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Ahmed HI, Heuberger M, Schoen A, Koo DH, Quiroz-Chavez J, Adhikari L, Raupp J, Cauet S, Rodde N, Cravero C, Callot C, Lazo GR, Kathiresan N, Sharma PK, Moot I, Yadav IS, Singh L, Saripalli G, Rawat N, Datla R, Athiyannan N, Ramirez-Gonzalez RH, Uauy C, Wicker T, Tiwari VK, Abrouk M, Poland J, Krattinger SG. Einkorn genomics sheds light on history of the oldest domesticated wheat. Nature 2023; 620:830-838. [PMID: 37532937 PMCID: PMC10447253 DOI: 10.1038/s41586-023-06389-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 06/29/2023] [Indexed: 08/04/2023]
Abstract
Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.
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Affiliation(s)
- Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Adam Schoen
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Charlotte Cravero
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Gerard R Lazo
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA, USA
| | - Nagarajan Kathiresan
- KAUST Supercomputing Core Lab (KSL), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Parva K Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Ian Moot
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Lovepreet Singh
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Gautam Saripalli
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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2
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Mascarenhas Dos Santos AC, Julian AT, Liang P, Juárez O, Pombert JF. Telomere-to-Telomere genome assemblies of human-infecting Encephalitozoon species. BMC Genomics 2023; 24:237. [PMID: 37142951 PMCID: PMC10158259 DOI: 10.1186/s12864-023-09331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Microsporidia are diverse spore forming, fungal-related obligate intracellular pathogens infecting a wide range of hosts. This diversity is reflected at the genome level with sizes varying by an order of magnitude, ranging from less than 3 Mb in Encephalitozoon species (the smallest known in eukaryotes) to more than 50 Mb in Edhazardia spp. As a paradigm of genome reduction in eukaryotes, the small Encephalitozoon genomes have attracted much attention with investigations revealing gene dense, repeat- and intron-poor genomes characterized by a thorough pruning of molecular functions no longer relevant to their obligate intracellular lifestyle. However, because no Encephalitozoon genome has been sequenced from telomere-to-telomere and since no methylation data is available for these species, our understanding of their overall genetic and epigenetic architectures is incomplete. METHODS In this study, we sequenced the complete genomes from telomere-to-telomere of three human-infecting Encephalitozoon spp. -E. intestinalis ATCC 50506, E. hellem ATCC 50604 and E. cuniculi ATCC 50602- using short and long read platforms and leveraged the data generated as part of the sequencing process to investigate the presence of epigenetic markers in these genomes. We also used a mixture of sequence- and structure-based computational approaches, including protein structure prediction, to help identify which Encephalitozoon proteins are involved in telomere maintenance, epigenetic regulation, and heterochromatin formation. RESULTS The Encephalitozoon chromosomes were found capped by TTAGG 5-mer telomeric repeats followed by telomere associated repeat elements (TAREs) flanking hypermethylated ribosomal RNA (rRNA) gene loci featuring 5-methylcytosines (5mC) and 5-hemimethylcytosines (5hmC), themselves followed by lesser methylated subtelomeres and hypomethylated chromosome cores. Strong nucleotide biases were identified between the telomeres/subtelomeres and chromosome cores with significant changes in GC/AT, GT/AC and GA/CT contents. The presence of several genes coding for proteins essential to telomere maintenance, epigenetic regulation, and heterochromatin formation was further confirmed in the Encephalitozoon genomes. CONCLUSION Altogether, our results strongly support the subtelomeres as sites of heterochromatin formation in Encephalitozoon genomes and further suggest that these species might shutdown their energy-consuming ribosomal machinery while dormant as spores by silencing of the rRNA genes using both 5mC/5hmC methylation and facultative heterochromatin formation at these loci.
