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Alabed D, Huo N, Gu Y, Thomson JG. Complete Genome of Agrobacterium fabrum Strain 1D1416. Microbiol Resour Announc 2023:e0026423. [PMID: 37338417 DOI: 10.1128/mra.00264-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023] Open
Abstract
This work reports the draft genome of Agrobacterium fabrum strain 1D1416. The assembled genome is composed of a 2,837,379-bp circular chromosome, a 2,043,296-bp linear chromosome, a 519,735-bp AT1 plasmid, a 188,396-bp AT2 plasmid, and a 196,706-bp Ti virulence plasmid. The nondisarmed strain produces gall-like structures in citrus tissue.
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Affiliation(s)
- Diaa Alabed
- USDA-ARS Crop Improvement and Genetics, Western Regional Research Center, Albany, California, USA
| | - Naxin Huo
- USDA-ARS Crop Improvement and Genetics, Western Regional Research Center, Albany, California, USA
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Yong Gu
- USDA-ARS Crop Improvement and Genetics, Western Regional Research Center, Albany, California, USA
| | - James G Thomson
- USDA-ARS Crop Improvement and Genetics, Western Regional Research Center, Albany, California, USA
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2
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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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3
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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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4
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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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5
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Xie J, Guo G, Wang Y, Hu T, Wang L, Li J, Qiu D, Li Y, Wu Q, Lu P, Chen Y, Dong L, Li M, Zhang H, Zhang P, Zhu K, Li B, Deal KR, Huo N, Zhang Y, Luo MC, Liu S, Gu YQ, Li H, Liu Z. A rare single nucleotide variant in Pm5e confers powdery mildew resistance in common wheat. New Phytol 2020; 228:1011-1026. [PMID: 32569398 DOI: 10.1111/nph.16762] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [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: 02/03/2020] [Accepted: 06/02/2020] [Indexed: 05/18/2023]
Abstract
Powdery mildew poses severe threats to wheat production. The most sustainable way to control this disease is through planting resistant cultivars. We report the map-based cloning of the powdery mildew resistance allele Pm5e from a Chinese wheat landrace. We applied a two-step bulked segregant RNA sequencing (BSR-Seq) approach in developing tightly linked or co-segregating markers to Pm5e. The first BSR-Seq used phenotypically contrasting bulks of recombinant inbred lines (RILs) to identify Pm5e-linked markers. The second BSR-Seq utilized bulks of genetic recombinants screened from a fine-mapping population to precisely quantify the associated genomic variation in the mapping interval, and identified the Pm5e candidate genes. The function of Pm5e was validated by transgenic assay, loss-of-function mutants and haplotype association analysis. Pm5e encodes a nucleotide-binding domain leucine-rich-repeat-containing (NLR) protein. A rare nonsynonymous single nucleotide variant (SNV) within the C-terminal leucine rich repeat (LRR) domain is responsible for the gain of powdery mildew resistance function of Pm5e, an allele endemic to wheat landraces of Shaanxi province of China. Results from this study demonstrate the value of landraces in discovering useful genes for modern wheat breeding. The key SNV associated with powdery mildew resistance will be useful for marker-assisted selection of Pm5e in wheat breeding programs.
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Affiliation(s)
- Jingzhong Xie
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanghao Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tiezhu Hu
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, 4530003, China
| | - Lili Wang
- China Agricultural University, Beijing, 100193, China
| | - Jingting Li
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China
| | - Dan Qiu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yahui Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - 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 Sciences, Beijing, 100101, China
| | - Ping Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, 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 Sciences, Beijing, 100101, China
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Miaomiao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huaizhi 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 Sciences, Beijing, 100101, China
- 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 Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keyu Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Beibei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Naxin Huo
- USDA-ARS West Regional Research Center, Albany, CA, 94710, USA
| | - Yan Zhang
- China Agricultural University, Beijing, 100193, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Yong Qiang Gu
- USDA-ARS West Regional Research Center, Albany, CA, 94710, USA
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, 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 Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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6
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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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7
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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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8
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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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9
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Dong XQ, Li J, Liu H, Wang YW, Wang H, Huo N, Wang Y, Zhao H. Hepatobiliary and Pancreatic: A rare cause of decompensated liver cirrhosis. J Gastroenterol Hepatol 2018; 33:1820. [PMID: 29862561 DOI: 10.1111/jgh.14273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 04/20/2018] [Indexed: 12/09/2022]
Affiliation(s)
- X Q Dong
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - J Li
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - H Liu
- Department of Pathology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Y W Wang
- Chinese Academy of Sciences Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, China
| | - H Wang
- Department of Radiology, Peking University First Hospital, Beijing, China
| | - N Huo
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - Y Wang
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - H Zhao
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
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10
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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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11
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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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12
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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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13
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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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14
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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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15
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Huo N, Wu Z, Li J, Zhang JH, Nong L, Liu WP, Zhao H. [A case of hepatitis C virus related diffuse large B cell lymphoma]. Zhonghua Gan Zang Bing Za Zhi 2017; 24:867-868. [PMID: 27978935 DOI: 10.3760/cma.j.issn.1007-3418.2016.11.014] [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)
- N Huo
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China(Huo N, Wu Z, Li J, Zhao H); Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China(Zhang JH); Department of Pathology, Peking University First Hospital, Beijing 100034, China(Nong L);Beijing Cancer Hospital, Beijing 100034, China(Liu WP)
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16
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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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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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18
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Huo N, Qian J. Associations of Herb And Non-Vitamin Dietary Supplements (NVDS) Use With Clinical Outcomes Among Patients With Asthma in the Unites States. Res Social Adm Pharm 2016. [DOI: 10.1016/j.sapharm.2016.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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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20
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Wang Y, Drader T, Tiwari VK, Dong L, Kumar A, Huo N, Ghavami F, Iqbal MJ, Lazo GR, Leonard J, Gill BS, Kianian SF, Luo MC, Gu YQ. Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics 2015; 16:646. [PMID: 26315263 PMCID: PMC4552153 DOI: 10.1186/s12864-015-1852-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 02/13/2015] [Accepted: 08/17/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome. RESULTS In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci. CONCLUSIONS In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website ( http://probes.pw.usda.gov/ATRJM/ ) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.
