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Abstract
An interesting and possibly unique pattern of genome evolution following polyploidy can be observed among allopolyploids of the Triticum and Aegilops genera (wheat group). Most polyploids in this group are presumed to share a common unaltered (pivotal) subgenome (U, D, or A) together with one or two modified (differential) subgenomes, a status that has been referred to as 'pivotal-differential' genome evolution. In this review we discuss various mechanisms that could be responsible for this evolutionary pattern, as well as evidence for and against the putative evolutionary mechanisms involved. We suggest that, in light of recent advances in genome sequencing and related technologies in the wheat group, the time has come to reopen the investigation into pivotal-differential genome evolution.
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Affiliation(s)
- Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, PO Box 416, Sanandaj, Iran
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Research Center for Biosystems, Land Use, and Nutrition (IFZ), Heinrich-Buff-Ring 26-32, Giessen 35392, Germany.
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202
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Zhang Y, Bai Y, Wu G, Zou S, Chen Y, Gao C, Tang D. Simultaneous modification of three homoeologs of TaEDR1 by genome editing enhances powdery mildew resistance in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:714-724. [PMID: 28502081 DOI: 10.1111/tpj.13599] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/23/2017] [Accepted: 05/03/2017] [Indexed: 05/18/2023]
Abstract
Wheat (Triticum aestivum L.) incurs significant yield losses from powdery mildew, a major fungal disease caused by Blumeria graminis f. sp. tritici (Bgt). enhanced disease resistance1 (EDR1) plays a negative role in the defense response against powdery mildew in Arabidopsis thaliana; however, the edr1 mutant does not show constitutively activated defense responses. This makes EDR1 an ideal target for approaches using new genome-editing tools to improve resistance to powdery mildew. We cloned TaEDR1 from hexaploid wheat and found high similarity among the three homoeologs of EDR1. Knock-down of TaEDR1 by virus-induced gene silencing or RNA interference enhanced resistance to powdery mildew, indicating that TaEDR1 negatively regulates powdery mildew resistance in wheat. We used CRISPR/Cas9 technology to generate Taedr1 wheat plants by simultaneous modification of the three homoeologs of wheat EDR1. No off-target mutations were detected in the Taedr1 mutant plants. The Taedr1 plants were resistant to powdery mildew and did not show mildew-induced cell death. Our study represents the successful generation of a potentially valuable trait using genome-editing technology in wheat and provides germplasm for disease resistance breeding.
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Affiliation(s)
- Yunwei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Bai
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guangheng Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecology and Resources Engineering, Wuyi University, Wuyishan, 354300, Fujian, China
| | - Shenghao Zou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongfang Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dingzhong Tang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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203
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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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204
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The wheat salinity-induced R2R3-MYB transcription factor TaSIM confers salt stress tolerance in Arabidopsis thaliana. Biochem Biophys Res Commun 2017; 491:642-648. [PMID: 28757414 DOI: 10.1016/j.bbrc.2017.07.150] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 07/26/2017] [Indexed: 11/24/2022]
Abstract
MYB transcription factors are a large family of proteins involved in plant development and responses to stress. In this study, the wheat salinity-induced R2R3-MYB transcription factor TaSIM was functionally characterized, with a focus on its role in salt stress tolerance. TaSIM protein enters the nucleus and binds to the MYB-binding site II motif. Expression analysis revealed that TaSIM was induced by drought, high salinity, low temperature, and abscisic acid treatment. Overexpression of TaSIM improved salt stress tolerance in transgenic plants. Furthermore, the transcript levels of genes involved in abscisic acid (ABA)-dependent (RD22) and ABA-independent (RD29A) signaling were higher in TaSIM-overexpressing plants than in the wild type. These results suggest that TaSIM positively modulates salt stress tolerance and has potential applications in molecular breeding to enhance salt tolerance in crops.
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205
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Talukder SK, Saha MC. Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses. FRONTIERS IN PLANT SCIENCE 2017; 8:1317. [PMID: 28798766 PMCID: PMC5526908 DOI: 10.3389/fpls.2017.01317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/12/2017] [Indexed: 05/13/2023]
Abstract
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.
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206
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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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207
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Majka M, Kwiatek MT, Majka J, Wiśniewska H. Aegilops tauschii Accessions with Geographically Diverse Origin Show Differences in Chromosome Organization and Polymorphism of Molecular Markers Linked to Leaf Rust and Powdery Mildew Resistance Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:1149. [PMID: 28702048 PMCID: PMC5487464 DOI: 10.3389/fpls.2017.01149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/15/2017] [Indexed: 06/02/2023]
Abstract
Aegilops tauschii (2n = 2x = 14) is a diploid wild species which is reported as a donor of the D-genome of cultivated bread wheat. The main goal of this study was to examine the differences and similarities in chromosomes organization among accessions of Ae. tauschii with geographically diversed origin, which is believed as a potential source of genes, especially determining resistance to fungal diseases (i.e., leaf rust and powdery mildew) for breeding of cereals. We established and compared the fluorescence in situ hybridization patterns of 21 accessions of Ae. tauschii using various repetitive sequences mainly from the BAC library of wheat cultivar Chinese Spring. Results obtained for Ae. tauschii chromosomes revealed many similarities between analyzed accessions, however, some hybridization patterns were specific for accessions, which become from cognate regions of the World. The most noticeable differences were observed for accessions from China which were characterized by presence of distinct signals of pTa-535 in the interstitial region of chromosome 3D, less intensity of pTa-86 signals in chromosome 2D, as well as lack of additional signals of pTa-86 in chromosomes 1D, 5D, or 6D. Ae. tauschii of Chinese origin appeared homogeneous and separate from landraces that originated in western Asia. Ae. tauschii chromosomes showed similar hybridization patterns to wheat D-genome chromosomes, but some differences were also observed among both species. What is more, we identified reciprocal translocation between short arm of chromosome 1D and long arm of chromosome 7D in accession with Iranian origin. High polymorphism between analyzed accessions and extensive allelic variation were revealed using molecular markers associated with resistance genes. Majority of the markers localized in chromosomes 1D and 2D showed the diversity of banding patterns between accessions. Obtained results imply, that there is a moderate or high level of polymorphism in the genome of Ae. tauschii determined by a geographical origin, which we proved by cytogenetic and molecular markers analysis. Therefore, selected accessions might constitute an accessible source of variation for improvement of Triticeae species like wheat and triticale.
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Affiliation(s)
- Maciej Majka
- Cereal Genomics Team, Department of Genomics, Institute of Plant Genetics, Polish Academy of SciencesPoznań, Poland
| | - Michał T. Kwiatek
- Cereal Genomics Team, Department of Genomics, Institute of Plant Genetics, Polish Academy of SciencesPoznań, Poland
| | - Joanna Majka
- Plant Molecular Physiology and Cytogenetics Team, Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of SciencesPoznań, Poland
| | - Halina Wiśniewska
- Cereal Genomics Team, Department of Genomics, Institute of Plant Genetics, Polish Academy of SciencesPoznań, Poland
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208
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Cui F, Zhang N, Fan XL, Zhang W, Zhao CH, Yang LJ, Pan RQ, Chen M, Han J, Zhao XQ, Ji J, Tong YP, Zhang HX, Jia JZ, Zhao GY, Li JM. Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep 2017. [PMID: 28630475 DOI: 10.1038/s41598-017-04028-63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.
