201
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Huang Q, Li L, Zheng M, Chen F, Long H, Deng G, Pan Z, Liang J, Li Q, Yu M, Zhang H. The Tryptophan decarboxylase 1 Gene From Aegilops variabilis No.1 Regulate the Resistance Against Cereal Cyst Nematode by Altering the Downstream Secondary Metabolite Contents Rather Than Auxin Synthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1297. [PMID: 30233630 PMCID: PMC6132075 DOI: 10.3389/fpls.2018.01297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/17/2018] [Indexed: 05/24/2023]
Abstract
Cereal cyst nematode (CCN, Heterodera avenae) is a most important pathogen of wheat and causes tremendous yield loss annually over the world. Since the lack of resistance materials among wheat cultivars, identification and characterization of the resistance-related genes from the relatives of wheat is a necessary and efficient way. As a close relative of wheat with high resistance against CCN, Aegilops variabilis No.1 is believed to be a valuable source for wheat breeding against this devastating disease. However so far, very few resistance-associated genes have been characterized from this species. In this study, we present that the tryptophan decarboxylase genes from Ae. variabilis No.1 (AeVTDC1 and AeVTDC2) were both induced by CCN juveniles at the early stage of resistance response (30 h post-inoculation), with AeVTDC1 more sensitive to CCN infection than AeVTDC2. Silencing of AeVTDC1 led to compromised immunity to CCN with more CCN intrusion into roots; while overexpression AeVTDC1 in Nicotiana tabacum dramatically enhanced the resistance of plants by reducing the knots formed on roots. Metabolism analysis showed that the contents of secondary metabolites with activity of resistance to varied pathogens correlated with the expression level of AeVTDC1 in both Ae. variabilis No.1 and the transgenic tobacco plants. In addition, the content of IAA was not affected by either silencing or overexpressing of AeVTDC1. Hence, our research provided AeVTDC1 a valuable target that mediates resistance to CCN and root knot nematode (RKN, Meloidogyne naasi) without influencing the auxin biosynthesis.
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Affiliation(s)
- Qiulan Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Lin Li
- School of Basic Medical Sciences, Zunyi Medical University, Zunyi, China
| | - Minghui Zheng
- School of Basic Medical Sciences, Zunyi Medical University, Zunyi, China
| | - Fang Chen
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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202
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Gilbert B, Bettgenhaeuser J, Upadhyaya N, Soliveres M, Singh D, Park RF, Moscou MJ, Ayliffe M. Components of Brachypodium distachyon resistance to nonadapted wheat stripe rust pathogens are simply inherited. PLoS Genet 2018; 14:e1007636. [PMID: 30265668 PMCID: PMC6161853 DOI: 10.1371/journal.pgen.1007636] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/15/2018] [Indexed: 11/19/2022] Open
Abstract
Phytopathogens have a limited range of host plant species that they can successfully parasitise ie. that they are adapted for. Infection of plants by nonadapted pathogens often results in an active resistance response that is relatively poorly characterised because phenotypic variation in this response often does not exist within a plant species, or is too subtle for genetic dissection. In addition, complex polygenic inheritance often underlies these resistance phenotypes and mutagenesis often does not impact upon this resistance, presumably due to genetic or mechanistic redundancy. Here it is demonstrated that phenotypic differences in the resistance response of Brachypodium distachyon to the nonadapted wheat stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst) are genetically tractable and simply inherited. Two dominant loci were identified on B. distachyon chromosome 4 that each reduce attempted Pst colonisation compared with sib and parent lines without these loci. One locus (Yrr1) is effective against diverse Australian Pst isolates and present in two B. distachyon mapping families as a conserved region that was reduced to 5 candidate genes by fine mapping. A second locus, Yrr2, shows Pst race-specificity and encodes a disease resistance gene family typically associated with host plant resistance. These data indicate that some components of resistance to nonadapted pathogens are genetically tractable in some instances and may mechanistically overlap with host plant resistance to avirulent adapted pathogens.
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Affiliation(s)
- Brian Gilbert
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Jan Bettgenhaeuser
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Narayana Upadhyaya
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Melanie Soliveres
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
| | - Davinder Singh
- University of Sydney, Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Robert F. Park
- University of Sydney, Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Matthew J. Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Michael Ayliffe
- CSIRO Agriculture and Food, Clunies Ross Drive, Canberra, ACT, Australia
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203
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Jordan KW, Wang S, He F, Chao S, Lun Y, Paux E, Sourdille P, Sherman J, Akhunova A, Blake NK, Pumphrey MO, Glover K, Dubcovsky J, Talbert L, Akhunov ED. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1039-1054. [PMID: 29952048 PMCID: PMC6174997 DOI: 10.1111/tpj.14009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/21/2018] [Accepted: 06/06/2018] [Indexed: 05/18/2023]
Abstract
Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence-based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome-wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans-acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans-acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low-recombining pericentromeric regions of chromosomes.
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Affiliation(s)
| | - Shichen Wang
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
TEES‐AgriLife Center for Bioinformatics and Genomic Systems EngineeringTexas A&M University101 Gateway, Suite ACollege StationTX77845USA
| | - Fei He
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Shiaoman Chao
- USDA‐ARS Cereal Crops Research Unit1605 Albrecht Blvd NFargoNDUSA
| | - Yanni Lun
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
TEES‐AgriLife Center for Bioinformatics and Genomic Systems EngineeringTexas A&M University101 Gateway, Suite ACollege StationTX77845USA
| | - Etienne Paux
- INRA GDEC Auvergne‐Rhône‐AlpesClermont‐FerrandFrance
| | | | | | - Alina Akhunova
- Integrated Genomics FacilityKansas State UniversityManhattanKSUSA
| | | | | | - Karl Glover
- Department of Agronomy, Horticulture and Plant ScienceSouth Dakota State UniversityBrookingsSDUSA
| | - Jorge Dubcovsky
- Department of Plant SciencesUniversity of CaliforniaDavis, DavisCAUSA
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
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204
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Keller B, Wicker T, Krattinger SG. Advances in Wheat and Pathogen Genomics: Implications for Disease Control. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:67-87. [PMID: 30149791 DOI: 10.1146/annurev-phyto-080516-035419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The gene pool of wheat and its wild and domesticated relatives contains a plethora of resistance genes that can be exploited to make wheat more resilient to pathogens. Only a few of these genes have been isolated and studied at the molecular level. In recent years, we have seen a shift from classical breeding to genomics-assisted breeding, which makes use of the enormous advancements in DNA sequencing and high-throughput molecular marker technologies for wheat improvement. These genomic advancements have the potential to transform wheat breeding in the near future and to significantly increase the speed and precision at which new cultivars can be bred. This review highlights the genomic improvements that have been made in wheat and its pathogens over the past years and discusses their implications for disease-resistance breeding.
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Affiliation(s)
- Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia;
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205
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Kumar A, Kaur G, Goel P, Bhati KK, Kaur M, Shukla V, Pandey AK. Genome-wide analysis of oligopeptide transporters and detailed characterization of yellow stripe transporter genes in hexaploid wheat. Funct Integr Genomics 2018; 19:75-90. [PMID: 30120602 DOI: 10.1007/s10142-018-0629-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 06/20/2018] [Accepted: 07/20/2018] [Indexed: 01/11/2023]
Abstract
Oligopeptide transporters (OPT) are integral cell membrane proteins that play a critical role in the transport of small peptides, secondary amino acids, glutathione conjugates, and mineral uptake. In the present study, 67 putative wheat yellow stripe-like transporter (YSL) proteins belonging to the subfamily of OPT transporters were identified. Phylogeny analysis resulted in the distribution of wheat YSLs into four discrete clades. The highest number of YSLs was present on the A genome and the chromosome 2 of hexaploid wheat. The identified wheat YSL genes showed differential expression in different tissues and during grain development suggesting the importance of this subfamily. Gene expression pattern of TaYSLs during iron starvation experiments suggested an early high transcript accumulation of TaYS1A, TaYS1B, TaYSL3, TaYSL5, and TaYSL6 in roots. In contrast, delayed expression was observed in shoots for TaYS1A, TaYS1B, TaYSL5, TaYSL12, and TaYSL19 as compared to control. Further, their expression under biotic and abiotic response emphasized their alternative functions during the plant growth and development. In conclusion, this work is the first comprehensive study of wheat YSL transporters and would be an important resource for prioritizing genes towards wheat biofortification.
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Affiliation(s)
- Anil Kumar
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Gazaldeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Parul Goel
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India
| | - Kaushal Kumar Bhati
- Copenhagen Plant Science Centre, PLEN, University of Copenhagen, Thorvaldsensvej, 40, 1871, Frederiksberg C, Denmark
| | - Mandeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Vishnu Shukla
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India.
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206
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Alaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, Paux E, Eversole K, Adam-Blondon AF, Quesneville H. Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biol 2018; 19:111. [PMID: 30115101 PMCID: PMC6097284 DOI: 10.1186/s13059-018-1491-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/23/2018] [Indexed: 01/24/2023] Open
Abstract
The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.
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Affiliation(s)
- Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France.
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge, CB23 1HE, UK
| | | | - Raphaël Flores
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | | | - Cyril Pommier
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Nacer Mohellibi
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Sophie Durand
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Erik Kimmel
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Célia Michotey
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Claire Guerche
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Mikaël Loaec
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Mathilde Lainé
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Delphine Steinbach
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
- Present address: GQE-Le Moulon UMR 320, INRA, Université Paris-Sud, Université Paris-Saclay, CNRS, AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Frédéric Choulet
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Hélène Rimbert
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Philippe Leroy
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Nicolas Guilhot
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Jérôme Salse
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Catherine Feuillet
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
- Present address: Inari Agriculture, 200 Sydney Street, Cambridge, MA, 02139, USA
| | - Etienne Paux
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, Maryland, 20816, USA
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207
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Wicker T, Gundlach H, Spannagl M, Uauy C, Borrill P, Ramírez-González RH, De Oliveira R, Mayer KFX, Paux E, Choulet F. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol 2018; 19:103. [PMID: 30115100 PMCID: PMC6097303 DOI: 10.1186/s13059-018-1479-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/11/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. RESULTS The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid. CONCLUSIONS Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.