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Affiliation(s)
| | | | - Pingdong Liang
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
| | - Oscar Juárez
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
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3
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Shrestha S, Koo DH, Evers B, Wu S, Walkowiak S, Hucl P, Pozniak C, Fritz A, Poland J. Wheat doubled haploids have a marked prevalence of chromosomal aberrations. THE PLANT GENOME 2023:e20309. [PMID: 37128182 DOI: 10.1002/tpg2.20309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/17/2022] [Indexed: 05/03/2023]
Abstract
Double haploid (DH) population development is widely used in many crops, including wheat (Triticum aestivum L.), to rapidly produce fixed germplasm for breeding and genetic studies. The genome shock that takes place during DH induction could induce chromosomal aberrations that can impact genome integrity and subsequently plant fitness and agronomic performance. To evaluate the extent of chromosomal aberrations that exist as a result of the DH process, we studied two wheat DH populations: CDC Stanley×CDC Landmark and KS13H9×SYMonument. We utilized high-throughput skim sequencing to construct digital karyotypes of these populations to quantify deletions and aneuploidy with high resolution and accuracy, which was confirmed in selected plants by cytological analysis. The two populations studied showed high proportion of abnormal primary DH lines, 55 and 45%, respectively, based on at least one abnormality per progeny. The chromosomal abnormalities are genetically unstable and were observed segregating in the subsequent generations. These observations have important implications for the use of DH lines in genetics and breeding.
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Affiliation(s)
- Sandesh Shrestha
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Dal-Hoe Koo
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Byron Evers
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Shuangye Wu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Sean Walkowiak
- Grain Research Laboratory, Canadian Grain Commission, Winnipeg, MB, Canada
| | - Pierre Hucl
- Crop Development Centre (CDC), University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis Pozniak
- Crop Development Centre (CDC), University of Saskatchewan, Saskatoon, SK, Canada
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Zhao J, Xie Y, Kong C, Lu Z, Jia H, Ma Z, Zhang Y, Cui D, Ru Z, Wang Y, Appels R, Jia J, Zhang X. Centromere repositioning and shifts in wheat evolution. PLANT COMMUNICATIONS 2023:100556. [PMID: 36739481 PMCID: PMC10398676 DOI: 10.1016/j.xplc.2023.100556] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/07/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms. Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat. Here, we comprehensively analyzed centromeres from the de novo-assembled common wheat cultivar Aikang58 (AK58), Chinese Spring (CS), and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing, whole-genome bisulfite sequencing, RNA sequencing, assay for transposase-accessible chromatin using sequencing, and comparative genomics. We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization. Centromeric repeats of wheat (CRWs) have undergone expansion during wheat evolution, with strong interweaving between the A and B subgenomes post tetraploidization. We found that CENH3 prefers to bind with younger CRWs, as directly supported by immunocolocalization on two chromosomes (1A and 2A) of wild emmer wheat with dicentromeric regions, only one of which bound with CENH3. In a comparison of AK58 with CS, obvious centromere repositioning was detected on chromosomes 1B, 3D, and 4D. The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels. We also found that centromeric chromatin was more open than pericentromeric chromatin, with higher levels of gene expression but lower gene density. Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome. This study also showed that active wheat centromeres were genetically and epigenetically determined.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chuizheng Kong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyan Jia
- Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Zhengqiang Ma
- Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dangqun Cui
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhengang Ru
- Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yuquan Wang
- Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Rudi Appels
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083, Australia
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China.
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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5
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Multiple wheat genomes reveal global variation in modern breeding. Nature 2020; 588:277-283. [PMID: 33239791 PMCID: PMC7759465 DOI: 10.1038/s41586-020-2961-x] [Citation(s) in RCA: 387] [Impact Index Per Article: 96.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022]
Abstract
Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars. Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.
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6
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Jordan KW, He F, de Soto MF, Akhunova A, Akhunov E. Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes. Genome Biol 2020; 21:176. [PMID: 32684157 PMCID: PMC7368981 DOI: 10.1186/s13059-020-02093-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Background Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome. Results Although open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs’ chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin. Conclusions Chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.
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Affiliation(s)
- Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Monica Fernandez de Soto
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA.,Genomic Sciences Laboratory, North Carolina State University, Raleigh, NC, USA
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
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Kopecky D, Lukaszewski AJ. Misdivision of Telocentrics and Isochromosomes in Wheat. Cytogenet Genome Res 2019; 157:179-188. [PMID: 30799400 DOI: 10.1159/000497301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2018] [Indexed: 11/19/2022] Open
Abstract
For normal transition through meiosis, chromosomes rely on pairing with their homologues. Chromosomes which fail to pair, univalents, behave irregularly and may undergo various types of breakage across their centromeres. Here, we analyzed the meiotic behavior of misdivision products themselves: isochromosomes and telocentrics in wheat. Both types of chromosomes behaved in the same fashion as standard 2-armed chromosomes. The 2 most frequent scenarios were separation of sister chromatids in anaphase I or monopolar/bipolar attachment of the univalent to the spindle apparatus with unseparated chromatids. Misdivision was rare, and its frequency appeared directly related to the size of the centromere. The previously deduced relationship between misdivision frequency and chromosome size was likely erroneous and can be explained by a general relationship between chromosome length and the size of its centromere. Pairing of identical arms in isochromosomes did not protect them from misdivision. It is not chiasmate pairing that protects from misdivision but mechanistic issues that arise through that pairing.