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Affiliation(s)
- Fa Cui
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong Unversity, Yan'tai, 264025, China
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xiao-Li Fan
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chun-Hua Zhao
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong Unversity, Yan'tai, 264025, China
| | - Li-Juan Yang
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453000, China
| | - Rui-Qing Pan
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Mei Chen
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jie Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xue-Qiang Zhao
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi-Ping Tong
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hong-Xia Zhang
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong Unversity, Yan'tai, 264025, China
| | - Ji-Zeng Jia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guang-Yao Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jun-Ming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
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209
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Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep 2017. [PMID: 28630475 PMCID: PMC5476560 DOI: 10.1038/s41598-017-04028-6] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.
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210
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Wang M, Wu H, Xu J, Li C, Wang Y, Wang Z. Five Fatty Acyl-Coenzyme A Reductases Are Involved in the Biosynthesis of Primary Alcohols in Aegilops tauschii Leaves. FRONTIERS IN PLANT SCIENCE 2017; 8:1012. [PMID: 28659955 PMCID: PMC5466989 DOI: 10.3389/fpls.2017.01012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 05/26/2017] [Indexed: 05/20/2023]
Abstract
The diploid Aegilops tauschii is the D-genome donor to hexaploid wheat (Triticum aestivum) and represents a potential source for genetic study in common wheat. The ubiquitous wax covering the aerial parts of plants plays an important role in protecting plants against non-stomatal water loss. Cuticular waxes are complex mixtures of very-long-chain fatty acids, alkanes, primary and/or secondary alcohols, aldehydes, ketones, esters, triterpenes, sterols, and flavonoids. In the present work, primary alcohols were identified as the major components of leaf cuticular wax in Ae. tauschii, with C26:0-OH being the dominant primary alcohol. Analysis by scanning electron microscope revealed that dense platelet-shaped wax crystals were deposited on leaf surfaces of Ae. tauschii. Ten putative wax biosynthetic genes encoding fatty acyl-coenzyme A reductase (FAR) were identified in the genome of Ae. tauschii. Five of these genes, Ae.tFAR1, Ae.tFAR2, Ae.tFAR3, Ae.tFAR4, and Ae.tFAR6, were found expressed in the leaf blades. Heterologous expression of the five Ae.tFARs in yeast (Saccharomyces cerevisiae) showed that Ae.tFAR1, Ae.tFAR2, Ae.tFAR3, Ae.tFAR4, and Ae.tFAR6 were predominantly responsible for the accumulation of C16:0, C18:0, C26:0, C24:0, and C28:0 primary alcohols, respectively. In addition, nine Ae.tFAR paralogous genes were located on D chromosome of wheat and the wheat nullisomic-tetrasomic lines with the loss of Ae.tFAR3 and Ae.tFAR4 paralogous genes had significantly reduced levels of primary alcohols in the leaf blades. Collectively, these data suggest that Ae.tFAR1, Ae.tFAR2, Ae.tFAR3, Ae.tFAR4, and Ae.tFAR6 encode alcohol-forming FARs involved in the biosynthesis of primary alcohols in the leaf blades of Ae. tauschii. The information obtained in Ae. tauschii enables us to better understand wax biosynthesis in common wheat.
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Affiliation(s)
- Meiling Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Hongqi Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Jing Xu
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural SciencesGuiyang, China
| | - Chunlian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Yong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
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211
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Majka J, Książczyk T, Kiełbowicz-Matuk A, Kopecký D, Kosmala A. Exploiting repetitive sequences and BAC clones in Festuca pratensis karyotyping. PLoS One 2017; 12:e0179043. [PMID: 28591168 PMCID: PMC5462415 DOI: 10.1371/journal.pone.0179043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/23/2017] [Indexed: 11/24/2022] Open
Abstract
The Festuca genus is thought to be the most numerous genus of the Poaceae family. One of the most agronomically important forage grasses, Festuca pratensis Huds. is treated as a model plant to study the molecular mechanisms associated with tolerance to winter stresses, including frost. However, the precise mapping of the genes governing stress tolerance in this species is difficult as its karyotype remains unrecognized. Only two F. pratensis chromosomes with 35S and 5S rDNA sequences can be easily identified, but its remaining chromosomes have not been distinguished to date. Here, two libraries derived from F. pratensis nuclear DNA with various contents of repetitive DNA sequences were used as sources of molecular probes for fluorescent in situ hybridisation (FISH), a BAC library and a library representing sequences most frequently present in the F. pratensis genome. Using FISH, six groups of DNA sequences were revealed in chromosomes on the basis of their signal position, including dispersed-like sequences, chromosome painting-like sequences, centromeric-like sequences, knob-like sequences, a group without hybridization signals, and single locus-like sequences. The last group was exploited to develop cytogenetic maps of diploid and tetraploid F. pratensis, which are presented here for the first time and provide a remarkable progress in karyotype characterization.
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Affiliation(s)
- Joanna Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
- * E-mail:
| | - Tomasz Książczyk
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | | | - David Kopecký
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Arkadiusz Kosmala
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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212
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Yuan Y, Bayer PE, Batley J, Edwards D. Improvements in Genomic Technologies: Application to Crop Genomics. Trends Biotechnol 2017; 35:547-558. [DOI: 10.1016/j.tibtech.2017.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 12/13/2022]
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213
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Zhang N, Fan X, Cui F, Zhao C, Zhang W, Zhao X, Yang L, Pan R, Chen M, Han J, Ji J, Liu D, Zhao Z, Tong Y, Zhang A, Wang T, Li J. Characterization of the temporal and spatial expression of wheat (Triticum aestivum L.) plant height at the QTL level and their influence on yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1235-1252. [PMID: 28349175 DOI: 10.1007/s00122-017-2884-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/21/2017] [Indexed: 05/05/2023]
Abstract
The temporal and spatial expression patterns of stable QTL for plant height and their influences on yield were characterized. Plant height (PH) is a complex trait in wheat (Triticum aestivum L.) that includes the spike length (SL) and the internode lengths from the first to the fifth internode, which are counted from the top and abbreviated as FIRITL, SECITL, THIITL, FOUITL, and FIFITL, respectively. This study identified eight putative additive quantitative trait loci (QTL) for PH. In addition, unconditional and conditional QTL mapping were used to analyze the temporal and spatial expression patterns of five stable QTL for PH. qPh-3A mainly regulated SL, FIRITL, and FIFITL to affect PH during the booting-heading stage (BS-HS); qPh-3D regulated all internode lengths to affect PH, especially during the BS-HS; before HS, qPh-4B mainly affected FIRITL, SECITL, THIITL, and FOUITL and qPh-5A.1 mainly affected SECITL, THIITL, and FOUITL to regulate PH; and qPh-6B mainly regulated FIRITL to affect the PH after the booting stage (BS). qPhdv-4B, a QTL for the response of PH to nitrogen stress, was stable and co-localized with qPh-4B. All five stable QTL, except for qPh-3A, were related to the 1000 kernel weight and yield per plant. Regions of qPh-3A, qPh-3D, qPh-4B, qPh-5A.1, and qPh-6B showed synteny to parts of rice chromosomes 1, 1, 3, 9, and 2, respectively. Based on comparative genomics analysis, Rht-B1b was cloned and mapped in the CI of qPh-4B. This report provides useful information for fine mapping of the stable QTL for PH and the genetic improvement of wheat plant type.