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Affiliation(s)
- Yi Wang
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Thomas Drader
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Vijay K Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. .,Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Lingli Dong
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. ajay.kumar.2.@ndsu.edu
| | - Naxin Huo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.,Molecular Breeding and Genomics Technology Laboratory, BioDiagnostics Inc., River Falls, WI, 54022, USA
| | - M Javed Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Gerard R Lazo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Jeff Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Bikram S Gill
- Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | | | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
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Liang Y, Zhang DY, Ouyang S, Xie J, Wu Q, Wang Z, Cui Y, Lu P, Zhang D, Liu ZJ, Zhu J, Chen YX, Zhang Y, Luo MC, Dvorak J, Huo N, Sun Q, Gu YQ, Liu Z. Dynamic evolution of resistance gene analogs in the orthologous genomic regions of powdery mildew resistance gene MlIW170 in Triticum dicoccoides and Aegilops tauschii. Theor Appl Genet 2015; 128:1617-29. [PMID: 25993896 DOI: 10.1007/s00122-015-2536-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/02/2015] [Indexed: 05/12/2023]
Abstract
Rapid evolution of powdery mildew resistance gene MlIW170 orthologous genomic regions in wheat subgenomes. Wheat is one of the most important staple grain crops in the world and also an excellent model for plant ploidy evolution research with different ploidy levels from diploid to hexaploid. Powdery mildew disease caused by Blumeria graminis f.sp. tritici can result in significant loss in both grain yield and quality in wheat. In this study, the wheat powdery mildew resistance gene MlIW170 locus located at the Triticum dicoccoides chromosome 2B short arm was further characterized by constructing and sequencing a BAC-based physical map contig covering a 0.3 cM genetic distance region (880 kb) and developing additional markers to delineate the resistance gene within a 0.16 cM genetic interval (372 kb). Comparative analyses of the T. dicoccoides 2BS region with the orthologous Aegilops tauschii 2DS region showed great gene colinearity, including the structure organization of both types of RGA1/2-like and RPS2-like resistance genes. Comparative analyses with the orthologous regions from Brachypodium and rice genomes revealed considerable dynamic evolutionary changes that have re-shaped this MlIW170 region in the wheat genome, resulting in a high number of non-syntenic genes including resistance-related genes. This result might reflect the rapid evolution in R-gene regions. Phylogenetic analysis on these resistance-related gene sequences indicated the duplication of these genes in the MlIW170 region, occurred before the separation of the wheat B and D genomes.
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Affiliation(s)
- Yong Liang
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
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22
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Ouyang S, Zhang D, Han J, Zhao X, Cui Y, Song W, Huo N, Liang Y, Xie J, Wang Z, Wu Q, Chen YX, Lu P, Zhang DY, Wang L, Sun H, Yang T, Keeble-Gagnere G, Appels R, Doležel J, Ling HQ, Luo M, Gu Y, Sun Q, Liu Z. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides). PLoS One 2014; 9:e100160. [PMID: 24955773 PMCID: PMC4067302 DOI: 10.1371/journal.pone.0100160] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 01/27/2014] [Accepted: 05/22/2014] [Indexed: 11/18/2022] Open
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90) via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172.
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Affiliation(s)
- Shuhong Ouyang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Dong Zhang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Jun Han
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
- Agriculture University of Beijing, Beijing, China
| | - Xiaojie Zhao
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Yu Cui
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Wei Song
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
- Maize Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Naxin Huo
- USDA-ARS West Regional Research Center, Albany, California, United States of America
| | - Yong Liang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Jingzhong Xie
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhenzhong Wang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Qiuhong Wu
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Yong-Xing Chen
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Ping Lu
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - De-Yun Zhang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Lili Wang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Hua Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institutes of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tsomin Yang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | | | - Rudi Appels
- Murdoch University, Perth, Western Australia, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institutes of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Yongqiang Gu
- USDA-ARS West Regional Research Center, Albany, California, United States of America
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhiyong Liu
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
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Noyszewski AK, Ghavami F, Alnemer LM, Soltani A, Gu YQ, Huo N, Meinhardt S, Kianian PMA, Kianian SF. Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat. BMC Genomics 2014; 15:67. [PMID: 24460856 PMCID: PMC3942274 DOI: 10.1186/1471-2164-15-67] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 02/27/2013] [Accepted: 01/15/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat is an excellent plant species for nuclear mitochondrial interaction studies due to availability of large collection of alloplasmic lines. These lines exhibit different vegetative and physiological properties than their parents. To investigate the level of sequence changes introduced into the mitochondrial genome under the alloplasmic condition, three mitochondrial genomes of the Triticum-Aegilops species were sequenced: 1) durum alloplasmic line with the Ae. longissima cytoplasm that carries the T. turgidum nucleus designated as (lo) durum, 2) the cytoplasmic donor line, and 3) the nuclear donor line. RESULTS The mitochondrial genome of the T. turgidum was 451,678 bp in length with high structural and nucleotide identity to the previously characterized T. aestivum genome. The assembled mitochondrial genome of the (lo) durum and the Ae. longissima were 431,959 bp and 399,005 bp in size, respectively. The high sequence coverage for all three genomes allowed analysis of heteroplasmy within each genome. The mitochondrial genome structure in the alloplasmic line was genetically distant from both maternal and paternal genomes. The alloplasmic durum and the Ae. longissima carry the same versions of atp6, nad6, rps19-p, cob and cox2 exon 2 which are different from the T. turgidum parent. Evidence of paternal leakage was also observed by analyzing nad9 and orf359 among all three lines. Nucleotide search identified a number of open reading frames, of which 27 were specific to the (lo) durum line. CONCLUSIONS Several heteroplasmic regions were observed within genes and intergenic regions of the mitochondrial genomes of all three lines. The number of rearrangements and nucleotide changes in the mitochondrial genome of the alloplasmic line that have occurred in less than half a century was significant considering the high sequence conservation between the T. turgidum and the T. aestivum that diverged from each other 10,000 years ago. We showed that the changes in genes were not limited to paternal leakage but were sufficiently significant to suggest that other mechanisms, such as recombination and mutation, were responsible. The newly formed ORFs, differences in gene sequences and copy numbers, heteroplasmy, and substoichiometric changes show the potential of the alloplasmic condition to accelerate evolution towards forming new mitochondrial genomes.