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8
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Keeble-Gagnère G, Rigault P, Tibbits J, Pasam R, Hayden M, Forrest K, Frenkel Z, Korol A, Huang BE, Cavanagh C, Taylor J, Abrouk M, Sharpe A, Konkin D, Sourdille P, Darrier B, Choulet F, Bernard A, Rochfort S, Dimech A, Watson-Haigh N, Baumann U, Eckermann P, Fleury D, Juhasz A, Boisvert S, Nolin MA, Doležel J, Šimková H, Toegelová H, Šafář J, Luo MC, Câmara F, Pfeifer M, Isdale D, Nyström-Persson J, IWGSC, Koo DH, Tinning M, Cui D, Ru Z, Appels R. Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. Genome Biol 2018; 19:112. [PMID: 30115128 PMCID: PMC6097218 DOI: 10.1186/s13059-018-1475-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 07/09/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. RESULTS Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. CONCLUSIONS Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
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Affiliation(s)
- Gabriel Keeble-Gagnère
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Philippe Rigault
- GYDLE, 1135 Grande Allée Ouest, Suite 220, Québec, QC G1S 1E7 Canada
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Josquin Tibbits
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Raj Pasam
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Matthew Hayden
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - B. Emma Huang
- CSIRO-Plant Industry, Black Mountain, Canberra, ACT 2601 Australia
| | - Colin Cavanagh
- CSIRO-Plant Industry, Black Mountain, Canberra, ACT 2601 Australia
| | - Jen Taylor
- CSIRO-Plant Industry, Black Mountain, Canberra, ACT 2601 Australia
| | - Michael Abrouk
- King Abdullah University of Science and Technology, Desert Agriculture Initiative, Thuwal, Saudi Arabia
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Andrew Sharpe
- Global Institute of Food Security, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK Canada
| | - David Konkin
- National Research Council of Canada, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK Canada
| | - Pierre Sourdille
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Benoît Darrier
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Frédéric Choulet
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Aurélien Bernard
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Simone Rochfort
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Adam Dimech
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Nathan Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Paul Eckermann
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Delphine Fleury
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064 Australia
| | - Angela Juhasz
- Veterinary and Agriculture, Murdoch University, 90 South St, Murdoch, Western Australia 6150 Australia
| | | | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Ming-Cheng Luo
- UC Davis Plant Sciences, Plant Genetics and Bioinformatics, 258A Hunt Hall, Davis, CA 95616 USA
| | - Francisco Câmara
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), 88 Dr. Aiguader, 08003 Barcelona, Spain
| | - Matthias Pfeifer
- Plant Genome and Systems Biology, Helmholtz Center, Munich, 85764 Neuherberg, Germany
| | - Don Isdale
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
| | - Johan Nyström-Persson
- Level Five Co. Ltd. GYB Akihabara, Kanda-Sudacho 2-25, Chiyoda-ku, Tokyo, 101-0041 Japan
| | - IWGSC
- International Wheat Genome Sequencing Consortium, 2841 NE Marywood Ct, Lee’s Summit, MO 64086 USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Matthew Tinning
- Australian Genome Research Facility, Suite 219, 55 Flemington Road, North Melbourne, VIC 3051 Australia
| | - Dangqun Cui
- Henan Agricultural University, Zhengzhou, China
| | - Zhengang Ru
- Henan Institute of Science and Technology, Zhengzhou, China
| | - Rudi Appels
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083 Australia
- Veterinary and Agriculture, Murdoch University, 90 South St, Murdoch, Western Australia 6150 Australia
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Padmanaban S, Zhang P, Hare RA, Sutherland MW, Martin A. Pentaploid Wheat Hybrids: Applications, Characterisation, and Challenges. FRONTIERS IN PLANT SCIENCE 2017; 8:358. [PMID: 28367153 PMCID: PMC5355473 DOI: 10.3389/fpls.2017.00358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/01/2017] [Indexed: 05/09/2023]
Abstract
Interspecific hybridisation between hexaploid and tetraploid wheat species leads to the development of F1 pentaploid hybrids with unique chromosomal constitutions. Pentaploid hybrids derived from bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum spp. durum Desf.) crosses can improve the genetic background of either parent by transferring traits of interest. The genetic variability derived from bread and durum wheat and transferred into pentaploid hybrids has the potential to improve disease resistance, abiotic tolerance, and grain quality, and to enhance agronomic characters. Nonetheless, pentaploid wheat hybrids have not been fully exploited in breeding programs aimed at improving crops. There are several potential barriers for efficient pentaploid wheat production, such as low pollen compatibility, poor seed set, failed seedling establishment, and frequent sterility in F1 hybrids. However, most of the barriers can be overcome by careful selection of the parental genotypes and by employing the higher ploidy level genotype as the maternal parent. In this review, we summarize the current research on pentaploid wheat hybrids and analyze the advantages and pitfalls of current methods used to assess pentaploid-derived lines. Furthermore, we discuss current and potential applications in commercial breeding programs and future directions for research into pentaploid wheat.