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Affiliation(s)
- Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Fa Cui
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong University, Yantai, 264025, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chunhua Zhao
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
| | - Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xueqiang Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lijuan Yang
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453000, China
| | - Ruiqing Pan
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Mei Chen
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jie Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zongwu Zhao
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453000, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
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214
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Wiersma AT, Pulman JA, Brown LK, Cowger C, Olson EL. Identification of Pm58 from Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1123-1133. [PMID: 28255671 DOI: 10.1007/s00122-017-2874-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/07/2017] [Indexed: 05/25/2023]
Abstract
A novel powdery mildew-resistance gene, designated Pm58, was introgressed directly from Aegilops tauschii to hexaploid wheat, mapped to chromosome 2DS, and confirmed to be effective under field conditions. Selectable KASP™ markers were developed for MAS. Powdery mildew caused by Blumeria graminis (DC.) f. sp. tritici (Bgt) remains a significant threat to wheat (Triticum aestivum L.) production. The rapid breakdown of race-specific resistance to Bgt reinforces the need to identify novel sources of resistance. The D-genome species, Aegilops tauschii, is an excellent source of disease resistance that is transferrable to T. aestivum. The powdery mildew-resistant Ae. tauschii accession TA1662 (2n = 2x = DD) was crossed directly with the susceptible hard white wheat line KS05HW14 (2n = 6x = AABBDD) followed by backcrossing to develop a population of 96 BC2F4 introgression lines (ILs). Genotyping-by-sequencing was used to develop a genome-wide genetic map that was anchored to the Ae. tauschii reference genome. A detached-leaf Bgt assay was used to screen BC2F4:6 ILs, and resistance was found to segregate as a single locus (χ = 2.0, P value = 0.157). The resistance gene, referred to as Pm58, mapped to chromosome 2DS. Pm58 was evaluated under field conditions in replicated trials in 2015 and 2016. In both years, a single QTL spanning the Pm58 locus was identified that reduced powdery mildew severity and explained 21% of field variation (P value < 0.01). KASP™ assays were developed from closely linked GBS-SNP markers, a refined genetic map was developed, and four markers that cosegregate with Pm58 were identified. This novel source of powdery mildew-resistance and closely linked genetic markers will support efforts to develop wheat varieties with powdery mildew resistance.
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Affiliation(s)
- Andrew T Wiersma
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, Room A286, East Lansing, MI, 48824, USA
| | - Jane A Pulman
- Department of Plant Biology and Center for Genomics-Enabled Plant Science, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA
| | - Linda K Brown
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, Room A286, East Lansing, MI, 48824, USA
| | - Christina Cowger
- Department of Plant Pathology, North Carolina State University, USDA-ARS Plant Science Research, 2510 Thomas Hall, Campus Box 7616, Raleigh, NC, 27695, USA
| | - Eric L Olson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, Room A286, East Lansing, MI, 48824, USA.
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215
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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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216
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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: 123] [Impact Index Per Article: 17.6] [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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217
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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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218
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Matsuda R, Iehisa JCM, Sakaguchi K, Ohno R, Yoshida K, Takumi S. Global gene expression profiling related to temperature-sensitive growth abnormalities in interspecific crosses between tetraploid wheat and Aegilops tauschii. PLoS One 2017; 12:e0176497. [PMID: 28463975 PMCID: PMC5413045 DOI: 10.1371/journal.pone.0176497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/10/2017] [Indexed: 12/17/2022] Open
Abstract
Triploid wheat hybrids between tetraploid wheat and Aegilops tauschii sometimes show abnormal growth phenotypes, and the growth abnormalities inhibit generation of wheat synthetic hexaploids. In type II necrosis, one of the growth abnormalities, necrotic cell death accompanied by marked growth repression occurs only under low temperature conditions. At normal temperature, the type II necrosis lines show grass-clump dwarfism with no necrotic symptoms, excess tillers, severe dwarfism and delayed flowering. Here, we report comparative expression analyses to elucidate the molecular mechanisms of the temperature-dependent phenotypic plasticity in the triploid wheat hybrids. We compared gene and small RNA expression profiles in crown tissues to characterize the temperature-dependent phenotypic plasticity. No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Some microRNAs, including miR156, were up-regulated, whereas the levels of transcripts of the miR156 target genes SPLs, known to inhibit tiller and branch number, were reduced in crown tissues of the grass-clump dwarf lines at the normal temperature. Unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype. Dramatic alteration of gene expression profiles, including miRNA levels, in crown tissues is associated with the temperature-dependent phenotypic plasticity in type II necrosis/grass-clump dwarf wheat hybrids.
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Affiliation(s)
- Ryusuke Matsuda
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Julio Cesar Masaru Iehisa
- Departmento de Biotecnología, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Kouhei Sakaguchi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Ryoko Ohno
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kentaro Yoshida
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shigeo Takumi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- * E-mail:
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219
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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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220
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Huang D, Feurtado JA, Smith MA, Flatman LK, Koh C, Cutler AJ. Long noncoding miRNA gene represses wheat β-diketone waxes. Proc Natl Acad Sci U S A 2017; 114:E3149-E3158. [PMID: 28351975 PMCID: PMC5393243 DOI: 10.1073/pnas.1617483114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The cuticle of terrestrial plants functions as a protective barrier against many biotic and abiotic stresses. In wheat and other Triticeae, β-diketone waxes are major components of the epicuticular layer leading to the bluish-white glaucous trait in reproductive-age plants. Glaucousness in durum wheat is controlled by a metabolic gene cluster at the WAX1 (W1) locus and a dominant suppressor INHIBITOR of WAX1 (Iw1) on chromosome 2B. The wheat D subgenome from progenitor Aegilops tauschii contains W2 and Iw2 paralogs on chromosome 2D. Here we identify the Iw1 gene from durum wheat and demonstrate the unique regulatory mechanism by which Iw1 acts to suppress a carboxylesterase-like protein gene, W1-COE, within the W1 multigene locus. Iw1 is a long noncoding RNA (lncRNA) containing an inverted repeat (IR) with >80% identity to W1-COE The Iw1 transcript forms a miRNA precursor-like long hairpin producing a 21-nt predominant miRNA, miRW1, and smaller numbers of related sRNAs associated with the nonglaucous phenotype. When Iw1 was introduced into glaucous bread wheat, miRW1 accumulated, W1-COE and its paralog W2-COE were down-regulated, and the phenotype was nonglaucous and β-diketone-depleted. The IR region of Iw1 has >94% identity to an IR region on chromosome 2 in Ae. tauschii that also produces miRW1 and lies within the marker-based location of Iw2 We propose the Iw loci arose from an inverted duplication of W1-COE and/or W2-COE in ancestral wheat to form evolutionarily young miRNA genes that act to repress the glaucous trait.