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Affiliation(s)
- Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Spannagl
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Philippa Borrill
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | | | - Romain De Oliveira
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France
| | - Klaus F X Mayer
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, Munich, Germany
| | - Etienne Paux
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France
| | - Frédéric Choulet
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France.
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208
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Thind AK, Wicker T, Müller T, Ackermann PM, Steuernagel B, Wulff BBH, Spannagl M, Twardziok SO, Felder M, Lux T, Mayer KFX, Keller B, Krattinger SG. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars. Genome Biol 2018; 19:104. [PMID: 30115097 PMCID: PMC6097286 DOI: 10.1186/s13059-018-1477-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/10/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the dynamics of wheat genomes on a megabase scale. RESULTS Here, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes-the old landrace Chinese Spring and the elite Swiss spring wheat line 'CH Campala Lr22a'. Both chromosomes were assembled into megabase-sized scaffolds. There is a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations reveals four large indels of more than 100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the molecular mechanisms that caused these indels. Three of the large indels affect copy number of NLRs, a gene family involved in plant immunity. Analysis of SNP density reveals four haploblocks of 4, 8, 9 and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Gene content across the two chromosomes was highly conserved. Ninety-nine percent of the genic sequences were present in both genotypes and the fraction of unique genes ranged from 0.4 to 0.7%. CONCLUSIONS This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations and gene content. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.
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Affiliation(s)
- Anupriya Kaur Thind
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | - Thomas Müller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | - Patrick M Ackermann
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | | | | | | | | | | | - Thomas Lux
- Helmholtz Zentrum Munich, Munich, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum Munich, Munich, Germany
- School of Life Sciences, Technical University Munich, Munich, Germany
- College of Science, King Saud University, Riad, Kingdom of Saudi Arabia
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland.
- King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
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209
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Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnère G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin AA, Stein N, Mascher M, Himmelbach A, Choulet F, Keeble-Gagnère G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin AA, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V, Choulet F, Keeble-Gagnère G, Mascher M, Josselin AA, Rogers J, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnère G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Šimková H, Wicker T, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L, Appels R, Rimbert H, Choulet F, Juhász A, Keeble-Gagnère G, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnère G, Mayer KFX, Wicker T, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M, Lang D, Spannagl M, Appels R, Fischer I, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D, Rogers J, Jacobs J, Alaux M, Appels R, Bartoš J, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen OA, Šimková H, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J, Tiwari V, Gill B, Paux E, Poland J, Doležel J, Číhalíková J, Šimková H, Toegelová H, Vrána J, Sourdille P, Darrier B, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G, Small I, Melonek J, Zhou R, Juhász A, Belova T, Appels R, Olsen OA, Kanyuka K, King R, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D, Rohde A, Golds T, Doležel J, Čížková J, Tibbits J, Budak H, Akpinar BA, Biyiklioglu S, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A, Doležel J, Šimková H, Číhalíková J, Kubaláková M, Šafář J, Vrána J, Berges H, Bellec A, Vautrin S, Alaux M, Alfama F, Adam-Blondon AF, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T, Choulet F, Paux E, Alberti A, Aury JM, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Gill B, Kaur G, Luo M, Sehgal S, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S, Gill B, Kaur G, Luo M, Sehgal S, Bartoš J, Holušová K, Plíhal O, Clark MD, Heavens D, Kettleborough G, Wright J, Valárik M, Abrouk M, Balcárková B, Holušová K, Hu Y, Luo M, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J, Appels R, Hayden M, Keeble-Gagnère G, Rigault P, Tibbits J, Olsen OA, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B, Šimková H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelová H, Tulpová Z, Visendi P, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Šimková H, Small I, Spannagl M, Swarbreck D, Uauy C. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 2018; 361:361/6403/eaar7191. [PMID: 30115783 DOI: 10.1126/science.aar7191] [Citation(s) in RCA: 1514] [Impact Index Per Article: 252.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/11/2018] [Indexed: 12/14/2022]
Abstract
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
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Affiliation(s)
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. .,Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Catherine Feuillet
- Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | | | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. .,Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Jesse Poland
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - Gil Ronen
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | | | - Curtis Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Gil Ronen
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Omer Barad
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Kobi Baruch
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Gil Ben-Zvi
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Ambre-Aurore Josselin
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - François Balfourier
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Juan Gutierrez-Gonzalez
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Matthew Hayden
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Ambre-Aurore Josselin
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - ChuShin Koh
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Raj K Pasam
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Philippe Rigault
- GYDLE, Suite 220, 1135 Grande Allée, Ouest, Québec, QC G1S 1E7, Canada
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Vijay Tiwari
- Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ambre-Aurore Josselin
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | | | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Georg Haberer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Danara Ormanbekova
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Verena Prade
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Hélène Rimbert
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Marius Felder
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Nicolas Guilhot
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Georg Haberer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Jens Keilwagen
- Julius Kühn-Institut, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Philippe Leroy
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Thomas Lux
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Sven Twardziok
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Luca Venturini
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Hélène Rimbert
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Angéla Juhász
- Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia.,Agricultural Institute, MTA Centre for Agricultural Research, Applied Genomics Department, 2 Brunszvik Street, Martonvásár H 2462, Hungary
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Georg Haberer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Iris Fischer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Cristobal Uauy
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Philippa Borrill
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Dominique Arnaud
- Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Smahane Chalabi
- Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Boulos Chalhoub
- Monsanto SAS, 28000 Boissay, France.,Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Aron Cory
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Raju Datla
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Mark W Davey
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Matthew Hayden
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - John Jacobs
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Vijay Tiwari
- Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | - Fred van Ex
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Brande B H Wulff
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Aron Cory
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | | | - Moussa Benhamed
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Abdelhafid Bendahmane
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | - Lorenzo Concia
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | - David Latrasse
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | | | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - John Jacobs
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Arnaud Bellec
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Hélène Berges
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Catherine Feuillet
- Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Abraham Korol
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | | | - Odd-Arne Olsen
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Kuldeep Singh
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | - Sonia Vautrin
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | | | - Abraham Korol
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Tzion Fahima
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | | | - Dina Raats
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | | | - Vijay Tiwari
- Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jesse Poland
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | | | - Benoit Darrier
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Iris Fischer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Danara Ormanbekova
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy
| | - Verena Prade
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Delfina Barabaschi
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy
| | | | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Consejo Superior de Investigaciones Científicas, Alameda del Obispo s/n, 14004 Córdoba, Spain
| | - Sergio Galvez
- Universidad de Málaga, Lenguajes y Ciencias de la Computación, Campus de Teatinos, 29071 Málaga, Spain
| | - Hikmet Budak
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | | | | | | | - Kamil Witek
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Brande B H Wulff
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Guotai Yu
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Ian Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Joanna Melonek
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Ruonan Zhou
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | | | - Angéla Juhász
- Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia.,Agricultural Institute, MTA Centre for Agricultural Research, Applied Genomics Department, 2 Brunszvik Street, Martonvásár H 2462, Hungary
| | - Tatiana Belova
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Odd-Arne Olsen
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | | | - Kostya Kanyuka
- Rothamsted Research, Biointeractions and Crop Protection, West Common, Harpenden AL5 2JQ, UK
| | - Robert King
- Rothamsted Research, Computational and Analytical Sciences, West Common, Harpenden AL5 2JQ, UK
| | | | - Kirby Nilsen
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Sean Walkowiak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Richard Cuthbert
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Box 1030, Swift Current, SK S9H 3X2, Canada
| | - Raju Datla
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Ron Knox
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Box 1030, Swift Current, SK S9H 3X2, Canada
| | - Krysta Wiebe
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Daoquan Xiang
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | | | - Antje Rohde
- Bayer CropScience, Breeding and Trait Development, Technologiepark 38, 9052 Gent, Belgium
| | - Timothy Golds
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Hikmet Budak
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Bala Ani Akpinar
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Sezgi Biyiklioglu
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | | | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Jesse Poland
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Liangliang Gao
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Juan Gutierrez-Gonzalez
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Amidou N'Daiye
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | - Hélène Berges
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Arnaud Bellec
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Sonia Vautrin
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | | | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | | | - Raphael Flores
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Claire Guerche
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | - Mikaël Loaec
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | | | | | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Andrew G Sharpe
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.,University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | | | - Hikmet Budak
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Janet Condie
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Jennifer Ens
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - ChuShin Koh
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Ron Maclachlan
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Yifang Tan
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Adriana Alberti
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - François Balfourier
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Valérie Barbe
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Arnaud Couloux
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Karine Labadie
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Sophie Mangenot
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Patrick Wincker
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France.,CNRS, UMR 8030, CP5706, 91057 Evry, France.,Université d'Evry, UMR 8030, CP5706, 91057 Evry, France
| | | | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Gaganpreet Kaur
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Sunish Sehgal
- Agronomy Horticulture and Plant Science, South Dakota State University, 2108 Jackrabbit Drive, Brookings, SD 57006, USA
| | | | - Kuldeep Singh
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Parveen Chhuneja
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Om Prakash Gupta
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Suruchi Jindal
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Parampreet Kaur
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Palvi Malik
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Priti Sharma
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Bharat Yadav
