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Sharma PK, Ahmed HI, Heuberger M, Koo DH, Quiroz-Chavez J, Adhikari L, Raupp J, Cauet S, Rodde N, Cravero C, Callot C, Yadav IS, Kathiresan N, Athiyannan N, Ramirez-Gonzalez RH, Uauy C, Wicker T, Abrouk M, Gu YQ, Poland J, Krattinger SG, Lazo GR, Tiwari VK. An online database for einkorn wheat to aid in gene discovery and functional genomics studies. Database (Oxford) 2023; 2023:baad079. [PMID: 37971714 PMCID: PMC10653128 DOI: 10.1093/database/baad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/02/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL https://wheat.pw.usda.gov/GG3/pangenome.
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Affiliation(s)
- Parva Kumar Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesus Quiroz-Chavez
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Charlotte Cravero
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | | | - Cristobal Uauy
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Yong Q Gu
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Gerard R Lazo
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
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2
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Jin NN, Chen XW, Gu YQ, Wang HL, Zhang Q, Liu L, Niu KJ. [Serum immunoglobulin concentration and the risk of type 2 diabetes mellitus in adults in Tianjin City: a prospective cohort study]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:1186-1193. [PMID: 37574311 DOI: 10.3760/cma.j.cn112150-20230210-00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Objective: To evaluate the association between immunoglobulin concentration and the risk of type 2 diabetes mellitus (T2DM) in adults in Tianjin City. Methods: Based on the Tianjin Chronic Low-grade Systemic Inflammation and Health (TCLSIHealth) cohort from January 2010 to December 2018, subjects who had completed the measurement of baseline immunoglobulin concentration and blood glucose concentration and not been diagnosed with any type of diabetes at baseline were selected in this study. The collected data included the concentration of serum immunoglobulin (IgG, IgM, IgA and IgE), fasting blood glucose and other potential confounders. The subjects were divided into four groups from Q1 to Q4 according to the quartiles of baseline immunoglobulin concentration. The multivariable Cox regression model was used to assess the association between the baseline immunoglobulin concentration and T2DM. Results: A total of 6 315 subjects aged (50.1±10.0) years were included. About 390 subjects were newly diagnosed with T2DM during the follow-up period. The incidence rate was 16.8/1 000 person-years. After adjusting for age, sex, waist circumference, smoking status, drinking status, eosinophil ratio, metabolic syndrome, first-or second-degree family history, and reciprocal adjusting for other immunoglobulin concentrations, compared to the lowest quartile concentration group Q1, subjects in group Q4 with the highest quartile of IgG concentration showed a lower risk of T2DM (HR=0.71, 95%CI: 0.52-0.97), and subjects in group Q4 with the highest quartile of IgM concentration also had a decreased risk of T2DM (HR=0.66, 95%CI: 0.47-0.91). Subjects in group Q4 with the highest quartile of IgA concentration had an increased risk of T2DM (HR=1.56, 95%CI: 1.18-2.07). The risk of T2DM decreased with the increase of serum IgG and IgM concentrations (Ptrend=0.018, Ptrend=0.010) and increased with the increase of serum IgA concentrations (Ptrend<0.001). No association was found between the concentration of IgE and T2DM risk (HR=0.99, 95%CI: 0.74-1.31, Ptrend=0.891). Conclusion: The concentration of IgG and IgM is negatively associated with the risk of T2DM, and the concentration of IgA is positively associated with the risk of T2DM in Tianjin City. The concentrations of IgG, IgM and IgA could be a predictor of hyperglycemia and T2DM.
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Affiliation(s)
- N N Jin
- Clinical Nutrition Department and geriatric Medicine Department, Tianjin Binhai People's Hospital, Tianjin 300280, China
| | - X W Chen
- School of Public Health, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China Nutritional Epidemiology Institute, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Y Q Gu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - H L Wang
- School of Public Health, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China Nutritional Epidemiology Institute, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Q Zhang
- Health Management Centre, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - L Liu
- Health Management Centre, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - K J Niu
- School of Public Health, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China Health Management Centre, Tianjin Medical University General Hospital, Tianjin 300052, China
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Yadav IS, Rawat N, Chhuneja P, Kaur S, Uauy C, Lazo G, Gu YQ, Doležel J, Tiwari VK. Comparative genomic analysis of 5M g chromosome of Aegilops geniculata and 5U u chromosome of Aegilops umbellulata reveal genic diversity in the tertiary gene pool. Front Plant Sci 2023; 14:1144000. [PMID: 37521926 PMCID: PMC10373596 DOI: 10.3389/fpls.2023.1144000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Wheat is one of the most important cereal crops for the global food security. Due to its narrow genetic base, modern bread wheat cultivars face challenges from increasing abiotic and biotic stresses. Since genetic improvement is the most sustainable approach, finding novel genes and alleles is critical for enhancing the genetic diversity of wheat. The tertiary gene pool of wheat is considered a gold mine for genetic diversity as novel genes and alleles can be identified and transferred to wheat cultivars. Aegilops geniculata and Ae. umbellulata are the key members of the tertiary gene pool of wheat and harbor important genes against abiotic and biotic stresses. Homoeologous-group five chromosomes (5Uu and 5Mg) have been extensively studied from Ae. geniculata and Ae. umbellulata as they harbor several important genes including Lr57, Lr76, Yr40, Yr70, Sr53 and chromosomal pairing loci. In the present study, using chromosome DNA sequencing and RNAseq datasets, we performed comparative analysis to study homoeologous gene evolution in 5Mg, 5Uu, and group 5 wheat chromosomes. Our findings highlight the diversity of transcription factors and resistance genes, resulting from the differential expansion of the gene families. Both the chromosomes were found to be enriched with the "response to stimulus" category of genes providing resistance against biotic and abiotic stress. Phylogenetic study positioned the M genome closer to the D genome, with higher proximity to the A genome than the B genome. Over 4000 genes were impacted by SNPs on 5D, with 4-5% of those genes displaying non-disruptive variations that affect gene function.
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Affiliation(s)
- Inderjit S. Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Gerard Lazo
- Agricultural Research Service, United States Department of Agriculture (USDA), Albany, CA, United States
| | - Yong Q. Gu
- Agricultural Research Service, United States Department of Agriculture (USDA), Albany, CA, United States
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Olomouc, Czechia
| | - Vijay K. Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
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Kim S, Sim JR, Gu YQ, Altenbach SB, Denery-Papini S, Pineau F, Tranquet O, Yang YJ, Park EJ, Lim SH, Kang CS, Choi C, Lee JY. Toward reducing the immunogenic potential of wheat flour: identification and characterization of wheat lines missing omega-5 gliadins encoded by the 1D chromosome. Theor Appl Genet 2023; 136:33. [PMID: 36897507 DOI: 10.1007/s00122-023-04295-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/18/2022] [Indexed: 06/18/2023]
Abstract
Eleven wheat lines that are missing genes for the 1D-encoded omega-5 gliadins will facilitate breeding efforts to reduce the immunogenic potential of wheat flour for patients susceptible to wheat allergy. Efforts to reduce the levels of allergens in wheat flour that cause wheat-dependent exercise-induced anaphylaxis are complicated by the presence of genes encoding omega-5 gliadins on both chromosomes 1B and 1D of hexaploid wheat. In this study, we screened 665 wheat germplasm samples using gene specific DNA markers for omega-5 gliadins encoded by the genes on 1D chromosome that were obtained from the reference wheat Chinese Spring. Eleven wheat lines missing the PCR product corresponding to 1D omega-5 gliadin gene sequences were identified. Two of the lines contained the 1BL·1RS translocation. Relative quantification of gene copy numbers by qPCR revealed that copy numbers of 1D omega-5 gliadins in the other nine lines were comparable to those in 1D null lines of Chinese Spring, while copy numbers of 1B omega-5 gliadins were like those of Chinese Spring. 2-D immunoblot analysis of total flour proteins from the selected lines using a specific monoclonal antibody against the N-terminal sequence of omega-5 gliadin showed no reactivity in regions of the blots containing previously identified 1D omega-5 gliadins. Interestingly, RP-UPLC analysis of the gliadin fractions of the selected lines indicated that the expression of omega-1,2 gliadins was also significantly reduced in seven of the lines, implying that 1D omega-5 gliadin and 1D omega-1,2 gliadin genes are tightly linked on the Gli-D1 loci of chromosome 1D. Wheat lines missing the omega-5 gliadins encoded by the genes on 1D chromosome should be useful in future breeding efforts to reduce the immunogenic potential of wheat flour.
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Affiliation(s)
- Sewon Kim
- National Institute of Agricultural Sciences, RDA, Jeonju, 54874, South Korea
| | - Jae-Ryeong Sim
- National Institute of Agricultural Sciences, RDA, Jeonju, 54874, South Korea
| | - Yong Q Gu
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Susan B Altenbach
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Sandra Denery-Papini
- UR1268 Biopolymers, Interactions, Assemblies, INRAE, Rue de la Géraudière, 44316, Nantes, France
| | - Florence Pineau
- UR1268 Biopolymers, Interactions, Assemblies, INRAE, Rue de la Géraudière, 44316, Nantes, France
| | - Olivier Tranquet
- UR1268 Biopolymers, Interactions, Assemblies, INRAE, Rue de la Géraudière, 44316, Nantes, France
| | - Yu-Jeong Yang
- National Institute of Agricultural Sciences, RDA, Jeonju, 54874, South Korea
| | - Eun Ji Park
- National Institute of Agricultural Sciences, RDA, Jeonju, 54874, South Korea
| | - Sun-Hyung Lim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, South Korea
| | - Chon-Sik Kang
- National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Changhyun Choi
- National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Jong-Yeol Lee
- National Institute of Agricultural Sciences, RDA, Jeonju, 54874, South Korea.
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5
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Wu Q, Cui Y, Jin X, Wang G, Yan L, Zhong C, Yu M, Li W, Wang Y, Wang L, Wang H, Dang C, Zhang X, Chen Y, Zhang P, Zhao X, Wu J, Fu D, Xia L, Nevo E, Vogel J, Huo N, Li D, Gu YQ, Jackson AO, Zhang Y, Liu Z. The CC-NB-LRR protein BSR1 from Brachypodium confers resistance to Barley stripe mosaic virus in gramineous plants by recognising TGB1 movement protein. New Phytol 2022; 236:2233-2248. [PMID: 36059081 DOI: 10.1111/nph.18457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Although some nucleotide binding, leucine-rich repeat immune receptor (NLR) proteins conferring resistance to specific viruses have been identified in dicot plants, NLR proteins involved in viral resistance have not been described in monocots. We have used map-based cloning to isolate the CC-NB-LRR (CNL) Barley stripe mosaic virus (BSMV) resistance gene barley stripe resistance 1 (BSR1) from Brachypodium distachyon Bd3-1 inbred line. Stable BSR1 transgenic Brachypodium line Bd21-3, barley (Golden Promise) and wheat (Kenong 199) plants developed resistance against BSMV ND18 strain. Allelic variation analyses indicated that BSR1 is present in several Brachypodium accessions collected from countries in the Middle East. Protein domain swaps revealed that the intact LRR domain and the C-terminus of BSR1 are required for resistance. BSR1 interacts with the BSMV ND18 TGB1 protein in planta and shows temperature-sensitive antiviral resistance. The R390 and T392 residues of TGB1ND (ND18 strain) and the G196 and K197 residues within the BSR1 P-loop motif are key amino acids required for immune activation. BSR1 is the first cloned virus resistance gene encoding a typical CNL protein in monocots, highlighting the utility of the Brachypodium model for isolation and analysis of agronomically important genes for crop improvement.
