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Tucker EJ, Baumann U, Kouidri A, Suchecki R, Baes M, Garcia M, Okada T, Dong C, Wu Y, Sandhu A, Singh M, Langridge P, Wolters P, Albertsen MC, Cigan AM, Whitford R. Molecular identification of the wheat male fertility gene Ms1 and its prospects for hybrid breeding. Nat Commun 2017; 8:869. [PMID: 29021581 PMCID: PMC5636796 DOI: 10.1038/s41467-017-00945-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 08/08/2017] [Indexed: 01/10/2023] Open
Abstract
The current rate of yield gain in crops is insufficient to meet the predicted demands. Capturing the yield boost from heterosis is one of the few technologies that offers rapid gain. Hybrids are widely used for cereals, maize and rice, but it has been a challenge to develop a viable hybrid system for bread wheat due to the wheat genome complexity, which is both large and hexaploid. Wheat is our most widely grown crop providing 20% of the calories for humans. Here, we describe the identification of Ms1, a gene proposed for use in large-scale, low-cost production of male-sterile (ms) female lines necessary for hybrid wheat seed production. We show that Ms1 completely restores fertility to ms1d, and encodes a glycosylphosphatidylinositol-anchored lipid transfer protein, necessary for pollen exine development. This represents a key step towards developing a robust hybridization platform in wheat.Heterosis can rapidly boost yield in crop species but development of hybrid-breeding systems for bread wheat remains a challenge. Here, Tucker et al. describe the molecular identification of the wheat Ms1 gene and discuss its potential for large-scale hybrid seed production in wheat.
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Affiliation(s)
- Elise J Tucker
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Ute Baumann
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Allan Kouidri
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Radoslaw Suchecki
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Mathieu Baes
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Melissa Garcia
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Takashi Okada
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Chongmei Dong
- Plant Breeding Institute, University of Sydney, PMB 4011, Narellan,, NSW 2567, Australia
| | - Yongzhong Wu
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA 50131-0552, USA
| | - Ajay Sandhu
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA 50131-0552, USA
| | - Manjit Singh
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA 50131-0552, USA
| | - Peter Langridge
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Petra Wolters
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA 50131-0552, USA
| | - Marc C Albertsen
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA 50131-0552, USA
| | - A Mark Cigan
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA 50131-0552, USA
| | - Ryan Whitford
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia.
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252
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Séguéla-Arnaud M, Choinard S, Larchevêque C, Girard C, Froger N, Crismani W, Mercier R. RMI1 and TOP3α limit meiotic CO formation through their C-terminal domains. Nucleic Acids Res 2017; 45:1860-1871. [PMID: 27965412 PMCID: PMC5389728 DOI: 10.1093/nar/gkw1210] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/23/2016] [Indexed: 01/04/2023] Open
Abstract
At meiosis, hundreds of programmed DNA double-strand breaks (DSBs) form and are repaired by homologous recombination. From this large number of DSBs, only a subset yields crossovers (COs), with a minimum of one CO per chromosome pair. All DSBs must be repaired and every recombination intermediate must be resolved to avoid subsequent entanglement and chromosome breakage. The conserved BLM-TOP3α-RMI1 (BTR) complex acts on early and late meiotic recombination intermediates to both limit CO outcome and promote chromosome integrity. In Arabidopsis, the BLM homologues RECQ4A and RECQ4B act redundantly to prevent meiotic extra COs, but recombination intermediates are fully resolved in their absence. In contrast, TOP3α is needed for both processes. Here we show through the characterization of specific mutants that RMI1 is a major anti-CO factor, in addition to being essential to prevent chromosome breakage and entanglement. Further, our findings suggest a specific role of the C-terminal domains of RMI1 and TOP3α, that respectively contain an Oligo Binding domain (OB2) and ZINC finger motifs, in preventing extra-CO. We propose that these domains of TOP3α and RMI1 define a sub-domain of the BTR complex which is dispensable for the resolution of recombination intermediates but crucial to limit extra-COs.
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Affiliation(s)
- Mathilde Séguéla-Arnaud
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Sandrine Choinard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Cécile Larchevêque
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Chloé Girard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Nicole Froger
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Wayne Crismani
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
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253
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Wang Y, Xie J, Zhang H, Guo B, Ning S, Chen Y, Lu P, Wu Q, Li M, Zhang D, Guo G, Zhang Y, Liu D, Zou S, Tang J, Zhao H, Wang X, Li J, Yang W, Cao T, Yin G, Liu Z. Mapping stripe rust resistance gene YrZH22 in Chinese wheat cultivar Zhoumai 22 by bulked segregant RNA-Seq (BSR-Seq) and comparative genomics analyses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2191-2201. [PMID: 28711956 DOI: 10.1007/s00122-017-2950-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/10/2017] [Indexed: 05/22/2023]
Abstract
A stripe rust resistance gene YrZH22 was mapped by combined BSR-Seq and comparative genomics analyses to a 5.92 centimorgan (cM) genetic interval spanning a 4 Mb physical genomic region on wheat chromosome 4BL1. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases of wheat and severely threatens wheat production worldwide. The widely grown Chinese wheat cultivar Zhoumai 22 is highly resistant to the current prevailing PST race CYR34 (V26). Genetic analysis of F5:6 and F6:7 recombinant inbred line (RIL) populations indicated that adult-plant stripe rust resistance in Zhoumai 22 is controlled by a single gene, temporarily designated YrZH22. By applying bulked segregant RNA-Seq (BSR-Seq), 7 SNP markers were developed and SNP mapping showed that YrZH22 is located between markers WGGB105 and WGGB112 on chromosome arm 4BL. The corresponding genomic regions of the Chinese Spring 4BL genome assembly and physical map of Aegilops tauschii 4DL were selected for comparative genomics analyses to develop nine new polymorphic markers that were used to construct a high-resolution genetic linkage map of YrZH22. YrZH22 was delimited in a 5.92 cM genetic interval between markers WGGB133 and WGGB146, corresponding to 4.1 Mb genomic interval in Chinese Spring 4BL and a 2.2 Mb orthologous genomic region in Ae. tauschii 4DL. The genetic linkage map of YrZH22 will be valuable for fine mapping and positional cloning of YrZH22, and can be used for marker-assisted selection in wheat breeding.
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Affiliation(s)
- Yong Wang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jingzhong Xie
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huaizhi Zhang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Bingmin Guo
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yongxing Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ping Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, 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
| | - Miaomiao Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Deyun Zhang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Guanghao Guo
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Yan Zhang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Shaokui Zou
- Zhoukou Academy of Agriculture Sciences, Zhoukou, 466001, Henan, China
| | - Jianwei Tang
- Zhoukou Academy of Agriculture Sciences, Zhoukou, 466001, Henan, China
| | - Hong Zhao
- Wheat Institute, Henan Academy of Agriculture Sciences, Zhengzhou, 450002, Henan, China
| | - Xicheng Wang
- Wheat Institute, Henan Academy of Agriculture Sciences, Zhengzhou, 450002, Henan, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agriculture Sciences, Chengdu, 610066, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agriculture Sciences, Chengdu, 610066, China
| | - Tingjie Cao
- Wheat Institute, Henan Academy of Agriculture Sciences, Zhengzhou, 450002, Henan, China.
| | - Guihong Yin
- Zhoukou Academy of Agriculture Sciences, Zhoukou, 466001, Henan, China.
| | - Zhiyong Liu
- 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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254
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Yan J, Su P, Wei Z, Nevo E, Kong L. Genome-wide identification, classification, evolutionary analysis and gene expression patterns of the protein kinase gene family in wheat and Aegilops tauschii. PLANT MOLECULAR BIOLOGY 2017; 95:227-242. [PMID: 28918554 DOI: 10.1007/s11103-017-0637-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/16/2017] [Indexed: 05/19/2023]
Abstract
In this study we systematically identified and classified PKs in Triticum aestivum, Triticum urartu and Aegilops tauschii. Domain distribution and exon-intron structure analyses of PKs were performed, and we found conserved exon-intron structures within the exon phases in the kinase domain. Collinearity events were determined, and we identified various T. aestivum PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed that some PKs might participate in the signaling pathways of stress response and developmental processes. QRT-PCR of 15 selected PKs were performed under drought treatment and with infection of Fusarium graminearum to validate the prediction of microarray. The protein kinase (PK) gene superfamily is one of the largest families in plants and participates in various plant processes, including growth, development, and stress response. To better understand wheat PKs, we conducted genome-wide identification, classification, evolutionary analysis and expression profiles of wheat and Ae. tauschii PKs. We identified 3269, 1213 and 1448 typical PK genes in T. aestivum, T. urartu and Ae. tauschii, respectively, and classified them into major groups and subfamilies. Domain distributions and gene structures were analyzed and visualized. Some conserved intron-exon structures within the conserved kinase domain were found in T. aestivum, T. urartu and Ae. tauschii, as well as the primitive land plants Selaginella moellendorffii and Physcomitrella patens, revealing the important roles and conserved evolutionary history of these PKs. We analyzed the collinearity events of T. aestivum PKs and identified PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed tissue-specific and stress-specific expression profiles, hinting that some wheat PKs may regulate abiotic and biotic stress response signaling pathways. QRT-PCR of 15 selected PKs were performed under drought treatment and with infection of F. graminearum to validate the prediction of microarray. Our results will provide the foundational information for further studies on the molecular functions of wheat PKs.
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Affiliation(s)
- Jun Yan
- College of Information Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Peisen Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhaoran Wei
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, 3498838, Haifa, Israel.
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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255
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Yang J, Moeinzadeh MH, Kuhl H, Helmuth J, Xiao P, Haas S, Liu G, Zheng J, Sun Z, Fan W, Deng G, Wang H, Hu F, Zhao S, Fernie AR, Boerno S, Timmermann B, Zhang P, Vingron M. Haplotype-resolved sweet potato genome traces back its hexaploidization history. NATURE PLANTS 2017; 3:696-703. [PMID: 28827752 DOI: 10.1038/s41477-017-0002-z] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 07/11/2017] [Indexed: 05/20/2023]
Abstract
Here we present the 15 pseudochromosomes of sweet potato, Ipomoea batatas, the seventh most important crop in the world and the fourth most significant in China. By using a novel haplotyping method based on genome assembly, we have produced a half haplotype-resolved genome from ~296 Gb of paired-end sequence reads amounting to roughly 67-fold coverage. By phylogenetic tree analysis of homologous chromosomes, it was possible to estimate the time of two recent whole-genome duplication events as occurring about 0.8 and 0.5 million years ago. This half haplotype-resolved hexaploid genome represents the first successful attempt to investigate the complexity of chromosome sequence composition directly in a polyploid genome, using sequencing of the polyploid organism itself rather than any of its simplified proxy relatives. Adaptation and application of our approach should provide higher resolution in future genomic structure investigations, especially for similarly complex genomes.