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | | | - Nagendra K Singh
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - JitendraP Khurana
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Chanderkant Chaudhary
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Paramjit Khurana
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Vinod Kumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Ajay Mahato
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Saloni Mathur
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Amitha Sevanthi
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Naveen Sharma
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Ram Sewak Tomar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | | | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - John Jacobs
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Arnaud Bellec
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Hélène Berges
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Catherine Feuillet
- Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Abraham Korol
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | | | - Sonia Vautrin
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | | | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Gaganpreet Kaur
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Sunish Sehgal
- Agronomy Horticulture and Plant Science, South Dakota State University, 2108 Jackrabbit Drive, Brookings, SD 57006, USA
| | | | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Ondřej Plíhal
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | | | - Matthew D Clark
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK.,Department of Lifesciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Darren Heavens
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Jon Wright
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Barbora Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Yuqin Hu
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | | | - Elena Salina
- The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikolai Ravin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia.,Faculty of Biology, Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia
| | - Konstantin Skryabin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia.,Faculty of Biology, Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia
| | - Alexey Beletsky
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Vitaly Kadnikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Andrey Mardanov
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Michail Nesterov
- The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Andrey Rakitin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Ekaterina Sergeeva
- The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | | | - Hirokazu Handa
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Satoshi Katagiri
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tsuyoshi Tanaka
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jianzhong Wu
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Matthew Hayden
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Philippe Rigault
- GYDLE, Suite 220, 1135 Grande Allée, Ouest, Québec, QC G1S 1E7, Canada
| | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Odd-Arne Olsen
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Tatiana Belova
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | | | - Min Jiumeng
- BGI-Shenzhen, BGI Genomics, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Karl Kugler
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Matthias Pfeifer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Simen Sandve
- Faculty of Bioscience, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Xu Xun
- BGI-Shenzhen, BGI Genomics, Yantian District, Shenzhen 518083, Guangdong, China
| | - Bujie Zhan
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | | | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Satomi Hayashi
- Queensland University of Technology, Earth, Environmental and Biological Sciences, Brisbane, QLD 4001, Australia
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Zuzana Tulpová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Paul Visendi
- University of Greenwich, Natural Resources Institute, Central Avenue, Chatham, Kent ME4 4TB, UK
| | | | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Xianghong Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Wei Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Le Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | | | - Philippa Borrill
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Sergio Galvez
- Universidad de Málaga, Lenguajes y Ciencias de la Computación, Campus de Teatinos, 29071 Málaga, Spain
| | | | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Thomas Lux
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Danara Ormanbekova
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy
| | - Verena Prade
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Cristobal Uauy
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Luca Venturini
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. .,Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - Philippa Borrill
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Consejo Superior de Investigaciones Científicas, Alameda del Obispo s/n, 14004 Córdoba, Spain
| | - Kostya Kanyuka
- Rothamsted Research, Biointeractions and Crop Protection, West Common, Harpenden AL5 2JQ, UK
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Kirby Nilsen
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | | | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Ian Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Cristobal Uauy
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
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210
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Zhu GR, Yan X, Zhu D, Deng X, Wu JS, Xia J, Yan YM. Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. J Proteomics 2018; 185:8-24. [DOI: 10.1016/j.jprot.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023]
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211
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Wang W, Chen D, Zhang X, Liu D, Cheng Y, Shen F. Role of plant respiratory burst oxidase homologs in stress responses. Free Radic Res 2018; 52:826-839. [DOI: 10.1080/10715762.2018.1473572] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Dongdong Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Dan Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Yingying Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, PR China
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212
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Singh K, Singh J, Jindal S, Sidhu G, Dhaliwal A, Gill K. Structural and functional evolution of an auxin efflux carrier PIN1 and its functional characterization in common wheat. Funct Integr Genomics 2018; 19:29-41. [PMID: 29968001 DOI: 10.1007/s10142-018-0625-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 10/28/2022]
Abstract
Particularly PIN1, PIN protein-mediated rate-limiting auxin distribution plays a critical role in plant differentiation. Although well-characterized in Arabidopsis, little is known about the structural and functional relationship of the PIN1 gene among other plants. Here, we report that the gene structure remained conserved among bryophytes and angiosperms while the gene size varied by ~ 17%. Although the positions were conserved, highly variable intron phase suggests preference for specific regions in the gene sequence for independent events of intron insertion. Significant variation was observed across gene length for insertions and deletions that were mainly localized to the exonic regions flanking intron 1, possibly demarcating the sequences prone to deletions/duplications. The N and C-terminals showed a higher protein sequence similarity (~ 80%) compared to the central hydrophilic loop (~ 26%). In addition to the signature domains and motifs, we identified four novel uncharacterized motifs in the central divergent loop of PIN1 protein. Three different homo-loci, one each on chromosome groups 4, 6, and 7, were identified in wheat each showing dramatically different expression patterns during different plant developmental stages. Virus-induced gene silencing of the TaPIN1 gene resulted up to 26% reduction in plant height. Because of its direct role in controlling plant height along with a higher expression during stem elongation, the TaPIN1 gene can be manipulated to regulate plant height.
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Affiliation(s)
- Kanwardeep Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.,Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Johar Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Suruchi Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gaganjot Sidhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | | | - Kulvinder Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
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213
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You FM, Xiao J, Li P, Yao Z, Jia G, He L, Zhu T, Luo MC, Wang X, Deyholos MK, Cloutier S. Chromosome-scale pseudomolecules refined by optical, physical and genetic maps in flax. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:371-384. [PMID: 29681136 DOI: 10.1111/tpj.13944] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 05/19/2023]
Abstract
Genomes of varying sizes have been sequenced with next-generation sequencing platforms. However, most reference sequences include draft unordered scaffolds containing chimeras caused by mis-scaffolding. A BioNano genome (BNG) optical map was constructed to improve the previously sequenced flax genome (Linum usitatissimum L., 2n = 30, about 373 Mb), which consisted of 3852 scaffolds larger than 1 kb and totalling 300.6 Mb. The high-resolution BNG map of cv. CDC Bethune totalled 317 Mb and consisted of 251 BNG contigs with an N50 of 2.15 Mb. A total of 622 scaffolds (286.6 Mb, 94.9%) aligned to 211 BNG contigs (298.6 Mb, 94.2%). Of those, 99 scaffolds, diagnosed to contain assembly errors, were refined into 225 new scaffolds. Using the newly refined scaffold sequences and the validated bacterial artificial chromosome-based physical map of CDC Bethune, the 211 BNG contigs were scaffolded into 94 super-BNG contigs (N50 of 6.64 Mb) that were further assigned to the 15 flax chromosomes using the genetic map. The pseudomolecules total about 316 Mb, with individual chromosomes of 15.6 to 29.4 Mb, and cover 97% of the annotated genes. Evidence from the chromosome-scale pseudomolecules suggests that flax has undergone palaeopolyploidization and mesopolyploidization events, followed by rearrangements and deletions or fusion of chromosome arms from an ancient progenitor with a haploid chromosome number of eight.
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Affiliation(s)
- Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jin Xiao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
- State Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Gaofeng Jia
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Liqiang He
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Xiue Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | | | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
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214
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Hurel A, Phillips D, Vrielynck N, Mézard C, Grelon M, Christophorou N. A cytological approach to studying meiotic recombination and chromosome dynamics in Arabidopsis thaliana male meiocytes in three dimensions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:385-396. [PMID: 29681056 DOI: 10.1111/tpj.13942] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/28/2018] [Accepted: 04/05/2018] [Indexed: 05/18/2023]
Abstract
During meiotic prophase I chromosomes undergo dramatic conformational changes that accompany chromosome condensation, pairing and recombination between homologs. These changes include the anchoring of telomeres to the nuclear envelope and their clustering to form a bouquet. In plants, these events have been studied and illustrated in intact meiocytes of species with large genomes. Arabidopsis thaliana is an excellent genetic model in which major molecular pathways that control synapsis and recombination between homologs have been uncovered. Yet the study of chromosome dynamics is hampered by current cytological methods that disrupt the three-dimensional (3D) architecture of the nucleus. Here we set up a protocol to preserve the 3D configuration of A. thaliana meiocytes. We showed that this technique is compatible with the use of a variety of antibodies that label structural and recombination proteins and were able to highlight the presence of clustered synapsis initiation centers at the nuclear periphery. By using fluorescence in situ hybridization we also studied the behavior of chromosomes during pre-meiotic G2 and prophase I, revealing the existence of a telomere bouquet during A. thaliana male meiosis. In addition we showed that the number of telomeres in a bouquet and its volume vary greatly, thus revealing the complexity of telomere behavior during meiotic prophase I. Finally, by using probes that label subtelomeric regions of individual chromosomes, we revealed differential localization behaviors of chromosome ends. Our protocol opens new areas of research for investigating chromosome dynamics in A. thaliana meiocytes.
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Affiliation(s)
- Aurélie Hurel
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Dylan Phillips
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3DA, UK
| | - Nathalie Vrielynck
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Christine Mézard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Nicolas Christophorou
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
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215
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Zhang Y, Zhao H, Zhou S, He Y, Luo Q, Zhang F, Qiu D, Feng J, Wei Q, Chen L, Chen M, Chang J, Yang G, He G. Expression of TaGF14b, a 14-3-3 adaptor protein gene from wheat, enhances drought and salt tolerance in transgenic tobacco. PLANTA 2018; 248:117-137. [PMID: 29616395 DOI: 10.1007/s00425-018-2887-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/29/2018] [Indexed: 05/22/2023]
Abstract
MAIN CONCLUSION TaGF14b enhances tolerance to multiple stresses through ABA signaling pathway by altering physiological and biochemical processes, including ROS-scavenging system, stomatal closure, compatible osmolytes, and stress-related gene expressions in tobaccos. The 14-3-3 proteins are involved in plant growth, development, and in responding to abiotic stresses. However, the precise functions of 14-3-3s in responding to drought and salt stresses remained unclear, especially in wheat. In this study, a 14-3-3 gene from wheat, designated TaGF14b, was cloned and characterized. TaGF14b was upregulated by polyethylene glycol 6000, sodium chloride, hydrogen peroxide, and abscisic acid (ABA) treatments. Ectopic expression of TaGF14b in tobacco conferred enhanced tolerance to drought and salt stresses. Transgenic tobaccos had longer root, better growth status, and higher relative water content, survival rate, photosynthetic rate, and water use efficiency than control plants under drought and salt stresses. The contribution of TaGF14b to drought and salt tolerance relies on the regulations of ABA biosynthesis and ABA signaling, as well as stomatal closure and stress-related gene expressions. Moreover, TaGF14b expression could significantly enhance the reactive oxygen species (ROS) scavenging system to ameliorate oxidative damage to cells. In addition, TaGF14b increased tolerance to osmotic stress evoked by drought and salinity through modifying water conservation and compatible osmolytes in plants. In conclusion, TaGF14b enhances tolerance to multiple abiotic stresses through the ABA signaling pathway in transgenic tobaccos by altering physiological and biochemical processes.