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Affiliation(s)
- Qiuhong Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
| | - Yu Cui
- Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Guoxin Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lijie Yan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chenchen Zhong
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Meihua Yu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wenli Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hao Wang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chen Dang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xinyu Zhang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongxing Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Panpan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofei Zhao
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jiajie Wu
- College of Agronomy, Shandong Agriculture University, Taian, 271018, China
| | - Daolin Fu
- College of Agronomy, Shandong Agriculture University, Taian, 271018, China
| | - Lanqin Xia
- Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Eviatar Nevo
- Institute of Evolution, Haifa University, Haifa, 31905, Israel
| | - John Vogel
- Joint Genome Institute, DOE, Walnut Creek, CA, 94598, USA
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yong Q Gu
- USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA
| | - Andrew O Jackson
- Department of Plant and Microbiology, University of California, Berkeley, CA, 94720, USA
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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6
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Du WX, Gu YQ, Meng G, Zhang Q, Liu L, Wu HZ, Niu KJ. [Associations between internet addiction, screen time and depressive symptoms]. Zhonghua Liu Xing Bing Xue Za Zhi 2022; 43:1731-1738. [PMID: 36444455 DOI: 10.3760/cma.j.cn112338-20220330-00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Objective: To understand the associations between internet addiction, screen time (computer/mobile devices use and television watching time) and depressive symptoms in adults. Methods: A total of 6 932 adults aged <60 years from the Tianjin Chronic Low-grade Sgstemic Inflammation and Health (TCLSIH) Cohort of 2013-2019 were surveyed. The information about their computer/mobile devices use and television watching time were collected by using a self-reported questionnaire. The depressive symptoms were assessed using the self-rating depression scale (SDS). The adults surveyed were divided into two groups: non-depressive symptom group (SDS score <45) and depressive symptom group (SDS score ≥45). The associations between internet addiction, screen time and depressive symptoms were estimated using Cox proportional hazard regression models, with adjusting for multiple confounders. Results: After adjusting for confounding factors, the hazard ratios (HRs) of depressive symptom in the adults who had internet addiction before, had light internet addiction and had moderate or severe internet addiction were 0.83 (95%CI: 0.56-1.23) , 1.20 (95%CI: 1.03-1.41) for light and 1.48 (95%CI: 1.16-1.89), respectively, compared with those without internet addiction. The linear trend test results of the association between internet addiction and depressive symptoms was significant (trend P<0.001). Compared with the adults who used computer/mobile devices for <1 hour/day, the HRs of depressive symptoms in those who used computer/mobile devices for >1 hour, >3 hours, >5 hours and >10 hours were 0.59 (95%CI: 0.40-0.88), 0.58 (95%CI: 0.40-0.85), 0.52 (95%CI: 0.36-0.76) and 0.69 (95%CI: 0.45-1.05) respectively, a U-shaped association was found between computer/mobile devices use time and depressive symptoms (trend P<0.001). Compared with the adults who never watch TV, the HR of depressive symptoms was 1.36 (95%CI:1.09-1.69) for those watching TV for ≥3 hours/day in crude model and 1.34 (95%CI: 1.07-1.68) for those watching TV for ≥3 hours/day in adjusted model (trend P<0.001). Conclusion: Our findings suggested that internet addiction and television watching time were associated with an increased risk of depressive symptoms, while computer/mobile device use time was associated with a reduced risk of depressive symptoms.
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Affiliation(s)
- W X Du
- Nutritional Epidemiology Institute/School of Public Health, Tianjin Medical University, Tianjin 300070, China School of Public Health of Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Y Q Gu
- Nutrition and Radiation Epidemiology Research Center, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, China
| | - G Meng
- Nutritional Epidemiology Institute/School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Q Zhang
- Health Management Centre, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - L Liu
- Health Management Centre, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - H Z Wu
- Nutritional Epidemiology Institute/School of Public Health, Tianjin Medical University, Tianjin 300070, China School of Public Health of Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - K J Niu
- Nutritional Epidemiology Institute/School of Public Health, Tianjin Medical University, Tianjin 300070, China School of Public Health of Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China Nutrition and Radiation Epidemiology Research Center, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, China Health Management Centre, Tianjin Medical University General Hospital, Tianjin 300052, China
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7
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Mohr T, Horstman J, Gu YQ, Elarabi NI, Abdallah NA, Thilmony R. CRISPR-Cas9 Gene Editing of the Sal1 Gene Family in Wheat. Plants 2022; 11:plants11172259. [PMID: 36079639 PMCID: PMC9460255 DOI: 10.3390/plants11172259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
The highly conserved Sal1 encodes a bifunctional enzyme with inositol polyphosphate-1-phosphatase and 3′ (2′), 5′-bisphosphate nucleotidase activity and has been shown to alter abiotic stress tolerance in plants when disrupted. Precise gene editing techniques were used to generate Sal1 mutants in hexaploid bread wheat. The CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) Cas9 system with three guide RNAs (gRNAs) was used to inactivate six Sal1 homologous genes within the Bobwhite wheat genome. The resulting mutant wheat plants with all their Sal1 genes disabled had slimmer stems, had a modest reduction in biomass and senesced more slowly in water limiting conditions, but did not exhibit improved yield under drought conditions. Our results show that multiplexed gRNAs enabled effective targeted gene editing of the Sal1 gene family in hexaploid wheat. These Sal1 mutant wheat plants will be a resource for further research studying the function of this gene family in wheat.
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Affiliation(s)
- Toni Mohr
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - James Horstman
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - Yong Q. Gu
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - Nagwa I. Elarabi
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Naglaa A. Abdallah
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Roger Thilmony
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
- Correspondence: ; Tel.: +1-(510)-559-5761
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8
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Wang AC, Xie JL, Wang YN, Sun XF, Lu LJ, Sun YF, Gu YQ. [Autopsies and placental examinations of perinatal fetal deaths: a clinicopathological analysis of 105 cases]. Zhonghua Bing Li Xue Za Zhi 2022; 51:431-436. [PMID: 35511639 DOI: 10.3760/cma.j.cn112151-20210908-00657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To summarize the clinicopathological factors related to perinatal fetal death and to evaluate importance of fetal autopsy and placental pathology. Methods: The clinicopathological data of 105 perinatal fetal deaths in Beijing Haidian Maternal and Child Health Hospital from November 2012 to December 2020 were retrospectively analyzed. Relevant literature was also reviewed. Results: The maternal age of the deceased fetuses ranged from 22 to 43 years with the average (31.35±4.04 years), and the gestational weeks were 28-40+6 weeks. Among them, 101 were singleton cases and 4 twin cases. 103 fetuses died in uterus and 2 died during delivery. Relevant factors analysis of the 105 perinatal fetal deaths showed that 86 cases (81.9%, 86/105) were related to umbilical cord/placental abnormality, 10 cases (9.5%, 10/105) uterine infection, 6 cases (5.7%, 6/105) fetal factors, 1 case was fetal maternal blood transfusion syndrome, 1 case twin blood transfusion syndrome, and 1 case died of complete uterine rupture. Among the 86 cases related to umbilical cord/placental abnormality, the diagnosis was most often based on the gross examination of placenta. The most common cause of death was umbilical cord torsion with thin root, followed by placental abruption, tight umbilical cord winding, vascular rupture and umbilical cord true knot. The morphology of placenta revealed mainly functional changes. Among the 10 cases related to intrauterine infections, the placenta generally showed lobular placental edema. The morphological characteristics of ascending infection were mainly acute chorioamnionitis, and the morphological characteristics of blood-borne infection were mainly acute or chronic villitis, as well as villous interstitial inflammation. Identification of viral inclusions suggested viral etiology, while the final diagnosis was relied on laboratory testing. Among the 6 cases related to fetal abnormality, the diagnostic value of placenta was limited and the diagnosis could be made with fetal autopsy. Conclusion: The causes of perinatal fetal death are complex, diverse, and often the synergistic result of multiple factors. Fetal autopsy and placental pathology are the key technical means to identify the cause of death and deserve more attention and utilization.
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Affiliation(s)
- A C Wang
- Department of Pathology, Haidian Maternal and Children Health Hospital, Beijing 100081, China
| | - J L Xie
- Department of Pathology, Haidian Maternal and Children Health Hospital, Beijing 100081, China
| | - Y N Wang
- Department of Pathology, Haidian Maternal and Children Health Hospital, Beijing 100081, China
| | - X F Sun
- Department of Pathology, Haidian Maternal and Children Health Hospital, Beijing 100081, China
| | - L J Lu
- Department of Pathology, Haidian Maternal and Children Health Hospital, Beijing 100081, China
| | - Y F Sun
- Department of Pathology, Haidian Maternal and Children Health Hospital, Beijing 100081, China
| | - Y Q Gu
- Department of Pathology, Haidian Maternal and Children Health Hospital, Beijing 100081, China
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9
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Wang AC, Xie JL, Wang YN, Sun XF, Lu LJ, Sun YF, Gu YQ. [Singleton placentas with abnormal shape: a clinicopathological analysis of 130 cases]. Zhonghua Bing Li Xue Za Zhi 2022; 51:39-43. [PMID: 34979752 DOI: 10.3760/cma.j.cn112151-20210508-00346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To investigate the pathological characteristics of singleton placenta with abnormal shape and its influence on the outcome of maternal-fetal pregnancy. Methods: The clinicopathological data of singleton placentas with abnormal shape from January 2014 to December 2020 in the Department of Pathology, Haidian Maternal and Children Health Hospital were analyzed retrospectively. Results: There were 130 singleton placentas with abnormal shape in this cohort, including 48 succenturiate placentas, 12 bilobed placentas, 50 marginate placentas, 13 circumvallate placentas, 3 annular placentas, 2 membranous placentas and 2 fenestrated placentas. Gestational age ranged from 29+5 to 40+4 weeks. There were 51 cases of premature rupture of membranes, 11 cases of placenta previa, 5 cases of placental abruption, 15 cases of placental adhesion/implantation and 27 cases of postpartum hemorrhage. There were 46 preterm fetuses,28 fetuses with fetal growth restriction, 22 fetuses with intrauterine distress, and 1 fetus with intrauterine death. Grossly, the placental lobules of succenturiate placentas had apparent size difference, while two lobules of bilobate placenta were more consistent. The chorionic plate size was smaller than the bottom plate of circumvallate placenta, the folded fetal membrane in the rim of placenta was thickened (termed marginate placenta if there was no thickening). The membranous placenta was characterized by a thin, large membrane-like shape. Annular placenta showed characteristic hollow cylinder, ring or horseshoe-shape. Fenestrated placenta was characterized by tissue defects near central area. Microscopically, functional/morphologic changes were the main manifestations of inadequate maternal-fetal perfusion, including villous infarction, distal villous dysplasia and excessive villous maturation. Conclusions: The abnormal shaped singleton placentas showed variable extent of inadequate maternal-fetal perfusion, which may lead to adverse pregnancy outcomes such as premature delivery, fetal growth restriction, intrauterine distress or fetal death.
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Affiliation(s)
- A C Wang
- Department of Pathology, Haidian Maternal & Children Health Hospital, Beijing 100081, China
| | - J L Xie
- Department of Pathology, Haidian Maternal & Children Health Hospital, Beijing 100081, China
| | - Y N Wang
- Department of Pathology, Haidian Maternal & Children Health Hospital, Beijing 100081, China
| | - X F Sun
- Department of Pathology, Haidian Maternal & Children Health Hospital, Beijing 100081, China
| | - L J Lu
- Department of Pathology, Haidian Maternal & Children Health Hospital, Beijing 100081, China
| | - Y F Sun
- Department of Pathology, Haidian Maternal & Children Health Hospital, Beijing 100081, China
| | - Y Q Gu
- Department of Pathology, Haidian Maternal & Children Health Hospital, Beijing 100081, China
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10
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Wang L, Zhu T, Rodriguez JC, Deal KR, Dubcovsky J, McGuire PE, Lux T, Spannagl M, Mayer KFX, Baldrich P, Meyers BC, Huo N, Gu YQ, Zhou H, Devos KM, Bennetzen JL, Unver T, Budak H, Gulick PJ, Galiba G, Kalapos B, Nelson DR, Li P, You FM, Luo MC, Dvorak J. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3 (Bethesda) 2021; 11:6369516. [PMID: 34515796 PMCID: PMC8664484 DOI: 10.1093/g3journal/jkab325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023]
Abstract
Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing acc. AL8/78 and release of the Aet v5.0 sequence assembly are reported here. Two new optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long-read contigs, decreasing the gap number by 38,899. Transposable elements and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. A total of 2245 biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat, was manually annotated and disease-resistance genes were annotated by a dedicated pipeline. Disease-resistance genes encoding nucleotide-binding site domains, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil proteins were dispersed more evenly along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. These advances enhance the utility of the Ae. tauschii genome sequence for wheat genetics, biotechnology, and breeding.
