both elites and the public; sensitive issues have been properly handled without obstructing the development of their bilateral relations. As ever closer ties are being built between China and Europe as a whole, the Beijing-Bern relationship can serve as a model for other European countries.

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat. © 2014 The Authors Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

The emergence of new sequencing technologies has provided fast and cost-efficient strategies for high-resolution mapping of complex genomes. Although these approaches hold great promise to accelerate genome analysis, their application in studying genetic variation in wheat has been hindered by the complexity of its polyploid genome. Here, we applied the next-generation sequencing of a wheat doubled-haploid mapping population for high-resolution gene mapping and tested its utility for ordering shotgun sequence contigs of a flow-sorted wheat chromosome. A bioinformatical pipeline was developed for reliable variant analysis of sequence data generated for polyploid wheat mapping populations. The results of variant mapping were consistent with the results obtained using the wheat 9000 SNP iSelect assay. A reference map of the wheat genome integrating 2740 gene-associated single-nucleotide polymorphisms from the wheat iSelect assay, 1351 diversity array technology, 118 simple sequence repeat/sequence-tagged sites, and 416,856 genotyping-by-sequencing markers was developed. By analyzing the sequenced megabase-size regions of the wheat genome we showed that mapped markers are located within 40−100 kb from genes providing a possibility for high-resolution mapping at the level of a single gene. In our population, gene loci controlling a seed color phenotype cosegregated with 2459 markers including one that was located within the red seed color gene. We demonstrate that the high-density reference map presented here is a useful resource for gene mapping and linking physical and genetic maps of the wheat genome.

The Arabidopsis ethylene-responsive element-binding factor (AtERF) family of transcription factors has approximately 120 members, all of which possess a highly conserved ERF domain. AtERF1, AtERF4, AtEBP and CBF1 are members from different phylogenetic subgroups within the family. Electrophoretic mobility shift assay analyses revealed that the ERF domains of these four proteins were capable of binding specifically to either GCC or dehydration-responsive element (DRE) motifs. In vitro and in vivo binding assays of the four AtERFs with the DRE motif showed that the recognition of the CG step was indispensable in all four of the specific binding reactions, implying that there may be a universal binding characteristic of various ERF domains binding to a given consensus (e.g. the DRE motif). In addition, the core DNA-binding motifs preferred by the four AtERFs were identified, and all of these motifs contained a conserved CG step core. Thus, conserved recognition of the CG step may be the foundation of the formation of the stable complex by the ERF domain with the DRE motif, which is probably determined by the highly conserved residues presented in the DNA contact surface among the whole AtERF family members. The different preferences at flanking bases of individual ERF domains, which appear to be attributed to the subfamily- or subgroup-specific residues, may be essential discrimination of the target binding motif from various similar sequences by divergent AtERF domains.

Extraction of plant proteins using typical extraction buffers leaves insoluble debris that cannot be investigated by conventional 2-DE technologies. In this paper, we present a scalable, off-line procedure for extraction of Arabidopsis thaliana homogenates that can be used in combination with both in-gel digestion and mass spectrometry. Based on sequential NaCl gradients and strong detergent fractionation, this new strategy allowed detection of 11 novel proteins from Arabidopsis thaliana that were altered in response to chilling stress.

Identification of downstream target genes of stress-relating transcription factors (TFs) is desirable in understanding cellular responses to various environmental stimuli. However, this has long been a difficult work for both experimental and computational practices. In this research, we presented a novel computational strategy which combined the analysis of the transcription factor binding site (TFBS) contexts and machine learning approach. Using this strategy, we conducted a genome-wide investigation into novel direct target genes of dehydration responsive element binding proteins (DREBs), the members of AP2-EREBPs transcription factor super family which is reported to be responsive to various abiotic stresses in Arabidopsis. The genome-wide searching yielded in total 474 target gene candidates. With reference to the microarray data for abiotic stresses-inducible gene expression profile, 268 target gene candidates out of the total 474 genes predicted, were induced during the 24-h exposure to abiotic stresses. This takes about 57% of total predicted targets. Furthermore, GO annotations revealed that these target genes are likely involved in protein amino acid phosphorylation, protein binding and Endomembrane sorting system. The results suggested that the predicted target gene candidates were adequate to meet the essential biological principle of stress-resistance in plants.