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Affiliation(s)
- Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Shanghai, 201602, China
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - M-Hossein Moeinzadeh
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Johannes Helmuth
- Max Planck Institute for Molecular Genetics, Otto-Warburg-Laboratory: Computational Epigenomics Group, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Peng Xiao
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Stefan Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Guiling Liu
- Tai'an Academy of Agricultural Sciences, 16 Tailai Road, Tai'an, 271000, Shandong, China
| | - Jianli Zheng
- Tai'an Academy of Agricultural Sciences, 16 Tailai Road, Tai'an, 271000, Shandong, China
| | - Zhe Sun
- Tai'an Academy of Agricultural Sciences, 16 Tailai Road, Tai'an, 271000, Shandong, China
| | - Weijuan Fan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Gaifang Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hongxia Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Fenhong Hu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shanshan Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Shanghai, 201602, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Stefan Boerno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany.
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256
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Botha AM, Kunert KJ, Cullis CA. Cysteine proteases and wheat (Triticum aestivum L) under drought: A still greatly unexplored association. PLANT, CELL & ENVIRONMENT 2017; 40:1679-1690. [PMID: 28664627 DOI: 10.1111/pce.12998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 05/13/2023]
Abstract
Bread wheat (Triticum aestivum L.) provides about 19% of global dietary energy. Environmental stress, such as drought, affects wheat growth causing premature plant senescence and ultimately plant death. A plant response to drought is an increase in protease-mediated proteolysis with rapid degradation of proteins required for metabolic processes. Among the plant proteases that are increased in their activity following stress, cysteine proteases are the best characterized. Very little is known about particular wheat cysteine protease sequences, their expression and also localization. The current knowledge on wheat cysteine proteases belonging to the five clans (CA, CD, CE, CF and CP) is outlined, in particular their expression and possible function under drought. The first successes in establishing an annotated wheat genome database are further highlighted which has allowed more detailed mining of cysteine proteases. We also share our thoughts on future research directions considering the growing availability of genomic resources of this very important food crop. Finally, we also outline future application of developed knowledge in transgenic wheat plants for environmental stress protection and also as senescence markers to monitor wheat growth under environmental stress conditions.
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Affiliation(s)
- Anna-Maria Botha
- Department of Genetics, University of Stellenbosch, Stellenbosch, 7601, South Africa
| | - Karl J Kunert
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Christopher A Cullis
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, 44106, USA
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257
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Seidl MF, Thomma BPHJ. Transposable Elements Direct The Coevolution between Plants and Microbes. Trends Genet 2017; 33:842-851. [PMID: 28800915 DOI: 10.1016/j.tig.2017.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/24/2017] [Accepted: 07/14/2017] [Indexed: 12/31/2022]
Abstract
Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as 'selfish' genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host-microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a 'two-speed' genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.
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Affiliation(s)
- Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
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258
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Díaz ML, Cuppari S, Soresi D, Carrera A. In Silico Analysis of Fatty Acid Desaturase Genes and Proteins in Grasses. Appl Biochem Biotechnol 2017; 184:484-499. [PMID: 28755245 DOI: 10.1007/s12010-017-2556-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/13/2017] [Indexed: 02/03/2023]
Abstract
Fatty acid desaturases (FADs) catalyze the introduction of a double bond into acyl chains. Two FAD groups have been identified in plants: acyl-acyl carrier proteins (ACPs) and acyl-lipid or membrane-bound FAD. The former catalyze the conversion of 18:0 to 18:1 and to date have only been identified in plants. The latter are found in eukaryotes and bacteria and are responsible for multiple desaturations. In this study, we identified 82 desaturase gene and protein sequences from 10 grass species deposited in GenBank that were analyzed using bioinformatic approaches. Subcellular localization predictions of desaturase family revealed their localization in plasma membranes, chloroplasts, endoplasmic reticula, and mitochondria. The in silico mapping showed multiple chromosomal locations in most species. Furthermore, the presence of the characteristic histidine domains, the predicted motifs, and the finding of transmembrane regions strongly support the protein functionality. The identification of putative regulatory sites in the promotor and the expression profiles revealed the wide range of pathways in which fatty acid desaturases are involved. This study is an updated survey on desaturases of grasses that provides a comprehensive insight into diversity and evolution. This characterization is a necessary first step before considering these genes as candidates for new biotechnological approaches.
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Affiliation(s)
- Marina Lucía Díaz
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina.
- Comisión de Investigaciones Científicas, Buenos Aires, Argentina.
| | - Selva Cuppari
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - Daniela Soresi
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - Alicia Carrera
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, San Andrés 800, Bahía Blanca, Argentina
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259
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Ma J, Yang Y, Luo W, Yang C, Ding P, Liu Y, Qiao L, Chang Z, Geng H, Wang P, Jiang Q, Wang J, Chen G, Wei Y, Zheng Y, Lan X. Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.). PLoS One 2017; 12:e0181443. [PMID: 28742823 PMCID: PMC5526560 DOI: 10.1371/journal.pone.0181443] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/02/2017] [Indexed: 11/18/2022] Open
Abstract
The MADS-box genes encode transcription factors with key roles in plant growth and development. A comprehensive analysis of the MADS-box gene family in bread wheat (Triticum aestivum) has not yet been conducted, and our understanding of their roles in stress is rather limited. Here, we report the identification and characterization of the MADS-box gene family in wheat. A total of 180 MADS-box genes classified as 32 Mα, 5 Mγ, 5 Mδ, and 138 MIKC types were identified. Evolutionary analysis of the orthologs among T. urartu, Aegilops tauschii and wheat as well as homeologous sequences analysis among the three sub-genomes in wheat revealed that gene loss and chromosomal rearrangements occurred during and/or after the origin of bread wheat. Forty wheat MADS-box genes that were expressed throughout the investigated tissues and development stages were identified. The genes that were regulated in response to both abiotic stresses (i.e., phosphorus deficiency, drought, heat, and combined drought and heat) and biotic stresses (i.e., Fusarium graminearum, Septoria tritici, stripe rust and powdery mildew) were detected as well. A few notable MADS-box genes were specifically expressed in a single tissue and those showed relatively higher expression differences between the stress and control treatment. The expression patterns of considerable MADS-box genes differed from those of their orthologs in Brachypodium, rice, and Arabidopsis. Collectively, the present study provides new insights into the possible roles of MADS-box genes in response to stresses and will be valuable for further functional studies of important candidate MADS-box genes.
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Affiliation(s)
- Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yujie Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wei Luo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Congcong Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Puyang Ding
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linyi Qiao
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Zhijian Chang
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Hongwei Geng
- College of Agronomy, Xinjiang Agriculture University, Urumqi, China
| | - Penghao Wang
- School of Veterinary and Life Sciences, Murdoch University, Murdoch WA, Australia
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
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Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress. Sci Rep 2017; 7:5461. [PMID: 28710348 PMCID: PMC5511167 DOI: 10.1038/s41598-017-04473-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/16/2017] [Indexed: 12/19/2022] Open
Abstract
Amino acid transporters have roles in amino acid uptake from soil, long-distance transport, remobilization from vegetative tissues and accumulation in grain. Critically, the majority of wheat grain nitrogen is derived from amino acids remobilized from vegetative organs. However, no systematic analysis of wheat AAT genes has been reported to date. Here, 283 full length wheat AAT genes representing 100 distinct groups of homeologs were identified and curated by selectively consolidating IWGSC CSSv2 and TGACv1 Triticum aestivum genome assemblies and reassembling or mapping of IWGSC CSS chromosome sorted reads to fill any gaps. Gene expression profiling was performed using public RNA-seq data from root, leaf, stem, spike, grain and grain cells (transfer cell (TC), aleurone cell (AL), and starchy endosperm (SE)). AATs highly expressed in roots are good candidates for amino acid uptake from soil whilst AATs highly expressed in senescing leaves and stems may be involved in translocation to grain. AATs in TC (TaAAP2 and TaAAP19) and SE (TaAAP13) may play important roles in determining grain protein content and grain yield. The expression levels of AAT homeologs showed unequal contributions in response to abiotic stresses and development, which may aid wheat adaptation to a wide range of environments.
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261
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Wan Y, King R, Mitchell RAC, Hassani-Pak K, Hawkesford MJ. Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress. Sci Rep 2017. [PMID: 28710348 DOI: 10.1038/s41598-017-04473-4473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Amino acid transporters have roles in amino acid uptake from soil, long-distance transport, remobilization from vegetative tissues and accumulation in grain. Critically, the majority of wheat grain nitrogen is derived from amino acids remobilized from vegetative organs. However, no systematic analysis of wheat AAT genes has been reported to date. Here, 283 full length wheat AAT genes representing 100 distinct groups of homeologs were identified and curated by selectively consolidating IWGSC CSSv2 and TGACv1 Triticum aestivum genome assemblies and reassembling or mapping of IWGSC CSS chromosome sorted reads to fill any gaps. Gene expression profiling was performed using public RNA-seq data from root, leaf, stem, spike, grain and grain cells (transfer cell (TC), aleurone cell (AL), and starchy endosperm (SE)). AATs highly expressed in roots are good candidates for amino acid uptake from soil whilst AATs highly expressed in senescing leaves and stems may be involved in translocation to grain. AATs in TC (TaAAP2 and TaAAP19) and SE (TaAAP13) may play important roles in determining grain protein content and grain yield. The expression levels of AAT homeologs showed unequal contributions in response to abiotic stresses and development, which may aid wheat adaptation to a wide range of environments.