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Affiliation(s)
- Daiqing Huang
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - J Allan Feurtado
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - Mark A Smith
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - Leah K Flatman
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - Chushin Koh
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
| | - Adrian J Cutler
- Wheat Improvement Flagship Program, National Research Council of Canada, Saskatoon, Saskatchewan, SK S7N 0W9, Canada
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221
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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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222
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Zhuang Y, Tripp EA. The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). DNA Res 2017; 24:179-192. [PMID: 28431014 PMCID: PMC5397612 DOI: 10.1093/dnares/dsw054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/13/2022] Open
Abstract
The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3'5'H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3'H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.
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Affiliation(s)
- Yongbin Zhuang
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA
- Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309, USA
| | - Erin A. Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA
- Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309, USA
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Miao L, Mao X, Wang J, Liu Z, Zhang B, Li W, Chang X, Reynolds M, Wang Z, Jing R. Elite Haplotypes of a Protein Kinase Gene TaSnRK2.3 Associated with Important Agronomic Traits in Common Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:368. [PMID: 28400774 PMCID: PMC5368224 DOI: 10.3389/fpls.2017.00368] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/01/2017] [Indexed: 05/19/2023]
Abstract
Plant-specific protein kinase SnRK2s play crucial roles in response to various environmental stimuli. TaSnRK2.3, a SnRK2 member, was involved in the response to multiple abiotic stresses in wheat. To facilitate the use of TaSnRK2.3 in wheat breeding, the three genomic sequences of TaSnRK2.3, originating from the A, B, and D genomes of hexaploid wheat, were obtained. Sequence polymorphism assays showing 4 and 10 variations were detected at TaSnRK2.3-1A and at TaSnRK2.3-1B, respectively, yet no variation was identified at TaSnRK2.3-1D. Three haplotypes for A genome, and two main haplotypes for B genome of TaSnRK2.3 were identified in 32 genotypes. Functional markers (2.3AM1, 2.3AM2, 2.3BM1, 2.3BM2) were successfully developed to distinguish different haplotypes. Association analysis was performed with the general linear model in TASSEL 2.1. The results showed that both TaSnRK2.3-1A and TaSnRK2.3-1B were significantly associated with plant height (PH), length of peduncle and penultimate node, as well as 1,000-grain weight (TGW) under different environments. Additionally, TaSnRK2.3-1B was significantly associated with stem water-soluble carbohydrates at flowering and mid-grain filling stages. Hap-1A-1 had higher TGW and lower PH; Hap-1B-1 had higher TGW and stem water-soluble carbohydrates, as well as lower PH, thus the two haplotypes were considered as elite haplotypes. Geographic distribution and allelic frequencies indicated that the two preferred haplotypes Hap-1A-1 and Hap-1B-1 were positively selected in the process of Chinese wheat breeding. These results could be valuable for genetic improvement and germplasm enhancement using molecular marker assisted selection in wheat breeding.
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Affiliation(s)
- Lili Miao
- College of Agronomy, Northeast Agricultural UniversityHarbin, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- College of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zicheng Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Bin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Weiyu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | | | - Zhenhua Wang
- College of Agronomy, Northeast Agricultural UniversityHarbin, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
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Gao L, Zhao G, Huang D, Jia J. Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array. Sci Rep 2017; 7:44530. [PMID: 28327671 PMCID: PMC5361097 DOI: 10.1038/srep44530] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/10/2017] [Indexed: 11/12/2022] Open
Abstract
Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions. This study will not only help future wheat breeding and evolutionary studies, but will also accelerate study of other crops, especially polyploids.
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Affiliation(s)
- Lifeng Gao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
| | - Guangyao Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
| | - Dawei Huang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing, 100081, China
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225
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Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KFX, Schmid K, Schön CC, Scholz U. Towards a whole-genome sequence for rye (Secale cereale L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:853-869. [PMID: 27888547 DOI: 10.1111/tpj.13436] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 05/18/2023]
Abstract
We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
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Affiliation(s)
- Eva Bauer
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Ivan Barilar
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mihaela M Martis
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Bernd Hackauf
- Julius Kühn-Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Andres Gordillo
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Peer Wilde
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Malthe Schmidt
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Viktor Korzun
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Karl Schmid
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Chris-Carolin Schön
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
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Xu T, Bian N, Wen M, Xiao J, Yuan C, Cao A, Zhang S, Wang X, Wang H. Characterization of a common wheat (Triticum aestivum L.) high-tillering dwarf mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:483-494. [PMID: 27866225 DOI: 10.1007/s00122-016-2828-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/12/2016] [Indexed: 05/05/2023]
Abstract
A novel high-tillering dwarf mutant in common wheat Wangshuibai was characterized and mapped to facilitate breeding for plant height and tiller and the future cloning of the causal gene. Tiller number and plant height are two major agronomic traits in cereal crops affecting plant architecture and grain yield. NAUH167, a mutant of common wheat landrace Wangshuibai induced by ethylmethyl sulfide (EMS) treatment, exhibits higher tiller number and reduced plant height. Microscope observation showed that the dwarf phenotype was attributed to the decrease in the number of cells and their length. The same as the wild type, the mutant was sensitive to exogenous gibberellins. Genetic analysis showed that the high-tillering number and dwarf phenotype were related and controlled by a partial recessive gene. Using a RIL2:6 population derived from the cross NAUH167/Sumai3, a molecular marker-based genetic map was constructed. The map consisted of 283 loci, spanning a total length of 1007.98 cM with an average markers interval of 3.56 cM. By composite interval mapping, a stable major QTL designated QHt.nau-2D controlling both traits, was mapped to the short arm of chromosome 2D flanked by markers Xcfd11 and Xgpw361. To further map the QHt.nau-2D loci, another population consisted of 180 F2 progeny from a cross 2011I-78/NAUH167 was constructed. Finally, QHt.nau-2D was located within a genetic region of 0.8 cM between markers QHT239 and QHT187 covering a predicted physical distance of 6.77 Mb. This research laid the foundation for map-based cloning of QHt.nau-2D and would facilitate the characterization of plant height and tiller number in wheat.
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Affiliation(s)
- Tao Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Nengfei Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Mingxing Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Chunxia Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Aizhong Cao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Shouzhong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.