International audience; Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.

Next-generation sequencing (NGS) provides a powerful tool for the discovery of important genes and alleles in crop plants and their wild relatives. Despite great advances in NGS technologies, whole-genome shotgun sequencing is cost-prohibitive for species with complex genomes. An attractive option is to reduce genome complexity to a single chromosome prior to sequencing. This work describes a strategy for studying the genomes of distant wild relatives of wheat by isolating single chromosomes from addition or substitution lines, followed by chromosome sorting using flow cytometry and sequencing of chromosomal DNA by NGS technology. We flow-sorted chromosome 5M(g) from a wheat/Aegilops geniculata disomic substitution line [DS5M(g) (5D)] and sequenced it using an Illumina HiSeq 2000 system at approximately 50 × coverage. Paired-end sequences were assembled and used for structural and functional annotation. A total of 4236 genes were annotated on 5M(g) , in close agreement with the predicted number of genes on wheat chromosome 5D (4286). Single-gene FISH indicated no major chromosomal rearrangements between chromosomes 5M(g) and 5D. Comparing chromosome 5M(g) with model grass genomes identified synteny blocks in Brachypodium distachyon, rice (Oryza sativa), sorghum (Sorghum bicolor) and barley (Hordeum vulgare). Chromosome 5M(g) -specific SNPs and cytogenetic probe-based resources were developed and validated. Deletion bin-mapped and ordered 5M(g) SNP markers will be useful to track 5M-specific introgressions and translocations. This study provides a detailed sequence-based analysis of the composition of a chromosome from a distant wild relative of bread wheat, and opens up opportunities to develop genomic resources for wild germplasm to facilitate crop improvement.

La liste complète des auteurs et leurs affiliations sont disponibles à la fin de l'article - 96 collaborateurs : Mayer KF, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P, Endo TR, Kubaláková M, Cíhalíková J, Dubská Z, Vrána J, Sperková R, Simková H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh NK, Khurana J, Akhunov E, Choulet F, Alberti A, Barbe V, Wincker P, Kanamori H, Kobayashi F, Itoh T, Matsumoto T, Sakai H, Tanaka T, Wu J, Ogihara Y, Handa H, Maclachlan PR, Sharpe A, Klassen D, Edwards D, Batley J, Olsen OA, Sandve SR, Lien S, Steuernagel B, Wulff B, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Pfeifer M, Spannagl M, Martis MM, Mascher M, Chapman J, Poland JA, Scholz U, Barry K, Waugh R, Rokhsar DS, Muehlbauer GJ, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca AM, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader KC, Rimbert H, Wang S, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B, Praud S.; International audience; An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Background Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). Results The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. Conclusion This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and monitoring of alien segments in crop breeding programs and further enable mapping and cloning novel genes from the wild relatives of crop plants.

Wheat leaf rust, caused by the basidiomycete Puccinia triticina, can cause yield losses of up to 20% in wheat producing regions. During infection, the fungus forms haustoria that secrete proteins into the plant cell and effect changes in plant transcription, metabolism, and defense. It is hypothesized that new races emerge as a result of overcoming plant resistance via changes in the secreted effector proteins. To understand gene expression during infection and find genetic differences associated with races, RNA from wheat leaves infected with six different rust races, at 6 days post inoculation, was sequenced using Illumina. As P. triticina is an obligate biotroph, RNA from both the host and fungi were present and separated by alignment to the P. triticina genome and a wheat EST reference. A total of 222,571 rust contigs were assembled from 165 million reads. An examination of the resulting contigs revealed 532 predicted secreted proteins among the transcripts. Of these, 456 were found in all races. Fifteen genes were found with amino acid changes, corresponding to putative avirulence effectors potentially recognized by 11 different leaf rust resistance (Lr) genes. Twelve of the potential avirulence effectors have no homology to known genes. One gene had significant similarity to cerato-platanin, a known fungal elicitor, and another showed similarity to fungal tyrosinase, an enzyme involved in melanin synthesis. Temporal expression profiles were developed for these genes by qRT-PCR and show that the genes expression patterns were consistent between races from infection initiation to just prior to spore eruption.