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Affiliation(s)
- Yongfang Wan
- Plant Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Robert King
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Rowan A C Mitchell
- Plant Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Keywan Hassani-Pak
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
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262
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Shi F, Tibbits J, Pasam RK, Kay P, Wong D, Petkowski J, Forrest KL, Hayes BJ, Akhunova A, Davies J, Webb S, Spangenberg GC, Akhunov E, Hayden MJ, Daetwyler HD. Exome sequence genotype imputation in globally diverse hexaploid wheat accessions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1393-1404. [PMID: 28378053 DOI: 10.1007/s00122-017-2895-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/18/2017] [Indexed: 06/07/2023]
Abstract
Imputing genotypes from the 90K SNP chip to exome sequence in wheat was moderately accurate. We investigated the factors that affect imputation and propose several strategies to improve accuracy. Imputing genetic marker genotypes from low to high density has been proposed as a cost-effective strategy to increase the power of downstream analyses (e.g. genome-wide association studies and genomic prediction) for a given budget. However, imputation is often imperfect and its accuracy depends on several factors. Here, we investigate the effects of reference population selection algorithms, marker density and imputation algorithms (Beagle4 and FImpute) on the accuracy of imputation from low SNP density (9K array) to the Infinium 90K single-nucleotide polymorphism (SNP) array for a collection of 837 hexaploid wheat Watkins landrace accessions. Based on these results, we then used the best performing reference selection and imputation algorithms to investigate imputation from 90K to exome sequence for a collection of 246 globally diverse wheat accessions. Accession-to-nearest-entry and genomic relationship-based methods were the best performing selection algorithms, and FImpute resulted in higher accuracy and was more efficient than Beagle4. The accuracy of imputing exome capture SNPs was comparable to imputing from 9 to 90K at approximately 0.71. This relatively low imputation accuracy is in part due to inconsistency between 90K and exome sequence formats. We also found the accuracy of imputation could be substantially improved to 0.82 when choosing an equivalent number of exome SNP, instead of 90K SNPs on the existing array, as the lower density set. We present a number of recommendations to increase the accuracy of exome imputation.
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Affiliation(s)
- Fan Shi
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.
| | - Josquin Tibbits
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Raj K Pasam
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Pippa Kay
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Debbie Wong
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Joanna Petkowski
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Kerrie L Forrest
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Ben J Hayes
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
- Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | | | | | - German C Spangenberg
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Matthew J Hayden
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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263
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Holušová K, Vrána J, Šafář J, Šimková H, Balcárková B, Frenkel Z, Darrier B, Paux E, Cattonaro F, Berges H, Letellier T, Alaux M, Doležel J, Bartoš J. Physical Map of the Short Arm of Bread Wheat Chromosome 3D. THE PLANT GENOME 2017; 10. [PMID: 28724077 DOI: 10.3835/plantgenome2017.03.0021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bread wheat ( L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning. It comprises 869 contigs with a cumulative length of 274.5 Mbp and represents 85.5% of the estimated chromosome arm size. Eighty-six Mbp of survey sequences from chromosome arm 3DS were assigned in silico to physical map contigs via next-generation sequencing of bacterial artificial chromosome pools, thus providing a high-density framework for physical map ordering along the chromosome arm. About 60% of the physical map was anchored in this single experiment. Finally, 1393 high-confidence genes were anchored to the physical map. Comparisons of gene space of the chromosome arm 3DS with genomes of closely related species [ (L.) P.Beauv., rice ( L.), and sorghum [ (L.) Moench] and homeologous wheat chromosomes provided information about gene movement on the chromosome arm.
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264
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Lu Y, Li R, Wang R, Wang X, Zheng W, Sun Q, Tong S, Dai S, Xu S. Comparative Proteomic Analysis of Flag Leaves Reveals New Insight into Wheat Heat Adaptation. FRONTIERS IN PLANT SCIENCE 2017; 8:1086. [PMID: 28676819 PMCID: PMC5476934 DOI: 10.3389/fpls.2017.01086] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/06/2017] [Indexed: 05/18/2023]
Abstract
Hexaploid wheat (Triticum aestivum L.) is an important food crop but it is vulnerable to heat. The heat-responsive proteome of wheat remains to be fully elucidated because of previous technical and genomic limitations, and this has hindered our understanding of the mechanisms of wheat heat adaptation and advances in improving thermotolerance. Here, flag leaves of wheat during grain filling stage were subjected to high daytime temperature stress, and 258 heat-responsive proteins (HRPs) were identified with iTRAQ analysis. Enrichment analysis revealed that chlorophyll synthesis, carbon fixation, protein turnover, and redox regulation were the most remarkable heat-responsive processes. The HRPs involved in chlorophyll synthesis and carbon fixation were significantly decreased, together with severe membrane damage, demonstrating the specific effects of heat on photosynthesis of wheat leaves. In addition, the decrease in chlorophyll content may result from the decrease in HRPs involved in chlorophyll precursor synthesis. Further analysis showed that the accumulated effect of heat stress played a critical role in photosynthesis reduction, suggested that improvement in heat tolerance of photosynthesis, and extending heat tolerant period would be major research targets. The significantly accumulation of GSTs and Trxs in response to heat suggested their important roles in redox regulation, and they could be the promising candidates for improving wheat thermotolerance. In summary, our results provide new insight into wheat heat adaption and provide new perspectives on thermotolerance improvement.
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Affiliation(s)
- Yunze Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Ruiqiong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Ruochen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Weijun Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Qixin Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Department of Plant Genetics and Breeding, China Agricultural UniversityBeijing, China
| | - Shaoming Tong
- College of Life Sciences, Liaoning Normal UniversityDalian, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal UniversityShanghai, China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
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265
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Peng FY, Yang RC. Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:108. [PMID: 28633642 PMCID: PMC5477749 DOI: 10.1186/s12870-017-1056-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/06/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND The resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens. At the molecular level, these three types of resistance may cover across the whole spectrum of pathogen specificities that are controlled by genes encoding different protein families in wheat. The objective of this study is to predict and analyze genes in three such families: NBS-LRR (nucleotide-binding sites and leucine-rich repeats or NLR), START (Steroidogenic Acute Regulatory protein [STaR] related lipid-transfer) and ABC (ATP-Binding Cassette) transporter. The focus of the analysis is on the patterns of relationships between these protein-coding genes within the gene families and QTLs detected for leaf rust resistance. RESULTS We predicted 526 ABC, 1117 NLR and 144 START genes in the hexaploid wheat genome through a domain analysis of wheat proteome. Of the 1809 SNPs from leaf rust resistance QTLs in seedling and adult stages of wheat, 126 SNPs were found within coding regions of these genes or their neighborhood (5 Kb upstream from transcription start site [TSS] or downstream from transcription termination site [TTS] of the genes). Forty-three of these SNPs for adult resistance and 18 SNPs for seedling resistance reside within coding or neighboring regions of the ABC genes whereas 14 SNPs for adult resistance and 29 SNPs for seedling resistance reside within coding or neighboring regions of the NLR gene. Moreover, we found 17 nonsynonymous SNPs for adult resistance and five SNPs for seedling resistance in the ABC genes, and five nonsynonymous SNPs for adult resistance and six SNPs for seedling resistance in the NLR genes. Most of these coding SNPs were predicted to alter encoded amino acids and such information may serve as a starting point towards more thorough molecular and functional characterization of the designated Lr genes. Using the primer sequences of 99 known non-SNP markers from leaf rust resistance QTLs, we found candidate genes closely linked to these markers, including Lr34 with distances to its two gene-specific markers being 1212 bases (to cssfr1) and 2189 bases (to cssfr2). CONCLUSION This study represents a comprehensive analysis of ABC, NLR and START genes in the hexaploid wheat genome and their physical relationships with QTLs for leaf rust resistance at seedling and adult stages. Our analysis suggests that the ABC (and START) genes are more likely to be co-located with QTLs for race-nonspecific, adult resistance whereas the NLR genes are more likely to be co-located with QTLs for race-specific resistance that would be often expressed at the seedling stage. Though our analysis was hampered by inaccurate or unknown physical positions of numerous QTLs due to the incomplete assembly of the complex hexaploid wheat genome that is currently available, the observed associations between (i) QTLs for race-specific resistance and NLR genes and (ii) QTLs for nonspecific resistance and ABC genes will help discover SNP variants for leaf rust resistance at seedling and adult stages. The genes containing nonsynonymous SNPs are promising candidates that can be investigated in future studies as potential new sources of leaf rust resistance in wheat breeding.
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Affiliation(s)
- Fred Y Peng
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Rong-Cai Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
- Feed Crops Section, Alberta Agriculture and Forestry, 7000 - 113 Street, Edmonton, AB, T6H 5T6, Canada.
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266
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Huang Y, Luo L, Hu X, Yu F, Yang Y, Deng Z, Wu J, Chen R, Zhang M. Characterization, Genomic Organization, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in Erianthus arundinaceus. FRONTIERS IN PLANT SCIENCE 2017; 8:924. [PMID: 28638390 PMCID: PMC5461294 DOI: 10.3389/fpls.2017.00924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/17/2017] [Indexed: 06/16/2023]
Abstract
Erianthus arundinaceus is an important wild species of the genus Saccharum with many valuable traits. However, the composition and structure of its genome are largely unknown, which have hindered its utilization in sugarcane breeding and evolutionary research. Retrotransposons constitute an appreciable fraction of plant genomes and may have played a significant role in the evolution and sequence organization of genomes. In the current study, we investigate the phylogenetic diversity and genomic abundance of Ty1-copia retrotransposons for the first time and inspect their chromosomal distribution patterns in E. arundinaceus. In total, 70 Ty1-copia reverse transcriptase (RT) sequences with significant levels of heterogeneity were obtained. The phylogenetic analysis revealed these Ty1-copia retrotransposons were classified into four distinct evolutionary lineages (Tork/TAR, Tork/Angela, Retrofit/Ale, and Sire/Maximus). Dot-blot analysis showed estimated the total copy number of Ty1-copia retrotransposons to be about 4.5 × 103 in the E. arundinaceus genome, indicating they were a significant component. Fluorescence in situ hybridization revealed that Ty1-copia retrotransposons from the four lineages had strikingly similar patterns of chromosomal enrichment, being exclusively enriched in the subterminal heterochromatic regions of most E. arundinaceus chromosomes. This is the first clear evidence of the presence of Ty1-copia retrotransposons in the subterminal heterochromatin of E. arundinaceus. Altogether, these results promote the understanding of the diversification of Ty1-copia retrotransposons and shed light on their chromosomal distribution patterns in E. arundinaceus.