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227
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Tulpan D, Leger S. The Plant Orthology Browser: An Orthology and Gene-Order Visualizer for Plant Comparative Genomics. THE PLANT GENOME 2017; 10. [PMID: 28464063 DOI: 10.3835/plantgenome2016.08.0078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Worldwide genome sequencing efforts for plants with medium and large genomes require identification and visualization of orthologous genes, while their syntenic conservation becomes the pinnacle of any comparative and functional genomics study. Using gene models for 20 fully sequenced plant genomes, including model organisms and staple crops such as Coss., (L.) Heynh., (L.) Beauv., turnip ( L.), barley ( L.), rice ( L.), sorghum [ (L.) Moench], wheat ( L.), red wild einkorn ( Tumanian ex Gandilyan), and maize ( L.), we computationally predicted 1,021,611 orthologs using stringent sequence similarity criteria. For each pair of plant species, we determined sets of conserved synteny blocks using strand orientation and physical mapping. Gene ontology (GO) annotations are added for each gene. Plant Orthology Browser (POB) includes three interconnected modules: (i) a gene-order visualization module implementing an interactive environment for exploration of gene order between any pair of chromosomes in two plant species, (ii) a synteny visualization module providing unique interactive dot plot representations of orthologous genes between a pair of chromosomes in two distinct plant species, and (iii) a search module that interconnects all modules via free-text search capability with online as-you-type suggestions and highlighting that allows exploration of the underlining information without constraint of interface-dependent search fields. The POB is a web-based orthology and annotation visualization tool, which currently supports 20 completely sequenced plant species with considerably large genomes and offers intuitive and highly interactive pairwise comparison and visualization of genomic traits via gene orthology.
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228
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Response of microRNAs to cold treatment in the young spikes of common wheat. BMC Genomics 2017; 18:212. [PMID: 28241738 PMCID: PMC5330121 DOI: 10.1186/s12864-017-3556-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 02/03/2017] [Indexed: 12/04/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important roles in biotic and abiotic stresses by regulating their target genes. For common wheat, spring frost damage frequently occurs, especially when low temperature coincides with plants at early floral organ differentiation, which may result in significant yield loss. Up to date, the role of miRNAs in wheat response to frost stress is not well understood. Results We report here the sequencing of small RNA transcriptomes from the young spikes that were treated with cold stress and the comparative analysis with those of the control. A total of 192 conserved miRNAs from 105 families and nine novel miRNAs were identified. Among them, 34 conserved and five novel miRNAs were differentially expressed between the cold-stressed samples and the controls. The expression patterns of 18 miRNAs were further validated by quantitative real time polymerase chain reaction (qRT-PCR). Moreover, nearly half of the miRNAs were cross inducible by biotic and abiotic stresses when compared with previously published work. Target genes were predicted and validated by degradome sequencing. Gene Ontology (GO) enrichment analysis showed that the target genes of differentially expressed miRNAs were enriched for response to the stimulus, regulation of transcription, and ion transport functions. Since many targets of differentially expressed miRNAs were transcription factors that are associated with floral development such as ARF, SPB (Squamosa Promoter Binding like protein), MADS-box (MCM1, AG, DEFA and SRF), MYB, SPX (SYG1, Pho81 and XPR1), TCP (TEOSINTE BRANCHED, Cycloidea and PCF), and PPR (PentatricoPeptide Repeat) genes, cold-altered miRNA expression may cause abnormal reproductive organ development. Conclusion Analysis of small RNA transcriptomes and their target genes provide new insight into miRNA regulation in developing wheat inflorescences under cold stress. MiRNAs provide another layer of gene regulation in cold stress response that can be genetically manipulated to reduce yield loss in wheat. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3556-2) contains supplementary material, which is available to authorized users.
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229
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Development of intron targeting (IT) markers specific for chromosome arm 4VS of Haynaldia villosa by chromosome sorting and next-generation sequencing. BMC Genomics 2017; 18:167. [PMID: 28202009 PMCID: PMC5310052 DOI: 10.1186/s12864-017-3567-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 02/07/2017] [Indexed: 12/31/2022] Open
Abstract
Background Haynaldia villosa (L.) Schur (syn. Dasypyrum villosum L. Candargy, 2n = 14, genome VV) is the tertiary gene pool of wheat, and thus a potential resource of genes for wheat improvement. Among other, wheat yellow mosaic (WYM) resistance gene Wss1 and a take-all resistance gene were identified on the short arm of chromosome 4 V (4VS) of H. villosa. We had obtained introgressions on 4VS chromosome arm, with the objective of utilizing the target genes. However, monitoring these introgressions has been a daunting task because of inadequate knowledge as to H.villosa genome, as reflected by the lack of specific markers. Results This study aims to develop 4VS-specific markers by combination of chromosome sorting and next-generation sequencing. The short arm of chromosome 4VS of H.villosa was flow-sorted using a FACSVantage SE flow cytometer and sorter, and then sequenced by Illumina sequencing. The sequence of H. villosa 4VS was assembled by the software Hecate, and then was compared with the sequence assemblies of wheat chromosome arms 4AL, 4BS and 4DS and Ae. tauschii 4DS, with the objectives of identifying exon-exon junctions and localizing introns on chromosome 4VS of H. villosa. The intron length polymorphisms suitable for designing H. villosa primers were evaluated with criteria. Consequently, we designed a total of 359 intron targeting (IT) markers, among which 232 (64.62%) markers were specific for tracing the 4VS chromatin in the wheat background. Conclusion The combination of chromosome sorting and next-generation sequencing to develop specific IT markers for 4VS of H. villosa has high success rate and specificity, thus being applicable for the development of chromosome-specific markers for alien chromatin in wheat breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3567-z) contains supplementary material, which is available to authorized users.
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230
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Hao M, Li A, Shi T, Luo J, Zhang L, Zhang X, Ning S, Yuan Z, Zeng D, Kong X, Li X, Zheng H, Lan X, Zhang H, Zheng Y, Mao L, Liu D. The abundance of homoeologue transcripts is disrupted by hybridization and is partially restored by genome doubling in synthetic hexaploid wheat. BMC Genomics 2017; 18:149. [PMID: 28187716 PMCID: PMC5303294 DOI: 10.1186/s12864-017-3558-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 02/07/2017] [Indexed: 11/10/2022] Open
Abstract
Background The formation of an allopolyploid is a two step process, comprising an initial wide hybridization event, which is later followed by a whole genome doubling. Both processes can affect the transcription of homoeologues. Here, RNA-Seq was used to obtain the genome-wide leaf transcriptome of two independent Triticum turgidum × Aegilops tauschii allotriploids (F1), along with their spontaneous allohexaploids (S1) and their parental lines. The resulting sequence data were then used to characterize variation in homoeologue transcript abundance. Results The hybridization event strongly down-regulated D-subgenome homoeologues, but this effect was in many cases reversed by whole genome doubling. The suppression of D-subgenome homoeologue transcription resulted in a marked frequency of parental transcription level dominance, especially with respect to genes encoding proteins involved in photosynthesis. Singletons (genes where no homoeologues were present) were frequently transcribed at both the allotriploid and allohexaploid plants. Conclusions The implication is that whole genome doubling helps to overcome the phenotypic weakness of the allotriploid, restoring a more favourable gene dosage in genes experiencing transcription level dominance in hexaploid wheat. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3558-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tongwei Shi
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Jiangtao Luo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xuechuan Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Deying Zeng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xingchen Kong
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiaolong Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Huaigang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China. .,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
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El Baidouri M, Murat F, Veyssiere M, Molinier M, Flores R, Burlot L, Alaux M, Quesneville H, Pont C, Salse J. Reconciling the evolutionary origin of bread wheat (Triticum aestivum). THE NEW PHYTOLOGIST 2017; 213:1477-1486. [PMID: 27551821 DOI: 10.1111/nph.14113] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/18/2016] [Indexed: 05/26/2023]
Abstract
The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.