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Affiliation(s)
- Le Wang
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Juan C Rodriguez
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Munich 85764, Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Munich 85764, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Munich 85764, Germany
| | - Patricia Baldrich
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.,University of Missouri, Columbia, Division of Plant Sciences, Columbia, Missouri 65211, USA
| | - Naxin Huo
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, California 94710, USA
| | - Yong Q Gu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, California 94710, USA
| | - Hongye Zhou
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics (Dept. of Crop & Soil Sciences) and Dept. of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | | | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, Ankara 06374, Turkey
| | - Hikmet Budak
- Montana BioAg Inc., Missoula, Montana 59801, USA
| | - Patrick J Gulick
- Department of Biology, Concordia University, Montreal, Quebec H3G 1M8, Canada
| | - Gabor Galiba
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, H-2462 Martonvásár, Hungary.,Department of Environmental Sustainability, IES, Hungarian University of Agriculture and Life Sciences, H-8360 Keszthely, Hungary
| | - Balázs Kalapos
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, H-2462 Martonvásár, Hungary
| | - David R Nelson
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Pingchuan Li
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C5, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C5, Canada
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
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11
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Cho K, Jang YR, Lim SH, Altenbach SB, Gu YQ, Simon-Buss A, Lee JY. Proteomic Determination of Low-Molecular-Weight Glutenin Subunit Composition in Aroona Near-Isogenic Lines and Standard Wheat Cultivars. Int J Mol Sci 2021; 22:ijms22147709. [PMID: 34299329 PMCID: PMC8306524 DOI: 10.3390/ijms22147709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
The low-molecular weight glutenin subunit (LMW-GS) composition of wheat (Triticum aestivum) flour has important effects on end-use quality. However, assessing the contributions of each LMW-GS to flour quality remains challenging because of the complex LMW-GS composition and allelic variation among wheat cultivars. Therefore, accurate and reliable determination of LMW-GS alleles in germplasm remains an important challenge for wheat breeding. In this study, we used an optimized reversed-phase HPLC method and proteomics approach comprising 2-D gels coupled with liquid chromatography–tandem mass spectrometry (MS/MS) to discriminate individual LMW-GSs corresponding to alleles encoded by the Glu-A3, Glu-B3, and Glu-D3 loci in the ‘Aroona’ cultivar and 12 ‘Aroona’ near-isogenic lines (ARILs), which contain unique LMW-GS alleles in the same genetic background. The LMW-GS separation patterns for ‘Aroona’ and ARILs on chromatograms and 2-D gels were consistent with those from a set of 10 standard wheat cultivars for Glu-3. Furthermore, 12 previously uncharacterized spots in ‘Aroona’ and ARILs were excised from 2-D gels, digested with chymotrypsin, and subjected to MS/MS. We identified their gene haplotypes and created a 2-D gel map of LMW-GS alleles in the germplasm for breeding and screening for desirable LMW-GS alleles for wheat quality improvement.
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Affiliation(s)
- Kyoungwon Cho
- Department of Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea;
| | - You-Ran Jang
- National Institute of Agricultural Science, RDA, Jeonju 54874, Korea;
| | - Sun-Hyung Lim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea;
| | - Susan B. Altenbach
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (S.B.A.); (Y.Q.G.); (A.S.-B.)
| | - Yong Q. Gu
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (S.B.A.); (Y.Q.G.); (A.S.-B.)
| | - Annamaria Simon-Buss
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (S.B.A.); (Y.Q.G.); (A.S.-B.)
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Jong-Yeol Lee
- National Institute of Agricultural Science, RDA, Jeonju 54874, Korea;
- Correspondence: ; Tel.: +82-62-238-4616
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12
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Zhu T, Wang L, Rimbert H, Rodriguez JC, Deal KR, De Oliveira R, Choulet F, Keeble‐Gagnère G, Tibbits J, Rogers J, Eversole K, Appels R, Gu YQ, Mascher M, Dvorak J, Luo M. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. Plant J 2021; 107:303-314. [PMID: 33893684 PMCID: PMC8360199 DOI: 10.1111/tpj.15289] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 05/09/2023]
Abstract
Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.
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Affiliation(s)
- Tingting Zhu
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Le Wang
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Hélène Rimbert
- GDECUniversité Clermont AuvergneINRAEClermont‐Ferrand63000France
| | | | - Karin R. Deal
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | | | - Frédéric Choulet
- GDECUniversité Clermont AuvergneINRAEClermont‐Ferrand63000France
| | | | - Josquin Tibbits
- Centre for AgriBioscienceAgriculture VictoriaAgriBioBundooraVIC3083Australia
| | - Jane Rogers
- International Wheat Genome Sequencing ConsortiumEau ClaireWI54701USA
| | - Kellye Eversole
- International Wheat Genome Sequencing ConsortiumEau ClaireWI54701USA
| | - Rudi Appels
- Centre for AgriBioscienceAgriculture VictoriaAgriBioBundooraVIC3083Australia
- International Wheat Genome Sequencing ConsortiumEau ClaireWI54701USA
| | - Yong Q. Gu
- Crop Improvement and Genetics Research UnitUSDA‐ARSAlbanyCA94710USA
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Jan Dvorak
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
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13
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Fu HX, Gu YQ, Lai YY, Qin YZ, Wang JZ, Chen H, Xu LP, Zhang XH, Liu KY, Huang XJ, Jiang H. [Hematologic malignancies with coexisting t(9;22) and inv(16) chromosomal abnormalities: report of three cases and literature review]. Zhonghua Xue Ye Xue Za Zhi 2021; 41:937-940. [PMID: 33333698 PMCID: PMC7767806 DOI: 10.3760/cma.j.issn.0253-2727.2020.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- H X Fu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - Y Q Gu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - Y Y Lai
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - Y Z Qin
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - J Z Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - H Chen
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - L P Xu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - X H Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - K Y Liu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - X J Huang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - H Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
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14
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He H, Liu R, Ma P, Du H, Zhang H, Wu Q, Yang L, Gong S, Liu T, Huo N, Gu YQ, Zhu S. Characterization of Pm68, a new powdery mildew resistance gene on chromosome 2BS of Greek durum wheat TRI 1796. Theor Appl Genet 2021; 134:53-62. [PMID: 32915283 DOI: 10.1007/s00122-020-03681-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/04/2020] [Indexed: 05/07/2023]
Abstract
New powdery mildew resistance gene Pm68 was found in the terminal region of chromosome 2BS of Greek durum wheat TRI 1796. The co-segregated molecular markers could be used for MAS. Durum wheat (Triticum turgidum L. var. durum Desf.) is not only an important cereal crop for pasta making, but also a genetic resource for common wheat improvement. In the present study, a Greek durum wheat TRI 1796 was found to confer high resistance to all 22 tested isolates of Blumeria graminis f. sp. tritici (Bgt). Inheritance study on the F1 plants and the F2 population derived from the cross TRI 1796/PI 584832 revealed that the resistance in TRI 1796 was controlled by a single dominant gene, herein designated Pm68. Using the bulked segregant RNA-Seq (BSR-Seq) analysis combined with molecular analysis, Pm68 was mapped to the terminal part of the short arm of chromosome 2B and flanked by markers Xdw04 and Xdw12/Xdw13 with genetic distances of 0.22 cM each. According to the reference genome of durum wheat cv. Svevo, the corresponding physical region spanned the Pm68 locus was about 1.78-Mb, in which a number of disease resistance-related genes were annotated. This study reports the new powdery mildew resistance gene Pm68 that would be a valuable resource for improvement of both common wheat and durum wheat. The co-segregated markers (Xdw05-Xdw11) developed here would be useful tools for marker-assisted selection (MAS) in breeding.
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Affiliation(s)
- Huagang He
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China.
- School of Environment, Jiangsu University, Zhenjiang, 212013, China.
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
| | - Renkang Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Haonan Du
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Huanhuan Zhang
- School of Environment, Jiangsu University, Zhenjiang, 212013, China
| | - Qiuhong Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lijun Yang
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Shuangjun Gong
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Tianlei Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Yong Q Gu
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
| | - Shanying Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China.
- School of Environment, Jiangsu University, Zhenjiang, 212013, China.
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
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15
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Song Z, Lin C, Xing P, Fen Y, Jin H, Zhou C, Gu YQ, Wang J, Li X. A high-quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes. Plant Genome 2020; 13:e20041. [PMID: 33217202 DOI: 10.1002/tpg2.20041] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/02/2020] [Accepted: 05/26/2020] [Indexed: 05/21/2023]
Abstract
Salvia miltiorrhiza Bunge, also known as red sage or Danshen, is an important traditional Chinese medicine (TCM) that has been used for thousands of years to treat cardiovascular and other diseases. It is also considered an important model TCM plant. Here, a high-quality reference genome of S. miltiorrhiza was generated by combining PacBio long-read sequencing and chromatin interaction mapping (Hi-C) technologies, resulting in the chromosome-scale assembly of a 594.75-Mb genome sequence with a contig N50 of 2.70 Mb. This assembly shows the highest level of continuity for a Danshen genome generated thus far. The S. miltiorrhiza genome contained 32,483 protein-coding genes, with a repetitive DNA content of approximately 64.84%. The high percentage of young LTRs suggests that multiple TE transposition bursts occurred recently in S. miltiorrhiza. Genes unique to secondary metabolism pathways were expanded in the S. miltiorrhiza genome. A new CYP450 gene cluster was identified in the phloem of red roots where active components were synthesized. This reference genome sequence will facilitate future studies aimed at the elucidation of the secondary metabolism synthesis pathway and the genetic improvement of S. miltiorrhiza.
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Affiliation(s)
- Zhenqiao Song
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Caicai Lin
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Piyi Xing
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Yuanyuan Fen
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Hua Jin
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Changhao Zhou
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Yong Q Gu
- Crop Improvement & Genetics Research, Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA
| | - Jianhua Wang
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Xingfeng Li
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271028, China
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16
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Gu YQ, Xia Y, Zhang SM, Bao X, Wu HM, Bian SS, Huang LY, Meng G, Niu KJ. [Method of dietary nutritional status assessment and its application in cohort study of nutritional epidemiology]. Zhonghua Liu Xing Bing Xue Za Zhi 2020; 41:1145-1150. [PMID: 32741185 DOI: 10.3760/cma.j.cn112338-20200110-00027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Minimizing the burden on study subjects and assessing the general dietary nutritional status as accurately as possible are the basis of a nutritional epidemiological cohort study in the general population. While introducing the main dietary nutrition assessment methods, this paper manly describes the basic contents and principles for the development of food frequency questionnaire, and briefly illustrates the problems and solutions for the development of area specific food frequency questionnaires by taking the example of Tianjin Chronic Low-grade Systemic Inflammation and Health (TCLSIH) cohort study. Finally, discusses preliminarily the necessity and possibility of developing a national food frequency questionnaire.
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Affiliation(s)
- Y Q Gu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China; Nutritional Epidemiology Institute and School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Y Xia
- Nutritional Epidemiology Institute and School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - S M Zhang
- Nutritional Epidemiology Institute and School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - X Bao
- Nutritional Epidemiology Institute and School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - H M Wu
- Nutritional Epidemiology Institute and School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - S S Bian
- Nutritional Epidemiology Institute and School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - L Y Huang
- Nutritional Epidemiology Institute and School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - G Meng
- Nutritional Epidemiology Institute and School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - K J Niu
- Nutritional Epidemiology Institute and School of Public Health, Tianjin Medical University, Tianjin 300070, China
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17
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Wang TH, Chen J, Wang GX, Lin X, Bao LJ, Zhao YM, Gu YQ, Liu N. [Prognosis analysis of 112 cases with Japanese encephalitis in adults]. Zhonghua Yi Xue Za Zhi 2020; 100:541-545. [PMID: 32164108 DOI: 10.3760/cma.j.issn.0376-2491.2020.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Objective: To analyze the improvement of clinical symptoms and recovery of neurological function in adult Japanese encephalitis, and study the prognostic factors. Methods: Follow-up was conducted for 112 hospitalized patients with Japanese encephalitis (JE) in adults at the Department of Neurology of three hospitals in Gansu province from July to October 2016, from July to October 2017, 6 months and 1 year after onset, respectively. The neurological functional recovery was evaluated by modified Ranking Scale (mRS).The influencing factors were analyzed by logistic regression model. Results: Among the 112 adult patients with JE after 1year follow-up, 57% (64/112) were completely recovered (mRS score=0), and 14%(16/112) had mild neurological dysfunction (mRS score=1 or 2 points), 20% (22/112) had moderate to severe neurological dysfunction (mRS score 3 to 5), and 9% (10/112) died. In 102 survivors, decreased consciousness were fully recovered (100%), 75% of the mental and behavior disorders, 64% of cognitive/memory impairment, 71% of language function disorder, 61% of paralysis, 73% of extrapyramidal symptoms were fully recovered, and 92% of the seizures were controlled. Comparison of clinical data of initial on-set between good prognosis group (mRS score≤2, 80 cases) and poor prognosis group (mRS score>2, 32 cases) showed that initial clinical manifestation with seizures, consciousness (GCS score), cerebrospinal fluid pressure, and lesion of MRI involved in midbrain had statistically significant differences (all P<0.05) . Multivariate analysis demonstrated that cerebrospinal fluid (CSF) pressure>250 mmH(2)O and lesion of midbrain in MRI were independent risk factors of poor prognosis in adult patients with JE. Conclusion: JE is an acute and infectious viral encephalitis of the central nervous system with high disability and mortality. Most patients were completely recovered, and some had neurological sequelae. CSF pressure>250 mmH(2)O and lesion of midbrain in MRI are independent risk factors for poor prognosis.