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Affiliation(s)
- Yongji Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Ling Luo
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xuguang Hu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Fan Yu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yongqing Yang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
- Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi UniversityNanning, China
| | - Jiayun Wu
- Guangdong Key Laboratory of Sugarcane Improvement and BiorefineryGuangzhou, China
- Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research InstituteGuangzhou, China
| | - Rukai Chen
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Muqing Zhang
- Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi UniversityNanning, China
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267
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Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization. Sci Rep 2017; 7:2581. [PMID: 28566710 PMCID: PMC5451465 DOI: 10.1038/s41598-017-01857-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 04/03/2017] [Indexed: 12/13/2022] Open
Abstract
Wheat (Triticum aestivum), one of the world’s most important crops, is facing unprecedented challenges due to global warming. To evaluate the gene resources for heat adaptation in hexaploid wheat, small heat shock proteins (sHSPs), the key plant heat protection genes, were comprehensively analysed in wheat and related species. We found that the sHSPs of hexaploid wheat were massively expanded in A and B subgenomes with intrachromosomal duplications during polyploidization. These expanded sHSPs were under similar purifying selection and kept the expressional patterns with the original copies. Generally, a strong purifying selection acted on the α-crystallin domain (ACD) and theoretically constrain conserved function. Meanwhile, weaker purifying selection and strong positive selection acted on the N-terminal region, which conferred sHSP flexibility, allowing adjustments to a wider range of substrates in response to genomic and environmental changes. Notably, in CI, CV, ER, MI and MII subfamilies, gene duplications, expression variations and functional divergence occurred before wheat polyploidization. Our results indicate the massive expansion of active sHSPs in hexaploid wheat may also provide more raw materials for evolving functional novelties and generating genetic diversity to face future global climate changes, and highlight the expansion of stress response genes with wheat polyploidization.
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268
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High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism. Genetics 2017; 206:1373-1388. [PMID: 28533438 DOI: 10.1534/genetics.116.196014] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 05/12/2017] [Indexed: 11/18/2022] Open
Abstract
During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry ∼60-70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (<26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals.
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269
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Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat Biotechnol 2017; 35:793-796. [PMID: 28504667 DOI: 10.1038/nbt.3877] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/11/2017] [Indexed: 11/08/2022]
Abstract
Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago long-range linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.
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270
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Xia C, Zhang L, Zou C, Gu Y, Duan J, Zhao G, Wu J, Liu Y, Fang X, Gao L, Jiao Y, Sun J, Pan Y, Liu X, Jia J, Kong X. A TRIM insertion in the promoter of Ms2 causes male sterility in wheat. Nat Commun 2017; 8:15407. [PMID: 28497807 PMCID: PMC5437302 DOI: 10.1038/ncomms15407] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/25/2017] [Indexed: 11/09/2022] Open
Abstract
The male-sterile ms2 mutant has been known for 40 years and has become extremely important in the commercial production of wheat. However, the gene responsible for this phenotype has remained unknown. Here we report the map-based cloning of the Ms2 gene. The Ms2 locus is remarkable in several ways that have implications in basic biology. Beyond having no functional annotation, barely detectable transcription in fertile wild-type wheat plants, and accumulated destructive mutations in Ms2 orthologs, the Ms2 allele in the ms2 mutant has acquired a terminal-repeat retrotransposon in miniature (TRIM) element in its promoter. This TRIM element is responsible for the anther-specific Ms2 activation that confers male sterility. The identification of Ms2 not only unravels the genetic basis of a historically important breeding trait, but also shows an example of how a TRIM element insertion near a gene can contribute to genetic novelty and phenotypic plasticity.
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Affiliation(s)
- Chuan Xia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lichao Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng Zou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongqiang Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California 94710, USA
| | - Jialei Duan
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangyao Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiajie Wu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yue Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaohua Fang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lifeng Gao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jiaqiang Sun
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinghong Pan
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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271
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Pelé A, Falque M, Trotoux G, Eber F, Nègre S, Gilet M, Huteau V, Lodé M, Jousseaume T, Dechaumet S, Morice J, Poncet C, Coriton O, Martin OC, Rousseau-Gueutin M, Chèvre AM. Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas. PLoS Genet 2017; 13:e1006794. [PMID: 28493942 PMCID: PMC5444851 DOI: 10.1371/journal.pgen.1006794] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 05/25/2017] [Accepted: 05/02/2017] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs.
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Affiliation(s)
- Alexandre Pelé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Matthieu Falque
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif sur Yvette, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Frédérique Eber
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Sylvie Nègre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Virginie Huteau
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Maryse Lodé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | | | - Sylvain Dechaumet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | | | - Olivier Coriton
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Olivier C. Martin
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif sur Yvette, France
| | | | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
- * E-mail:
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272
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Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Res 2017; 27:885-896. [PMID: 28420692 PMCID: PMC5411782 DOI: 10.1101/gr.217117.116] [Citation(s) in RCA: 244] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/14/2017] [Indexed: 01/16/2023]
Abstract
Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Tom Barker
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
| | - Fu-Hao Lu
- John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | | | - Dina Raats
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
| | | | | | - Ned Peel
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
| | | | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley Western Australia 6009, Australia
| | - Josua Trösch
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley Western Australia 6009, Australia
| | - Guotai Yu
- John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Dan M Bolser
- EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, United Kingdom
| | - Guy Namaati
- EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, United Kingdom
| | - Arnaud Kerhornou
- EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, United Kingdom
| | - Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Robert P Davey
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | | | - Federica Di Palma
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | | | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley Western Australia 6009, Australia
| | - Paul J Kersey
- EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, United Kingdom
| | | | - Ksenia V Krasileva
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
- The Sainsbury Laboratory, Norwich, NR4 7UH, United Kingdom
| | - David Swarbreck
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | | | - Matthew D Clark
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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273
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Steffan PM, Torp AM, Borgen A, Backes G, Rasmussen SK. Mapping of common bunt resistance gene Bt9 in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1031-1040. [PMID: 28238022 PMCID: PMC5395592 DOI: 10.1007/s00122-017-2868-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/26/2017] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE The Bt9 resistance locus was mapped and shown to be distinct from the Bt10 locus. New markers linked to Bt9 have been identified and may be used to breed for resistance towards the seed-borne disease. Increasing organic wheat production in Denmark, and in other wheat-producing areas, in conjunction with legal requirements for organic seed production, may potentially lead to a rise in common bunt occurrence. As systemic pesticides are not used in organic farming, organic wheat production systems may benefit from genetic resistances. However, little is known about the underlying genetic mechanisms and locations of the resistance factors for common bunt resistance in wheat. A double haploid (DH) population segregating for common bunt resistance was used to identify the chromosomal location of common bunt resistance gene Bt9. DH lines were phenotyped in three environments and genotyped with DArTseq and SSR markers. The total length of the resulting linkage map was 2882 cM distributed across all 21 wheat chromosomes. Bt9 was mapped to the distal end of chromosome 6DL. Since wheat common bunt resistance gene Bt10 is also located on chromosome 6D, the possibility of their co-location was investigated. A comparison of marker sequences linked to Bt9 and Bt10 on physical maps of chromosome 6D confirmed that Bt9 and Bt10 are two distinct resistance factors located at the distal (6DL) and proximal (6DS) end, respectively, of chromosome 6D. Five new SSR markers Xgpw4005-1, Xgpw7433, Xwmc773, Xgpw7303 and Xgpw362 and many SNP and PAV markers flanking the Bt9 resistance locus were identified and they may be used in the future for marker-assisted selection.
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Affiliation(s)
- Philipp Matthias Steffan
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Mons, Germany
| | - Anna Maria Torp
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Anders Borgen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Agrologica, Houvej 55, 9550, Mariager, Denmark
| | - Gunter Backes
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Department of Organic Agricultural Sciences, University of Kassel, Nordbahnhofstraße 1a, 37213, Witzenhausen, Germany
| | - Søren K Rasmussen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark.
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274
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Debernardi JM, Lin H, Chuck G, Faris JD, Dubcovsky J. microRNA172 plays a crucial role in wheat spike morphogenesis and grain threshability. Development 2017; 144:1966-1975. [PMID: 28455375 PMCID: PMC5482987 DOI: 10.1242/dev.146399] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/18/2017] [Indexed: 12/12/2022]
Abstract
Wheat domestication from wild species involved mutations in the Q gene. The q allele (wild wheats) is associated with elongated spikes and hulled grains, whereas the mutant Q allele (domesticated wheats) confers subcompact spikes and free-threshing grains. Previous studies showed that Q encodes an AP2-like transcription factor, but the causal polymorphism of the domestication traits remained unclear. Here, we show that the interaction between microRNA172 (miR172) and the Q allele is reduced by a single nucleotide polymorphism in the miRNA binding site. Inhibition of miR172 activity by a miRNA target mimic resulted in compact spikes and transition from glumes to florets in apical spikelets. By contrast, overexpression of miR172 was sufficient to induce elongated spikes and non-free-threshing grains, similar to those observed in three Q loss-of-function mutations. These lines showed transitions from florets to glumes in the basal spikelets. These localized homeotic changes were associated with opposing miR172/Q gradients along the spike. We propose that the selection of a nucleotide change at the miR172 binding site of Q contributed to subcompact spikes and free-threshing grains during wheat domestication. Highlighted Article: A nucleotide change in the microRNA172 binding site of the AP2 gene Q played a critical role in wheat domestication and the origin of free-threshing modern wheats. See also Greenwood et al. in this issue.