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Affiliation(s)
- Yang Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongyan Zhao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shiyi Zhou
- Hubei Key Laboratory of Purification and Application of Plant Anticancer Active Ingredients, School of Chemistry and Life Sciences, Hubei University of Education, Wuhan, 430205, China
| | - Yuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qingchen Luo
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fan Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Ding Qiu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jialu Feng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qiuhui Wei
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lihong Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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216
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Morata J, Tormo M, Alexiou KG, Vives C, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM. The Evolutionary Consequences of Transposon-Related Pericentromer Expansion in Melon. Genome Biol Evol 2018; 10:1584-1595. [PMID: 29901717 PMCID: PMC6009578 DOI: 10.1093/gbe/evy115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) are a major driver of plant genome evolution. A part from being a rich source of new genes and regulatory sequences, TEs can also affect plant genome evolution by modifying genome size and shaping chromosome structure. TEs tend to concentrate in heterochromatic pericentromeric regions and their proliferation may expand these regions. Here, we show that after the split of melon and cucumber, TEs have expanded the pericentromeric regions of melon chromosomes that, probably as a consequence, show a very low recombination frequency. In contrast, TEs have not proliferated to a high extent in cucumber, which has small TE-dense pericentromeric regions and shows a relatively constant recombination rate along chromosomes. These differences in chromosome structure also translate in differences in gene nucleotide diversity. Although gene nucleotide diversity is essentially constant along cucumber chromosomes, melon chromosomes show a bimodal pattern of genetic variability, with a gene-poor region where variability is negatively correlated with gene density. Interestingly, genes are not homogeneously distributed in melon, and the high variable low-recombining pericentromeric regions show a higher concentration of melon-specific genes whereas genes shared with cucumber and other plants are essentially found in gene-rich chromosomal arms. The results presented here suggest that melon pericentromeric regions may allow gene sequences to evolve more freely than in other chromosomal compartments which may allow new ORFs to arise and eventually be selected. These results show that TEs can drastically change the structure of chromosomes creating different chromosomal compartments imposing different constraints for gene evolution.
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Affiliation(s)
- Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Marc Tormo
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Konstantinos G Alexiou
- Institut de Recerca i Tecnologia Agroalimentàries, Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Cristina Vives
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Sebastián E Ramos-Onsins
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Jordi Garcia-Mas
- Institut de Recerca i Tecnologia Agroalimentàries, Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
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217
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Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics. BIOLOGY 2018; 7:biology7020032. [PMID: 29799487 PMCID: PMC6022998 DOI: 10.3390/biology7020032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/16/2018] [Accepted: 05/22/2018] [Indexed: 12/22/2022]
Abstract
One particular class of Transposable Elements (TEs), called Long Terminal Repeats (LTRs), retrotransposons, comprises the most abundant mobile elements in plant genomes. Their copy number can vary from several hundreds to up to a few million copies per genome, deeply affecting genome organization and function. The detailed classification of LTR retrotransposons is an essential step to precisely understand their effect at the genome level, but remains challenging in large-sized genomes, requiring the use of optimized bioinformatics tools that can take advantage of supercomputers. Here, we propose a new tool: Inpactor, a parallel and scalable pipeline designed to classify LTR retrotransposons, to identify autonomous and non-autonomous elements, to perform RT-based phylogenetic trees and to analyze their insertion times using High Performance Computing (HPC) techniques. Inpactor was tested on the classification and annotation of LTR retrotransposons in pineapple, a recently-sequenced genome. The pineapple genome assembly comprises 44% of transposable elements, of which 23% were classified as LTR retrotransposons. Exceptionally, 16.4% of the pineapple genome assembly corresponded to only one lineage of the Gypsy superfamily: Del, suggesting that this particular lineage has undergone a significant increase in its copy numbers. As demonstrated for the pineapple genome, Inpactor provides comprehensive data of LTR retrotransposons’ classification and dynamics, allowing a fine understanding of their contribution to genome structure and evolution. Inpactor is available at https://github.com/simonorozcoarias/Inpactor.
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218
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Ling HQ, Ma B, Shi X, Liu H, Dong L, Sun H, Cao Y, Gao Q, Zheng S, Li Y, Yu Y, Du H, Qi M, Li Y, Lu H, Yu H, Cui Y, Wang N, Chen C, Wu H, Zhao Y, Zhang J, Li Y, Zhou W, Zhang B, Hu W, van Eijk MJT, Tang J, Witsenboer HMA, Zhao S, Li Z, Zhang A, Wang D, Liang C. Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 2018. [PMID: 29743678 DOI: 10.1038/s41586‐018‐0108‐0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Triticum urartu (diploid, AA) is the progenitor of the A subgenome of tetraploid (Triticum turgidum, AABB) and hexaploid (Triticum aestivum, AABBDD) wheat1,2. Genomic studies of T. urartu have been useful for investigating the structure, function and evolution of polyploid wheat genomes. Here we report the generation of a high-quality genome sequence of T. urartu by combining bacterial artificial chromosome (BAC)-by-BAC sequencing, single molecule real-time whole-genome shotgun sequencing 3 , linked reads and optical mapping4,5. We assembled seven chromosome-scale pseudomolecules and identified protein-coding genes, and we suggest a model for the evolution of T. urartu chromosomes. Comparative analyses with genomes of other grasses showed gene loss and amplification in the numbers of transposable elements in the T. urartu genome. Population genomics analysis of 147 T. urartu accessions from across the Fertile Crescent showed clustering of three groups, with differences in altitude and biostress, such as powdery mildew disease. The T. urartu genome assembly provides a valuable resource for studying genetic variation in wheat and related grasses, and promises to facilitate the discovery of genes that could be useful for wheat improvement.
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Affiliation(s)
- Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Bin Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hui Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hua Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yinghao Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ye Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ying Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huilong Du
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ming Qi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongwei Lu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hua Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chunlin Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Juncheng Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenjuan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bairu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Weijuan Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | | | | | | | | | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Chengzhi Liang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
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219
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Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 2018; 557:424-428. [PMID: 29743678 PMCID: PMC6784869 DOI: 10.1038/s41586-018-0108-0] [Citation(s) in RCA: 272] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Triticum urartu (diploid, AA) is the progenitor of the A subgenome of tetraploid (Triticum turgidum, AABB) and hexaploid (Triticum aestivum, AABBDD) wheat1,2. Genomic studies of T. urartu have been useful for investigating the structure, function and evolution of polyploid wheat genomes. Here we report the generation of a high-quality genome sequence of T. urartu by combining bacterial artificial chromosome (BAC)-by-BAC sequencing, single molecule real-time whole-genome shotgun sequencing3, linked reads and optical mapping4,5. We assembled seven chromosome-scale pseudomolecules and identified protein-coding genes, and we suggest a model for the evolution of T. urartu chromosomes. Comparative analyses with genomes of other grasses showed gene loss and amplification in the numbers of transposable elements in the T. urartu genome. Population genomics analysis of 147 T. urartu accessions from across the Fertile Crescent showed clustering of three groups, with differences in altitude and biostress, such as powdery mildew disease. The T. urartu genome assembly provides a valuable resource for studying genetic variation in wheat and related grasses, and promises to facilitate the discovery of genes that could be useful for wheat improvement. The genome sequence of Triticum urartu, the progenitor of the A subgenome of hexaploid wheat, provides insight into genome duplication during grass evolution.
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220
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Liu M, Zhao Q, Qi F, Stiller J, Tang S, Miao J, Vrána J, Holušová K, Liu D, Doležel J, Manners JM, Han B, Liu C. Sequence divergence between spelt and common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1125-1132. [PMID: 29427242 DOI: 10.1007/s00122-018-3064-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Sequence comparison between spelt and common wheat reveals that the former has huge potential in enriching the genetic variation of the latter. Genetic variation is the foundation of crop improvement. By comparing genome sequences of a Triticum spelta accession and one of its derived hexaploid lines with the sequences of the international reference genotype Chinese Spring, we detected variants more than tenfold higher than those present among common wheat (T. aestivum L) genotypes. Furthermore, different from the typical 'V-shaped' pattern of variant distribution often observed along wheat chromosomes, the sequence variation detected in this study was more evenly distributed along the 3B chromosome. This was also the case between T. spelta and the wild emmer genome. Genetic analysis showed that T. spelta and common wheat formed discrete groups. These results showed that, although it is believed that the spelt and common wheat are evolutionarily closely related and belong to the same species, a significant sequence divergence exists between them. Thus, the values of T. spelta in enriching the genetic variation of common wheat can be huge.