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Affiliation(s)
- T H Wang
- Department of Neurology, the First Hospital of Lanzhou University, Lanzhou 730000, China
| | - J Chen
- Department of Neurology, the First Hospital of Lanzhou University, Lanzhou 730000, China
| | - G X Wang
- The First Department of Neurology, the First People's Hospital of Tianshui City, Tianshui 741000, China
| | - X Lin
- The First Department of Neurology, the First People's Hospital of Tianshui City, Tianshui 741000, China
| | - L J Bao
- Department of Cadre Ward Neurology, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - Y M Zhao
- Department of Cadre Ward Neurology, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - Y Q Gu
- Department of Neurology, the First Hospital of Lanzhou University, Lanzhou 730000, China
| | - N Liu
- Department of Neurology, the First Hospital of Lanzhou University, Lanzhou 730000, China
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18
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Yang SJ, Gu YQ, Luo T, Qi LX, Zhang CC, Tong Z, Wang DS, Wu ZJ. Left subclavian artery stenosis treated with covered stent. J BIOL REG HOMEOS AG 2020; 33:1875-1878. [PMID: 31984686 DOI: 10.23812/19-219-l] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- S J Yang
- Department of Vascular Surgery, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Y Q Gu
- Department of Vascular Surgery, Xuanwu Hospital of Capital Medical University, Beijing, China.,Institute of Vascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - T Luo
- Department of Human Resources, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - L X Qi
- Department of Vascular Surgery, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - C C Zhang
- Department of Vascular Surgery, Xuanwu Hospital of Capital Medical University, Beijing, China.,Institute of Vascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Z Tong
- Department of Vascular Surgery, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - D S Wang
- Department of Vascular Surgery, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Z J Wu
- Institute of Vascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
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19
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Blake VC, Woodhouse MR, Lazo GR, Odell SG, Wight CP, Tinker NA, Wang Y, Gu YQ, Birkett CL, Jannink JL, Matthews DE, Hane DL, Michel SL, Yao E, Sen TZ. GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. Database (Oxford) 2020; 2019:5513438. [PMID: 31210272 DOI: 10.1093/database/baz065] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/18/2019] [Accepted: 04/22/2019] [Indexed: 11/13/2022]
Abstract
GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discovery. Since 1992, GrainGenes has served geneticists and breeders in both the public and private sectors on six continents. Recently, several new datasets were curated into the database along with new tools for analysis. The GrainGenes homepage was enhanced by making it more visually intuitive and by adding links to commonly used pages. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes, including the Triticum aestivum (bread wheat) cv. 'Chinese Spring' IWGSC RefSeq v1.0 genome assembly, the Aegilops tauschii (D genome progenitor) Aet v4.0 genome assembly, the Triticum turgidum ssp. dicoccoides (wild emmer wheat) cv. 'Zavitan' WEWSeq v.1.0 genome assembly, a T. aestivum (bread wheat) pangenome, the Hordeum vulgare (barley) cv. 'Morex' IBSC genome assembly, the Secale cereale (rye) select 'Lo7' assembly, a partial hexaploid Avena sativa (oat) assembly and the Triticum durum cv. 'Svevo' (durum wheat) RefSeq Release 1.0 assembly. New genetic maps and markers were added and can be displayed through CMAP. Quantitative trait loci, genetic maps and genes from the Wheat Gene Catalogue are indexed and linked through the Wheat Information System (WheatIS) portal. Training videos were created to help users query and reach the data they need. GSP (Genome Specific Primers) and PIECE2 (Plant Intron Exon Comparison and Evolution) tools were implemented and are available to use. As more small grains reference sequences become available, GrainGenes will play an increasingly vital role in helping researchers improve crops.
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Affiliation(s)
- Victoria C Blake
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Margaret R Woodhouse
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Gerard R Lazo
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Sarah G Odell
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA.,Department of Plant Sciences, University of California, Davis, CA, USA
| | - Charlene P Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Yi Wang
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Yong Q Gu
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Clay L Birkett
- Robert Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - Jean-Luc Jannink
- Robert Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA.,Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Dave E Matthews
- Robert Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - David L Hane
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Steve L Michel
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Eric Yao
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Taner Z Sen
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA.,Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
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20
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Jang YR, Cho K, Kim S, Sim JR, Lee SB, Kim BG, Gu YQ, Altenbach SB, Lim SH, Goo TW, Lee JY. Comparison of MALDI-TOF-MS and RP-HPLC as Rapid Screening Methods for Wheat Lines With Altered Gliadin Compositions. Front Plant Sci 2020; 11:600489. [PMID: 33343602 PMCID: PMC7746642 DOI: 10.3389/fpls.2020.600489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/13/2020] [Indexed: 05/05/2023]
Abstract
The wheat gliadins are a complex group of flour proteins that can trigger celiac disease and serious food allergies. As a result, mutation breeding and biotechnology approaches are being used to develop new wheat lines with reduced immunogenic potential. Key to these efforts is the development of rapid, high-throughput methods that can be used as a first step in selecting lines with altered gliadin contents. In this paper, we optimized matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and reversed-phase high-performance liquid chromatography (RP-HPLC) methods for the separation of gliadins from Triticum aestivum cv. Chinese Spring (CS). We evaluated the quality of the resulting profiles using the complete set of gliadin gene sequences recently obtained from this cultivar as well as a set of aneuploid lines in CS. The gliadins were resolved into 13 peaks by MALDI-TOF-MS. α- or γ-gliadins that contain abundant celiac disease epitopes and are likely targets for efforts to reduce the immunogenicity of flour were found in several peaks. However, other peaks contained multiple α- and γ-gliadins, including one peak with as many as 12 different gliadins. In comparison, separation of proteins by RP-HPLC yielded 28 gliadin peaks, including 13 peaks containing α-gliadins and eight peaks containing γ-gliadins. While the separation of α- and γ-gliadins gliadins achieved by RP-HPLC was better than that achieved by MALDI-TOF-MS, it was not possible to link peaks with individual protein sequences. Both MALDI-TOF-MS and RP-HPLC provided adequate separation of ω-gliadins. While MALDI-TOF-MS is faster and could prove useful in studies that target specific gliadins, RP-HPLC is an effective method that can be applied more broadly to detect changes in gliadin composition.
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Affiliation(s)
- You-Ran Jang
- National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Kyoungwon Cho
- Department of Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Sewon Kim
- National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Jae-Ryeong Sim
- National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Su-Bin Lee
- National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Beom-Gi Kim
- National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Yong Q. Gu
- USDA-ARS, Western Regional Research Center, Albany, CA, United States
| | | | - Sun-Hyung Lim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong, South Korea
| | - Tae-Won Goo
- Department of Biochemistry, School of Medicine, Dongguk University, Gyeongju, South Korea
| | - Jong-Yeol Lee
- National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
- *Correspondence: Jong-Yeol Lee,
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21
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Wang YN, Gu YQ, Wang AC, Xie JL, Shi LL, Sun YF, Wang L. [Left ventricular diverticulum in an fetus: report of a case]. Zhonghua Bing Li Xue Za Zhi 2019; 48:564-565. [PMID: 31288316 DOI: 10.3760/cma.j.issn.0529-5807.2019.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Y N Wang
- Department of Pathology, Haidian Maternal and Child Health Hospital, Beijing 100080, China
| | - Y Q Gu
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - A C Wang
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - J L Xie
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - L L Shi
- Department of Ultrasound, Haidian Maternal and Child Health Hospital, Beijing 100080, China
| | - Y F Sun
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - L Wang
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
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22
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Xu L, Dong Z, Fang L, Luo Y, Wei Z, Guo H, Zhang G, Gu YQ, Coleman-Derr D, Xia Q, Wang Y. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52-W58. [PMID: 31053848 PMCID: PMC6602458 DOI: 10.1093/nar/gkz333] [Citation(s) in RCA: 540] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/16/2019] [Accepted: 04/25/2019] [Indexed: 12/28/2022] Open
Abstract
OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.
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Affiliation(s)
- Ling Xu
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Zhaobin Dong
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94710, USA
- USDA-ARS, Plant Gene Expression Center, Albany, CA 94706, USA
| | - Lu Fang
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Yongjiang Luo
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Zhaoyuan Wei
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Hailong Guo
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Guoqing Zhang
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94706, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94710, USA
- USDA-ARS, Plant Gene Expression Center, Albany, CA 94706, USA
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Yi Wang
- Biological Science Research Center, Southwest University, Chongqing 400715, China
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23
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Altenbach SB, Chang HC, Simon-Buss A, Mohr T, Huo N, Gu YQ. Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring. Funct Integr Genomics 2019; 20:1-16. [PMID: 31250230 PMCID: PMC6954139 DOI: 10.1007/s10142-019-00694-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/12/2019] [Accepted: 05/31/2019] [Indexed: 12/18/2022]
Abstract
Although the economic value of wheat flour is determined by the complement of gluten proteins, these proteins have been challenging to study because of the complexity of the major protein groups and the tremendous sequence diversity among wheat cultivars. The completion of a high-quality wheat genome sequence from the reference wheat Chinese Spring recently facilitated the assembly and annotation of a complete set of gluten protein genes from a single cultivar, making it possible to link individual proteins in the flour to specific gene sequences. In a proteomic analysis of total wheat flour protein from Chinese Spring using quantitative two-dimensional gel electrophoresis combined with tandem mass spectrometry, gliadins or low-molecular-weight glutenin subunits were identified as the predominant proteins in 72 protein spots. Individual spots were associated with 40 of 56 Chinese Spring gene sequences, including 16 of 26 alpha gliadins, 10 of 11 gamma gliadins, six of seven omega gliadins, one of two delta gliadins, and nine of ten LMW-GS. Most genes that were not associated with protein spots were either expressed at low levels in endosperm or encoded proteins with high similarity to other proteins. A wide range of protein accumulation levels were observed and discrepancies between transcript levels and protein levels were noted. This work together with similar studies using other commercial cultivars should provide new insight into the molecular basis of wheat flour quality and allergenic potential.
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Affiliation(s)
- Susan B Altenbach
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
| | - Han-Chang Chang
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Annamaria Simon-Buss
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Toni Mohr
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Yong Q Gu
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
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24
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Huo N, Zhu T, Zhang S, Mohr T, Luo MC, Lee JY, Distelfeld A, Altenbach S, Gu YQ. Rapid evolution of α-gliadin gene family revealed by analyzing Gli-2 locus regions of wild emmer wheat. Funct Integr Genomics 2019; 19:993-1005. [PMID: 31197605 PMCID: PMC6797660 DOI: 10.1007/s10142-019-00686-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
α-Gliadins are a major group of gluten proteins in wheat flour that contribute to the end-use properties for food processing and contain major immunogenic epitopes that can cause serious health-related issues including celiac disease (CD). α-Gliadins are also the youngest group of gluten proteins and are encoded by a large gene family. The majority of the gene family members evolved independently in the A, B, and D genomes of different wheat species after their separation from a common ancestral species. To gain insights into the origin and evolution of these complex genes, the genomic regions of the Gli-2 loci encoding α-gliadins were characterized from the tetraploid wild emmer, a progenitor of hexaploid bread wheat that contributed the AABB genomes. Genomic sequences of Gli-2 locus regions for the wild emmer A and B genomes were first reconstructed using the genome sequence scaffolds along with optical genome maps. A total of 24 and 16 α-gliadin genes were identified for the A and B genome regions, respectively. α-Gliadin pseudogene frequencies of 86% for the A genome and 69% for the B genome were primarily caused by C to T substitutions in the highly abundant glutamine codons, resulting in the generation of premature stop codons. Comparison with the homologous regions from the hexaploid wheat cv. Chinese Spring indicated considerable sequence divergence of the two A genomes at the genomic level. In comparison, conserved regions between the two B genomes were identified that included α-gliadin pseudogenes containing shared nested TE insertions. Analyses of the genomic organization and phylogenetic tree reconstruction indicate that although orthologous gene pairs derived from speciation were present, large portions of α-gliadin genes were likely derived from differential gene duplications or deletions after the separation of the homologous wheat genomes ~ 0.5 MYA. The higher number of full-length intact α-gliadin genes in hexaploid wheat than that in wild emmer suggests that human selection through domestication might have an impact on α-gliadin evolution. Our study provides insights into the rapid and dynamic evolution of genomic regions harboring the α-gliadin genes in wheat.