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Affiliation(s)
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - George Chuck
- Plant Gene Expression Center, University of California, Berkeley, Albany, CA 94710, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND 58102, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616, USA .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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275
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Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N. A chromosome conformation capture ordered sequence of the barley genome. Nature 2017; 544:427-433. [DOI: 10.1038/nature22043] [Citation(s) in RCA: 966] [Impact Index Per Article: 138.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/03/2017] [Indexed: 02/06/2023]
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276
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Mutti JS, Bhullar RK, Gill KS. Evolution of Gene Expression Balance Among Homeologs of Natural Polyploids. G3 (BETHESDA, MD.) 2017; 7:1225-1237. [PMID: 28193629 PMCID: PMC5386871 DOI: 10.1534/g3.116.038711] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/11/2017] [Indexed: 11/18/2022]
Abstract
Polyploidy is a major evolutionary process in eukaryotes, yet the expression balance of homeologs in natural polyploids is largely unknown. To study this expression balance, the expression patterns of 2180 structurally well-characterized genes of wheat were studied, of which 813 had the expected three copies and 375 had less than three. Copy numbers of the remaining 992 ranged from 4 to 14, including homeologs, orthologs, and paralogs. Of the genes with three structural copies corresponding to homeologs, 55% expressed from all three, 38% from two, and the remaining 7% expressed from only one of the three copies. Homeologs of 76-87% of the genes showed differential expression patterns in different tissues, thus have evolved different gene expression controls, possibly resulting in novel functions. Homeologs of 55% of the genes showed tissue-specific expression, with the largest percentage (14%) in the anthers and the smallest (7%) in the pistils. The highest number (1.72/3) of homeologs/gene expression was in the roots and the lowest (1.03/3) in the anthers. As the expression of homeologs changed with changes in structural copy number, about 30% of the genes showed dosage dependence. Chromosomal location also impacted expression pattern as a significantly higher proportion of genes in the proximal regions showed expression from all three copies compared to that present in the distal regions.
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Affiliation(s)
- Jasdeep S Mutti
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Ramanjot K Bhullar
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
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277
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Jiang Q, Li X, Niu F, Sun X, Hu Z, Zhang H. iTRAQ-based quantitative proteomic analysis of wheat roots in response to salt stress. Proteomics 2017; 17. [PMID: 28191739 DOI: 10.1002/pmic.201600265] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 12/28/2016] [Accepted: 02/07/2017] [Indexed: 11/05/2022]
Abstract
Salinity is a major abiotic stress that affects plant growth and development. Plant roots are the sites of salt uptake. Here, an isobaric tag for a relative and absolute quantitation based proteomic technique was employed to identify the differentially expressed proteins (DEPs) from seedling roots of the salt-tolerant genotype Han 12 and the salt-sensitive genotype Jimai 19 in response to salt treatment. A total of 121 NaCl-responsive DEPs were observed in Han 12 and Jimai 19. The main DEPs were ubiquitination-related proteins, transcription factors, pathogen-related proteins, membrane intrinsic protein transporters and antioxidant enzymes, which may work together to obtain cellular homeostasis in roots and to determine the overall salt tolerance of different wheat varieties in response to salt stress. Functional analysis of three salt-responsive proteins was performed in transgenic plants as a case study to confirm the salt-related functions of the detected proteins. Taken together, the results of this study may be helpful in further elucidating salt tolerance mechanisms in wheat.
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Affiliation(s)
- Qiyan Jiang
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R., China
| | - Xiaojuan Li
- College of Life Sciences, Agriculture University of Hebei, Baoding, P. R., China
| | - Fengjuan Niu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R., China
| | - Xianjun Sun
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R., China
| | - Zheng Hu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R., China
| | - Hui Zhang
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R., China
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278
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Pavy N, Lamothe M, Pelgas B, Gagnon F, Birol I, Bohlmann J, Mackay J, Isabel N, Bousquet J. A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:189-203. [PMID: 28090692 DOI: 10.1111/tpj.13478] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/23/2016] [Accepted: 01/03/2017] [Indexed: 05/21/2023]
Abstract
Over the last decade, extensive genetic and genomic resources have been developed for the conifer white spruce (Picea glauca, Pinaceae), which has one of the largest plant genomes (20 Gbp). Draft genome sequences of white spruce and other conifers have recently been produced, but dense genetic maps are needed to comprehend genome macrostructure, delineate regions involved in quantitative traits, complement functional genomic investigations, and assist the assembly of fragmented genomic sequences. A greatly expanded P. glauca composite linkage map was generated from a set of 1976 full-sib progeny, with the positioning of 8793 expressed genes. Regions with significant low or high gene density were identified. Gene family members tended to be mapped on the same chromosomes, with tandemly arrayed genes significantly biased towards specific functional classes. The map was integrated with transcriptome data surveyed across eight tissues. In total, 69 clusters of co-expressed and co-localising genes were identified. A high level of synteny was found with pine genetic maps, which should facilitate the transfer of structural information in the Pinaceae. Although the current white spruce genome sequence remains highly fragmented, dozens of scaffolds encompassing more than one mapped gene were identified. From these, the relationship between genetic and physical distances was examined and the genome-wide recombination rate was found to be much smaller than most estimates reported for angiosperm genomes. This gene linkage map shall assist the large-scale assembly of the next-generation white spruce genome sequence and provide a reference resource for the conifer genomics community.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Betty Pelgas
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanç Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - John Mackay
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, 0X1 3RB, UK
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
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279
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Underwood CJ, Henderson IR, Martienssen RA. Genetic and epigenetic variation of transposable elements in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:135-141. [PMID: 28343122 PMCID: PMC5746046 DOI: 10.1016/j.pbi.2017.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 05/03/2023]
Abstract
Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation. Together, epigenetic modification and the forces of selection define the scope within which transposable elements can contribute to, and control, genome evolution.
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Affiliation(s)
- Charles J Underwood
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Ian R Henderson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Robert A Martienssen
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; HHMI-GBMF, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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280
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Acevedo‐Garcia J, Spencer D, Thieron H, Reinstädler A, Hammond‐Kosack K, Phillips AL, Panstruga R. mlo-based powdery mildew resistance in hexaploid bread wheat generated by a non-transgenic TILLING approach. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:367-378. [PMID: 27565953 PMCID: PMC5316926 DOI: 10.1111/pbi.12631] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 08/12/2016] [Accepted: 08/24/2016] [Indexed: 05/03/2023]
Abstract
Wheat is one of the most widely grown cereal crops in the world and is an important food grain source for humans. However, wheat yields can be reduced by many abiotic and biotic stress factors, including powdery mildew disease caused by Blumeria graminis f.sp. tritici (Bgt). Generating resistant varieties is thus a major effort in plant breeding. Here, we took advantage of the non-transgenic Targeting Induced Lesions IN Genomes (TILLING) technology to select partial loss-of-function alleles of TaMlo, the orthologue of the barley Mlo (Mildew resistance locus o) gene. Natural and induced loss-of-function alleles (mlo) of barley Mlo are known to confer durable broad-spectrum powdery mildew resistance, typically at the expense of pleiotropic phenotypes such as premature leaf senescence. We identified 16 missense mutations in the three wheat TaMlo homoeologues, TaMlo-A1, TaMlo-B1 and TaMlo-D1 that each lead to single amino acid exchanges. Using transient gene expression assays in barley single cells, we functionally analysed the different missense mutants and identified the most promising candidates affecting powdery mildew susceptibility. By stacking of selected mutant alleles we generated four independent lines with non-conservative mutations in each of the three TaMlo homoeologues. Homozygous triple mutant lines and surprisingly also some of the homozygous double mutant lines showed enhanced, yet incomplete, Bgt resistance without the occurrence of discernible pleiotropic phenotypes. These lines thus represent an important step towards the production of commercial non-transgenic, powdery mildew-resistant bread wheat varieties.
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Affiliation(s)
- Johanna Acevedo‐Garcia
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - David Spencer
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - Hannah Thieron
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - Anja Reinstädler
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - Kim Hammond‐Kosack
- Department of Plant Biology and Crop ScienceRothamsted ResearchWest CommonHarpendenHertfordshireAL5 2JQ, UK
| | - Andrew L. Phillips
- Department of Plant Biology and Crop ScienceRothamsted ResearchWest CommonHarpendenHertfordshireAL5 2JQ, UK
| | - Ralph Panstruga
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
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281
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Saidi MN, Mergby D, Brini F. Identification and expression analysis of the NAC transcription factor family in durum wheat (Triticum turgidum L. ssp. durum). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 112:117-128. [PMID: 28064119 DOI: 10.1016/j.plaphy.2016.12.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 12/29/2016] [Accepted: 12/31/2016] [Indexed: 05/05/2023]
Abstract
The NAC (NAM, ATAF and CUC) proteins belong to one of the largest plant-specific transcription factor (TF) families and play important roles in plant development processes, response to biotic and abiotic cues and hormone signaling. Our analysis led to the identification of 168 NAC genes in durum wheat, including nine putative membrane-bound TFs and 48 homeologous genes pairs. Phylogenetic analyses of TtNACs along with their Arabidopsis, grape, barley and rice counterparts divided these proteins into 8 phylogenetic groups and allowed the identification of TtNAC-A7, TtNAC-B35, TtNAC-A68, TtNAC-B69 and TtNAC-A43 as homologs of OsNAC1, OsNAC8, OsNTL2, OsNTL5 and ANAC025/NTL14, respectively. In silico expression analysis, using RNA-seq data, revealed tissue-specific and stress responsive TtNAC genes. The expression of ten selected genes was analyzed under salt and drought stresses in two contrasting tolerance cultivars. This analysis is the first report of NAC gene family in durum wheat and will be useful for the identification and selection of candidate genes associated with stress tolerance.
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Affiliation(s)
- Mohammed Najib Saidi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, PO Box 1177, Road Sidi Mansour 6 km, Sfax 3018, Tunisia.
| | - Dhawya Mergby
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, PO Box 1177, Road Sidi Mansour 6 km, Sfax 3018, Tunisia
| | - Faiçal Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, PO Box 1177, Road Sidi Mansour 6 km, Sfax 3018, Tunisia
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282
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Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, Clissold L, Simmonds J, Ramirez-Gonzalez RH, Wang X, Borrill P, Fosker C, Ayling S, Phillips AL, Uauy C, Dubcovsky J. Uncovering hidden variation in polyploid wheat. Proc Natl Acad Sci U S A 2017; 114:E913-E921. [PMID: 28096351 PMCID: PMC5307431 DOI: 10.1073/pnas.1619268114] [Citation(s) in RCA: 324] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations. Here we exploited this property to sequence and catalog more than 10 million mutations in the protein-coding regions of 2,735 mutant lines of tetraploid and hexaploid wheat. We detected, on average, 2,705 and 5,351 mutations per tetraploid and hexaploid line, respectively, which resulted in 35-40 mutations per kb in each population. With these mutation densities, we identified an average of 23-24 missense and truncation alleles per gene, with at least one truncation or deleterious missense mutation in more than 90% of the captured wheat genes per population. This public collection of mutant seed stocks and sequence data enables rapid identification of mutations in the different copies of the wheat genes, which can be combined to uncover previously hidden variation. Polyploidy is a central phenomenon in plant evolution, and many crop species have undergone recent genome duplication events. Therefore, the general strategy and methods developed herein can benefit other polyploid crops.