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Affiliation(s)
- Miao Liu
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Jinjiang District, Chengdu, 610066, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Qiang Zhao
- National Center for Gene Research, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Feng Qi
- National Center for Gene Research, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Jiri Stiller
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Shican Tang
- National Center for Gene Research, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Jiashun Miao
- National Center for Gene Research, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - John M Manners
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Bin Han
- National Center for Gene Research, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
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221
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Zhang G, Hua Z. Genome comparison implies the role of Wsm2 in membrane trafficking and protein degradation. PeerJ 2018; 6:e4678. [PMID: 29707435 PMCID: PMC5918131 DOI: 10.7717/peerj.4678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/09/2018] [Indexed: 02/01/2023] Open
Abstract
Wheat streak mosaic virus (WSMV) causes streak mosaic disease in wheat (Triticum aestivum L.) and has been an important constraint limiting wheat production in many regions around the world. Wsm2 is the only resistance gene discovered in wheat genome and has been located in a short genomic region of its chromosome 3B. However, the sequence nature and the biological function of Wsm2 remain unknown due to the difficulty of genetic manipulation in wheat. In this study, we tested WSMV infectivity among wheat and its two closely related grass species, rice (Oryza sativa) and Brachypodium distachyon. Based on the phenotypic result and previous genomic studies, we developed a novel bioinformatics pipeline for interpreting a potential biological function of Wsm2 and its ancestor locus in wheat. In the WSMV resistance tests, we found that rice has a WMSV resistance gene while Brachypodium does not, which allowed us to hypothesize the presence of a Wsm2 ortholog in rice. Our OrthoMCL analysis of protein coding genes on wheat chromosome 3B and its syntenic chromosomes in rice and Brachypodium discovered 4,035 OrthoMCL groups as preliminary candidates of Wsm2 orthologs. Given that Wsm2 is likely duplicated through an intrachromosomal illegitimate recombination and that Wsm2 is dominant, we inferred that this new WSMV-resistance gene acquired an activation domain, lost an inhibition domain, or gained high expression compared to its ancestor locus. Through comparison, we identified that 67, 16, and 10 out of 4,035 OrthoMCL orthologous groups contain a rice member with 25% shorter or longer in length, or 10 fold more expression, respectively, than those from wheat and Brachypodium. Taken together, we predicted a total of 93 good candidates for a Wsm2 ancestor locus. All of these 93 candidates are not tightly linked with Wsm2, indicative of the role of illegitimate recombination in the birth of Wsm2. Further sequence analysis suggests that the protein products of Wsm2 may combat WSMV disease through a molecular mechanism involving protein degradation and/or membrane trafficking. The 93 putative Wsm2 ancestor loci discovered in this study could serve as good candidates for future genetic isolation of the true Wsm2 locus.
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Affiliation(s)
- Guorong Zhang
- Agricultural Research Center-Hays, Kansas State University, Hays, KS, United States of America
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States of America.,Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, United States of America
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222
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Loginova DB, Silkova OG. The Genome of Bread Wheat Triticum aestivum L.: Unique Structural and Functional Properties. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418040105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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223
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Choi K, Zhao X, Tock AJ, Lambing C, Underwood CJ, Hardcastle TJ, Serra H, Kim J, Cho HS, Kim J, Ziolkowski PA, Yelina NE, Hwang I, Martienssen RA, Henderson IR. Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res 2018; 28:532-546. [PMID: 29530928 PMCID: PMC5880243 DOI: 10.1101/gr.225599.117] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 02/08/2018] [Indexed: 02/02/2023]
Abstract
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes and allows SPO11-1 access. A positive relationship was observed between SPO11-1-oligos and crossovers genome-wide, although fine-scale correlations were weaker. This may reflect the influence of interhomolog polymorphism on crossover formation, downstream from DSB formation. Although H3K4me3 is enriched in proximity to SPO11-1-oligo hotspots at gene 5' ends, H3K4me3 levels do not correlate with DSBs. Repetitive transposons are thought to be recombination silenced during meiosis, to prevent nonallelic interactions and genome instability. Unexpectedly, we found high SPO11-1-oligo levels in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. High SPO11-1-oligo transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin in SPO11-1-oligo distributions. Epigenetic activation of meiotic DSBs in proximity to centromeres and transposons occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription, and H3K4me3. Together, our work reveals a complex relationship between chromatin and meiotic DSBs within A. thaliana genes and transposons, with significance for the diversity and evolution of plant genomes.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom;,Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Andrew J. Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Charles J. Underwood
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom;,Howard Hughes Medical Institute–Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Thomas J. Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Juhyun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Piotr A. Ziolkowski
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Nataliya E. Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Robert A. Martienssen
- Howard Hughes Medical Institute–Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R. Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
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224
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Underwood CJ, Choi K, Lambing C, Zhao X, Serra H, Borges F, Simorowski J, Ernst E, Jacob Y, Henderson IR, Martienssen RA. Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation. Genome Res 2018; 28:519-531. [PMID: 29530927 PMCID: PMC5880242 DOI: 10.1101/gr.227116.117] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/15/2018] [Indexed: 02/02/2023]
Abstract
Eukaryotic centromeres contain the kinetochore, which connects chromosomes to the spindle allowing segregation. During meiosis, centromeres are suppressed for inter-homolog crossover, as recombination in these regions can cause chromosome missegregation and aneuploidy. Plant centromeres are surrounded by transposon-dense pericentromeric heterochromatin that is epigenetically silenced by histone 3 lysine 9 dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. However, the role of these chromatin modifications in control of meiotic recombination in the pericentromeres is not fully understood. Here, we show that disruption of Arabidopsis thaliana H3K9me2 and non-CG DNA methylation pathways, for example, via mutation of the H3K9 methyltransferase genes KYP/SUVH4 SUVH5 SUVH6, or the CHG DNA methyltransferase gene CMT3, increases meiotic recombination in proximity to the centromeres. Using immunocytological detection of MLH1 foci and genotyping by sequencing of recombinant plants, we observe that H3K9me2 and non-CG DNA methylation pathway mutants show increased pericentromeric crossovers. Increased pericentromeric recombination in H3K9me2/non-CG mutants occurs in hybrid and inbred backgrounds and likely involves contributions from both the interfering and noninterfering crossover repair pathways. We also show that meiotic DNA double-strand breaks (DSBs) increase in H3K9me2/non-CG mutants within the pericentromeres, via purification and sequencing of SPO11-1-oligonucleotides. Therefore, H3K9me2 and non-CG DNA methylation exert a repressive effect on both meiotic DSB and crossover formation in plant pericentromeric heterochromatin. Our results may account for selection of enhancer trap Dissociation (Ds) transposons into the CMT3 gene by recombination with proximal transposon launch-pads.
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Affiliation(s)
- Charles J. Underwood
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;,Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Filipe Borges
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joe Simorowski
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Evan Ernst
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yannick Jacob
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R. Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Robert A. Martienssen
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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225
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Identification of Wheat Inflorescence Development-Related Genes Using a Comparative Transcriptomics Approach. Int J Genomics 2018; 2018:6897032. [PMID: 29581960 PMCID: PMC5822904 DOI: 10.1155/2018/6897032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/26/2017] [Accepted: 12/03/2017] [Indexed: 12/14/2022] Open
Abstract
Inflorescence represents the highly specialized plant tissue producing the grains. Although key genes regulating flower initiation and development are conserved, the mechanism regulating fertility is still not well explained. To identify genes and gene network underlying inflorescence morphology and fertility of bread wheat, expressed sequence tags (ESTs) from different tissues were analyzed using a comparative transcriptomics approach. Based on statistical comparison of EST frequencies of individual genes in EST pools representing different tissues and verification with RT-PCR and RNA-seq data, 170 genes of 59 gene sets predominantly expressed in the inflorescence were obtained. Nearly one-third of the gene sets displayed differentiated expression profiles in terms of their subgenome orthologs. The identified genes, most of which were predominantly expressed in anthers, encode proteins involved in wheat floral identity determination, anther and pollen development, pollen-pistil interaction, and others. Particularly, 25 annotated gene sets are associated with pollen wall formation, of which 18 encode enzymes or proteins participating in lipid metabolic pathway, including fatty acid ω-hydroxylation, alkane and fatty alcohol biosynthesis, and glycerophospholipid metabolism. We showed that the comparative transcriptomics approach was effective in identifying genes for reproductive development and found that lipid metabolism was particularly active in wheat anthers.
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226
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Fernandes JB, Séguéla-Arnaud M, Larchevêque C, Lloyd AH, Mercier R. Unleashing meiotic crossovers in hybrid plants. Proc Natl Acad Sci U S A 2018; 115:2431-2436. [PMID: 29183972 DOI: 10.1101/159640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana that rely on the activity of FANCM [Crismani W, et al. (2012) Science 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) Proc Natl Acad Sci USA 112:4713-4718], and FIGL1 [Girard C, et al. (2015) PLoS Genet 11:e1005369]. Here we analyzed recombination in plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining recq4 and figl1 mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways did not further increase recombination, suggesting that some upper limit had been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, although in wild type recombination is much higher in male meiosis than in female meiosis (490 cM vs. 290 cM), female recombination is higher than male recombination in recq4 figl1 (3,200 cM vs. 2,720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase in recombination observed in recq4 figl1 hybrids opens the possibility of manipulating recombination to enhance plant breeding efficiency.
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Affiliation(s)
- Joiselle Blanche Fernandes
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
- Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Mathilde Séguéla-Arnaud
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Cécile Larchevêque
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Andrew H Lloyd
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France;
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227
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Fernandes JB, Séguéla-Arnaud M, Larchevêque C, Lloyd AH, Mercier R. Unleashing meiotic crossovers in hybrid plants. Proc Natl Acad Sci U S A 2018; 115:2431-2436. [PMID: 29183972 PMCID: PMC5877974 DOI: 10.1073/pnas.1713078114] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana that rely on the activity of FANCM [Crismani W, et al. (2012) Science 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) Proc Natl Acad Sci USA 112:4713-4718], and FIGL1 [Girard C, et al. (2015) PLoS Genet 11:e1005369]. Here we analyzed recombination in plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining recq4 and figl1 mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways did not further increase recombination, suggesting that some upper limit had been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, although in wild type recombination is much higher in male meiosis than in female meiosis (490 cM vs. 290 cM), female recombination is higher than male recombination in recq4 figl1 (3,200 cM vs. 2,720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase in recombination observed in recq4 figl1 hybrids opens the possibility of manipulating recombination to enhance plant breeding efficiency.