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Affiliation(s)
- Sriram Padmanaban
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Peng Zhang
- Plant Breeding Institute, The University of Sydney, SydneyNSW, Australia
| | - Ray A. Hare
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Mark W. Sutherland
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
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Koo DH, Tiwari VK, Hřibová E, Doležel J, Friebe B, Gill BS. Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat. Cytogenet Genome Res 2016; 148:314-21. [PMID: 27403741 DOI: 10.1159/000447471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2016] [Indexed: 11/19/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) provides an efficient system for cytogenetic analysis of wild relatives of wheat for individual chromosome identification, elucidation of homoeologous relationships, and for monitoring alien gene transfers into wheat. This study is aimed at developing cytogenetic markers for chromosome identification of wheat and Aegilops geniculata (2n = 4x = 28, UgUgMgMg) using satellite DNAs obtained from flow-sorted chromosome 5Mg. FISH was performed to localize the satellite DNAs on chromosomes of wheat and selected Aegilops species. The FISH signals for satellite DNAs on chromosome 5Mg were generally associated with constitutive heterochromatin regions corresponding to C-band-positive chromatin including telomeric, pericentromeric, centromeric, and interstitial regions of all the 14 chromosome pairs of Ae. geniculata. Most satellite DNAs also generated FISH signals on wheat chromosomes and provided diagnostic chromosome arm-specific cytogenetic markers that significantly improved chromosome identification in wheat. The newly identified satellite DNA CL36 produced localized Mg genome chromosome-specific FISH signals in Ae. geniculata and in the M genome of the putative diploid donor species Ae. comosa subsp. subventricosa but not in Ae. comosa subsp. comosa, suggesting that the Mg genome of Ae. geniculata was probably derived from subsp. subventricosa.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, Kans., USA
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Schubert V, Ruban A, Houben A. Chromatin Ring Formation at Plant Centromeres. FRONTIERS IN PLANT SCIENCE 2016; 7:28. [PMID: 26913037 PMCID: PMC4753331 DOI: 10.3389/fpls.2016.00028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/10/2016] [Indexed: 05/11/2023]
Abstract
We observed the formation of chromatin ring structures at centromeres of somatic rye and Arabidopsis chromosomes. To test whether this behavior is present also in other plant species and tissues we analyzed Arabidopsis, rye, wheat, Aegilops and barley centromeres during cell divisions and in interphase nuclei by immunostaining and FISH. Furthermore, structured illumination microscopy (super-resolution) was applied to investigate the ultrastructure of centromere chromatin beyond the classical refraction limit of light. It became obvious, that a ring formation at centromeres may appear during mitosis, meiosis and in interphase nuclei in all species analyzed. However, varying centromere structures, as ring formations or globular organized chromatin fibers, were identified in different tissues of one and the same species. In addition, we found that a chromatin ring formation may also be caused by subtelomeric repeats in barley. Thus, we conclude that the formation of chromatin rings may appear in different plant species and tissues, but that it is not specific for centromere function. Based on our findings we established a model describing the ultrastructure of plant centromeres and discuss it in comparison to previous models proposed for animals and plants.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenStadt Seeland, Germany
- *Correspondence: Veit Schubert
| | - Alevtina Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenStadt Seeland, Germany
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural AcademyMoscow, Russia
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenStadt Seeland, Germany
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