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24
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Nigro D, Gu YQ, Huo N, Marcotuli I, Blanco A, Gadaleta A, Anderson OD. Structural analysis of the wheat genes encoding NADH-dependent glutamine-2-oxoglutarate amidotransferases and correlation with grain protein content. PLoS One 2013; 8:e73751. [PMID: 24069228 PMCID: PMC3775782 DOI: 10.1371/journal.pone.0073751] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 05/03/2013] [Accepted: 07/21/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Nitrogen uptake and the efficient absorption and metabolism of nitrogen are essential elements in attempts to breed improved cereal cultivars for grain or silage production. One of the enzymes related to nitrogen metabolism is glutamine-2-oxoglutarate amidotransferase (GOGAT). Together with glutamine synthetase (GS), GOGAT maintains the flow of nitrogen from NH4 (+) into glutamine and glutamate, which are then used for several aminotransferase reactions during amino acid synthesis. RESULTS The aim of the present work was to identify and analyse the structure of wheat NADH-GOGAT genomic sequences, and study the expression in two durum wheat cultivars characterized by low and high kernel protein content. The genomic sequences of the three homoeologous A, B and D NADH-GOGAT genes were obtained for hexaploid Triticum aestivum and the tetraploid A and B genes of Triticum turgidum ssp. durum. Analysis of the gene sequences indicates that all wheat NADH-GOGAT genes are composed of 22 exons and 21 introns. The three hexaploid wheat homoeologous genes have high conservation of sequence except intron 13 which shows differences in both length and sequence. A comparative analysis of sequences among di- and mono-cotyledonous plants shows both regions of high conservation and of divergence. qRT-PCR performed with the two durum wheat cvs Svevo and Ciccio (characterized by high and low protein content, respectively) indicates different expression levels of the two NADH-GOGAT-3A and NADH-GOGAT-3B genes. CONCLUSION The three hexaploid wheat homoeologous NADH-GOGAT gene sequences are highly conserved - consistent with the key metabolic role of this gene. However, the dicot and monocot amino acid sequences show distinctive patterns, particularly in the transit peptide, the exon 16-17 junction, and the C-terminus. The lack of conservation in the transit peptide may indicate subcellular differences between the two plant divisions - while the sequence conservation within enzyme functional domains remains high. Higher expression levels of NADH-GOGAT are associated with higher grain protein content in two durum wheats.
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Affiliation(s)
- Domenica Nigro
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari “Aldo Moro”, Bari, Italy
| | - Yong Q. Gu
- Genomics and Gene Discovery Research Unit, Western Regional Research Center, USDA-ARS, Albany, California, United States of America
| | - Naxin Huo
- Genomics and Gene Discovery Research Unit, Western Regional Research Center, USDA-ARS, Albany, California, United States of America
| | - Ilaria Marcotuli
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari “Aldo Moro”, Bari, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari “Aldo Moro”, Bari, Italy
| | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari “Aldo Moro”, Bari, Italy
- * E-mail: (AG); (OA)
| | - Olin D. Anderson
- Genomics and Gene Discovery Research Unit, Western Regional Research Center, USDA-ARS, Albany, California, United States of America
- * E-mail: (AG); (OA)
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25
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Anderson OD, Huo N, Gu YQ. The gene space in wheat: the complete γ-gliadin gene family from the wheat cultivar Chinese Spring. Funct Integr Genomics 2013; 13:261-73. [PMID: 23564033 DOI: 10.1007/s10142-013-0321-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/14/2013] [Accepted: 03/19/2013] [Indexed: 12/20/2022]
Abstract
The complete set of unique γ-gliadin genes is described for the wheat cultivar Chinese Spring using a combination of expressed sequence tag (EST) and Roche 454 DNA sequences. Assemblies of Chinese Spring ESTs yielded 11 different γ-gliadin gene sequences. Two of the sequences encode identical polypeptides and are assumed to be the result of a recent gene duplication. One gene has a 3' coding mutation that changes the reading frame in the final eight codons. A second assembly of Chinese Spring γ-gliadin sequences was generated using Roche 454 total genomic DNA sequences. The 454 assembly confirmed the same 11 active genes as the EST assembly plus two pseudogenes not represented by ESTs. These 13 γ-gliadin sequences represent the complete unique set of γ-gliadin genes for cv Chinese Spring, although not ruled out are additional genes that are exact duplications of these 13 genes. A comparison with the ESTs of two other hexaploid cultivars (Butte 86 and Recital) finds that the most active genes are present in all three cultivars, with exceptions likely due to too few ESTs for detection in Butte 86 and Recital. A comparison of the numbers of ESTs per gene indicates differential levels of expression within the γ-gliadin gene family. Genome assignments were made for 6 of the 13 Chinese Spring γ-gliadin genes, i.e., one assignment from a match to two γ-gliadin genes found within a tetraploid wheat A genome BAC and four genes that match four distinct γ-gliadin sequences assembled from Roche 454 sequences from Aegilops tauschii, the hexaploid wheat D-genome ancestor.
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Affiliation(s)
- Olin D Anderson
- Genomics and Gene Discovery Research Unit, Western Regional Research Unit, Agricultural Research Service, US Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA.
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Zheng YY, Wang LF, Fan XH, Wu CH, Huo N, Lu HY, Xu XY, Wei L. Association of suppressor of cytokine signalling 3 polymorphisms with insulin resistance in patients with chronic hepatitis C. J Viral Hepat 2013; 20:273-80. [PMID: 23490372 DOI: 10.1111/j.1365-2893.2012.01644.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 05/01/2012] [Indexed: 01/07/2023]
Abstract
Suppressor of cytokine signalling 3 is thought to be associated with insulin resistance in patients with chronic hepatitis C. We evaluated the role of suppressor of cytokine signalling 3 polymorphisms in determining insulin resistance in patients with chronic hepatitis C. Two hundred and ninety untreated hepatitis C virus-infected patients without diabetes and cirrhosis were genotyped for the SNPs rs4969168, rs4969170 and rs12952093 of suppressor of cytokine signalling 3 using the TaqMan Genotyping Assay. We found that the rs4969170 AA genotype and rs4969170 A allele frequency were significantly more common in the insulin-resistant group than the non-insulin-resistant group (89.5% vs 76.1%, OR = 2.693, 95% CI: 1.221-5.939, P = 0.012 and 94.8% vs 88.0%, OR = 2.463, 95% CI: 1.151-5.271, P = 0.017, respectively). Haplotype G-C was likely associated with non-insulin resistance (adjusted P = 0.011). Multiple logistic regression analysis indicates that the independent risk factors for insulin resistance are the SNP rs4969170 AA genotype (OR = 3.005, 95% CI: 1.194-7.560, P = 0.019), HCV genotype 1 (OR = 2.524, 95% CI: 1.099-5.794, P = 0.029) and BMI (OR = 0.514, 95% CI: 0.265-0.999, P = 0.05).