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Affiliation(s)
- Joiselle Blanche Fernandes
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
- Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Mathilde Séguéla-Arnaud
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Cécile Larchevêque
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Andrew H Lloyd
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France;
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228
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Bilichak A, Luu J, Jiang F, Eudes F. Identification of BABY BOOM homolog in bread wheat. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aggene.2017.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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229
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A large-scale multiomics analysis of wheat stem solidness and the wheat stem sawfly feeding response, and syntenic associations in barley, Brachypodium, and rice. Funct Integr Genomics 2018; 18:241-259. [PMID: 29470681 PMCID: PMC5908820 DOI: 10.1007/s10142-017-0585-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 01/12/2023]
Abstract
The wheat stem sawfly (WSS), Cephus cinctus Norton (Hymenoptera: Cephidae), is an important pest of wheat and other cereals, threatening the quality and quantity of grain production. WSS larvae feed and develop inside the stem where they are protected from the external environment; therefore, pest management strategies primarily rely on host plant resistance. A major locus on the long arm of wheat chromosome 3B underlies most of the variation in stem solidness; however, the impact of stem solidness on WSS feeding has not been completely characterized. Here, we used a multiomics approach to examine the response to WSS in both solid- and semi-solid-stemmed wheat varieties. The combined transcriptomic, proteomic, and metabolomic data revealed that two important molecular pathways, phenylpropanoid and phosphate pentose, are involved in plant defense against WSS. We also detected a general downregulation of several key defense transcripts, including those encoding secondary metabolites such as DIMBOA, tricetin, and lignin, which suggested that the WSS larva might interfere with plant defense. We comparatively analyzed the stem solidness genomic region known to be associated with WSS tolerance in wild emmer, durum, and bread wheats, and described syntenic regions in the close relatives barley, Brachypodium, and rice. Additionally, microRNAs identified from the same genomic region revealed potential regulatory pathways associated with the WSS response. We propose a model outlining the molecular responses of the WSS–wheat interactions. These findings provide insight into the link between stem solidness and WSS feeding at the molecular level.
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230
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Genetic improvement of heat tolerance in wheat: Recent progress in understanding the underlying molecular mechanisms. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.cj.2017.09.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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231
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Jia M, Guan J, Zhai Z, Geng S, Zhang X, Mao L, Li A. Wheat functional genomics in the era of next generation sequencing: An update. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.cj.2017.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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232
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Abstract
PLAZA 3.0 is an online resource for comparative genomics and offers a versatile platform to study gene functions and gene families or to analyze genome organization and evolution in the green plant lineage. Starting from genome sequence information for over 35 plant species, precomputed comparative genomic data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, and genomic colinearity information within and between species. Complementary functional data sets, a Workbench, and interactive visualization tools are available through a user-friendly web interface, making PLAZA an excellent starting point to translate sequence or omics data sets into biological knowledge. PLAZA is available at http://bioinformatics.psb.ugent.be/plaza/ .
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Affiliation(s)
- Klaas Vandepoele
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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233
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Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 2018; 357:93-97. [PMID: 28684525 DOI: 10.1126/science.aan0032] [Citation(s) in RCA: 478] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/08/2017] [Indexed: 01/07/2023]
Abstract
Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.
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Affiliation(s)
- Raz Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Moran Nave
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Iago Hale
- University of New Hampshire, Durham, NH, USA
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Manuel Spannagl
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | | | | | - Guy Golan
- The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jasline Deek
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Batsheva Ben-Zvi
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany
| | | | - Andrew G Sharpe
- University of Saskatchewan, Saskatoon, Canada.,Global Institute for Food Security, Saskatoon, SK, Canada
| | | | - Roi Ben-David
- Agricultural Research Organization (ARO), Bet Dagan, Israel
| | | | | | | | - Justin D Faris
- U.S. Department of Agriculture (USDA)-Agricultural Research Service, Fargo, ND, USA
| | | | | | | | | | | | | | - Luigi Cattivelli
- Council of Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Primetta Faccioli
- Council of Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Aldo Ceriotti
- CNR-National Research Council, Institute of Agricultural Biology and Biotechnology, Milano, Italy
| | | | | | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Tamar Eilam
- The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.,The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Nir Ohad
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Daniel A Chamovitz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany
| | | | - Zvi Peleg
- The Hebrew University of Jerusalem, Rehovot, Israel
| | | | | | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.,The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
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234
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High throughput SNP discovery and genotyping in hexaploid wheat. PLoS One 2018; 13:e0186329. [PMID: 29293495 PMCID: PMC5749704 DOI: 10.1371/journal.pone.0186329] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/13/2017] [Indexed: 12/03/2022] Open
Abstract
Because of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms (SNPs) are powerful tools for efficient genetics and genomics studies, including characterization of genetic resources, genome-wide association studies and genomic selection. In wheat, most of the previous SNP discovery initiatives targeted the coding fraction, leaving almost 98% of the wheat genome largely unexploited. Here we report on the use of whole-genome resequencing data from eight wheat lines to mine for SNPs in the genic, the repetitive and non-repetitive intergenic fractions of the wheat genome. Eventually, we identified 3.3 million SNPs, 49% being located on the B-genome, 41% on the A-genome and 10% on the D-genome. We also describe the development of the TaBW280K high-throughput genotyping array containing 280,226 SNPs. Performance of this chip was examined by genotyping a set of 96 wheat accessions representing the worldwide diversity. Sixty-nine percent of the SNPs can be efficiently scored, half of them showing a diploid-like clustering. The TaBW280K was proven to be a very efficient tool for diversity analyses, as well as for breeding as it can discriminate between closely related elite varieties. Finally, the TaBW280K array was used to genotype a population derived from a cross between Chinese Spring and Renan, leading to the construction a dense genetic map comprising 83,721 markers. The results described here will provide the wheat community with powerful tools for both basic and applied research.
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235
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Kim D, Alptekin B, Budak H. CRISPR/Cas9 genome editing in wheat. Funct Integr Genomics 2018; 18:31-41. [PMID: 28918562 DOI: 10.1007/s10142-017-0572-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 12/20/2022]
Abstract
Genome editing has been a long-term challenge for molecular biology research, particularly for plants possess complex genome. The recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile tool for genome editing which enables editing of multiple genes based on the guidance of small RNAs. Even though the efficiency of CRISPR/Cas9 system has been shown with several studies from diploid plants, its application remains a challenge for plants with polyploid and complex genome. Here, we applied CRISPR/Cas9 genome editing system in wheat protoplast to conduct the targeted editing of stress-responsive transcription factor genes, wheat dehydration responsive element binding protein 2 (TaDREB2) and wheat ethylene responsive factor 3 (TaERF3). Targeted genome editing of TaDREB2 and TaERF3 was achieved with transient expression of small guide RNA and Cas9 protein in wheat protoplast. The effectiveness of mutagenesis in wheat protoplast was confirmed with restriction enzyme digestion assay, T7 endonuclease assay, and sequencing. Furthermore, several off-target regions for designed sgRNAs were analyzed, and the specificity of genome editing was confirmed with amplicon sequencing. Overall results suggested that CRISPR/Cas9 genome editing system can easily be established on wheat protoplast and it has a huge potentiality for targeted manipulation of wheat genome for crop improvement purposes.
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Affiliation(s)
- Dongjin Kim
- Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Burcu Alptekin
- Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Hikmet Budak
- Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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236
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Barley Genome Sequencing and Assembly—A First Version Reference Sequence. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-92528-8_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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237
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Wang Z, Cheng J, Fan A, Zhao J, Yu Z, Li Y, Zhang H, Xiao J, Muhammad F, Wang H, Cao A, Xing L, Wang X. LecRK-V, an L-type lectin receptor kinase in Haynaldia villosa, plays positive role in resistance to wheat powdery mildew. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:50-62. [PMID: 28436098 PMCID: PMC5811777 DOI: 10.1111/pbi.12748] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/21/2017] [Accepted: 04/14/2017] [Indexed: 05/25/2023]
Abstract
Plant sense potential microbial pathogen using pattern recognition receptors (PRRs) to recognize pathogen-associated molecular patterns (PAMPs). The Lectin receptor-like kinase genes (LecRKs) are involved in various cellular processes mediated by signal transduction pathways. In the present study, an L-type lectin receptor kinase gene LecRK-V was cloned from Haynaldia villosa, a diploid wheat relative which is highly resistant to powdery mildew. The expression of LecRK-V was rapidly up-regulated by Bgt inoculation and chitin treatment. Its transcript level was higher in the leaves than in roots, culms, spikes and callus. Single-cell transient overexpression of LecRK-V led to decreased haustorium index in wheat variety Yangmai158, which is powdery mildew susceptible. Stable transformation LecRK-V into Yangmai158 significantly enhanced the powdery mildew resistance at both seedling and adult stages. At seedling stage, the transgenic line was highly resistance to 18 of the tested 23 Bgt isolates, hypersensitive responses (HR) were observed for 22 Bgt isolates, and more ROS at the Bgt infection sites was accumulated. These indicated that LecRK-V confers broad-spectrum resistance to powdery mildew, and ROS and SA pathways contribute to the enhanced powdery mildew resistance in wheat.