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Affiliation(s)
- Naxin Huo
- United States Department of Agriculture-Agricultural Research Service USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Shengli Zhang
- Hena Institute of Science and Technology, Xinxiang, Hena Province, 453003, China
| | - Toni Mohr
- United States Department of Agriculture-Agricultural Research Service USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Jong-Yeol Lee
- National Institute of Agricultural Sciences, RDA, Jeonju, 54874, South Korea
| | - Assaf Distelfeld
- Institute for Crop Improvement, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Susan Altenbach
- United States Department of Agriculture-Agricultural Research Service USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
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25
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Altenbach SB, Chang HC, Simon-Buss A, Jang YR, Denery-Papini S, Pineau F, Gu YQ, Huo N, Lim SH, Kang CS, Lee JY. Towards reducing the immunogenic potential of wheat flour: omega gliadins encoded by the D genome of hexaploid wheat may also harbor epitopes for the serious food allergy WDEIA. BMC Plant Biol 2018; 18:291. [PMID: 30463509 PMCID: PMC6249860 DOI: 10.1186/s12870-018-1506-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/26/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Omega-5 gliadins are a group of highly repetitive gluten proteins in wheat flour encoded on the 1B chromosome of hexaploid wheat. These proteins are the major sensitizing allergens in a severe form of food allergy called wheat-dependent exercise-induced anaphylaxis (WDEIA). The elimination of omega-5 gliadins from wheat flour through biotechnology or breeding approaches could reduce the immunogenic potential and adverse health effects of the flour. RESULTS A mutant line missing low-molecular weight glutenin subunits encoded at the Glu-B3 locus was selected previously from a doubled haploid population generated from two Korean wheat cultivars. Analysis of flour from the mutant line by 2-dimensional gel electrophoresis coupled with tandem mass spectrometry revealed that the omega-5 gliadins and several gamma gliadins encoded by the closely linked Gli-B1 locus were also missing as a result of a deletion of at least 5.8 Mb of chromosome 1B. Two-dimensional immunoblot analysis of flour proteins using sera from WDEIA patients showed reduced IgE reactivity in the mutant relative to the parental lines due to the absence of the major omega-5 gliadins. However, two minor proteins showed strong reactivity to patient sera in both the parental and the mutant lines and also reacted with a monoclonal antibody against omega-5 gliadin. Analysis of the two minor reactive proteins by mass spectrometry revealed that both proteins correspond to omega-5 gliadin genes encoded on chromosome 1D that were thought previously to be pseudogenes. CONCLUSIONS While breeding approaches can be used to reduce the levels of the highly immunogenic omega-5 gliadins in wheat flour, these approaches are complicated by the genetic linkage of different classes of gluten protein genes and the finding that omega-5 gliadins may be encoded on more than one chromosome. The work illustrates the importance of detailed knowledge about the genomic regions harboring the major gluten protein genes in individual wheat cultivars for future efforts aimed at reducing the immunogenic potential of wheat flour.
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Affiliation(s)
- Susan B. Altenbach
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710 USA
| | - Han-Chang Chang
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710 USA
| | - Annamaria Simon-Buss
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710 USA
| | - You-Ran Jang
- National Institute of Agricultural Sciences, RDA, Jeonju, 54874 South Korea
| | - Sandra Denery-Papini
- UR1268 Biopolymers, Interactions, Assemblies, Institut National de la Recherche Agronomique, Rue de la Géraudière, F-44316 Nantes, France
| | - Florence Pineau
- UR1268 Biopolymers, Interactions, Assemblies, Institut National de la Recherche Agronomique, Rue de la Géraudière, F-44316 Nantes, France
| | - Yong Q. Gu
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710 USA
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710 USA
| | - Sun-Hyung Lim
- National Institute of Agricultural Sciences, RDA, Jeonju, 54874 South Korea
| | - Chon-Sik Kang
- National Institute of Crop Science, RDA, Jeonju, 55365 South Korea
| | - Jong-Yeol Lee
- National Institute of Agricultural Sciences, RDA, Jeonju, 54874 South Korea
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Dvorak J, Wang L, Zhu T, Jorgensen CM, Luo MC, Deal KR, Gu YQ, Gill BS, Distelfeld A, Devos KM, Qi P, McGuire PE. Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B. Theor Appl Genet 2018; 131:2451-2462. [PMID: 30141064 PMCID: PMC6208953 DOI: 10.1007/s00122-018-3165-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 08/13/2018] [Indexed: 05/02/2023]
Abstract
Comparison of genome sequences of wild emmer wheat and Aegilops tauschii suggests a novel scenario of the evolution of rearranged wheat chromosomes 4A, 5A, and 7B. Past research suggested that wheat chromosome 4A was subjected to a reciprocal translocation T(4AL;5AL)1 that occurred in the diploid progenitor of the wheat A subgenome and to three major rearrangements that occurred in polyploid wheat: pericentric inversion Inv(4AS;4AL)1, paracentric inversion Inv(4AL;4AL)1, and reciprocal translocation T(4AL;7BS)1. Gene collinearity along the pseudomolecules of tetraploid wild emmer wheat (Triticum turgidum ssp. dicoccoides, subgenomes AABB) and diploid Aegilops tauschii (genomes DD) was employed to confirm these rearrangements and to analyze the breakpoints. The exchange of distal regions of chromosome arms 4AS and 4AL due to pericentric inversion Inv(4AS;4AL)1 was detected, and breakpoints were validated with an optical Bionano genome map. Both breakpoints contained satellite DNA. The breakpoints of reciprocal translocation T(4AL;7BS)1 were also found. However, the breakpoints that generated paracentric inversion Inv(4AL;4AL)1 appeared to be collocated with the 4AL breakpoints that had produced Inv(4AS;4AL)1 and T(4AL;7BS)1. Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 either originated sequentially, and Inv(4AL;4AL)1 was produced by recurrent chromosome breaks at the same breakpoints that generated Inv(4AS;4AL)1 and T(4AL;7BS)1, or Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 originated simultaneously. We prefer the latter hypothesis since it makes fewer assumptions about the sequence of events that produced these chromosome rearrangements.
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Affiliation(s)
- Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Chad M. Jorgensen
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Karin R. Deal
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Yong Q. Gu
- Crop Improvement and Genetics Research, USDA-ARS, Albany, CA USA
| | - Bikram S. Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA USA
- Department of Plant Biology, University of Georgia, Athens, GA USA
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA USA
- Department of Plant Biology, University of Georgia, Athens, GA USA
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27
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Wu YC, Zhu B, Li G, Zhang XH, Yu MH, Dong KG, Zhang TK, Yang Y, Bi B, Yang J, Yan YH, Tan F, Fan W, Lu F, Wang SY, Zhao ZQ, Zhou WM, Cao LF, Gu YQ. Towards high-energy, high-resolution computed tomography via a laser driven micro-spot gamma-ray source. Sci Rep 2018; 8:15888. [PMID: 30367090 PMCID: PMC6203838 DOI: 10.1038/s41598-018-33844-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/02/2018] [Indexed: 02/04/2023] Open
Abstract
Computed Tomography (CT) is a powerful method for non-destructive testing (NDT) and metrology awakes with expanding application fields. To improve the spatial resolution of high energy CT, a micro-spot gamma-ray source based on bremsstrahlung from a laser wakefield accelerator was developed. A high energy CT using the source was performed, which shows that the resolution of reconstruction can reach 100 μm at 10% contrast. Our proof-of-principle demonstration indicates that laser driven micro-spot gamma-ray sources provide a prospective way to increase the spatial resolution and toward to high energy micro CT. Due to the advantage in spatial resolution, laser based high energy CT represents a large potential for many NDT applications.
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Affiliation(s)
- Y C Wu
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China.,IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - B Zhu
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - G Li
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - X H Zhang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China.,Department of Engineering Physics, Tsinghua University, Beijing, 100084, China
| | - M H Yu
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - K G Dong
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - T K Zhang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - Y Yang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - B Bi
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - J Yang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - Y H Yan
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - F Tan
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China.,University of Science and Technology of China, Hefei, 230026, China
| | - W Fan
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - F Lu
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - S Y Wang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China
| | - Z Q Zhao
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China.,IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - W M Zhou
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China.,IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - L F Cao
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China.,IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Y Q Gu
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang, Sichuan, 621900, China. .,IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
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28
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Li D, Jin H, Zhang K, Wang Z, Wang F, Zhao Y, Huo N, Liu X, Gu YQ, Wang D, Dong L. Analysis of the Gli-D2 locus identifies a genetic target for simultaneously improving the breadmaking and health-related traits of common wheat. Plant J 2018; 95:414-426. [PMID: 29752764 DOI: 10.1111/tpj.13956] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 05/22/2023]
Abstract
Gliadins are a major component of wheat seed proteins. However, the complex homoeologous Gli-2 loci (Gli-A2, -B2 and -D2) that encode the α-gliadins in commercial wheat are still poorly understood. Here we analyzed the Gli-D2 locus of Xiaoyan 81 (Xy81), a winter wheat cultivar. A total of 421.091 kb of the Gli-D2 sequence was assembled from sequencing multiple bacterial artificial clones, and 10 α-gliadin genes were annotated. Comparative genomic analysis showed that Xy81 carried only eight of the α-gliadin genes of the D genome donor Aegilops tauschii, with two of them each experiencing a tandem duplication. A mutant line lacking Gli-D2 (DLGliD2) consistently exhibited better breadmaking quality and dough functionalities than its progenitor Xy81, but without penalties in other agronomic traits. It also had an elevated lysine content in the grains. Transcriptome analysis verified the lack of Gli-D2 α-gliadin gene expression in DLGliD2. Furthermore, the transcript and protein levels of protein disulfide isomerase were both upregulated in DLGliD2 grains. Consistent with this finding, DLGliD2 had increased disulfide content in the flour. Our work sheds light on the structure and function of Gli-D2 in commercial wheat, and suggests that the removal of Gli-D2 and the gliadins specified by it is likely to be useful for simultaneously enhancing the end-use and health-related traits of common wheat. Because gliadins and homologous proteins are widely present in grass species, the strategy and information reported here may be broadly useful for improving the quality traits of diverse cereal crops.
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Affiliation(s)
- Da Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huaibing Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kunpu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Agronomy and State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhaojun Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Faming Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yue Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California, 94710, USA
| | - Xin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California, 94710, USA
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- College of Agronomy and State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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29
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Dvorak J, Wang L, Zhu T, Jorgensen CM, Deal KR, Dai X, Dawson MW, Müller HG, Luo MC, Ramasamy RK, Dehghani H, Gu YQ, Gill BS, Distelfeld A, Devos KM, Qi P, You FM, Gulick PJ, McGuire PE. Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size. Plant J 2018; 95:487-503. [PMID: 29770515 DOI: 10.1111/tpj.13964] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 05/05/2023]
Abstract
Homology was searched with genes annotated in the Aegilops tauschii pseudomolecules against genes annotated in the pseudomolecules of tetraploid wild emmer wheat, Brachypodium distachyon, sorghum and rice. Similar searches were performed with genes annotated in the rice pseudomolecules. Matrices of collinear genes and rearrangements in their order were constructed. Optical BioNano genome maps were constructed and used to validate rearrangements unique to the wild emmer and Ae. tauschii genomes. Most common rearrangements were short paracentric inversions and short intrachromosomal translocations. Intrachromosomal translocations outnumbered segmental intrachromosomal duplications. The densities of paracentric inversion lengths were approximated by exponential distributions in all six genomes. Densities of collinear genes along the Ae. tauschii chromosomes were highly correlated with meiotic recombination rates but those of rearrangements were not, suggesting different causes of the erosion of gene collinearity and evolution of major chromosome rearrangements. Frequent rearrangements sharing breakpoints suggested that chromosomes have been rearranged recurrently at some sites. The distal 4 Mb of the short arms of rice chromosomes Os11 and Os12 and corresponding regions in the sorghum, B. distachyon and Triticeae genomes contain clusters of interstitial translocations including from 1 to 7 collinear genes. The rates of acquisition of major rearrangements were greater in the large wild emmer wheat and Ae. tauschii genomes than in the lineage preceding their divergence or in the B. distachyon, rice and sorghum lineages. It is suggested that synergy between large quantities of dynamic transposable elements and annual growth habit have been the primary causes of the fast evolution of the Triticeae genomes.
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Affiliation(s)
- Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Chad M Jorgensen
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Xiongtao Dai
- Department of Statistics, University of California, Davis, CA, USA
| | - Matthew W Dawson
- Department of Statistics, University of California, Davis, CA, USA
| | | | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Ramesh K Ramasamy
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Hamid Dehghani
- Department of Plant Sciences, University of California, Davis, CA, USA
- Department of Plant Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Yong Q Gu
- Crop Improvement & Genetics Research, USDA-ARS, Albany, CA, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop & Soil Sciences), University of Georgia, Athens, GA, USA
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop & Soil Sciences), University of Georgia, Athens, GA, USA
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Frank M You
- Agriculture & Agri-Food Canada, Morden, MB, Canada
| | - Patrick J Gulick
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA, USA
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30
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Shan LQ, Cai HB, Zhang WS, Tang Q, Zhang F, Song ZF, Bi B, Ge FJ, Chen JB, Liu DX, Wang WW, Yang ZH, Qi W, Tian C, Yuan ZQ, Zhang B, Yang L, Jiao JL, Cui B, Zhou WM, Cao LF, Zhou CT, Gu YQ, Zhang BH, Zhu SP, He XT. Experimental Evidence of Kinetic Effects in Indirect-Drive Inertial Confinement Fusion Hohlraums. Phys Rev Lett 2018; 120:195001. [PMID: 29799245 DOI: 10.1103/physrevlett.120.195001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 01/19/2018] [Indexed: 06/08/2023]
Abstract
We present the first experimental evidence supported by simulations of kinetic effects launched in the interpenetration layer between the laser-driven hohlraum plasma bubbles and the corona plasma of the compressed pellet at the Shenguang-III prototype laser facility. Solid plastic capsules were coated with carbon-deuterium layers; as the implosion neutron yield is quenched, DD fusion yield from the corona plasma provides a direct measure of the kinetic effects inside the hohlraum. An anomalous large energy spread of the DD neutron signal (∼282 keV) and anomalous scaling of the neutron yield with the thickness of the carbon-deuterium layers cannot be explained by the hydrodynamic mechanisms. Instead, these results can be attributed to kinetic shocks that arise in the hohlraum-wall-ablator interpenetration region, which result in efficient acceleration of the deuterons (∼28.8 J, 0.45% of the total input laser energy). These studies provide novel insight into the interactions and dynamics of a vacuum hohlraum and near-vacuum hohlraum.