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Affiliation(s)
- Y-Y Zheng
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
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Hastie AR, Dong L, Smith A, Finklestein J, Lam ET, Huo N, Cao H, Kwok PY, Deal KR, Dvorak J, Luo MC, Gu Y, Xiao M. Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome. PLoS One 2013; 8:e55864. [PMID: 23405223 PMCID: PMC3566107 DOI: 10.1371/journal.pone.0055864] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 01/03/2013] [Indexed: 02/04/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75% to 95% complete.
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Affiliation(s)
- Alex R. Hastie
- BioNano Genomics, San Diego, California, United States of America
| | - Lingli Dong
- Genomics and Gene Discovery Research Unit, United States Department of Agriculture - Agricultural Research Service, Albany, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Alexis Smith
- BioNano Genomics, San Diego, California, United States of America
| | - Jeff Finklestein
- BioNano Genomics, San Diego, California, United States of America
| | - Ernest T. Lam
- BioNano Genomics, San Diego, California, United States of America
| | - Naxin Huo
- Genomics and Gene Discovery Research Unit, United States Department of Agriculture - Agricultural Research Service, Albany, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Han Cao
- BioNano Genomics, San Diego, California, United States of America
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Karin R. Deal
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Jan Dvorak
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Yong Gu
- Genomics and Gene Discovery Research Unit, United States Department of Agriculture - Agricultural Research Service, Albany, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- * E-mail: (MX); (YG)
| | - Ming Xiao
- BioNano Genomics, San Diego, California, United States of America
- * E-mail: (MX); (YG)
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Abstract
The utility of mining DNA sequence data to understand the structure and expression of cereal prolamin genes is demonstrated by the identification of a new class of wheat prolamins. This previously unrecognized wheat prolamin class, given the name δ-gliadins, is the most direct ortholog of barley γ3-hordeins. Phylogenetic analysis shows that the orthologous δ-gliadins and γ3-hordeins form a distinct prolamin branch that existed separate from the γ-gliadins and γ-hordeins in an ancestral Triticeae prior to the branching of wheat and barley. The expressed δ-gliadins are encoded by a single gene in each of the hexaploid wheat genomes. This single δ-gliadin/γ3-hordein ortholog may be a general feature of the Triticeae tribe since examination of ESTs from three barley cultivars also confirms a single γ3-hordein gene. Analysis of ESTs and cDNAs shows that the genes are expressed in at least five hexaploid wheat cultivars in addition to diploids Triticum monococcum and Aegilops tauschii. The latter two sequences also allow assignment of the δ-gliadin genes to the A and D genomes, respectively, with the third sequence type assumed to be from the B genome. Two wheat cultivars for which there are sufficient ESTs show different patterns of expression, i.e., with cv Chinese Spring expressing the genes from the A and B genomes, while cv Recital has ESTs from the A and D genomes. Genomic sequences of Chinese Spring show that the D genome gene is inactivated by tandem premature stop codons. A fourth δ-gliadin sequence occurs in the D genome of both Chinese Spring and Ae. tauschii, but no ESTs match this sequence and limited genomic sequences indicates a pseudogene containing frame shifts and premature stop codons. Sequencing of BACs covering a 3 Mb region from Ae. tauschii locates the δ-gliadin gene to the complex Gli-1 plus Glu-3 region on chromosome 1.
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Affiliation(s)
- Olin D Anderson
- Genomics and Gene Discovery Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA, USA.
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Brenchley R, Spannagl M, Pfeifer M, Barker GLA, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KFX, Edwards KJ, Bevan MW, Hall N. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 2012; 491:705-10. [PMID: 23192148 PMCID: PMC3510651 DOI: 10.1038/nature11650] [Citation(s) in RCA: 689] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 10/01/2012] [Indexed: 11/17/2022]
Abstract
Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.
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Affiliation(s)
- Rachel Brenchley
- Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK
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Cui Y, Lee MY, Huo N, Bragg J, Yan L, Yuan C, Li C, Holditch SJ, Xie J, Luo MC, Li D, Yu J, Martin J, Schackwitz W, Gu YQ, Vogel JP, Jackson AO, Liu Z, Garvin DF. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One 2012; 7:e38333. [PMID: 22675544 PMCID: PMC3366947 DOI: 10.1371/journal.pone.0038333] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [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: 03/14/2012] [Accepted: 05/03/2012] [Indexed: 11/18/2022] Open
Abstract
The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25°C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F6∶7 recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F2 population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.
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Affiliation(s)
- Yu Cui
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Mi Yeon Lee
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Jennifer Bragg
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Lijie Yan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Cheng Yuan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Cui Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Sara J. Holditch
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Jingzhong Xie
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Joel Martin
- US DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Wendy Schackwitz
- US DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Yong Qiang Gu
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Andrew O. Jackson
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
- * E-mail: (AOJ); (ZL)
| | - Zhiyong Liu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
- * E-mail: (AOJ); (ZL)
| | - David F. Garvin
- USDA-ARS Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
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Belknap WR, Wang Y, Huo N, Wu J, Rockhold DR, Gu YQ, Stover E. Characterizing the citrus cultivar Carrizo genome through 454 shotgun sequencing. Genome 2011; 54:1005-15. [DOI: 10.1139/g11-070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The citrus cultivar Carrizo is the single most important rootstock to the US citrus industry and has resistance or tolerance to a number of major citrus diseases, including citrus tristeza virus, foot rot, and Huanglongbing (HLB, citrus greening). A Carrizo genomic sequence database providing approximately 3.5× genome coverage (haploid genome size approximately 367 Mb) was populated through 454 GS FLX shotgun sequencing. Analysis of the repetitive DNA fraction indicated a total interspersed repeat fraction of 36.5%. Assembly and characterization of abundant citrus Ty3/gypsy elements revealed a novel type of element containing open reading frames encoding a viral RNA-silencing suppressor protein (RNA binding protein, rbp) and a plant cytokinin riboside 5′-monophosphate phosphoribohydrolase-related protein (LONELY GUY, log). Similar gypsy elements were identified in the Populus trichocarpa genome. Gene-coding region analysis indicated that 24.4% of the nonrepetitive reads contained genic regions. The depth of genome coverage was sufficient to allow accurate assembly of constituent genes, including a putative phloem-expressed gene. The development of the Carrizo database ( http://citrus.pw.usda.gov/ ) will contribute to characterization of agronomically significant loci and provide a publicly available genomic resource to the citrus research community.