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Affiliation(s)
- Moaine El Baidouri
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Florent Murat
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Maeva Veyssiere
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Mélanie Molinier
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Raphael Flores
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Laura Burlot
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Michael Alaux
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Hadi Quesneville
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Caroline Pont
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
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232
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Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res 2017; 27:787-792. [PMID: 28130360 PMCID: PMC5411773 DOI: 10.1101/gr.213405.116] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/18/2017] [Indexed: 01/12/2023]
Abstract
Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data alone, particularly with highly repetitive plant genomes. Errors in the raw data can lead to insertion or deletion errors (indels) in the consensus genome sequence, which in turn create significant problems for downstream analysis; for example, a single indel may shift the reading frame and incorrectly truncate a protein sequence. Here, we describe an algorithm that solves the high error rate problem by combining long, high-error reads with shorter but much more accurate Illumina sequencing reads, whose error rates average <1%. Our hybrid assembly algorithm combines these two types of reads to construct mega-reads, which are both long and accurate, and then assembles the mega-reads using the CABOG assembler, which was designed for long reads. We apply this technique to a large data set of Illumina and PacBio sequences from the species Aegilops tauschii, a large and extremely repetitive plant genome that has resisted previous attempts at assembly. We show that the resulting assembled contigs are far larger than in any previous assembly, with an N50 contig size of 486,807 nucleotides. We compare the contigs to independently produced optical maps to evaluate their large-scale accuracy, and to a set of high-quality bacterial artificial chromosome (BAC)-based assemblies to evaluate base-level accuracy.
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Affiliation(s)
- Aleksey V Zimin
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Guillaume Marçais
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA.,Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - James A Yorke
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA.,Departments of Mathematics and Physics, University of Maryland, College Park, Maryland 20742, USA
| | - Jan Dvořák
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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233
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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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234
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Taylor RS, Tarver JE, Foroozani A, Donoghue PCJ. MicroRNA annotation of plant genomes − Do it right or not at all. Bioessays 2017; 39. [DOI: 10.1002/bies.201600113] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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235
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Spannagl M, Nussbaumer T, Bader K, Gundlach H, Mayer KFX. PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data. Methods Mol Biol 2017; 1533:33-44. [PMID: 27987163 DOI: 10.1007/978-1-4939-6658-5_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Plant Genome and Systems Biology (PGSB), formerly Munich Institute for Protein Sequences (MIPS) PlantsDB, is a database framework for the integration and analysis of plant genome data, developed and maintained for more than a decade now. Major components of that framework are genome databases and analysis resources focusing on individual (reference) genomes providing flexible and intuitive access to data. Another main focus is the integration of genomes from both model and crop plants to form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny). Data exchange and integrated search functionality with/over many plant genome databases is provided within the transPLANT project.
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Affiliation(s)
- Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany.
| | - Thomas Nussbaumer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Kai Bader
- Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
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236
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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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237
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Sun S, Wang J, Yu J, Meng F, Xia R, Wang L, Wang Z, Ge W, Liu X, Li Y, Liu Y, Yang N, Wang X. Alignment of Common Wheat and Other Grass Genomes Establishes a Comparative Genomics Research Platform. FRONTIERS IN PLANT SCIENCE 2017; 8:1480. [PMID: 28912789 PMCID: PMC5582351 DOI: 10.3389/fpls.2017.01480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 08/09/2017] [Indexed: 05/06/2023]
Abstract
Grass genomes are complicated structures as they share a common tetraploidization, and particular genomes have been further affected by extra polyploidizations. These events and the following genomic re-patternings have resulted in a complex, interweaving gene homology both within a genome, and between genomes. Accurately deciphering the structure of these complicated plant genomes would help us better understand their compositional and functional evolution at multiple scales. Here, we build on our previous research by performing a hierarchical alignment of the common wheat genome vis-à-vis eight other sequenced grass genomes with most up-to-date assemblies, and annotations. With this data, we constructed a list of the homologous genes, and then, in a layer-by-layer process, separated their orthology, and paralogy that were established by speciations and recursive polyploidizations, respectively. Compared with the other grasses, the far fewer collinear outparalogous genes within each of three subgenomes of common wheat suggest that homoeologous recombination, and genomic fractionation should have occurred after its formation. In sum, this work contributes to the establishment of an important and timely comparative genomics platform for researchers in the grass community and possibly beyond. Homologous gene list can be found in Supplemental material.
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Affiliation(s)
- Sangrong Sun
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Ruiyan Xia
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Li Wang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Zhenyi Wang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Weina Ge
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Xiaojian Liu
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Yuxian Li
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Yinzhe Liu
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Nanshan Yang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
- *Correspondence: Xiyin Wang
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238
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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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239
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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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240
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Quraishi UM, Pont C, Ain QU, Flores R, Burlot L, Alaux M, Quesneville H, Salse J. Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1843. [PMID: 29184557 PMCID: PMC5694560 DOI: 10.3389/fpls.2017.01843] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/10/2017] [Indexed: 05/18/2023]
Abstract
The high resolution integration of bread wheat genetic and genomic resources accumulated during the last decades offers the opportunity to unveil candidate genes driving major agronomical traits to an unprecedented scale. We combined 27 public quantitative genetic studies and four genetic maps to deliver an exhaustive consensus map consisting of 140,315 molecular markers hosting 221, 73, and 82 Quantitative Trait Loci (QTL) for respectively yield, baking quality, and grain protein content (GPC) related traits. Projection of the consensus genetic map and associated QTLs onto the wheat syntenome made of 99,386 genes ordered on the 21 chromosomes delivered a complete and non-redundant repertoire of 18, 8, 6 metaQTLs for respectively yield, baking quality and GPC, altogether associated to 15,772 genes (delivering 28,630 SNP-based makers) including 37 major candidates. Overall, this study illustrates a translational research approach in transferring information gained from grass relatives to dissect the genomic regions hosting major loci governing key agronomical traits in bread wheat, their flanking markers and associated candidate genes to be now considered as a key resource for breeding programs.