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Affiliation(s)
- Ksenia V Krasileva
- Department of Plant Sciences, University of California, Davis, CA 95616
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Paul Bailey
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | - Francine Paraiso
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Leah Clissold
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | - Ricardo H Ramirez-Gonzalez
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
- John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Xiaodong Wang
- Department of Plant Sciences, University of California, Davis, CA 95616
| | | | | | - Sarah Ayling
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | | | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616;
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
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283
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Genome-wide exploration of metal tolerance protein (MTP) genes in common wheat (Triticum aestivum): insights into metal homeostasis and biofortification. Biometals 2017; 30:217-235. [PMID: 28150142 DOI: 10.1007/s10534-017-9997-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 01/21/2017] [Indexed: 10/20/2022]
Abstract
Metal transport process in plants is a determinant of quality and quantity of the harvest. Although it is among the most important of staple crops, knowledge about genes that encode for membrane-bound metal transporters is scarce in wheat. Metal tolerance proteins (MTPs) are involved in trace metal homeostasis at the sub-cellular level, usually by providing metal efflux out of the cytosol. Here, by using various bioinformatics approaches, genes that encode for MTPs in the hexaploid wheat genome (Triticum aestivum, abbreviated as Ta) were identified and characterized. Based on the comparison with known rice MTPs, the wheat genome contained 20 MTP sequences; named as TaMTP1-8A, B and D. All TaMTPs contained a cation diffusion facilitator (CDF) family domain and most members harbored a zinc transporter dimerization domain. Based on motif, phylogeny and alignment analysis, A, B and D genomes of TaMTP3-7 sequences demonstrated higher homology compared to TaMTP1, 2 and 8. With reference to their rice orthologs, TaMTP1s and TaMTP8s belonged to Zn-CDFs, TaMTP2s to Fe/Zn-CDFs and TaMTP3-7s to Mn-CDFs. Upstream regions of TaMTP genes included diverse cis-regulatory motifs, indicating regulation by developmental stage, tissue type and stresses. A scan of the coding sequences of 20 TaMTPs against published miRNAs predicted a total of 14 potential miRNAs, mainly targeting the members of most diverged groups. Expression analysis showed that several TaMTPs were temporally and spatially regulated during the developmental time-course. In grains, MTPs were preferentially expressed in the aleurone layer, which is known as a reservoir for high concentrations of iron and zinc. The work identified and characterized metal tolerance proteins in common wheat and revealed a potential involvement of MTPs in providing a sink for trace element storage in wheat grains.
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284
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Abrouk M, Balcárková B, Šimková H, Komínkova E, Martis MM, Jakobson I, Timofejeva L, Rey E, Vrána J, Kilian A, Järve K, Doležel J, Valárik M. The in silico identification and characterization of a bread wheat/Triticum militinae introgression line. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:249-256. [PMID: 27510270 PMCID: PMC5259550 DOI: 10.1111/pbi.12610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 07/21/2016] [Accepted: 08/08/2016] [Indexed: 05/23/2023]
Abstract
The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies.
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Affiliation(s)
- Michael Abrouk
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Barbora Balcárková
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Hana Šimková
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Eva Komínkova
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Mihaela M. Martis
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems BiologyInstitute for Bioinformatics and Systems BiologyHelmholtz Center MunichNeuherbergGermany
- Division of Cell BiologyDepartment of Clinical and Experimental Medicine, Bioinformatics Infrastructure for Life SciencesLinköping UniversityLinköpingSweden
| | - Irena Jakobson
- Department of Gene TechnologyTallinn University of TechnologyTallinnEstonia
| | | | - Elodie Rey
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Jan Vrána
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | | | - Kadri Järve
- Department of Gene TechnologyTallinn University of TechnologyTallinnEstonia
| | - Jaroslav Doležel
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Miroslav Valárik
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
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285
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Hao C, Wang Y, Chao S, Li T, Liu H, Wang L, Zhang X. The iSelect 9 K SNP analysis revealed polyploidization induced revolutionary changes and intense human selection causing strong haplotype blocks in wheat. Sci Rep 2017; 7:41247. [PMID: 28134278 PMCID: PMC5278348 DOI: 10.1038/srep41247] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 12/19/2016] [Indexed: 01/05/2023] Open
Abstract
A Chinese wheat mini core collection was genotyped using the wheat 9 K iSelect SNP array. Total 2420 and 2396 polymorphic SNPs were detected on the A and the B genome chromosomes, which formed 878 haplotype blocks. There were more blocks in the B genome, but the average block size was significantly (P < 0.05) smaller than those in the A genome. Intense selection (domestication and breeding) had a stronger effect on the A than on the B genome chromosomes. Based on the genetic pedigrees, many blocks can be traced back to a well-known Strampelli cross, which was made one century ago. Furthermore, polyploidization of wheat (both tetraploidization and hexaploidization) induced revolutionary changes in both the A and the B genomes, with a greater increase of gene diversity compared to their diploid ancestors. Modern breeding has dramatically increased diversity in the gene coding regions, though obvious blocks were formed on most of the chromosomes in both tetraploid and hexaploid wheats. Tag-SNP markers identified in this study can be used for marker assisted selection using haplotype blocks as a wheat breeding strategy. This strategy can also be employed to facilitate genome selection in other self-pollinating crop species.
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Affiliation(s)
- Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuquan Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shiaoman Chao
- US Department of Agriculture-Agricultural Research Service Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lanfen Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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286
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Molecular cloning and characterization of two novel genes from hexaploid wheat that encode double PR-1 domains coupled with a receptor-like protein kinase. Mol Genet Genomics 2017; 292:435-452. [DOI: 10.1007/s00438-017-1287-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/03/2017] [Indexed: 11/26/2022]
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287
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Balcárková B, Frenkel Z, Škopová M, Abrouk M, Kumar A, Chao S, Kianian SF, Akhunov E, Korol AB, Doležel J, Valárik M. A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A. FRONTIERS IN PLANT SCIENCE 2017; 7:2063. [PMID: 28119729 PMCID: PMC5222868 DOI: 10.3389/fpls.2016.02063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/26/2016] [Indexed: 05/18/2023]
Abstract
Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.
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Affiliation(s)
- Barbora Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Zeev Frenkel
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Monika Škopová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, FargoND, USA
| | - Shiaoman Chao
- Biosciences Research Laboratory, United States Department of Agriculture-Agricultural Research Service, FargoND, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, University of Minnesota, St. PaulMN, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, ManhattanKS, USA
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
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288
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Ma J, Gao X, Liu Q, Shao Y, Zhang D, Jiang L, Li C. Overexpression of TaWRKY146 Increases Drought Tolerance through Inducing Stomatal Closure in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:2036. [PMID: 29225611 PMCID: PMC5706409 DOI: 10.3389/fpls.2017.02036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/14/2017] [Indexed: 05/02/2023]
Abstract
As a superfamily of transcription factors, the tryptophan-arginine-lysine-tyrosine (WRKY) transcription factors have been found to be essential for abiotic and biotic stress responses in plants. Currently, only 76 WRKY transcription factors in wheat could be identified in the NCBI database, among which only a few have been functionally analyzed. Herein, a total of 188 WRKY transcription factors were identified from the wheat genome database, which included 123 full-length coding sequences, and all of them were used for detailed evolution studies. By bioinformatics analysis, a WRKY transcription factor, named TaWRKY146, was found to be the homologous gene of AtWRKY46, overexpression of which leads to hypersensitivity to drought and salt stress in Arabidopsis. Consequently, the full length of TaWRKY146 was cloned, and the expression levels of TaWRKY146 were found significantly up-regulated in the leaves and roots of wheat seedlings, which were subjected to osmotic stress. Overexpression of TaWRKY146 in Arabidopsis was shown to enhance drought tolerance by the induction of stomatal closure that reduced the transpiration rate. All these results provide a firm foundation for further identification of WRKY transcription factors with important functions in wheat.
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Affiliation(s)
| | | | | | | | | | - Lina Jiang
- *Correspondence: Chunxi Li, ; Lina Jiang,
| | - Chunxi Li
- *Correspondence: Chunxi Li, ; Lina Jiang,
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289
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Bhalla PL, Sharma A, Singh MB. Enabling Molecular Technologies for Trait Improvement in Wheat. Methods Mol Biol 2017; 1679:3-24. [PMID: 28913791 DOI: 10.1007/978-1-4939-7337-8_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Wheat is the major staple food crop and a source of calories for humans worldwide. A steady increase in the wheat production is essential to meet the demands of an ever-increasing global population and to achieve food security. The large size and structurally intricate genome of polyploid wheat had hindered the genomic analysis. However, with the advent of new genomic technologies such as next generation sequencing has led to genome drafts for bread wheat and its progenitors and has paved the way to design new strategies for crop improvement. Here we provide an overview of the advancements made in wheat genomics together with the available "omics approaches" and bioinformatics resources developed for wheat research. Advances in genomic, transcriptomic, and metabolomic technologies are highlighted as options to circumvent existing bottlenecks in the phenotypic and genomic selection and gene transfer. The contemporary reverse genetics approaches, including the novel genome editing techniques to inform targeted manipulation of a single/multiple genes and strategies for generating marker-free transgenic wheat plants, emphasize potential to revolutionize wheat improvement shortly.