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Affiliation(s)
| | - Yi Wang
- USDA-ARS, Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Naxin Huo
- USDA-ARS, Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jiajie Wu
- USDA-ARS, Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | | | - Yong Q. Gu
- USDA-ARS, Western Regional Research Center, Albany, CA 94710, USA
| | - Ed Stover
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
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Huo N, Garvin DF, You FM, McMahon S, Luo MC, Gu YQ, Lazo GR, Vogel JP. Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. Theor Appl Genet 2011; 123:455-64. [PMID: 21597976 DOI: 10.1007/s00122-011-1598-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 04/08/2011] [Indexed: 05/25/2023]
Abstract
The small annual grass Brachypodium distachyon (Brachypodium) is rapidly emerging as a powerful model system to study questions unique to the grasses. Many Brachypodium resources have been developed including a whole genome sequence, highly efficient transformation and a large germplasm collection. We developed a genetic linkage map of Brachypodium using single nucleotide polymorphism (SNP) markers and an F(2) mapping population of 476 individuals. SNPs were identified by targeted resequencing of single copy genomic sequences. Using the Illumina GoldenGate Genotyping platform we placed 558 markers into five linkage groups corresponding to the five chromosomes of Brachypodium. The unusually long total genetic map length, 1,598 centiMorgans (cM), indicates that the Brachypodium mapping population has a high recombination rate. By comparing the genetic map to genome features we found that the recombination rate was positively correlated with gene density and negatively correlated with repetitive regions and sites of ancestral chromosome fusions that retained centromeric repeat sequences. A comparison of adjacent genome regions with high versus low recombination rates revealed a positive correlation between interspecific synteny and recombination rate.
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Affiliation(s)
- Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA
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You FM, Huo N, Deal KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OD. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics 2011; 12:59. [PMID: 21266061 PMCID: PMC3041743 DOI: 10.1186/1471-2164-12-59] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [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: 08/24/2010] [Accepted: 01/25/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Many plants have large and complex genomes with an abundance of repeated sequences. Many plants are also polyploid. Both of these attributes typify the genome architecture in the tribe Triticeae, whose members include economically important wheat, rye and barley. Large genome sizes, an abundance of repeated sequences, and polyploidy present challenges to genome-wide SNP discovery using next-generation sequencing (NGS) of total genomic DNA by making alignment and clustering of short reads generated by the NGS platforms difficult, particularly in the absence of a reference genome sequence. RESULTS An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions from repetitive sequences and sequences shared by paralogous genes. Multiple genome equivalents of shotgun reads of another genotype generated with SOLiD or Solexa are then mapped to the annotated Roche 454 reads to identify putative SNPs. A pipeline program package, AGSNP, was developed and used for genome-wide SNP discovery in Aegilops tauschii-the diploid source of the wheat D genome, and with a genome size of 4.02 Gb, of which 90% is repetitive sequences. Genomic DNA of Ae. tauschii accession AL8/78 was sequenced with the Roche 454 NGS platform. Genomic DNA and cDNA of Ae. tauschii accession AS75 was sequenced primarily with SOLiD, although some Solexa and Roche 454 genomic sequences were also generated. A total of 195,631 putative SNPs were discovered in gene sequences, 155,580 putative SNPs were discovered in uncharacterized single-copy regions, and another 145,907 putative SNPs were discovered in repeat junctions. These SNPs were dispersed across the entire Ae. tauschii genome. To assess the false positive SNP discovery rate, DNA containing putative SNPs was amplified by PCR from AL8/78 and AS75 and resequenced with the ABI 3730 xl. In a sample of 302 randomly selected putative SNPs, 84.0% in gene regions, 88.0% in repeat junctions, and 81.3% in uncharacterized regions were validated. CONCLUSION An annotation-based genome-wide SNP discovery pipeline for NGS platforms was developed. The pipeline is suitable for SNP discovery in genomic libraries of complex genomes and does not require a reference genome sequence. The pipeline is applicable to all current NGS platforms, provided that at least one such platform generates relatively long reads. The pipeline package, AGSNP, and the discovered 497,118 Ae. tauschii SNPs can be accessed at (http://avena.pw.usda.gov/wheatD/agsnp.shtml).
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Affiliation(s)
- Frank M You
- Department of Plant Sciences, University of California, Davis, CA 95616, USA.
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Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Deal KR, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo H, Huo N, Lazo GR, Luo MC, Ma YQ, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics 2010; 11:702. [PMID: 21156062 PMCID: PMC3022916 DOI: 10.1186/1471-2164-11-702] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [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: 04/27/2010] [Accepted: 12/14/2010] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. RESULTS Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. CONCLUSIONS In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.
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Affiliation(s)
- Eduard D Akhunov
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Department of Plant Pathology, KSU, Manhattan, KS 66506, USA
| | - Alina R Akhunova
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Department of Plant Pathology, KSU, Manhattan, KS 66506, USA
| | - Olin D Anderson
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Nancy Blake
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Michael T Clegg
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Devin Coleman-Derr
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Emily J Conley
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Curt C Crossman
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan KS 66506, USA
| | - Yong Q Gu
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Jakub Hadam
- Department of Plant Pathology, Kansas State University, Manhattan KS 66506, USA
| | - Hwayoung Heo
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Naxin Huo
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Gerard R Lazo
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Yaqin Q Ma
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Calvin O Qualset
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - James Renfro
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Dindo Tabanao
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Philippine Rice Research Institute, Maligaya, Nueva Ecija, Philippines
| | - Luther E Talbert
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Chao Tian
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Donna M Toleno
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Marilyn L Warburton
- The International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico, D.F., Mexico
- Corn Host Plant Research Resistance Unit, USDA/ARS MSU MS 39762, USA
| | - Frank M You
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Deal KR, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo H, Huo N, Lazo GR, Luo MC, Ma YQ, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics 2010. [PMID: 21156062 DOI: 10.1186/1471‐2164‐11‐702] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. RESULTS Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. CONCLUSIONS In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.