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Affiliation(s)
- L Q Shan
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - H B Cai
- Institute of Applied Physics and Computational Mathematics, Beijing 100094, China
- HEDPS, Center for Applied Physics and Technology, Peking University, Beijing 100871, China
- IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - W S Zhang
- Graduate School, China Academy of Engineering Physics, P.O. Box 2101, Beijing 100088, China
| | - Q Tang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - F Zhang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - Z F Song
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - B Bi
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - F J Ge
- Institute of Applied Physics and Computational Mathematics, Beijing 100094, China
| | - J B Chen
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - D X Liu
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - W W Wang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - Z H Yang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - W Qi
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - C Tian
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - Z Q Yuan
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - B Zhang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - L Yang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - J L Jiao
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - B Cui
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - W M Zhou
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
- IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - L F Cao
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - C T Zhou
- Institute of Applied Physics and Computational Mathematics, Beijing 100094, China
| | - Y Q Gu
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
- IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - B H Zhang
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
| | - S P Zhu
- Science and Technology on Plasma Physics Laboratory, Research Center of Laser Fusion, CAEP, Mianyang 621900, China
- Institute of Applied Physics and Computational Mathematics, Beijing 100094, China
- Graduate School, China Academy of Engineering Physics, P.O. Box 2101, Beijing 100088, China
| | - X T He
- Institute of Applied Physics and Computational Mathematics, Beijing 100094, China
- HEDPS, Center for Applied Physics and Technology, Peking University, Beijing 100871, China
- IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China
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31
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Valdes Franco JA, Wang Y, Huo N, Ponciano G, Colvin HA, McMahan CM, Gu YQ, Belknap WR. Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes. BMC Genomics 2018; 19:271. [PMID: 29673330 PMCID: PMC5907723 DOI: 10.1186/s12864-018-4653-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 04/10/2018] [Indexed: 12/30/2022] Open
Abstract
Background Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. Results The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50 = 22 kb), maps > 95% of the shotgun reads and is essentially complete. Approximately 40,000 transcribed, protein encoding genes were annotated on the assembly. Further characterization of this genome revealed 15 families of small, microsatellite-associated, transposable elements (TEs) with unexpected chromosomal distribution profiles. These SaTar (Satellite Targeted) elements, which are non-autonomous Mu-like elements (MULEs), were frequently observed in multimeric linear arrays of unrelated individual elements within which no individual element is interrupted by another. This uniformly non-nested TE multimer architecture has not been previously described in either eukaryotic or prokaryotic genomes. Five families of similarly distributed non-autonomous MULEs (microsatellite associated, modularly assembled) were characterized in the rice genome. Families of TEs with similar structures and distribution profiles were identified in sorghum and citrus. Conclusion The sequencing and assembly of the guayule genome provides a foundation for application of current crop improvement technologies to this plant. In addition, characterization of this genome revealed SaTar elements with distribution profiles unique among TEs. Satar targeting appears based on an alternative MULE recombination mechanism with the potential to impact gene evolution. Electronic supplementary material The online version of this article (10.1186/s12864-018-4653-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José A Valdes Franco
- Universidad Autónoma de Nuevo León, Monterrey, NL, Mexico.,Present Address: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Yi Wang
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | - Naxin Huo
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | - Grisel Ponciano
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | | | - Colleen M McMahan
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | - Yong Q Gu
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA.
| | - William R Belknap
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
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32
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Huo N, Zhu T, Altenbach S, Dong L, Wang Y, Mohr T, Liu Z, Dvorak J, Luo MC, Gu YQ. Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat. Sci Rep 2018; 8:5181. [PMID: 29581476 PMCID: PMC5980091 DOI: 10.1038/s41598-018-23570-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/13/2018] [Indexed: 12/21/2022] Open
Abstract
Wheat Gli-2 loci encode complex groups of α-gliadin prolamins that are important for breadmaking, but also major triggers of celiac disease (CD). Elucidation of α-gliadin evolution provides knowledge to produce wheat with better end-use properties and reduced immunogenic potential. The Gli-2 loci contain a large number of tandemly duplicated genes and highly repetitive DNA, making sequence assembly of their genomic regions challenging. Here, we constructed high-quality sequences spanning the three wheat homeologous α-gliadin loci by aligning PacBio-based sequence contigs with BioNano genome maps. A total of 47 α-gliadin genes were identified with only 26 encoding intact full-length protein products. Analyses of α-gliadin loci and phylogenetic tree reconstruction indicate significant duplications of α-gliadin genes in the last ~2.5 million years after the divergence of the A, B and D genomes, supporting its rapid lineage-independent expansion in different Triticeae genomes. We showed that dramatic divergence in expression of α-gliadin genes could not be attributed to sequence variations in the promoter regions. The study also provided insights into the evolution of CD epitopes and identified a single indel event in the hexaploid wheat D genome that likely resulted in the generation of the highly toxic 33-mer CD epitope.
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Affiliation(s)
- Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California, 94710, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Susan Altenbach
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California, 94710, USA
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California, 94710, USA
| | - Toni Mohr
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California, 94710, USA
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California, 94710, USA.
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33
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Huo N, Zhang S, Zhu T, Dong L, Wang Y, Mohr T, Hu T, Liu Z, Dvorak J, Luo MC, Wang D, Lee JY, Altenbach S, Gu YQ. Gene Duplication and Evolution Dynamics in the Homeologous Regions Harboring Multiple Prolamin and Resistance Gene Families in Hexaploid Wheat. Front Plant Sci 2018; 9:673. [PMID: 29875781 PMCID: PMC5974169 DOI: 10.3389/fpls.2018.00673] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/03/2018] [Indexed: 05/19/2023]
Abstract
Improving end-use quality and disease resistance are important goals in wheat breeding. The genetic loci controlling these traits are highly complex, consisting of large families of prolamin and resistance genes with members present in all three homeologous A, B, and D genomes in hexaploid bread wheat. Here, orthologous regions harboring both prolamin and resistance gene loci were reconstructed and compared to understand gene duplication and evolution in different wheat genomes. Comparison of the two orthologous D regions from the hexaploid wheat Chinese Spring and the diploid progenitor Aegilops tauschii revealed their considerable difference due to the presence of five large structural variations with sizes ranging from 100 kb to 2 Mb. As a result, 44% of the Ae. tauschii and 71% of the Chinese Spring sequences in the analyzed regions, including 79 genes, are not shared. Gene rearrangement events, including differential gene duplication and deletion in the A, B, and D regions, have resulted in considerable erosion of gene collinearity in the analyzed regions, suggesting rapid evolution of prolamin and resistance gene families after the separation of the three wheat genomes. We hypothesize that this fast evolution is attributed to the co-evolution of the two gene families dispersed within a high recombination region. The identification of a full set of prolamin genes facilitated transcriptome profiling and revealed that the A genome contributes the least to prolamin expression because of its smaller number of expressed intact genes and their low expression levels, while the B and D genomes contribute similarly.
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Affiliation(s)
- Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Shengli Zhang
- Hena Institute of Science and Technology, Xinxiang, China
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Toni Mohr
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Tiezhu Hu
- Hena Institute of Science and Technology, Xinxiang, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jong-Yeol Lee
- National Institute of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Susan Altenbach
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
- *Correspondence: Susan Altenbach, Yong Q. Gu,
| | - Yong Q. Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
- *Correspondence: Susan Altenbach, Yong Q. Gu,
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Huo N, Dong L, Zhang S, Wang Y, Zhu T, Mohr T, Altenbach S, Liu Z, Dvorak J, Anderson OD, Luo MC, Wang D, Gu YQ. New insights into structural organization and gene duplication in a 1.75-Mb genomic region harboring the α-gliadin gene family in Aegilops tauschii, the source of wheat D genome. Plant J 2017; 92:571-583. [PMID: 28857322 DOI: 10.1111/tpj.13675] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Among the wheat prolamins important for its end-use traits, α-gliadins are the most abundant, and are also a major cause of food-related allergies and intolerances. Previous studies of various wheat species estimated that between 25 and 150 α-gliadin genes reside in the Gli-2 locus regions. To better understand the evolution of this complex gene family, the DNA sequence of a 1.75-Mb genomic region spanning the Gli-2 locus was analyzed in the diploid grass, Aegilops tauschii, the ancestral source of D genome in hexaploid bread wheat. Comparison with orthologous regions from rice, sorghum, and Brachypodium revealed rapid and dynamic changes only occurring to the Ae. tauschii Gli-2 region, including insertions of high numbers of non-syntenic genes and a high rate of tandem gene duplications, the latter of which have given rise to 12 copies of α-gliadin genes clustered within a 550-kb region. Among them, five copies have undergone pseudogenization by various mutation events. Insights into the evolutionary relationship of the duplicated α-gliadin genes were obtained from their genomic organization, transcription patterns, transposable element insertions and phylogenetic analyses. An ancestral glutamate-like receptor (GLR) gene encoding putative amino acid sensor in all four grass species has duplicated only in Ae. tauschii and generated three more copies that are interspersed with the α-gliadin genes. Phylogenetic inference and different gene expression patterns support functional divergence of the Ae. tauschii GLR copies after duplication. Our results suggest that the duplicates of α-gliadin and GLR genes have likely taken different evolutionary paths; conservation for the former and neofunctionalization for the latter.
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Affiliation(s)
- Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shengli Zhang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Toni Mohr
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Susan Altenbach
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Olin D Anderson
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
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Zhang CJ, Hua JF, Wan Y, Pai CH, Guo B, Zhang J, Ma Y, Li F, Wu YP, Chu HH, Gu YQ, Xu XL, Mori WB, Joshi C, Wang J, Lu W. Femtosecond Probing of Plasma Wakefields and Observation of the Plasma Wake Reversal Using a Relativistic Electron Bunch. Phys Rev Lett 2017; 119:064801. [PMID: 28949606 DOI: 10.1103/physrevlett.119.064801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Indexed: 06/07/2023]
Abstract
We show that a high-energy electron bunch can be used to capture the instantaneous longitudinal and transverse field structures of the highly transient, microscopic, laser-excited relativistic wake with femtosecond resolution. The spatiotemporal evolution of wakefields in a plasma density up ramp is measured and the reversal of the plasma wake, where the wake wavelength at a particular point in space increases until the wake disappears completely only to reappear at a later time but propagating in the opposite direction, is observed for the first time by using this new technique.
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Affiliation(s)
- C J Zhang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Department of Electrical Engineering, University of California Los Angeles, Los Angeles, California 90095, USA
| | - J F Hua
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Y Wan
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - C-H Pai
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - B Guo
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - J Zhang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Y Ma
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - F Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Y P Wu
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - H-H Chu
- Department of Physics, National Central University, Jhong-Li 32001, Taiwan
| | - Y Q Gu
- Science and Technology on Plasma Physics Laboratory, Laser Fusion Research Center, CAEP, Mianyang 621900, China
| | - X L Xu
- Department of Electrical Engineering, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095, USA
| | - W B Mori
- Department of Electrical Engineering, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095, USA
| | - C Joshi
- Department of Electrical Engineering, University of California Los Angeles, Los Angeles, California 90095, USA
| | - J Wang
- Department of Physics, National Central University, Jhong-Li 32001, Taiwan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - W Lu
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- IFSA Collaborative Center, Shanghai Jiao Tong University, Shanghai 200240, China
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36
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Chang HX, Qiao B, Huang TW, Xu Z, Zhou CT, Gu YQ, Yan XQ, Zepf M, He XT. Brilliant petawatt gamma-ray pulse generation in quantum electrodynamic laser-plasma interaction. Sci Rep 2017; 7:45031. [PMID: 28338010 PMCID: PMC5364473 DOI: 10.1038/srep45031] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/20/2017] [Indexed: 11/17/2022] Open
Abstract
We show a new resonance acceleration scheme for generating ultradense relativistic electron bunches in helical motions and hence emitting brilliant vortical γ-ray pulses in the quantum electrodynamic (QED) regime of circularly-polarized (CP) laser-plasma interactions. Here the combined effects of the radiation reaction recoil force and the self-generated magnetic fields result in not only trapping of a great amount of electrons in laser-produced plasma channel, but also significant broadening of the resonance bandwidth between laser frequency and that of electron betatron oscillation in the channel, which eventually leads to formation of the ultradense electron bunch under resonant helical motion in CP laser fields. Three-dimensional PIC simulations show that a brilliant γ-ray pulse with unprecedented power of 6.7 PW and peak brightness of 1025 photons/s/mm2/mrad2/0.1% BW (at 15 MeV) is emitted at laser intensity of 1.9 × 1023 W/cm2.