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Affiliation(s)
- Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Akanksha Sharma
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
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290
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Wei Q, Luo Q, Wang R, Zhang F, He Y, Zhang Y, Qiu D, Li K, Chang J, Yang G, He G. A Wheat R2R3-type MYB Transcription Factor TaODORANT1 Positively Regulates Drought and Salt Stress Responses in Transgenic Tobacco Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1374. [PMID: 28848578 PMCID: PMC5550715 DOI: 10.3389/fpls.2017.01374] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/24/2017] [Indexed: 05/18/2023]
Abstract
MYB transcription factors play important roles in plant responses to biotic and abiotic stress. In this study, TaODORANT1, a R2R3-MYB gene, was cloned from wheat (Triticum aestivum L.). TaODORANT1 was localized in the nucleus and functioned as a transcriptional activator. TaODORANT1 was up-regulated in wheat under PEG6000, NaCl, ABA, and H2O2 treatments. TaODORANT1-overexpressing transgenic tobacco plants exhibited higher relative water content and lower water loss rate under drought stress, as well as lower Na+ accumulation in leaves under salt stress. The transgenic plants showed higher CAT activity but lower ion leakage, H2O2 and malondialdehyde contents under drought and salt stresses. Besides, the transgenic plants also exhibited higher SOD activity under drought stress. Our results also revealed that TaODORANT1 overexpression up-regulated the expression of several ROS- and stress-related genes in response to both drought and salt stresses, thus enhancing transgenic tobacco plants tolerance. Our studies demonstrate that TaODORANT1 positively regulates plant tolerance to drought and salt stresses.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Junli Chang
- *Correspondence: Guangyuan He, Guangxiao Yang, Junli Chang,
| | - Guangxiao Yang
- *Correspondence: Guangyuan He, Guangxiao Yang, Junli Chang,
| | - Guangyuan He
- *Correspondence: Guangyuan He, Guangxiao Yang, Junli Chang,
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291
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Lv GY, Guo XG, Xie LP, Xie CG, Zhang XH, Yang Y, Xiao L, Tang YY, Pan XL, Guo AG, Xu H. Molecular Characterization, Gene Evolution, and Expression Analysis of the Fructose-1, 6-bisphosphate Aldolase (FBA) Gene Family in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1030. [PMID: 28659962 PMCID: PMC5470051 DOI: 10.3389/fpls.2017.01030] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/29/2017] [Indexed: 05/17/2023]
Abstract
Fructose-1, 6-bisphosphate aldolase (FBA) is a key plant enzyme that is involved in glycolysis, gluconeogenesis, and the Calvin cycle. It plays significant roles in biotic and abiotic stress responses, as well as in regulating growth and development processes. In the present paper, 21 genes encoding TaFBA isoenzymes were identified, characterized, and categorized into three groups: class I chloroplast/plastid FBA (CpFBA), class I cytosol FBA (cFBA), and class II chloroplast/plastid FBA. By using a prediction online database and genomic PCR analysis of Chinese Spring nulli-tetrasomic lines, we have confirmed the chromosomal location of these genes in 12 chromosomes of four homologous groups. Sequence and genomic structure analysis revealed the high identity of the allelic TaFBA genes and the origin of different TaFBA genes. Numerous putative environment stimulus-responsive cis-elements have been identified in 1,500-bp regions of TaFBA gene promoters, of which the most abundant are the light-regulated elements (LREs). Phylogenetic reconstruction using the deduced protein sequence of 245 FBA genes indicated an independent evolutionary pathway for the class I and class II groups. Although, earlier studies have indicated that class II FBA only occurs in prokaryote and fungi, our results have demonstrated that a few class II CpFBAs exist in wheat and other closely related species. Class I TaFBA was predicted to be tetramers and class II to be dimers. Gene expression analysis based on microarray and transcriptome databases suggested the distinct role of TaFBAs in different tissues and developmental stages. The TaFBA 4-9 genes were highly expressed in leaves and might play important roles in wheat development. The differential expression patterns of the TaFBA genes in light/dark and a few abiotic stress conditions were also analyzed. The results suggested that LRE cis-elements of TaFBA gene promoters were not directly related to light responses. Most TaFBA genes had higher expression levels in the roots than in the shoots when under various stresses. Class I cytosol TaFBA genes, particularly TaFBA10/12/18 and TaFBA13/16, and three class II TaFBA genes are involved in responses to various abiotic stresses. Class I CpFBA genes in wheat are apparently sensitive to different stress conditions.
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Affiliation(s)
- Geng-Yin Lv
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Xiao-Guang Guo
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Li-Ping Xie
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Chang-Gen Xie
- College of Life Sciences, Northwest A & F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - Xiao-Hong Zhang
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Yuan Yang
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Lei Xiao
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Yu-Ying Tang
- College of Life Sciences, Northwest A & F UniversityYangling, China
| | - Xing-Lai Pan
- Department of Food Crop Science, Cotton Research Institute, Shanxi Academy of Agricultural Sciences (CAAS)Yuncheng, China
| | - Ai-Guang Guo
- College of Life Sciences, Northwest A & F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - Hong Xu
- College of Life Sciences, Northwest A & F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
- *Correspondence: Hong Xu
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292
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Wen W, He Z, Gao F, Liu J, Jin H, Zhai S, Qu Y, Xia X. A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array. FRONTIERS IN PLANT SCIENCE 2017; 8:1389. [PMID: 28848588 PMCID: PMC5552701 DOI: 10.3389/fpls.2017.01389] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/25/2017] [Indexed: 05/04/2023]
Abstract
A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding.
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Affiliation(s)
- Weie Wen
- College of Agronomy, Xinjiang Agricultural UniversityUrumqi, China
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT)Beijing, China
| | - Fengmei Gao
- Crop Breeding Institute, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Jindong Liu
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Hui Jin
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shengnan Zhai
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural UniversityUrumqi, China
- *Correspondence: Yanying Qu, Xianchun Xia,
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Yanying Qu, Xianchun Xia,
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293
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Matros A, Liu G, Hartmann A, Jiang Y, Zhao Y, Wang H, Ebmeyer E, Korzun V, Schachschneider R, Kazman E, Schacht J, Longin F, Reif JC, Mock HP. Genome-metabolite associations revealed low heritability, high genetic complexity, and causal relations for leaf metabolites in winter wheat (Triticum aestivum). JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:415-428. [PMID: 28007948 PMCID: PMC5441906 DOI: 10.1093/jxb/erw441] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We investigated associations between the metabolic phenotype, consisting of quantitative data of 76 metabolites from 135 contrasting winter wheat (Triticum aestivum) lines, and 17 372 single nucleotide polymorphism (SNP) markers. Metabolite profiles were generated from flag leaves of plants from three different environments, with average repeatabilities of 0.5-0.6. The average heritability of 0.25 was unaffected by the heading date. Correlations among metabolites reflected their functional grouping, highlighting the strict coordination of various routes of the citric acid cycle. Genome-wide association studies identified significant associations for six metabolic traits, namely oxalic acid, ornithine, L-arginine, pentose alcohol III, L-tyrosine, and a sugar oligomer (oligo II), with between one and 17 associated SNPs. Notable associations with genes regulating transcription or translation explained between 2.8% and 32.5% of the genotypic variance (pG). Further candidate genes comprised metabolite carriers (pG 32.5-38.1%), regulatory proteins (pG 0.3-11.1%), and metabolic enzymes (pG 2.5-32.5%). The combinatorial use of genomic and metabolic data to construct partially directed networks revealed causal inferences in the correlated metabolite traits and associated SNPs. The evaluated causal relationships will provide a basis for predicting the effects of genetic interferences on groups of correlated metabolic traits, and thus on specific metabolic phenotypes.
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Affiliation(s)
- Andrea Matros
- Department of Physiology and Cell Biology, Applied Biochemistry, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Guozheng Liu
- Department of Breeding Research, Quantitative Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Anja Hartmann
- Department of Physiology and Cell Biology, Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Yong Jiang
- Department of Breeding Research, Quantitative Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Quantitative Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Huange Wang
- Biometris, Department of Plant Sciences, Wageningen University, PB Wageningen, The Netherlands
| | | | | | | | - Ebrahim Kazman
- Lantmännen SW Seed Hadmersleben GmbH, Hadmersleben, Germany
| | | | - Friedrich Longin
- University of Hohenheim, State Plant Breeding Institute, Stuttgart, Germany
| | - Jochen Christoph Reif
- Department of Breeding Research, Quantitative Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Hans-Peter Mock
- Department of Physiology and Cell Biology, Applied Biochemistry, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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294
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Abstract
In the past two decades, Chinese scientists have achieved significant progress on three aspects of wheat genetic transformation. First, the wheat transformation platform has been established and optimized to improve the transformation efficiency, shorten the time required from starting of transformation procedure to the fertile transgenic wheat plants obtained as well as to overcome the problem of genotype-dependent for wheat genetic transformation in wide range of wheat elite varieties. Second, with the help of many emerging techniques such as CRISPR/cas9 function of over 100 wheat genes has been investigated. Finally, modern technology has been combined with the traditional breeding technique such as crossing to accelerate the application of wheat transformation. Overall, the wheat end-use quality and the characteristics of wheat stress tolerance have been improved by wheat genetic engineering technique. So far, wheat transgenic lines integrated with quality-improved genes and stress tolerant genes have been on the way of Production Test stage in the field. The debates and the future studies on wheat transformation have been discussed, and the brief summary of Chinese wheat breeding research history has also been provided in this review.
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295
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Leitwein M, Gagnaire PA, Desmarais E, Guendouz S, Rohmer M, Berrebi P, Guinand B. Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations. JOURNAL OF FISH BIOLOGY 2016; 89:2717-2734. [PMID: 27666575 DOI: 10.1111/jfb.13131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/01/2016] [Indexed: 06/06/2023]
Abstract
A genome-wide assessment of diversity is provided for wild Mediterranean brown trout Salmo trutta populations from headwater tributaries of the Orb River and from Atlantic and Mediterranean hatchery-reared strains that have been used for stocking. Double-digest restriction-site-associated DNA sequencing (dd-RADseq) was performed and the efficiency of de novo and reference-mapping approaches to obtain individual genotypes was compared. Large numbers of single nucleotide polymorphism (SNP) markers with similar genome-wide distributions were discovered using both approaches (196 639 v. 121 016 SNPs, respectively), with c. 80% of the loci detected de novo being also found with reference mapping, using the Atlantic salmon Salmo salar genome as a reference. Lower mapping density but larger nucleotide diversity (π) was generally observed near extremities of linkage groups, consistent with regions of residual tetrasomic inheritance observed in salmonids. Genome-wide diversity estimates revealed reduced polymorphism in hatchery strains (π = 0·0040 and π = 0·0029 in Atlantic and Mediterranean strains, respectively) compared to wild populations (π = 0·0049), a pattern that was congruent with allelic richness estimated from microsatellite markers. Finally, pronounced heterozygote deficiency was found in hatchery strains (Atlantic FIS = 0·18; Mediterranean FIS = 0·42), indicating that stocking practices may affect the genetic diversity in wild populations. These new genomic resources will provide important tools to define better conservation strategies in S. trutta.