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Affiliation(s)
- Umar M. Quraishi
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Institut National de la Recherche Agronomique, Université Clermont Auvergne, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, France
- *Correspondence: Umar M. Quraishi ;
| | - Caroline Pont
- Institut National de la Recherche Agronomique, Université Clermont Auvergne, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Qurat-ul Ain
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Raphael Flores
- Institut National de la Recherche Agronomique UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, France
| | - Laura Burlot
- Institut National de la Recherche Agronomique UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, France
| | - Michael Alaux
- Institut National de la Recherche Agronomique UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, France
| | - Hadi Quesneville
- Institut National de la Recherche Agronomique UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, France
| | - Jerome Salse
- Institut National de la Recherche Agronomique, Université Clermont Auvergne, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, France
- Jerome Salse
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241
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Bolser DM, Staines DM, Perry E, Kersey PJ. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data. Methods Mol Biol 2017; 1533:1-31. [PMID: 27987162 DOI: 10.1007/978-1-4939-6658-5_1] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for 39 sequenced plant species. Available data includes genome sequence, gene models, functional annotation, and polymorphic loci; for the latter, additional information including population structure, individual genotypes, linkage, and phenotype data is available for some species. Comparative data is also available, including genomic alignments and "gene trees," which show the inferred evolutionary history of each gene family represented in the resource. Access to the data is provided through a genome browser, which incorporates many specialist interfaces for different data types, through a variety of programmatic interfaces, and via a specialist data mining tool supporting rapid filtering and retrieval of bulk data. Genomic data from many non-plant species, including those of plant pathogens, pests, and pollinators, is also available via the same interfaces through other divisions of Ensembl.Ensembl Plants is updated 4-6 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.eu ).
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Affiliation(s)
- Dan M Bolser
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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242
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Zhang J, Yu D, Zhang Y, Liu K, Xu K, Zhang F, Wang J, Tan G, Nie X, Ji Q, Zhao L, Li C. Vacuum and Co-cultivation Agroinfiltration of (Germinated) Seeds Results in Tobacco Rattle Virus (TRV) Mediated Whole-Plant Virus-Induced Gene Silencing (VIGS) in Wheat and Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:393. [PMID: 28382049 PMCID: PMC5360694 DOI: 10.3389/fpls.2017.00393] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/07/2017] [Indexed: 05/06/2023]
Abstract
Tobacco rattle virus (TRV)-mediated virus-induced gene silencing (VIGS) has been frequently used in dicots. Here we show that it can also be used in monocots, by presenting a system involving use of a novel infiltration solution (containing acetosyringone, cysteine, and Tween 20) that enables whole-plant level VIGS of (germinated) seeds in wheat and maize. Using the established system, phytoene desaturase (PDS) genes were successfully silenced, resulting in typical photo-bleaching symptoms in the leaves of treated wheat and maize. In addition, three wheat homoeoalleles of MLO, a key gene repressing defense responses to powdery mildew in wheat, were simultaneously silenced in susceptible wheat with this system, resulting in it becoming resistant to powdery mildew. The system has the advantages generally associated with TRV-mediated VIGS systems (e.g., high-efficiency, mild virus infection symptoms, and effectiveness in different organs). However, it also has the following further advantages: (germinated) seed-stage agroinfiltration; greater rapidity and convenience; whole-plant level gene silencing; adequately stable transformation; and suitability for studying functions of genes involved in seed germination and early plant development stages.
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Affiliation(s)
- Ju Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Deshui Yu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Yi Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Kun Liu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Fuli Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Jian Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Guangxuan Tan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Xianhui Nie
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Qiaohua Ji
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Lu Zhao
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Chengwei Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Technology, Henan Institute of Science and Technology, XinxiangChina
- *Correspondence: Chengwei Li,
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243
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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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244
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Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L. Genes (Basel) 2016; 8:genes8010013. [PMID: 28042823 PMCID: PMC5295008 DOI: 10.3390/genes8010013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/09/2016] [Accepted: 12/20/2016] [Indexed: 11/17/2022] Open
Abstract
RNA editing is an important way to convert cytidine (C) to uridine (U) at specific sites within RNA molecules at a post-transcriptional level in the chloroplasts of higher plants. Although it has been systematically studied in many plants, little is known about RNA editing in the wheat D genome donor Aegilops tauschii L. Here, we investigated the chloroplast RNA editing of Ae. tauschii and compared it with other wheat relatives to trace the evolution of wheat. Through bioinformatics prediction, a total of 34 C-to-U editing sites were identified, 17 of which were validated using RT-PCR product sequencing. Furthermore, 60 sites were found by the RNA-Seq read mapping approach, 24 of which agreed with the prediction and six were validated experimentally. The editing sites were biased toward tCn or nCa trinucleotides and 5′-pyrimidines, which were consistent with the flanking bases of editing sites of other seed plants. Furthermore, the editing events could result in the alteration of the secondary structures and topologies of the corresponding proteins, suggesting that RNA editing might impact the function of target genes. Finally, comparative analysis found some evolutionarily conserved editing sites in wheat and two species-specific sites were also obtained. This study is the first to report on RNA editing in Aegilops tauschii L, which not only sheds light on the evolution of wheat from the point of view of RNA editing, but also lays a foundation for further studies to identify the mechanisms of C-to-U alterations.
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Li L, Sun F, Wu D, Zhen F, Bai G, Gao D, Li T. High-throughput development of genome-wide locus-specific informative SSR markers in wheat. SCIENCE CHINA-LIFE SCIENCES 2016; 60:671-673. [PMID: 28000017 DOI: 10.1007/s11427-016-0252-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 10/31/2016] [Indexed: 11/25/2022]
Affiliation(s)
- Lei Li
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops; Key Laboratory of Plant Functional Genomics of Chinese Ministry of Education; Wheat Research Center, Yangzhou University, Yangzhou, 225009, China
| | - Fayu Sun
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops; Key Laboratory of Plant Functional Genomics of Chinese Ministry of Education; Wheat Research Center, Yangzhou University, Yangzhou, 225009, China
| | - Di Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops; Key Laboratory of Plant Functional Genomics of Chinese Ministry of Education; Wheat Research Center, Yangzhou University, Yangzhou, 225009, China
| | - Fei Zhen
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops; Key Laboratory of Plant Functional Genomics of Chinese Ministry of Education; Wheat Research Center, Yangzhou University, Yangzhou, 225009, China
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.,USDA-ARS Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Derong Gao
- Lixiahe Academy of Agricultural Sciences, Yangzhou, 225000, China
| | - Tao Li
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops; Key Laboratory of Plant Functional Genomics of Chinese Ministry of Education; Wheat Research Center, Yangzhou University, Yangzhou, 225009, China.