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Affiliation(s)
- H X Chang
- Center for Applied Physics and Technology, HEDPS, State Key Laboratory of Nuclear Physics and Technology, and School of Physics, Peking University, Beijing, 100871, China
| | - B Qiao
- Center for Applied Physics and Technology, HEDPS, State Key Laboratory of Nuclear Physics and Technology, and School of Physics, Peking University, Beijing, 100871, China.,Collaborative Innovation Center of IFSA (CICIFSA), Shanghai Jiao Tong University, Shanghai 200240, China
| | - T W Huang
- Center for Applied Physics and Technology, HEDPS, State Key Laboratory of Nuclear Physics and Technology, and School of Physics, Peking University, Beijing, 100871, China
| | - Z Xu
- Center for Applied Physics and Technology, HEDPS, State Key Laboratory of Nuclear Physics and Technology, and School of Physics, Peking University, Beijing, 100871, China
| | - C T Zhou
- Center for Applied Physics and Technology, HEDPS, State Key Laboratory of Nuclear Physics and Technology, and School of Physics, Peking University, Beijing, 100871, China.,Institute of Applied Physics and Computational Mathematics, Beijing 100094, China
| | - Y Q Gu
- Science and Technology on Plasma Physics Laboratory, Mianyang 621900, China
| | - X Q Yan
- Center for Applied Physics and Technology, HEDPS, State Key Laboratory of Nuclear Physics and Technology, and School of Physics, Peking University, Beijing, 100871, China
| | - M Zepf
- Department of Physics and Astronomy, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - X T He
- Center for Applied Physics and Technology, HEDPS, State Key Laboratory of Nuclear Physics and Technology, and School of Physics, Peking University, Beijing, 100871, China.,Collaborative Innovation Center of IFSA (CICIFSA), Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Applied Physics and Computational Mathematics, Beijing 100094, China
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37
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Deng ZG, Zhang ZM, Zhang B, He SK, Teng J, Hong W, Dong KG, Wu YC, Zhu B, Gu YQ. Large-charge quasimonoenergetic electron beams produced by off-axis colliding laser pulses in underdense plasma. Phys Rev E 2017; 95:023206. [PMID: 28297850 DOI: 10.1103/physreve.95.023206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 11/07/2022]
Abstract
Electrons can be efficiently injected into a plasma wave by colliding two counterpropagating laser pulses in a laser wakefield acceleration. However, the generation of a high-quality electron beam with a large charge is difficult in the traditional on-axis colliding scheme due to the growth of the electron beam duration coming from the increase of the beam charge. To solve this problem, we propose an off-axis colliding scheme, in which the collision point is away from the axis of the driver pulse. We show that the electrons injected from the off-axis region are highly concentered on the tail of the bubble even for a large trapped charge, thus feeling almost the same accelerating field. As a result, quasimonoenergetic electron beams with a large charge can be produced. The validity of this scheme is confirmed by both the particle-in-cell simulations and the Hamiltonian model. Furthermore, it is shown that a Laguerre-Gauss (LG) laser can be adopted as the injection pulse to realize the off-axis colliding injection in three dimensions symmetrically, which may be useful in simplifying the technical layout of the real experiment setup.
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Affiliation(s)
- Z G Deng
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China
| | - Z M Zhang
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China
| | - B Zhang
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China
| | - S K He
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China
| | - J Teng
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China
| | - W Hong
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China
| | - K G Dong
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China
| | - Y C Wu
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China.,IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - B Zhu
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China
| | - Y Q Gu
- Research Center of Laser Fusion, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900, People's Republic of China.,IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China
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38
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Muñoz-Amatriaín M, Mirebrahim H, Xu P, Wanamaker SI, Luo M, Alhakami H, Alpert M, Atokple I, Batieno BJ, Boukar O, Bozdag S, Cisse N, Drabo I, Ehlers JD, Farmer A, Fatokun C, Gu YQ, Guo YN, Huynh BL, Jackson SA, Kusi F, Lawley CT, Lucas MR, Ma Y, Timko MP, Wu J, You F, Barkley NA, Roberts PA, Lonardi S, Close TJ. Genome resources for climate-resilient cowpea, an essential crop for food security. Plant J 2017; 89:1042-1054. [PMID: 27775877 DOI: 10.1111/tpj.13404] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 05/20/2023]
Abstract
Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Hamid Mirebrahim
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Pei Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou, 310021, China
| | - Steve I Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Hind Alhakami
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Matthew Alpert
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Ibrahim Atokple
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, Tamale, Ghana
| | - Benoit J Batieno
- Institut de l'Environnement et de Recherches Agricoles, Saria, Burkina Faso
| | - Ousmane Boukar
- International Institute of Tropical Agriculture, Kano, Nigeria
| | - Serdar Bozdag
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, USA
| | - Ndiaga Cisse
- Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Issa Drabo
- Institut de l'Environnement et de Recherches Agricoles, Saria, Burkina Faso
| | - Jeffrey D Ehlers
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
- The Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - Yong Q Gu
- USDA-ARS Western Regional Research Center, Albany, CA, USA
| | - Yi-Ning Guo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Bao-Lam Huynh
- Department of Nematology, University of California, Riverside, CA, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Francis Kusi
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, Tamale, Ghana
| | | | - Mitchell R Lucas
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Jiajie Wu
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Frank You
- Department of Plant Sciences, University of California, Davis, CA, USA
- Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Noelle A Barkley
- USDA-ARS Plant Genetic Resources Conservation Unit, Griffin, GA, USA
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
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39
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Wan Y, Pai CH, Zhang CJ, Li F, Wu YP, Hua JF, Lu W, Gu YQ, Silva LO, Joshi C, Mori WB. Physical Mechanism of the Transverse Instability in Radiation Pressure Ion Acceleration. Phys Rev Lett 2016; 117:234801. [PMID: 27982647 DOI: 10.1103/physrevlett.117.234801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Indexed: 06/06/2023]
Abstract
The transverse stability of the target is crucial for obtaining high quality ion beams using the laser radiation pressure acceleration (RPA) mechanism. In this Letter, a theoretical model and supporting two-dimensional (2D) particle-in-cell (PIC) simulations are presented to clarify the physical mechanism of the transverse instability observed in the RPA process. It is shown that the density ripples of the target foil are mainly induced by the coupling between the transverse oscillating electrons and the quasistatic ions, a mechanism similar to the oscillating two stream instability in the inertial confinement fusion research. The predictions of the mode structure and the growth rates from the theory agree well with the results obtained from the PIC simulations in various regimes, indicating the model contains the essence of the underlying physics of the transverse breakup of the target.
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Affiliation(s)
- Y Wan
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Laser Fusion Research Center, China Academy of Engineering Physics, Mianyang, Sichuan 621900, China
- IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - C-H Pai
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - C J Zhang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - F Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Y P Wu
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - J F Hua
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - W Lu
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Y Q Gu
- Laser Fusion Research Center, China Academy of Engineering Physics, Mianyang, Sichuan 621900, China
| | - L O Silva
- GoLP/instituto de Plasmas e Fusao Nuclear, Instituto Superior Tecnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - C Joshi
- University of California Los Angeles, Los Angeles, California 90095, USA
| | - W B Mori
- University of California Los Angeles, Los Angeles, California 90095, USA
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40
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Yin XH, Li YY, Fu J, Jiang D, Feng SY, Gu YQ, Cheng Y, Lyu B, Shi YJ, Ye MY, Wan BN. Improved spatial calibration for the CXRS system on EAST. Rev Sci Instrum 2016; 87:11E539. [PMID: 27910672 DOI: 10.1063/1.4962054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A Charge eXchange Recombination Spectroscopy (CXRS) diagnostic system has been developed to measure profiles of ion temperature and rotation since 2014 on EAST. Several techniques have been developed to improve the spatial calibration of the CXRS diagnostic. The sightline location was obtained by measuring the coordinates of three points on each sightline using an articulated flexible coordinate measuring arm when the vessel was accessible. After vacuum pumping, the effect of pressure change in the vacuum vessel was evaluated by observing the movement of the light spot from back-illuminated sightlines on the first wall using the newly developed articulated inspection arm. In addition, the rotation of the periscope after vacuum pumping was derived by using the Doppler shift of neutral beam emission spectra without magnetic field. Combining these techniques, improved spatial calibration was implemented to provide a complete and accurate description of the EAST CXRS system. Due to the effects of the change of air pressure, a ∼0.4° periscope rotation, yielding a ∼20 mm movement of the major radius of observation positions to the lower field side, was derived. Results of Zeeman splitting of neutral beam emission spectra with magnetic field also showed good agreement with the calibration results.
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Affiliation(s)
- X H Yin
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Y Y Li
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - J Fu
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - D Jiang
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - S Y Feng
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Y Q Gu
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - Y Cheng
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - B Lyu
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - Y J Shi
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - M Y Ye
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - B N Wan
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
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41
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Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Res 2016; 45:1015-1020. [PMID: 27742820 PMCID: PMC5210635 DOI: 10.1093/nar/gkw935] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/04/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022] Open
Abstract
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.
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Affiliation(s)
- Yi Wang
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Ling Xu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Roger Thilmony
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden R6M 1Y5 MB, Canada
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA .,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
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42
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Xie J, Huo N, Zhou S, Wang Y, Guo G, Deal KR, Ouyang S, Liang Y, Wang Z, Xiao L, Zhu T, Hu T, Tiwari V, Zhang J, Li H, Ni Z, Yao Y, Peng H, Zhang S, Anderson OD, McGuire PE, Dvorak J, Luo MC, Liu Z, Gu YQ, Sun Q. Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes. J Genet Genomics 2016; 44:51-61. [PMID: 27765484 DOI: 10.1016/j.jgg.2016.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 11/18/2022]
Abstract
Bread wheat (Triticum aestivum, AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path (MTP) of 3176 BAC clones from the short arm of Ae. tauschii chromosome 3 (At3DS). The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B (Ta3BS) is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element (TE) bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D (Ta3DS), there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.
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Affiliation(s)
- Jingzhong Xie
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Naxin Huo
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA; Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Shenghui Zhou
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Guanghao Guo
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Karin R Deal
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Shuhong Ouyang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yong Liang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Zhenzhong Wang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Lichan Xiao
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Tiezhu Hu
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Vijay Tiwari
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ 85721, USA
| | - Hongxia Li
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Shengli Zhang
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Olin D Anderson
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Patrick E McGuire
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
| | - Zhiyong Liu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
| | - Yong Q Gu
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA.
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
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43
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He LC, Li PH, Ma X, Sui SP, Gao S, Kim SW, Gu YQ, Huang Y, Ding NS, Huang RH. Identification of new single nucleotide polymorphisms affecting total number born and candidate genes related to ovulation rate in Chinese Erhualian pigs. Anim Genet 2016; 48:48-54. [PMID: 27615062 DOI: 10.1111/age.12492] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2016] [Indexed: 01/08/2023]
Abstract
The Chinese Erhualian pig has the highest record for litter size in the world. However, the genetic mechanism of its high prolificacy remains poorly understood. In our study, large phenotypic variations in litter size were found among Erhualian sows. Significant differences in total number born (TNB) and corpora lutea numbers were observed between sows with high and low estimated breeding values (EBVs) for TNB. To identify single nucleotide polymorphisms (SNPs) associated with TNB, a selective genomic scan was conducted on 18 sows representing the top 10% and 18 sows representing the bottom 10% of EBVs of 177 sows using Illumina Porcine SNP60 genotype data. Genome-wide fixation coefficient (FST ) values were calculated for each SNP between the high- and low-EBV groups. A total of 154 SNPs were significantly differentiated loci between the two groups. Of the top 10 highest FST SNPs, rs81399474, rs81400131 and rs81405013 on SSC8 and rs81434499 and rs81434489 on SSC 12 corresponded to previously reported QTL for litter size. The other five SNPs, rs81367039 on SSC2, rs80891106 on SSC7, rs81477883 on SSC12 and rs80938898 and rs80971725 on SSC14, appeared to be novel QTL for TNB. Significant associations between rs81399474 on SSC8 and TNB were confirmed in 313 Erhualian sows. Forty genes were identified around the top 10 highest FST SNPs, of which UCHL1, adjacent to rs81399474, and RPS6KB1 and CLTC, adjacent to rs81434499, have been reported to affect the ovulation rate in pig. The findings can advance understanding of the genetic variations in litter size of pigs.