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Affiliation(s)
- Zongkuan Wang
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Jiangyue Cheng
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Anqi Fan
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Jia Zhao
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Zhongyu Yu
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Yingbo Li
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Heng Zhang
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Jin Xiao
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Faheem Muhammad
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Haiyan Wang
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Aizhong Cao
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Liping Xing
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
| | - Xiue Wang
- State Key Lab of Crop Genetics and Germplasm EnhancementCytogenetics InstituteNanjing Agricultural University/JCIC‐MCPNanjingJiangsuChina
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238
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Lambing C, Heckmann S. Tackling Plant Meiosis: From Model Research to Crop Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:829. [PMID: 29971082 PMCID: PMC6018109 DOI: 10.3389/fpls.2018.00829] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2018] [Indexed: 05/04/2023]
Abstract
Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| | - Stefan Heckmann
- Independent Research Group Meiosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- *Correspondence: Christophe Lambing, Stefan Heckmann,
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Zhou Y, Chen Z, Cheng M, Chen J, Zhu T, Wang R, Liu Y, Qi P, Chen G, Jiang Q, Wei Y, Luo M, Nevo E, Allaby RG, Liu D, Wang J, Dvorák J, Zheng Y. Uncovering the dispersion history, adaptive evolution and selection of wheat in China. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:280-291. [PMID: 28635103 PMCID: PMC5785339 DOI: 10.1111/pbi.12770] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 05/18/2023]
Abstract
Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro-ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27 933 DArTseq (for 717 landraces) and 312 831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome-wide divergence at the population level in Chinese wheat landraces. In total, 148 regions of the wheat genome show signs of selection in at least one geographic area. Our data show adaptive events across geographic areas, from the xeric northwest to the mesic south, along and among homoeologous chromosomes, with fewer variations in the D genome than in the A and B genomes. Multiple variations in interdependent functional genes such as regulatory and metabolic genes controlling germination and flowering time were characterized, showing clear allelic frequency changes corresponding to the dispersion of wheat in China. Population structure and selection data reveal that Chinese wheat spread from the northwestern Caspian Sea region to South China, adapting during its agricultural trajectory to increasingly mesic and warm climatic areas.
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Affiliation(s)
- Yong Zhou
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Zhongxu Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Mengping Cheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Jian Chen
- Chengdu City Institute of ArchaeologyChengduSichuanChina
| | - Tingting Zhu
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Rui Wang
- State Key Lab of CAD&CGZhejiang UniversityHangzhouZhejiangChina
| | - Yaxi Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Pengfei Qi
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Guoyue Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Qiantao Jiang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Yuming Wei
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaHaifaIsrael
| | | | - Dengcai Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityYaanSichuanChina
| | - Jirui Wang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityYaanSichuanChina
| | - Jan Dvorák
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Youliang Zheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityYaanSichuanChina
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240
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Aggarwal S, Kumar A, Bhati KK, Kaur G, Shukla V, Tiwari S, Pandey AK. RNAi-Mediated Downregulation of Inositol Pentakisphosphate Kinase ( IPK1) in Wheat Grains Decreases Phytic Acid Levels and Increases Fe and Zn Accumulation. FRONTIERS IN PLANT SCIENCE 2018; 9:259. [PMID: 29559984 PMCID: PMC5845732 DOI: 10.3389/fpls.2018.00259] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/14/2018] [Indexed: 05/18/2023]
Abstract
Enhancement of micronutrient bioavailability is crucial to address the malnutrition in the developing countries. Various approaches employed to address the micronutrient bioavailability are showing promising signs, especially in cereal crops. Phytic acid (PA) is considered as a major antinutrient due to its ability to chelate important micronutrients and thereby restricting their bioavailability. Therefore, manipulating PA biosynthesis pathway has largely been explored to overcome the pleiotropic effect in different crop species. Recently, we reported that functional wheat inositol pentakisphosphate kinase (TaIPK1) is involved in PA biosynthesis, however, the functional roles of the IPK1 gene in wheat remains elusive. In this study, RNAi-mediated gene silencing was performed for IPK1 transcripts in hexaploid wheat. Four non-segregating RNAi lines of wheat were selected for detailed study (S3-D-6-1; S6-K-3-3; S6-K-6-10 and S16-D-9-5). Homozygous transgenic RNAi lines at T4 seeds with a decreased transcript of TaIPK1 showed 28-56% reduction of the PA. Silencing of IPK1 also resulted in increased free phosphate in mature grains. Although, no phenotypic changes in the spike was observed but, lowering of grain PA resulted in the reduced number of seeds per spikelet. The lowering of grain PA was also accompanied by a significant increase in iron (Fe) and zinc (Zn) content, thereby enhancing their molar ratios (Zn:PA and Fe:PA). Overall, this work suggests that IPK1 is a promising candidate for employing genome editing tools to address the mineral accumulation in wheat grains.
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Affiliation(s)
- Sipla Aggarwal
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Anil Kumar
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Kaushal K. Bhati
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
- Copenhagen Plant Science Centre, PLEN, University of Copenhagen, Copenhagen, Denmark
| | - Gazaldeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Vishnu Shukla
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Siddharth Tiwari
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Ajay K. Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
- *Correspondence: Ajay K. Pandey, ;
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241
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Sarno R, Vicq Y, Uematsu N, Luka M, Lapierre C, Carroll D, Bastianelli G, Serero A, Nicolas A. Programming sites of meiotic crossovers using Spo11 fusion proteins. Nucleic Acids Res 2017; 45:e164. [PMID: 28977556 PMCID: PMC5737382 DOI: 10.1093/nar/gkx739] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/17/2017] [Indexed: 12/05/2022] Open
Abstract
Meiotic recombination shapes the genetic diversity transmitted upon sexual reproduction. However, its non-random distribution along the chromosomes constrains the landscape of potential genetic combinations. For a variety of purposes, it is desirable to expand the natural repertoire by changing the distribution of crossovers in a wide range of eukaryotes. Toward this end, we report the local stimulation of meiotic recombination at a number of chromosomal sites by tethering the natural Spo11 protein to various DNA-binding modules: full-length DNA binding proteins, zinc fingers (ZFs), transcription activator-like effector (TALE) modules, and the CRISPR-Cas9 system. In the yeast Saccharomyces cerevisiae, each strategy is able to stimulate crossover frequencies in naturally recombination-cold regions. The binding and cleavage efficiency of the targeting Spo11 fusions (TSF) are variable, being dependent on the chromosomal regions and potential competition with endogenous factors. TSF-mediated genome interrogation distinguishes naturally recombination-cold regions that are flexible and can be warmed-up (gene promoters and coding sequences), from those that remain refractory (gene terminators and centromeres). These results describe new generic experimental strategies to increase the genetic diversity of gametes, which should prove useful in plant breeding and other applications.
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Affiliation(s)
- Roberta Sarno
- Institut Curie, PSL Research University, CNRS UMR3244, Recombination and Genetic Instability, Paris F-75005, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS UMR3244, Paris F-75005, France
| | - Yoan Vicq
- Institut Curie, PSL Research University, CNRS UMR3244, Recombination and Genetic Instability, Paris F-75005, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS UMR3244, Paris F-75005, France
| | - Norio Uematsu
- Institut Curie, PSL Research University, CNRS UMR3244, Recombination and Genetic Instability, Paris F-75005, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS UMR3244, Paris F-75005, France
| | - Marine Luka
- Institut Curie, PSL Research University, CNRS UMR3244, Recombination and Genetic Instability, Paris F-75005, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS UMR3244, Paris F-75005, France
| | - Clement Lapierre
- Institut Curie, PSL Research University, CNRS UMR3244, Recombination and Genetic Instability, Paris F-75005, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS UMR3244, Paris F-75005, France
| | - Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
| | | | - Alexandre Serero
- Institut Curie, PSL Research University, CNRS UMR3244, Recombination and Genetic Instability, Paris F-75005, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS UMR3244, Paris F-75005, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, CNRS UMR3244, Recombination and Genetic Instability, Paris F-75005, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS UMR3244, Paris F-75005, France
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242
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Tyagi S, Sharma S, Taneja M, Shumayla, Kumar R, Sembi JK, Upadhyay SK. Superoxide dismutases in bread wheat ( Triticum aestivum L.): Comprehensive characterization and expression analysis during development and, biotic and abiotic stresses. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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243
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Zhao G, Zou C, Li K, Wang K, Li T, Gao L, Zhang X, Wang H, Yang Z, Liu X, Jiang W, Mao L, Kong X, Jiao Y, Jia J. The Aegilops tauschii genome reveals multiple impacts of transposons. NATURE PLANTS 2017; 3:946-955. [PMID: 29158546 DOI: 10.1038/s41477-017-0067-8] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/30/2017] [Indexed: 05/19/2023]
Abstract
Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes. In addition to the discovery of a wave of very recent gene duplications, we detected that TEs occurred in about half of the genes, and found that such genes are expressed at lower levels than those without TEs, presumably because of their elevated methylation levels. We mapped all wheat molecular markers and constructed a high-resolution integrated genetic map corresponding to genome sequences, thereby placing previously detected agronomically important genes/quantitative trait loci (QTLs) on the Ae. tauschii genome for the first time.
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Affiliation(s)
- 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, 100081, Beijing, 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, 100081, Beijing, China
| | - Kui Li
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Kai Wang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Tianbao Li
- Agronomy College, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 450002, Zhengzhou, 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, 100081, Beijing, China
| | - Xiaoxia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 100093, Beijing, China
| | - Hongjin Wang
- Center for Information in Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 610054, Chengdu, China
| | - Zujun Yang
- Center for Information in Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 610054, Chengdu, 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, 100081, Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China.
| | - Long Mao
- 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, 100081, Beijing, 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, 100081, Beijing, China.
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 100093, Beijing, 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, 100081, Beijing, China.
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244
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Choi K. Advances towards Controlling Meiotic Recombination for Plant Breeding. Mol Cells 2017; 40:814-822. [PMID: 29179262 PMCID: PMC5712510 DOI: 10.14348/molcells.2017.0171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/10/2017] [Accepted: 11/17/2017] [Indexed: 12/28/2022] Open
Abstract
Meiotic homologous recombination generates new combinations of preexisting genetic variation and is a crucial process in plant breeding. Within the last decade, our understanding of plant meiotic recombination and genome diversity has advanced considerably. Innovation in DNA sequencing technology has led to the exploration of high-resolution genetic and epigenetic information in plant genomes, which has helped to accelerate plant breeding practices via high-throughput genotyping, and linkage and association mapping. In addition, great advances toward understanding the genetic and epigenetic control mechanisms of meiotic recombination have enabled the expansion of breeding programs and the unlocking of genetic diversity that can be used for crop improvement. This review highlights the recent literature on plant meiotic recombination and discusses the translation of this knowledge to the manipulation of meiotic recombination frequency and location with regards to crop plant breeding.