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Affiliation(s)
- Eduard D Akhunov
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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You FM, Wanjugi H, Huo N, Lazo GR, Luo MC, Anderson OD, Dvorak J, Gu YQ. RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development. Nucleic Acids Res 2010; 38:W313-20. [PMID: 20497996 PMCID: PMC2896120 DOI: 10.1093/nar/gkq425] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [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] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TE) exist in the genomes of nearly all eukaryotes. TE mobilization through ‘cut-and-paste’ or ‘copy-and-paste’ mechanisms causes their insertions into other repetitive sequences, gene loci and other DNA. An insertion of a TE commonly creates a unique TE junction in the genome. TE junctions are also randomly distributed along chromosomes and therefore useful for genome-wide marker development. Several TE-based marker systems have been developed and applied to genetic diversity assays, and to genetic and physical mapping. A software tool ‘RJPrimers’ reported here allows for accurate identification of unique repeat junctions using BLASTN against annotated repeat databases and a repeat junction finding algorithm, and then for fully automated high-throughput repeat junction-based primer design using Primer3 and BatchPrimer3. The software was tested using the rice genome and genomic sequences of Aegilops tauschii. Over 90% of repeat junction primers designed by RJPrimers were unique. At least one RJM marker per 10 Kb sequence of A. tauschii was expected with an estimate of over 0.45 million such markers in a genome of 4.02 Gb, providing an almost unlimited source of molecular markers for mapping large and complex genomes. A web-based server and a command line-based pipeline for RJPrimers are both available at http://wheat.pw.usda.gov/demos/RJPrimers/.
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Affiliation(s)
- Frank M You
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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37
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Garvin DF, McKenzie N, Vogel JP, Mockler TC, Blankenheim ZJ, Wright J, Cheema JJS, Dicks J, Huo N, Hayden DM, Gu Y, Tobias C, Chang JH, Chu A, Trick M, Michael TP, Bevan MW, Snape JW. An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome 2010; 53:1-13. [PMID: 20130744 DOI: 10.1139/g09-079] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The grass species Brachypodium distachyon (hereafter, Brachypodium) has been adopted as a model system for grasses. Here, we describe the development of a genetic linkage map of Brachypodium. The genetic linkage map was developed with an F2 population from a cross between the diploid Brachypodium lines Bd3-1 and Bd21. The map was populated with polymorphic simple sequence repeat (SSR) markers from Brachypodium expressed sequence tag (EST) and bacterial artificial chromosome (BAC) end sequences and conserved orthologous sequence (COS) markers from other grass species. The map is 1386 cM in length and consists of 139 marker loci distributed across 20 linkage groups. Five of the linkage groups exceed 100 cM in length, with the largest being 231 cM long. Assessment of colinearity between the Brachypodium linkage map and the rice genome sequence revealed significant regions of macrosynteny between the two genomes, as well as rearrangements similar to those reported in other grass comparative structural genomics studies. The Brachypodium genetic linkage map described here will serve as a new tool to pursue a range of molecular genetic analyses and other applications in this new model plant system.
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Affiliation(s)
- David F Garvin
- USDA-ARS Plant Science Research Unit, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
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38
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Qian H, Zhao Y, Peng Y, Han C, Li S, Huo N, Ding Y, Duan Y, Xiong L, Sang H. Activation of cannabinoid receptor CB2 regulates osteogenic and osteoclastogenic gene expression in human periodontal ligament cells. J Periodontal Res 2010; 45:504-11. [DOI: 10.1111/j.1600-0765.2009.01265.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Gu YQ, Ma Y, Huo N, Vogel JP, You FM, Lazo GR, Nelson WM, Soderlund C, Dvorak J, Anderson OD, Luo MC. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics 2009; 10:496. [PMID: 19860896 PMCID: PMC2774330 DOI: 10.1186/1471-2164-10-496] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [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: 04/28/2009] [Accepted: 10/27/2009] [Indexed: 11/13/2022] Open
Abstract
Background Brachypodium distachyon (Brachypodium) has been recognized as a new model species for comparative and functional genomics of cereal and bioenergy crops because it possesses many biological attributes desirable in a model, such as a small genome size, short stature, self-pollinating habit, and short generation cycle. To maximize the utility of Brachypodium as a model for basic and applied research it is necessary to develop genomic resources for it. A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence. Results A total of 67,151 Brachypodium BAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of the Brachypodium genome was constructed. The map consisted of 671 contigs and 2,161 clones remained as singletons. The contigs and singletons spanned 414 Mb. A total of 13,970 gene-related sequences were detected in the BAC end sequences (BES). These gene tags aligned 345 contigs with 336 Mb of rice genome sequence, showing that Brachypodium and rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot of Brachypodium contigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum. Brachypodium contigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door to Brachypodium-Triticeae comparative genomics. Conclusion The construction of the Brachypodium physical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion of Brachypodium genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at .
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Affiliation(s)
- Yong Q Gu
- 1Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710,USA.
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You FM, Huo N, Gu YQ, Lazo GR, Dvorak J, Anderson OD. ConservedPrimers 2.0: a high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery. BMC Bioinformatics 2009; 10:331. [PMID: 19825183 PMCID: PMC2765976 DOI: 10.1186/1471-2105-10-331] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [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: 05/18/2009] [Accepted: 10/13/2009] [Indexed: 01/18/2023] Open
Abstract
Background In some genomic applications it is necessary to design large numbers of PCR primers in exons flanking one or several introns on the basis of orthologous gene sequences in related species. The primer pairs designed by this target gene approach are called "intron-flanking primers" or because they are located in exonic sequences which are usually conserved between related species, "conserved primers". They are useful for large-scale single nucleotide polymorphism (SNP) discovery and marker development, especially in species, such as wheat, for which a large number of ESTs are available but for which genome sequences and intron/exon boundaries are not available. To date, no suitable high-throughput tool is available for this purpose. Results We have developed, the ConservedPrimers 2.0 pipeline, for designing intron-flanking primers for large-scale SNP discovery and marker development, and demonstrated its utility in wheat. This tool uses non-redundant wheat EST sequences, such as wheat contigs and singleton ESTs, and related genomic sequences, such as those of rice, as inputs. It aligns the ESTs to the genomic sequences to identify unique colinear exon blocks and predicts intron lengths. Intron-flanking primers are then designed based on the intron/exon information using the Primer3 core program or BatchPrimer3. Finally, a tab-delimited file containing intron-flanking primer pair sequences and their primer properties is generated for primer ordering and their PCR applications. Using this tool, 1,922 bin-mapped wheat ESTs (31.8% of the 6,045 in total) were found to have unique colinear exon blocks suitable for primer design and 1,821 primer pairs were designed from these single- or low-copy genes for PCR amplification and SNP discovery. With these primers and subsequently designed genome-specific primers, a total of 1,527 loci were found to contain one or more genome-specific SNPs. Conclusion The ConservedPrimers 2.0 pipeline for designing intron-flanking primers was developed and its utility demonstrated. The tool can be used for SNP discovery, genetic variation assays and marker development for any target genome that has abundant ESTs and a related reference genome that has been fully sequenced. The ConservedPrimers 2.0 pipeline has been implemented as a command-line tool as well as a web application. Both versions are freely available at .