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Affiliation(s)
- L C He
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - P H Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - X Ma
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - S P Sui
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - S Gao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - S W Kim
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Y Q Gu
- Changzhou Jiaoxi Cooperatives of Erhualian pigs, Changzhou, 213116, China
| | - Y Huang
- Changzhou Jiaoxi Cooperatives of Erhualian pigs, Changzhou, 213116, China
| | - N S Ding
- College of Animal Science and Veterinary Medicine, Jiangxi Agricultural University, Nanchang, 330045, China
| | - R H Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, 210095, China
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44
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Dong L, Huo N, Wang Y, Deal K, Wang D, Hu T, Dvorak J, Anderson OD, Luo MC, Gu YQ. Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii. Plant J 2016; 87:495-506. [PMID: 27228577 DOI: 10.1111/tpj.13214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 06/05/2023]
Abstract
Prolamin and resistance gene families are important in wheat food use and in defense against pathogen attacks, respectively. To better understand the evolution of these multi-gene families, the DNA sequence of a 2.8-Mb genomic region, representing an 8.8 cM genetic interval and harboring multiple prolamin and resistance-like gene families, was analyzed in the diploid grass Aegilops tauschii, the D-genome donor of bread wheat. Comparison with orthologous regions from rice, Brachypodium, and sorghum showed that the Ae. tauschii region has undergone dramatic changes; it has acquired more than 80 non-syntenic genes and only 13 ancestral genes are shared among these grass species. These non-syntenic genes, including prolamin and resistance-like genes, originated from various genomic regions and likely moved to their present locations via sequence evolution processes involving gene duplication and translocation. Local duplication of non-syntenic genes contributed significantly to the expansion of gene families. Our analysis indicates that the insertion of prolamin-related genes occurred prior to the separation of the Brachypodieae and Triticeae lineages. Unlike in Brachypodium, inserted prolamin genes have rapidly evolved and expanded to encode different classes of major seed storage proteins in Triticeae species. Phylogenetic analyses also showed that the multiple insertions of resistance-like genes and subsequent differential expansion of each R gene family. The high frequency of non-syntenic genes and rapid local gene evolution correlate with the high recombination rate in the 2.8-Mb region with nine-fold higher than the genome-wide average. Our results demonstrate complex evolutionary dynamics in this agronomically important region of Triticeae species.
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Affiliation(s)
- Lingli Dong
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Karin Deal
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tiezhu Hu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Olin D Anderson
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA.
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45
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Wang Y, Xu L, Gu YQ, Coleman-Derr D. MetaCoMET: a web platform for discovery and visualization of the core microbiome. Bioinformatics 2016; 32:3469-3470. [DOI: 10.1093/bioinformatics/btw507] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/09/2016] [Accepted: 07/26/2016] [Indexed: 11/12/2022] Open
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46
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Bassi FM, Ghavami F, Hayden MJ, Wang Y, Forrest KL, Kong S, Dizon R, Michalak de Jimenez MK, Meinhardt SW, Mergoum M, Gu YQ, Kianian SF. Fast-forward genetics by radiation hybrids to saturate the locus regulating nuclear-cytoplasmic compatibility in Triticum. Plant Biotechnol J 2016; 14:1716-1726. [PMID: 26915753 PMCID: PMC5067624 DOI: 10.1111/pbi.12532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 11/24/2015] [Accepted: 12/24/2015] [Indexed: 05/29/2023]
Abstract
The nuclear-encoded species cytoplasm specific (scs) genes control nuclear-cytoplasmic compatibility in wheat (genus Triticum). Alloplasmic cells, which have nucleus and cytoplasm derived from different species, produce vigorous and vital organisms only when the correct version of scs is present in their nucleus. In this study, bulks of in vivo radiation hybrids segregating for the scs phenotype have been genotyped by sequencing with over 1.9 million markers. The high marker saturation obtained for a critical region of chromosome 1D allowed identification of 3318 reads that mapped in close proximity of the scs. A novel in silico approach was deployed to extend these short reads to sequences of up to 70 Kb in length and identify candidate open reading frames (ORFs). Markers were developed to anchor the short contigs containing ORFs to a radiation hybrid map of 650 individuals with resolution of 288 Kb. The region containing the scs locus was narrowed to a single Bacterial Artificial Chromosome (BAC) contig of Aegilops tauschii. Its sequencing and assembly by nano-mapping allowed rapid identification of a rhomboid gene as the only ORF existing within the refined scs locus. Resequencing of this gene from multiple germplasm sources identified a single nucleotide mutation, which gives rise to a functional amino acid change. Gene expression characterization revealed that an active copy of this rhomboid exists on all homoeologous chromosomes of wheat, and depending on the specific cytoplasm each copy is preferentially expressed. Therefore, a new methodology was applied to unique genetic stocks to rapidly identify a strong candidate gene for the control of nuclear-cytoplasmic compatibility in wheat.
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Affiliation(s)
- Filippo M Bassi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- International Center for the Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- Eurofins BioDiagnostics, Inc., River Falls, WI, USA
| | - Matthew J Hayden
- Department of Environment and Primary Industries, AgriBiosciences Center, Bundoora, Vic, Australia
| | - Yi Wang
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Kerrie L Forrest
- Department of Environment and Primary Industries, AgriBiosciences Center, Bundoora, Vic, Australia
| | - Stephan Kong
- Department of Environment and Primary Industries, AgriBiosciences Center, Bundoora, Vic, Australia
| | - Rhoderissa Dizon
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | | | - Steven W Meinhardt
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Mohamed Mergoum
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Shahryar F Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, USA
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47
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Nigro D, Fortunato S, Giove SL, Paradiso A, Gu YQ, Blanco A, de Pinto MC, Gadaleta A. Glutamine synthetase in Durum Wheat: Genotypic Variation and Relationship with Grain Protein Content. Front Plant Sci 2016; 7:971. [PMID: 27468287 PMCID: PMC4942471 DOI: 10.3389/fpls.2016.00971] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/20/2016] [Indexed: 05/29/2023]
Abstract
Grain protein content (GPC), is one of the most important trait in wheat and its characterized by a very complex genetic control. The identification of wheat varieties with high GPC (HGPC), as well as the characterization of central enzymes involved in these processes, are important for more sustainable agricultural practices. In this study, we focused on Glutamine synthetase (GS) as a candidate to study GPC in wheat. We analyzed GS expression and its enzymatic activity in different tissues and phenological stages in 10 durum wheat genotypes with different GPC. Although each genotype performed quite differently from the others, both because their genetic variability and their adaptability to specific environmental conditions, the highest GS activity and expression were found in genotypes with HGPC and vice versa the lowest ones in genotypes with low GPC (LGPC). Moreover, in genotypes contrasting in GPC bred at different nitrogen regimes (0, 60, 140 N Unit/ha) GS behaved differently in diverse organs. Nitrogen supplement increased GS expression and activity in roots of all genotypes, highlighting the key role of this enzyme in nitrogen assimilation and ammonium detoxification in roots. Otherwise, nitrogen treatments decreased GS expression and activity in the leaves of HGPC genotypes and did not affect GS in the leaves of LGPC genotypes. Finally, no changes in GS and soluble protein content occurred at the filling stage in the caryopses of all analyzed genotypes.
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Affiliation(s)
- Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo MoroBari, Italy
| | - Stefania Fortunato
- Department of Soil, Plant and Food Sciences, University of Bari Aldo MoroBari, Italy
- Department of Agricultural and Environmental Sciences, Research Unity of Genetic and Plant Biotechnology, University of Bari Aldo MoroBari, Italy
| | - Stefania L. Giove
- Department of Soil, Plant and Food Sciences, University of Bari Aldo MoroBari, Italy
| | | | - Yong Q. Gu
- Crop Improvement and Genetics Research, Western Regional Research Center, United States Department of Agriculture – Agricultural Research Service, AlbanyCA, USA
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, University of Bari Aldo MoroBari, Italy
| | | | - Agata Gadaleta
- Department of Agricultural and Environmental Sciences, Research Unity of Genetic and Plant Biotechnology, University of Bari Aldo MoroBari, Italy
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48
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Zhang CJ, Hua JF, Xu XL, Li F, Pai CH, Wan Y, Wu YP, Gu YQ, Mori WB, Joshi C, Lu W. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe. Sci Rep 2016; 6:29485. [PMID: 27403561 PMCID: PMC4939525 DOI: 10.1038/srep29485] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/20/2016] [Indexed: 11/15/2022] Open
Abstract
A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. The capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method.
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Affiliation(s)
- C J Zhang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China.,Laser Fusion Research Center, China Academy of Engineering Physics, Mianyang, Sichuan 621900, China.,IFSA Collaborative Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - J F Hua
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - X L Xu
- University of California, Los Angeles, California 90095, USA
| | - F Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - C-H Pai
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Y Wan
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Y P Wu
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Y Q Gu
- Laser Fusion Research Center, China Academy of Engineering Physics, Mianyang, Sichuan 621900, China
| | - W B Mori
- University of California, Los Angeles, California 90095, USA
| | - C Joshi
- University of California, Los Angeles, California 90095, USA
| | - W Lu
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China.,IFSA Collaborative Center, Shanghai Jiao Tong University, Shanghai 200240, China
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49
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Wang Y, Tiwari VK, Rawat N, Gill BS, Huo N, You FM, Coleman-Derr D, Gu YQ. GSP: a web-based platform for designing genome-specific primers in polyploids. ACTA ACUST UNITED AC 2016; 32:2382-3. [PMID: 27153733 DOI: 10.1093/bioinformatics/btw134] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/04/2016] [Indexed: 11/15/2022]
Abstract
MOTIVATION The sequences among subgenomes in a polyploid species have high similarity, making it difficult to design genome-specific primers for sequence analysis. RESULTS We present GSP, a web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome. GSP uses BLAST to extract homeologous sequences of the subgenomes in existing databases, performs a multiple sequence alignment, and design primers based on sequence variants in the alignment. An interactive primers diagram, a sequence alignment viewer and a virtual electrophoresis are displayed as parts of the primer design result. GSP also designs specific primers from multiple sequences uploaded by users. AVAILABILITY AND IMPLEMENTATION GSP is a user-friendly and efficient web platform freely accessible at http://probes.pw.usda.gov/GSP Source code and command-line application are available at https://github.com/bioinfogenome/GSP CONTACTS: yong.gu@ars.usda.gov or devin.coleman-derr@ars.usda.gov SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yi Wang
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Vijay K Tiwari
- Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Nidhi Rawat
- Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Bikram S Gill
- Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Naxin Huo
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
| | | | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
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50
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Pearce S, Vazquez-Gross H, Herin SY, Hane D, Wang Y, Gu YQ, Dubcovsky J. WheatExp: an RNA-seq expression database for polyploid wheat. BMC Plant Biol 2015; 15:299. [PMID: 26705106 PMCID: PMC4690421 DOI: 10.1186/s12870-015-0692-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND For functional genomics studies, it is important to understand the dynamic expression profiles of transcribed genes in different tissues, stages of development and in response to environmental stimuli. The proliferation in the use of next-generation sequencing technologies by the plant research community has led to the accumulation of large volumes of expression data. However, analysis of these datasets is complicated by the frequent occurrence of polyploidy among economically-important crop species. In addition, processing and analyzing such large volumes of sequence data is a technical and time-consuming task, limiting their application in functional genomics studies, particularly for smaller laboratories which lack access to high-powered computing infrastructure. Wheat is a good example of a young polyploid species with three similar genomes (97 % identical among homoeologous genes), rapidly accumulating RNA-seq datasets and a large research community. DESCRIPTION We present WheatExp, an expression database and visualization tool to analyze and compare homoeologue-specific transcript profiles across a broad range of tissues from different developmental stages in polyploid wheat. Beginning with publicly-available RNA-seq datasets, we developed a pipeline to distinguish between homoeologous transcripts from annotated genes in tetraploid and hexaploid wheat. Data from multiple studies is processed and compiled into a database which can be queried either by BLAST or by searching for a known gene of interest by name or functional domain. Expression data of multiple genes can be displayed side-by-side across all expression datasets providing immediate access to a comprehensive panel of expression data for specific subsets of wheat genes. CONCLUSIONS The development of a publicly accessible expression database hosted on the GrainGenes website - http://wheat.pw.usda.gov/WheatExp/ - coupled with a simple and readily-comparable visualization tool will empower the wheat research community to use RNA-seq data and to perform functional analyses of target genes. The presented expression data is homoeologue-specific allowing for the analysis of relative contributions from each genome to the overall expression of a gene, a critical consideration for breeding applications. Our approach can be expanded to other polyploid species by adjusting sequence mapping parameters according to the specific divergence of their genomes.
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Affiliation(s)
- Stephen Pearce
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Hans Vazquez-Gross
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Sayer Y Herin
- USDA-Agriculture Research Service, Western Regional Research Center, Albany, CA, 94710, USA.
| | - David Hane
- USDA-Agriculture Research Service, Western Regional Research Center, Albany, CA, 94710, USA.
| | - Yi Wang
- USDA-Agriculture Research Service, Western Regional Research Center, Albany, CA, 94710, USA.
| | - Yong Q Gu
- USDA-Agriculture Research Service, Western Regional Research Center, Albany, CA, 94710, USA.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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