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Affiliation(s)
- Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
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245
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Lawrence EJ, Griffin CH, Henderson IR. Modification of meiotic recombination by natural variation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5471-5483. [PMID: 28992351 DOI: 10.1093/jxb/erx306] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Meiosis is a specialized cell division that produces haploid gametes required for sexual reproduction. During the first meiotic division, homologous chromosomes pair and undergo reciprocal crossing over, which recombines linked sequence variation. Meiotic recombination frequency varies extensively both within and between species. In this review, we will examine the molecular basis of meiotic recombination rate variation, with an emphasis on plant genomes. We first consider cis modification caused by polymorphisms at the site of recombination, or elsewhere on the same chromosome. We review cis effects caused by mismatches within recombining joint molecules, the effect of structural hemizygosity, and the role of specific DNA sequence motifs. In contrast, trans modification of recombination is exerted by polymorphic loci encoding diffusible molecules, which are able to modulate recombination on the same and/or other chromosomes. We consider trans modifiers that act to change total recombination levels, hotspot locations, or interactions between homologous and homeologous chromosomes in polyploid species. Finally, we consider the significance of genetic variation that modifies meiotic recombination for adaptation and evolution of plant species.
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Affiliation(s)
- Emma J Lawrence
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Catherine H Griffin
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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246
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Kaur S, Dhugga KS, Beech R, Singh J. Genome-wide analysis of the cellulose synthase-like (Csl) gene family in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:193. [PMID: 29100539 PMCID: PMC5670714 DOI: 10.1186/s12870-017-1142-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 10/26/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Hemicelluloses are a diverse group of complex, non-cellulosic polysaccharides, which constitute approximately one-third of the plant cell wall and find use as dietary fibres, food additives and raw materials for biofuels. Genes involved in hemicellulose synthesis have not been extensively studied in small grain cereals. RESULTS In efforts to isolate the sequences for the cellulose synthase-like (Csl) gene family from wheat, we identified 108 genes (hereafter referred to as TaCsl). Each gene was represented by two to three homeoalleles, which are named as TaCslXY_ZA, TaCslXY_ZB, or TaCslXY_ZD, where X denotes the Csl subfamily, Y the gene number and Z the wheat chromosome where it is located. A quarter of these genes were predicted to have 2 to 3 splice variants, resulting in a total of 137 putative translated products. Approximately 45% of TaCsl genes were located on chromosomes 2 and 3. Sequences from the subfamilies C and D were interspersed between the dicots and grasses but those from subfamily A clustered within each group of plants. Proximity of the dicot-specific subfamilies B and G, to the grass-specific subfamilies H and J, respectively, points to their common origin. In silico expression analysis in different tissues revealed that most of the genes were expressed ubiquitously and some were tissue-specific. More than half of the genes had introns in phase 0, one-third in phase 2, and a few in phase 1. CONCLUSION Detailed characterization of the wheat Csl genes has enhanced the understanding of their structural, functional, and evolutionary features. This information will be helpful in designing experiments for genetic manipulation of hemicellulose synthesis with the goal of developing improved cultivars for biofuel production and increased tolerance against various stresses.
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Affiliation(s)
- Simerjeet Kaur
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
| | - Kanwarpal S. Dhugga
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Estado de México Mexico
| | - Robin Beech
- Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Montreal, QC Canada
| | - Jaswinder Singh
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
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247
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Rampino P, De Pascali M, De Caroli M, Luvisi A, De Bellis L, Piro G, Perrotta C. Td4IN2: A drought-responsive durum wheat (Triticum durum Desf.) gene coding for a resistance like protein with serine/threonine protein kinase, nucleotide binding site and leucine rich domains. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 120:223-231. [PMID: 29065389 DOI: 10.1016/j.plaphy.2017.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/01/2017] [Accepted: 10/13/2017] [Indexed: 06/07/2023]
Abstract
Wheat, the main food source for a third of world population, appears strongly under threat because of predicted increasing temperatures coupled to drought. Plant complex molecular response to drought stress relies on the gene network controlling cell reactions to abiotic stress. In the natural environment, plants are subjected to the combination of abiotic and biotic stresses. Also the response of plants to biotic stress, to cope with pathogens, involves the activation of a molecular network. Investigations on combination of abiotic and biotic stresses indicate the existence of cross-talk between the two networks and a kind of overlapping can be hypothesized. In this work we describe the isolation and characterization of a drought-related durum wheat (Triticum durum Desf.) gene, identified in a previous study, coding for a protein combining features of NBS-LRR type resistance protein with a S/TPK domain, involved in drought stress response. This is one of the few examples reported where all three domains are present in a single protein and, to our knowledge, it is the first report on a gene specifically induced by drought stress and drought-related conditions, with this particular structure.
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Affiliation(s)
- Patrizia Rampino
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy.
| | - Mariarosaria De Pascali
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Monica De Caroli
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Andrea Luvisi
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Luigi De Bellis
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Gabriella Piro
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Carla Perrotta
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
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248
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Sun F, Fan G, Hu Q, Zhou Y, Guan M, Tong C, Li J, Du D, Qi C, Jiang L, Liu W, Huang S, Chen W, Yu J, Mei D, Meng J, Zeng P, Shi J, Liu K, Wang X, Wang X, Long Y, Liang X, Hu Z, Huang G, Dong C, Zhang H, Li J, Zhang Y, Li L, Shi C, Wang J, Lee SMY, Guan C, Xu X, Liu S, Liu X, Chalhoub B, Hua W, Wang H. The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:452-468. [PMID: 28849613 DOI: 10.1111/tpj.13669] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/05/2017] [Accepted: 08/11/2017] [Indexed: 05/04/2023]
Abstract
Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (Ar ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with Ar , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia.
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Affiliation(s)
- Fengming Sun
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Qiong Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, BeiBei District, Chongqing, 400715, China
| | - Dezhi Du
- Qinghai Academy of Agricultural and Forestry, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, 810016, China
| | - Cunkou Qi
- Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Liangcai Jiang
- Shichun Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Weiqing Liu
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Shunmou Huang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wenbin Chen
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jingyin Yu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Desheng Mei
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peng Zeng
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jiaqin Shi
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xi Wang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Xinfa Wang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinming Liang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Zhiyong Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Guodong Huang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Caihua Dong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - He Zhang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jun Li
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yaolei Zhang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Liangwei Li
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Chengcheng Shi
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jiahao Wang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Xun Xu
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xin Liu
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
| | - Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA), Unité de Recherche en Génomique Végétale (URGV), UMR1165, Organization and Evolution of Plant Genomes (OEPG), 2 rue Gaston Crémieux, 91057, Evry, France
| | - Wei Hua
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Hanzhong Wang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
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POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat. Sci Rep 2017; 7:14315. [PMID: 29085014 PMCID: PMC5662734 DOI: 10.1038/s41598-017-14591-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/12/2017] [Indexed: 01/08/2023] Open
Abstract
POPSEQ Ordered Triticum aestivum Gene Expression (POTAGE) is a web application which accelerates the process of identifying candidate genes for quantitative trait loci (QTL) in hexaploid wheat. This is achieved by leveraging several of the most commonly used data sets in wheat research. These include the Chromosome Survey Sequences, their order along the chromosomes determined by the population sequencing (POPSEQ) approach, the gene predictions and RNA-Seq expression data. POTAGE aggregates those data sets and provides an intuitive interface for biologists to explore the expression of the predicted genes and their functional annotation in a chromosomal context. The interface accelerates some of the laborious and repetitive tasks commonly undertaken in the process of identifying and prioritising genes which may underlie QTL. We illustrate the utility of POTAGE by showing how a short-list of candidate genes can quickly be identified for a QTL linked to pre-harvest sprouting - a major cause of quality and yield loss in wheat production. The candidate genes identified using POTAGE included TaMKK3, which was recently reported as a causal gene for seed dormancy in wheat, and a mutation in its barley ortholog has been shown to reduce pre-harvest sprouting. POTAGE is available at http://crobiad.agwine.adelaide.edu.au/potage .
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Xiao J, Dai K, Fu L, Vrána J, Kubaláková M, Wan W, Sun H, Zhao J, Yu C, Wu Y, Abrouk M, Wang H, Doležel J, Wang X. Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order. BMC Genomics 2017; 18:791. [PMID: 29037165 PMCID: PMC5644170 DOI: 10.1186/s12864-017-4211-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 10/12/2017] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and application. RESULTS In this work, the short arm of H. villosa chromosome 4V (4VS) was sorted by flow cytometry and sequenced using Illumina platform. About 170.6 Mb assembled sequences were obtained. Further analysis showed that repetitive elements accounted for about 64.6% of 4VS, while the coding fraction, which is corresponding to 1977 annotated genes, represented 1.5% of the arm. The syntenic regions of the 4VS were searched and identified on wheat group 4 chromosomes 4AL, 4BS, 4DS, Brachypodium chromosomes 1 and 4, rice chromosomes 3 and 11, and sorghum chromosomes 1, 5 and 8. Based on genome-zipper analysis, a virtual gene order comprising 735 gene loci on 4VS genome was built by referring to the Brachypodium genome, which was relatively consistent with the scaffold order determined for Ae. tauschii chromosome 4D. The homologous alleles of several cloned genes on wheat group 4 chromosomes including Rht-1 gene were identified. CONCLUSIONS The sequences provided valuable information for mapping and positional-cloning genes located on 4VS, such as the wheat yellow mosaic virus resistance gene Wss1. The work on 4VS provided detailed insights into the genome of H. villosa, and may also serve as a model for sequencing the remaining parts of H. villosa genome.
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Affiliation(s)
- Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Keli Dai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Lian Fu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671 Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671 Olomouc, Czech Republic
| | - Wentao Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Jing Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Chunyan Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671 Olomouc, Czech Republic
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671 Olomouc, Czech Republic
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
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