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Affiliation(s)
- Frank M You
- Department of Plant Sciences, University of California, Davis, CA 95616, USA.
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Wanjugi H, Coleman-Derr D, Huo N, Kianian SF, Luo MC, Wu J, Anderson O, Gu YQ. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome 2009; 52:576-87. [PMID: 19483776 DOI: 10.1139/g09-033] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17 000 Mb), repeat DNA accounts for approximately 90% of the genome, of which transposable elements (TEs) constitute 60%-80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (3%) amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88% were successfully assigned to individual chromosomes of the hexaploid D genome. Among the 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome.
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Affiliation(s)
- Humphrey Wanjugi
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
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42
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Vogel JP, Tuna M, Budak H, Huo N, Gu YQ, Steinwand MA. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biol 2009; 9:88. [PMID: 19594938 PMCID: PMC2719641 DOI: 10.1186/1471-2229-9-88] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 07/13/2009] [Indexed: 05/19/2023]
Abstract
BACKGROUND Brachypodium distachyon (Brachypodium) is rapidly emerging as a powerful model system to facilitate research aimed at improving grass crops for grain, forage and energy production. To characterize the natural diversity of Brachypodium and provide a valuable new tool to the growing list of resources available to Brachypodium researchers, we created and characterized a large, diverse collection of inbred lines. RESULTS We developed 84 inbred lines from eight locations in Turkey. To enable genotypic characterization of this collection, we created 398 SSR markers from BAC end and EST sequences. An analysis of 187 diploid lines from 56 locations with 43 SSR markers showed considerable genotypic diversity. There was some correlation between SSR genotypes and broad geographic regions, but there was also a high level of genotypic diversity at individual locations. Phenotypic analysis of this new germplasm resource revealed considerable variation in flowering time, seed size, and plant architecture. The inbreeding nature of Brachypodium was confirmed by an extremely high level of homozygosity in wild plants and a lack of cross-pollination under laboratory conditions. CONCLUSION Taken together, the inbreeding nature and genotypic diversity observed at individual locations suggest a significant amount of long-distance seed dispersal. The resources developed in this study are freely available to the research community and will facilitate experimental applications based on natural diversity.
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Affiliation(s)
- John P Vogel
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Metin Tuna
- Namik Kemal University, Department of Field Crops, Tekirdag, Turkey
| | - Hikmet Budak
- Sabanci University, Biological Science and Bioengineering Program, Istanbul, Turkey
| | - Naxin Huo
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
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Wei B, Cai T, Zhang R, Li A, Huo N, Li S, Gu YQ, Vogel J, Jia J, Qi Y, Mao L. Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Funct Integr Genomics 2009; 9:499-511. [PMID: 19499258 DOI: 10.1007/s10142-009-0128-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 05/17/2009] [Indexed: 12/31/2022]
Abstract
The small RNA transcriptomes of bread wheat and its emerging model Brachypodium distachyon were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNAs) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of expressed sequence tags, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' rapid amplification of complementary DNA ends experiments demonstrated their capability to cleave predicted target genes including three disease-resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in B. distachyon.
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Affiliation(s)
- Bo Wei
- National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, Pr China
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Wanjugi H, Coleman-Derr D, Huo N, Kianian SF, Luo MC, Wu J, Anderson O, Gu YQ. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome 2009. [PMID: 19483776 DOI: 10.1139/g09‐033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17 000 Mb), repeat DNA accounts for approximately 90% of the genome, of which transposable elements (TEs) constitute 60%-80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (3%) amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88% were successfully assigned to individual chromosomes of the hexaploid D genome. Among the 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome.
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Affiliation(s)
- Humphrey Wanjugi
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
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Huo N, Vogel JP, Lazo GR, You FM, Ma Y, McMahon S, Dvorak J, Anderson OD, Luo MC, Gu YQ. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Mol Biol 2009; 70:47-61. [PMID: 19184460 DOI: 10.1007/s11103-009-9456-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 01/07/2009] [Indexed: 05/22/2023]
Abstract
Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecules. The analysis revealed that approximately 26.4% of BES have significant matches with the rice genome and 82.4% of the matches were homologous to known genes. Further analysis of paired-end BES and approximately 1.0 Mb sequences from nine selected BACs proved to be useful in revealing conserved regions and regions that have undergone considerable genomic changes. Differential gene amplification, insertions/deletions and inversions appeared to be the common evolutionary events that caused variations of microcolinearity at different orthologous genomic regions. It was found that approximately 17% of genes in the two genomes are not colinear in the orthologous regions. Analysis of BAC sequences also revealed higher gene density (approximately 9 kb/gene) and lower repeat DNA content (approximately 13.1%) in Brachypodium when compared to the orthologous rice regions, consistent with the smaller size of the Brachypodium genome. The 119 annotated Brachypodium genes were BLASTN compared against the wheat EST database and deletion bin mapped wheat ESTs. About 77% of the genes retrieved significant matches in the EST database, while 9.2% matched to the bin mapped ESTs. In some cases, genes in single Brachypodium BACs matched to multiple ESTs that were mapped to the same deletion bins, suggesting that the Brachypodium genome will be useful for ordering wheat ESTs within the deletion bins and developing specific markers at targeted regions in the wheat genome.
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Affiliation(s)
- Naxin Huo
- Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
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You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 2008; 9:253. [PMID: 18510760 PMCID: PMC2438325 DOI: 10.1186/1471-2105-9-253] [Citation(s) in RCA: 484] [Impact Index Per Article: 30.3] [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: 10/26/2007] [Accepted: 05/29/2008] [Indexed: 01/25/2023] Open
Abstract
Background Microsatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded. Results A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories. Conclusion BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at .