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Nesterov MA, Afonnikov DA, Sergeeva EM, Miroshnichenko LA, Bragina MK, Bragin AO, Vasiliev GV, Salina EA. Identification of microsatellite loci based on BAC sequencing data and their physical mapping into the soft wheat 5B chromosome. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s2079059716070078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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247
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Recurrence of Chromosome Rearrangements and Reuse of DNA Breakpoints in the Evolution of the Triticeae Genomes. G3-GENES GENOMES GENETICS 2016; 6:3837-3847. [PMID: 27729435 PMCID: PMC5144955 DOI: 10.1534/g3.116.035089] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Chromosomal rearrangements (CRs) play important roles in karyotype diversity and speciation. While many CR breakpoints have been characterized at the sequence level in yeast, insects, and primates, little is known about the structure of evolutionary CR breakpoints in plant genomes, which are much more dynamic in genome size and sequence organization. Here, we report identification of breakpoints of a translocation between chromosome arms 4L and 5L of Triticeae, which is fixed in several species, including diploid wheat and rye, by comparative mapping and analysis of the draft genome and chromosome survey sequences of the Triticeae species. The wheat translocation joined the ends of breakpoints downstream of a WD40 gene on 4AL and a gene of the PMEI family on 5AL. A basic helix-loop-helix transcription factor gene in 5AL junction was significantly restructured. Rye and wheat share the same position for the 4L breakpoint, but the 5L breakpoint positions are not identical, although very close in these two species, indicating the recurrence of 4L/5L translocations in the Triticeae. Although barley does not carry the translocation, collinearity across the breakpoints was violated by putative inversions and/or transpositions. Alignment with model grass genomes indicated that the translocation breakpoints coincided with ancient inversion junctions in the Triticeae ancestor. Our results show that the 4L/5L translocation breakpoints represent two CR hotspots reused during Triticeae evolution, and support breakpoint reuse as a widespread mechanism in all eukaryotes. The mechanisms of the recurrent translocation and its role in Triticeae evolution are also discussed.
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Transcriptomics analysis of hulless barley during grain development with a focus on starch biosynthesis. Funct Integr Genomics 2016; 17:107-117. [PMID: 27913887 PMCID: PMC5203864 DOI: 10.1007/s10142-016-0537-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 11/09/2016] [Accepted: 11/15/2016] [Indexed: 10/29/2022]
Abstract
Hulless barley, with its unique nutritional value and potential health benefits, has increasingly attracted attentions in recent years. However, the transcription dynamics during hulless barley grain development is not well understood. In the present study, we investigated the transcriptome changes during barley grain development using Illumina paired-end RNA-sequencing. Two datasets of the developing grain transcriptomes from two barley landraces with the differential seed starch synthesis traits were generated, and comparative transcriptome approach in both genotypes was performed. The results showed that 38 differentially expressed genes (DEGs) were found co-modulated in both genotypes during the barley grain development. Of those, the proteins encoded by most of those DGEs were found, such as alpha-amylase-related proteins, lipid-transfer protein, homeodomain leucine zipper (HD-Zip), NUCLEAR FACTOR-Y, subunit B (NF-YBs), as well as MYB transcription factors. More interestingly, two genes Hvulgare_GLEAN_10012370 and Hvulgare_GLEAN_10021199 encoding SuSy, AGPase (Hvulgare_GLEAN_10033640 and Hvulgare_GLEAN_10056301), as well as SBE2b (Hvulgare_GLEAN_10018352) were found to significantly contribute to the regulatory mechanism during grain development in both genotypes. Moreover, six co-expression modules associated with specific biological processes or pathways (M1 to M6) were identified by consensus co-expression network. Significantly enriched pathways of those module genes showed difference in both genotypes. These results will expand our understanding of the complex molecular mechanism of starch synthesis during barley grain development.
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Wiersma AT, Brown LK, Brisco EI, Liu TL, Childs KL, Poland JA, Sehgal SK, Olson EL. Fine mapping of the stem rust resistance gene SrTA10187. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2369-2378. [PMID: 27581540 DOI: 10.1007/s00122-016-2776-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
SrTA10187 was fine-mapped to a 1.1 cM interval, candidate genes were identified in the region of interest, and molecular markers were developed for marker-assisted selection and Sr gene pyramiding. Stem rust (Puccinia graminis f. sp. tritici, Pgt) races belonging to the Ug99 (TTKSK) race group pose a serious threat to global wheat (Triticum aestivum L.) production. To improve Pgt host resistance, the Ug99-effective resistance gene SrTA10187 previously identified in Aegilops tauschii Coss. was introgressed into wheat, and mapped to the short arm of wheat chromosome 6D. In this study, high-resolution mapping of SrTA10187 was done using a population of 1,060 plants. Pgt resistance was screened using race QFCSC. PCR-based SNP and STS markers were developed from genotyping-by-sequencing tags and SNP sequences available in online databases. SrTA10187 segregated as expected in a 3:1 ratio of resistant to susceptible individuals in three out of six BC3F2 families, and was fine-mapped to a 1.1 cM region on wheat chromosome 6DS. Marker context sequence was aligned to the reference Ae. tauschii genome to identify the physical region encompassing SrTA10187. Due to the size of the corresponding region, candidate disease resistance genes could not be identified with confidence. Comparisons with the Ae. tauschii genetic map developed by Luo et al. (PNAS 110(19):7940-7945, 2013) enabled identification of a discrete genetic locus and a BAC minimum tiling path of the region spanning SrTA10187. Annotation of pooled BAC library sequences led to the identification of candidate genes in the region of interest-including a single NB-ARC-LRR gene. The shorter genetic interval and flanking KASP™ and STS markers developed in this study will facilitate marker-assisted selection, gene pyramiding, and positional cloning of SrTA10187.
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Affiliation(s)
- Andrew T Wiersma
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, Room A286, East Lansing, MI, 48824, USA
| | - Linda K Brown
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, Room A286, East Lansing, MI, 48824, USA
| | - Elizabeth I Brisco
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, Room A286, East Lansing, MI, 48824, USA
| | - Tiffany L Liu
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Plant Biology and Center for Genomics-Enabled Plant Science, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA
| | - Jesse A Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, 4011 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA
| | - Sunish K Sehgal
- Department of Plant Science, South Dakota State University, Plant Science-Box 2140C, Brookings, SD, 57007, USA
| | - Eric L Olson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, Room A286, East Lansing, MI, 48824, USA.
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Akpinar BA, Lucas S, Budak H. A large-scale chromosome-specific SNP discovery guideline. Funct Integr Genomics 2016; 17:97-105. [PMID: 27900504 DOI: 10.1007/s10142-016-0536-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/06/2016] [Accepted: 11/09/2016] [Indexed: 12/01/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae. tauschii accessions, including AL8/78, the only genotype for which a draft genome sequence is available at present. We also suggest a workflow to compare SNP positions in homologous regions on the 5D chromosome of Triticum aestivum, bread wheat, to mark single nucleotide variations between these closely related species. Overall, the identified SNPs define a density of 4.49 SNPs per kilobyte, among the highest reported for the genic regions of Ae. tauschii so far. To our knowledge, this study also presents the first chromosome-specific SNP catalog in Ae. tauschii that should facilitate the association of these SNPs with morphological traits on chromosome 5D to be ultimately targeted for wheat improvement.
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Affiliation(s)
- Bala Ani Akpinar
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Orhanlı, 34956, Tuzla, Istanbul, Turkey
| | - Stuart Lucas
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Orhanlı, 34956, Tuzla, Istanbul, Turkey
| | - Hikmet Budak
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Orhanlı, 34956, Tuzla, Istanbul, Turkey. .,Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
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