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Affiliation(s)
- M Leitwein
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
| | - P-A Gagnaire
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
- Station Biologique Marine, 2 Avenue des Chantiers, 34200, Sète, France
| | - E Desmarais
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
| | - S Guendouz
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, 141 rue de Cardonille, 34094, Montpellier Cedex 5, France
| | - M Rohmer
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, 141 rue de Cardonille, 34094, Montpellier Cedex 5, France
| | - P Berrebi
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
| | - B Guinand
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
- Département Biologie-Ecologie, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
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296
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Xiao J, Sekhwal MK, Li P, Ragupathy R, Cloutier S, Wang X, You FM. Pseudogenes and Their Genome-Wide Prediction in Plants. Int J Mol Sci 2016; 17:E1991. [PMID: 27916797 PMCID: PMC5187791 DOI: 10.3390/ijms17121991] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/20/2016] [Accepted: 11/22/2016] [Indexed: 11/17/2022] Open
Abstract
Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes). Pseudogenes are primarily identified by comparison to their parent genes. Bioinformatics tools for pseudogene prediction have been developed, among which PseudoPipe, PSF and Shiu's pipeline are publicly available. We compared these three tools using the well-annotated Arabidopsis thaliana genome and its known 924 pseudogenes as a test data set. PseudoPipe and Shiu's pipeline identified ~80% of A. thaliana pseudogenes, of which 94% were shared, while PSF failed to generate adequate results. A need for improvement of the bioinformatics tools for pseudogene prediction accuracy in plant genomes was thus identified, with the ultimate goal of improving the quality of genome annotation in plants.
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Affiliation(s)
- Jin Xiao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Manoj Kumar Sekhwal
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Raja Ragupathy
- Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada.
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Xiue Wang
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
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297
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Taneja M, Tyagi S, Sharma S, Upadhyay SK. Ca 2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1775. [PMID: 27965686 PMCID: PMC5124604 DOI: 10.3389/fpls.2016.01775] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/10/2016] [Indexed: 05/05/2023]
Abstract
The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. Molecular characterization of these proteins has been performed in certain plants, but they are still not characterized in Triticum aestivum (bread wheat). Herein, we identified 34 TaCaCA superfamily proteins, which were classified into TaCAX, TaCCX, TaNCL, and TaMHX protein families based on their structural organization and evolutionary relation with earlier reported proteins. Since the T. aestivum comprises an allohexaploid genome, TaCaCA genes were derived from each A, B, and D subgenome and homeologous chromosome (HC), except chromosome-group 1. Majority of genes were derived from more than one HCs in each family that were considered as homeologous genes (HGs) due to their high similarity with each other. These HGs showed comparable gene and protein structures in terms of exon/intron organization and domain architecture. Majority of TaCaCA proteins comprised two Na_Ca_ex domains. However, TaNCLs consisted of an additional EF-hand domain with calcium binding motifs. Each TaCaCA protein family consisted of about 10 transmembrane and two α-repeat regions with specifically conserved signature motifs except TaNCL, which had single α-repeat. Variable expression of most of the TaCaCA genes during various developmental stages suggested their specified role in development. However, constitutively high expression of a few genes like TaCAX1-A and TaNCL1-B indicated their role throughout the plant growth and development. The modulated expression of certain genes during biotic (fungal infections) and abiotic stresses (heat, drought, salt) suggested their role in stress response. Majority of TaCCX and TaNCL family genes were found highly affected during various abiotic stresses. However, the role of individual gene needs to be established. The present study unfolded the opportunity for detail functional characterization of TaCaCA proteins and their utilization in future crop improvement programs.
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Affiliation(s)
- Mehak Taneja
- Department of Botany, Panjab UniversityChandigarh, India
| | - Shivi Tyagi
- Department of Botany, Panjab UniversityChandigarh, India
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298
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Li X, Feng B, Zhang F, Tang Y, Zhang L, Ma L, Zhao C, Gao S. Bioinformatic Analyses of Subgroup-A Members of the Wheat bZIP Transcription Factor Family and Functional Identification of TabZIP174 Involved in Drought Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 7:1643. [PMID: 27899926 PMCID: PMC5110565 DOI: 10.3389/fpls.2016.01643] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/18/2016] [Indexed: 05/03/2023]
Abstract
Extensive studies in Arabidopsis and rice have demonstrated that Subgroup-A members of the bZIP transcription factor family play important roles in plant responses to multiple abiotic stresses. Although common wheat (Triticum aestivum) is one of the most widely cultivated and consumed food crops in the world, there are limited investigations into Subgroup A of the bZIP family in wheat. In this study, we performed bioinformatic analyses of the 41 Subgroup-A members of the wheat bZIP family. Phylogenetic and conserved motif analyses showed that most of the Subgroup-A bZIP proteins involved in abiotic stress responses of wheat, Arabidopsis, and rice clustered in Clade A1 of the phylogenetic tree, and shared a majority of conserved motifs, suggesting the potential importance of Clade-A1 members in abiotic stress responses. Gene structure analysis showed that TabZIP genes with close phylogenetic relationships tended to possess similar exon-intron compositions, and the positions of introns in the hinge regions of the bZIP domains were highly conserved, whereas introns in the leucine zipper regions were at variable positions. Additionally, eleven groups of homologs and two groups of tandem paralogs were also identified in Subgroup A of the wheat bZIP family. Expression profiling analysis indicated that most Subgroup-A TabZIP genes were responsive to abscisic acid and various abiotic stress treatments. TabZIP27, TabZIP74, TabZIP138, and TabZIP174 proteins were localized in the nucleus of wheat protoplasts, whereas TabZIP9-GFP fusion protein was simultaneously present in the nucleus, cytoplasm, and cell membrane. Transgenic Arabidopsis overexpressing TabZIP174 displayed increased seed germination rates and primary root lengths under drought treatments. Overexpression of TabZIP174 in transgenic Arabidopsis conferred enhanced drought tolerance, and transgenic plants exhibited lower water loss rates, higher survival rates, higher proline, soluble sugar, and leaf chlorophyll contents, as well as more stable osmotic potential under drought conditions. Additionally, overexpression of TabZIP174 increased the expression of stress-responsive genes (RD29A, RD29B, RAB18, DREB2A, COR15A, and COR47). The improved drought resistance might be attributed to the increased osmotic adjustment capacity. Our results indicate that TabZIP174 may participate in regulating plant response to drought stress and holds great potential for genetic improvement of abiotic stress tolerance in crops.
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Affiliation(s)
- Xueyin Li
- College of Agronomy, Northwest A & F UniversityYangling, China
- Beijing Municipal Key Laboratory of Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Biane Feng
- Beijing Municipal Key Laboratory of Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- College of Agriculture, Shanxi Agricultural UniversityTaigu, China
| | - Fengjie Zhang
- Beijing Municipal Key Laboratory of Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- College of Agriculture, Shanxi Agricultural UniversityTaigu, China
| | - Yimiao Tang
- Beijing Municipal Key Laboratory of Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Liping Zhang
- Beijing Municipal Key Laboratory of Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Lingjian Ma
- College of Agronomy, Northwest A & F UniversityYangling, China
| | - Changping Zhao
- Beijing Municipal Key Laboratory of Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Shiqing Gao
- Beijing Municipal Key Laboratory of Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
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299
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Liu M, Stiller J, Holušová K, Vrána J, Liu D, Doležel J, Liu C. Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat. Sci Rep 2016; 6:36398. [PMID: 27821854 PMCID: PMC5099574 DOI: 10.1038/srep36398] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/14/2016] [Indexed: 12/22/2022] Open
Abstract
The hexaploid wheat genotype Chinese Spring (CS) has been used worldwide as the reference base for wheat genetics and genomics, and significant resources have been used by the international community to generate a reference wheat genome based on this genotype. By sequencing flow-sorted 3B chromosome from a hexaploid wheat genotype CRNIL1A and comparing the obtained sequences with those available for CS, we detected that a large number of sequences in the former were missing in the latter. If the distribution of such sequences in the hexaploid wheat genome is random, CRNILA sequences missing in CS could be as much as 159.3 Mb even if only fragments of 50 bp or longer were considered. Analysing RNA sequences available in the public domains also revealed that dispensable genes are common in hexaploid wheat. Together with those extensive intra- and interchromosomal rearrangements in CS, the existence of such dispensable genes is another factor highlighting potential issues with the use of reference genomes in various studies. Strong deviation in distributions of these dispensable sequences among genotypes with different geographical origins provided the first evidence indicating that they could be associated with adaptation in wheat.
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Affiliation(s)
- Miao Liu
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD 4067, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jiri Stiller
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD 4067, Australia
- School of Plant Biology, The University of Western Australia, Perth, WA 6009, Australia
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300
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Sánchez-Martín J, Steuernagel B, Ghosh S, Herren G, Hurni S, Adamski N, Vrána J, Kubaláková M, Krattinger SG, Wicker T, Doležel J, Keller B, Wulff BBH. Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biol 2016; 17:221. [PMID: 27795210 PMCID: PMC5087116 DOI: 10.1186/s13059-016-1082-1] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/10/2016] [Indexed: 11/18/2022] Open
Abstract
Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to parental chromosomes. We apply MutChromSeq to six mutants each of the barley Eceriferum-q gene and the wheat Pm2 genes. This approach unambiguously identified single candidate genes that were verified by Sanger sequencing of additional mutants. MutChromSeq enables reference-free forward genetics in barley and wheat, thus opening up their pan-genomes to functional genomics.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | | | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Severine Hurni
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Nikolai Adamski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Simon G. Krattinger
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
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