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Affiliation(s)
- Frank M You
- Department of Plant Sciences, University of California, CA 95616, USA.
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You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 2008. [PMID: 18510760 DOI: 10.1186/1471‐2105‐9‐253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded. RESULTS A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories. CONCLUSION BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/.
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Affiliation(s)
- Frank M You
- Department of Plant Sciences, University of California, CA 95616, USA.
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Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD, Luo MC, Gu YQ. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genomics 2007; 8:135-47. [PMID: 17985162 DOI: 10.1007/s10142-007-0062-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 10/04/2007] [Accepted: 10/06/2007] [Indexed: 10/22/2022]
Abstract
Due in part to its small genome (approximately 350 Mb), Brachypodium distachyon is emerging as a model system for temperate grasses, including important crops like wheat and barley. We present the analysis of 10.9% of the Brachypodium genome based on 64,696 bacterial artificial chromosome (BAC) end sequences (BES). Analysis of repeat DNA content in BES revealed that approximately 11.0% of the genome consists of known repetitive DNA. The vast majority of the Brachypodium repetitive elements are LTR retrotransposons. While Bare-1 retrotransposons are common to wheat and barley, Brachypodium repetitive element sequence-1 (BRES-1), closely related to Bare-1, is also abundant in Brachypodium. Moreover, unique Brachypodium repetitive element sequences identified constitute approximately 7.4% of its genome. Simple sequence repeats from BES were analyzed, and flanking primer sequences for SSR detection potentially useful for genetic mapping are available at http://brachypodium.pw.usda.gov . Sequence analyses of BES indicated that approximately 21.2% of the Brachypodium genome represents coding sequence. Furthermore, Brachypodium BES have more significant matches to ESTs from wheat than rice or maize, although these species have similar sizes of EST collections. A phylogenetic analysis based on 335 sequences shared among seven grass species further revealed a closer relationship between Brachypodium and Triticeae than Brachypodium and rice or maize.
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Affiliation(s)
- Naxin Huo
- Genomics and Gene Discovery Research Unit, USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
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Gao S, Gu YQ, Wu J, Coleman-Derr D, Huo N, Crossman C, Jia J, Zuo Q, Ren Z, Anderson OD, Kong X. Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome. Plant Mol Biol 2007; 65:189-203. [PMID: 17629796 DOI: 10.1007/s11103-007-9208-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 07/02/2007] [Indexed: 05/04/2023]
Abstract
Genes encoding wheat prolamins belong to complicated multi-gene families in the wheat genome. To understand the structural complexity of storage protein loci, we sequenced and analyzed orthologous regions containing both gliadin and LMW-glutenin genes from the A and B genomes of a tetraploid wheat species, Triticum turgidum ssp. durum. Despite their physical proximity to one another, the gliadin genes and LMW-glutenin genes are organized quite differently. The gliadin genes are found to be more clustered than the LMW-glutenin genes which are separated from each other by much larger distances. The separation of the LMW-glutenin genes is the result of both the insertion of large blocks of repetitive DNA owing to the rapid amplification of retrotransposons and the presence of genetic loci interspersed between them. Sequence comparisons of the orthologous regions reveal that gene movement could be one of the major factors contributing to the violation of microcolinearity between the homoeologous A and B genomes in wheat. The rapid sequence rearrangements and differential insertion of repetitive DNA has caused the gene islands to be not conserved in compared regions. In addition, we demonstrated that the i-type LMW-glutenin originated from a deletion of 33-bps in the 5' coding region of the m-type gene. Our results show that multiple rounds of segmental duplication of prolamin genes have driven the amplification of the omega-gliadin genes in the region; such segmental duplication could greatly increase the repetitive DNA content in the genome depending on the amount of repetitive DNA present in the original duplicate region.
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Affiliation(s)
- Shuangcheng Gao
- Key Laboratory of Crop Germplasm & Biotechnology, MOA, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Zhongguancun, Beijing, PR China
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Huo N, Gu YQ, Lazo GR, Vogel JP, Coleman-Derr D, Luo MC, Thilmony R, Garvin DF, Anderson OD. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome 2007; 49:1099-108. [PMID: 17110990 DOI: 10.1139/g06-087] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Brachypodium is well suited as a model system for temperate grasses because of its compact genome and a range of biological features. In an effort to develop resources for genome research in this emerging model species, we constructed 2 bacterial artificial chromosome (BAC) libraries from an inbred diploid Brachypodium distachyon line, Bd21, using restriction enzymes HindIII and BamHI. A total of 73,728 clones (36,864 per BAC library) were picked and arrayed in 192,384-well plates. The average insert size for the BamHI and HindIII libraries is estimated to be 100 and 105 kb, respectively, and inserts of chloroplast origin account for 4.4% and 2.4%, respectively. The libraries individually represent 9.4- and 9.9-fold haploid genome equivalents with combined 19.3-fold genome coverage, based on a genome size of 355 Mb reported for the diploid Brachypodium, implying a 99.99% probability that any given specific sequence will be present in each library. Hybridization of the libraries with 8 starch biosynthesis genes was used to empirically evaluate this theoretical genome coverage; the frequency at which these genes were present in the library clones gave an estimated coverage of 11.6- and 19.6-fold genome equivalents. To obtain a first view of the sequence composition of the Brachypodium genome, 2185 BAC end sequences (BES) representing 1.3 Mb of random genomic sequence were compared with the NCBI GenBank database and the GIRI repeat database. Using a cutoff expectation value of E<10-10, only 3.3% of the BESs showed similarity to repetitive sequences in the existing database, whereas 40.0% had matches to the sequences in the EST database, suggesting that a considerable portion of the Brachypodium genome is likely transcribed. When the BESs were compared with individual EST databases, more matches hit wheat than maize, although their EST collections are of a similar size, further supporting the close relationship between Brachypodium and the Triticeae. Moreover, 122 BESs have significant matches to wheat ESTs mapped to individual chromosome bin positions. These BACs represent colinear regions containing the mapped wheat ESTs and would be useful in identifying additional markers for specific wheat chromosome regions.
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Affiliation(s)
- Naxin Huo
- United States Department of Agriculture - Agricultural Research Service, Western Regional Research Center, 800 Buchanan St., Albany, CA 94710, USA
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