Cycles of whole-genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied by comparing the patterns of gene structure changes, alternative splicing (AS), and codon substitution rates among wheat and model grass genomes. In orthologous gene sets, significantly more acquired and lost exonic sequences were detected in wheat than in model grasses. In wheat, 35% of these gene structure rearrangements resulted in frame-shift mutations and premature termination codons. An increased codon mutation rate in the wheat lineage compared with Brachypodium distachyon was found for 17% of orthologs. The discovery of premature termination codons in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. The rates of AS within the individual wheat subgenomes (21%–25%) were similar to diploid plants. However, we uncovered a high level of AS pattern divergence between the duplicated homeologous copies of genes. Our results are consistent with the accelerated accumulation of AS isoforms, nonsynonymous mutations, and gene structure rearrangements in the wheat lineage, likely due to genetic redundancy created by WGDs. Whereas these processes mostly contribute to the degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variations, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits.

The Maoling deposit, with average grade of 2 g/t Au and reserves of over 45 m.t., is a disseminated Au deposit hosted in Proterozoic sedimentary rocks in the Southern Liaoning Province of the North China Platform. The hidden ore bodies at Maoling were discovered in 1985 through a combination of geophysical and geochemical studies in the area which showed anomalies during the reconnaissance soil geochemical survey. The ore bodies show high magnetic susceptibility, low resistivity and high chargeability compared to unaltered host rocks and they are enriched in As, Ag, Pb, Co, Ni and Sb. The soils overlying the deposit show secondary halos of Au, As, Ag, Pb and Sb. All Au deposits in the area are in and around Mesozoic granitic intrusions and the Maoling deposit is underlain by the Wo-Longquan batholith. The occurrences of Au deposits and cross-cutting relationships between alteration zones and dykes suggest that the Au mineralization took place after the peak intrusive event during the Jurassic tectonic activity. The ore bodies at Maoling are composed mostly of fine dissemination of arsenopyrite and pyrrhotite and they are accompanied by intense sericitization and silicification with minor biotitization. The characteristics of the deposit are akin to those of Carlin-type Au deposits in North America, including intense regional silification, high tonnage/grade ratio, high As and Ag, low base metal contents, and dissemination of fine-grained metallic minerals in sedimentary rocks. Whereas the host rocks of North American Carlin-type deposits are unmetamorphosed, those of the Maoling deposit have undergone greenschist- to amphibolite-facies regional metamorphism and some ores occur within the andalusite-grade contact metamorphic rocks of the intrusion. The lack of cristobalite, opaline silica, clays, and cinnabar which are common in Carlin-type deposits together with the evidence of brittle-ductile deformation in the Maoling deposit is consistent with the mineralization at Maoling at higher temperatures and deeper crustal level than Carlin-type deposits.

CYP82E4, a cytochrome P450 monooxygenase, has nicotine N-demethylase (NND) activity, which mediates the bioconversion of nicotine into nornicotine in senescing tobacco leaves. Nornicotine is a precursor of the carcinogen, tobacco-specific nitrosamine. CYP82E3 is an ortholog of CYP82E4 with 95% sequence identity, but it lacks NND activity. A recent site-directed mutagenesis study revealed that a single amino acid substitution, i.e., cysteine to tryptophan at the 330 position in the middle of protein, restores the NND activity of CYP82E3 entirely. However, the same amino acid change caused the loss of the NND activity of CYP82E4. To determine the mechanism of the functional turnover of the two molecules, four 3D structures, i.e., the two molecules and their corresponding cys–trp mutants were modeled. The resulting structures exhibited that the mutation site is far from the active site, which suggests that no direct interaction occurs between the two sites. Simulation studies in different biological scenarios revealed that the mutation introduces a conformation drift with the largest change at the F-G loop. The dynamics trajectories analysis using principal component analysis and covariance analysis suggests that the single amino acid change causes the opening and closing of the transfer channels of the substrates, products, and water by altering the motion of the F-G and B-C loops. The motion of helix I is also correlated with the motion of both the F-G loop and the B-C loop and; the single amino acid mutation resulted in the curvature of helix I. These results suggest that the single amino acid mutation outside the active site region may have indirectly mediated the flexibility of the F-G and B-C loops through helix I, causing a functional turnover of the P450 monooxygenase.

The Arabidopsis ethylene-responsive element-binding factor (AtERF) family of transcription factors has approximately 120 members, all of which possess a highly conserved ERF domain. AtERF1, AtERF4, AtEBP and CBF1 are members from different phylogenetic subgroups within the family. Electrophoretic mobility shift assay analyses revealed that the ERF domains of these four proteins were capable of binding specifically to either GCC or dehydration-responsive element (DRE) motifs. In vitro and in vivo binding assays of the four AtERFs with the DRE motif showed that the recognition of the CG step was indispensable in all four of the specific binding reactions, implying that there may be a universal binding characteristic of various ERF domains binding to a given consensus (e.g. the DRE motif). In addition, the core DNA-binding motifs preferred by the four AtERFs were identified, and all of these motifs contained a conserved CG step core. Thus, conserved recognition of the CG step may be the foundation of the formation of the stable complex by the ERF domain with the DRE motif, which is probably determined by the highly conserved residues presented in the DNA contact surface among the whole AtERF family members. The different preferences at flanking bases of individual ERF domains, which appear to be attributed to the subfamily- or subgroup-specific residues, may be essential discrimination of the target binding motif from various similar sequences by divergent AtERF domains.

Arabidopsis ethylene responsive element binding factors (AtERFs) form a transcription factor super family. While the functions of most AtERFs are unknown, a number of AtERFs appear to be involved in regulation of stress-related genes through their DNA binding domains (DBD), namely ERF domains, which recognize a consensus motif GCC-box at the regulatory region. In this study, molecular dynamics simulations were performed on the four ERF domain-GCC-box complexes, AtERF1, AtERF4, AtEBP and CFBF1, to determine disparity in specific binding to the GCC-box by the AtERFs. Our results suggested that three amino acid residues Arg29, Glu39 and Arg41, played a vital role in direct readout of DNA. The position of the consensus sequence GCCGCC has an intrinsic disparity on binding with ERF domains. The third C, fourth G and the last C in the GCC motif was compulsory for recognition by ERF domains. Our results provide structural evidence for a sequence-dependent recognition mechanism for AtERFs. Copyright © 2009 John Wiley & Sons, Ltd.

Background Eight diverse sorghum (Sorghum bicolor L. Moench) accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs). Two strategies were used for DNA library preparation. Missing SNP genotype data were imputed by local haplotype comparison. The effect of library type and genomic diversity on SNP discovery and imputation are evaluated. Results Alignment of eight genome equivalents (6 Gb) to the public reference genome revealed 283,000 SNPs at ≥82% confirmation probability. Sequencing from libraries constructed to limit sequencing to start at defined restriction sites led to genotyping 10-fold more SNPs in all 8 accessions, and correctly imputing 11% more missing data, than from semirandom libraries. The SNP yield advantage of the reduced-representation method was less than expected, since up to one fifth of reads started at noncanonical restriction sites and up to one third of restriction sites predicted in silico to yield unique alignments were not sampled at near-saturation. For imputation accuracy, the availability of a genomically similar accession in the germplasm panel was more important than panel size or sequencing coverage. Conclusions A sequence quantity of 3 million 50-base reads per accession using a BsrFI library would conservatively provide satisfactory genotyping of 96,000 sorghum SNPs. For most reliable SNP-genotype imputation in shallowly sequenced genomes, germplasm panels should consist of pairs or groups of genomically similar entries. These results may help in designing strategies for economical genotyping-by-sequencing of large numbers of plant accessions.

Background: The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. Results: A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing.Conclusions: Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies. Fil: Krasileva, Ksenia V.. University of California at Davis; Estados Unidos Fil: Buffalo, Vince. University of California at Davis; Estados Unidos Fil: Bailey, Paul. Norwich Research Park; Estados Unidos Fil: Pearce, Stephen. University of California at Davis; Estados Unidos Fil: Ayling, Sarah. Norwich Research Park; Estados Unidos Fil: Tabbita, Facundo. University of California at Davis; Estados Unidos Fil: Soria, Marcelo Abel. University of California at Davis; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales; Argentina Fil: Wang, Shichen. Kansas State University; Estados Unidos Fil: Akhunov, Eduard. Kansas State University; Estados Unidos Fil: Uauy, Cristobal. Norwich Research Park; Estados Unidos Fil: Dubcovsky, Jorge. University of California at Davis; Estados Unidos. Howard Hughes Medical Institute; Estados Unidos