Multiple wheat genomes reveal global variation in modern breeding.
Acclimatization
/ genetics
Animals
Centromere
/ genetics
Chromosome Mapping
Cloning, Molecular
DNA Copy Number Variations
/ genetics
DNA Transposable Elements
/ genetics
Edible Grain
/ genetics
Genes, Plant
/ genetics
Genetic Introgression
Genetic Variation
Genome, Plant
/ genetics
Genomics
Haplotypes
Insecta
/ pathogenicity
Internationality
NLR Proteins
/ genetics
Plant Breeding
/ methods
Plant Diseases
/ genetics
Plant Proteins
/ genetics
Polymorphism, Single Nucleotide
/ genetics
Polyploidy
Triticum
/ classification
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
12 2020
12 2020
Historique:
received:
03
04
2020
accepted:
09
09
2020
pubmed:
27
11
2020
medline:
3
2
2021
entrez:
26
11
2020
Statut:
ppublish
Résumé
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 genome
Identifiants
pubmed: 33239791
doi: 10.1038/s41586-020-2961-x
pii: 10.1038/s41586-020-2961-x
pmc: PMC7759465
doi:
Substances chimiques
DNA Transposable Elements
0
NLR Proteins
0
Plant Proteins
0
Types de publication
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
277-283Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/J/000C0628
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/J/000CA352
Pays : United Kingdom
Références
The International Wheat Genome Sequencing Consortium. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361, eaar7191 (2018).
doi: 10.1126/science.aar7191
Montenegro, J. D. et al. The pangenome of hexaploid bread wheat. Plant J. 90, 1007–1013 (2017).
pubmed: 28231383
doi: 10.1111/tpj.13515
International Wheat Genome Sequencing Consortium (IWGSC). A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345, 1251788 (2014).
doi: 10.1126/science.1251788
He, F. et al. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat. Genet. 51, 896–904 (2019); correction 51, 1194 (2019).
pubmed: 31197271
doi: 10.1038/s41588-019-0463-2
Pont, C. et al. Tracing the ancestry of modern bread wheats. Nat. Genet. 51, 905–911 (2019).
pubmed: 31043760
doi: 10.1038/s41588-019-0393-z
Kassa, M. T. et al. A saturated SNP linkage map for the orange wheat blossom midge resistance gene Sm1. Theor. Appl. Genet. 129, 1507–1517 (2016).
pubmed: 27160855
doi: 10.1007/s00122-016-2720-4
Tadesse, W. et al. Genetic gains in wheat breeding and its role in feeding the world. Crop Breed. Genet. Genom. 1, e190005 (2019).
Zhao, Q. et al. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat. Genet. 50, 278–284 (2018).
pubmed: 29335547
doi: 10.1038/s41588-018-0041-z
Dubcovsky, J. & Dvorak, J. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316, 1862–1866 (2007).
pubmed: 17600208
pmcid: 4737438
doi: 10.1126/science.1143986
Marcussen, T. et al. Ancient hybridizations among the ancestral genomes of bread wheat. Science 345, 1250092 (2014).
pubmed: 25035499
doi: 10.1126/science.1250092
Avni, R. et al. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357, 93–97 (2017).
doi: 10.1126/science.aan0032
pubmed: 28684525
Maccaferri, M. et al. Durum wheat genome highlights past domestication signatures and future improvement targets. Nat. Genet. 51, 885–895 (2019).
pubmed: 30962619
doi: 10.1038/s41588-019-0381-3
Zimin, A. V. et al. The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. Gigascience 6, 1–7 (2017).
pubmed: 29069494
pmcid: 5691383
Winfield, M. O. et al. Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnol. J. 10, 733–742 (2012).
pubmed: 22703335
doi: 10.1111/j.1467-7652.2012.00713.x
Arora, D., Gross, T. & Brueggeman, R. Allele characterization of genes required for rpg4-mediated wheat stem rust resistance identifies Rpg5 as the R gene. Phytopathology 103, 1153–1161 (2013).
pubmed: 23841622
doi: 10.1094/PHYTO-01-13-0030-R
Adamski, N. M. et al. A roadmap for gene functional characterisation in crops with large genomes: lessons from polyploid wheat. eLife 9, e55646 (2020).
Uauy, C. Wheat genomics comes of age. Curr. Opin. Plant Biol. 36, 142–148 (2017).
pubmed: 28346895
doi: 10.1016/j.pbi.2017.01.007
Mascher, M. et al. A chromosome conformation capture ordered sequence of the barley genome. Nature 544, 427–433 (2017).
pubmed: 28447635
doi: 10.1038/nature22043
Edwards, D. et al. Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnol. J. 10, 703–708 (2012).
pubmed: 22681313
doi: 10.1111/j.1467-7652.2012.00717.x
Jordan, K. W. et al. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol. 16, 48 (2015).
pubmed: 25886949
pmcid: 4389885
doi: 10.1186/s13059-015-0606-4
Paape, T. et al. Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica. Nat. Commun. 9, 3909 (2018).
pubmed: 30254374
pmcid: 6156220
doi: 10.1038/s41467-018-06108-1
Paape, T. et al. Conserved but attenuated parental gene expression in allopolyploids: Constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica. Mol. Biol. Evol. 33, 2781–2800 (2016).
pubmed: 27413047
pmcid: 5062318
doi: 10.1093/molbev/msw141
Melonek, J., Stone, J. D. & Small, I. Evolutionary plasticity of restorer-of-fertility-like proteins in rice. Sci. Rep. 6, 35152 (2016).
pubmed: 27775031
pmcid: 5075784
doi: 10.1038/srep35152
Bernhard, T., Koch, M., Snowdon, R. J., Friedt, W. & Wittkop, B. Undesired fertility restoration in msm1 barley associates with two mTERF genes. Theor. Appl. Genet. 132, 1335–1350 (2019).
pubmed: 30659305
doi: 10.1007/s00122-019-03281-9
Whitford, R. et al. Hybrid breeding in wheat: technologies to improve hybrid wheat seed production. J. Exp. Bot. 64, 5411–5428 (2013).
pubmed: 24179097
doi: 10.1093/jxb/ert333
Keller, B., Wicker, T. & Krattinger, S. G. Advances in wheat and pathogen genomics: Implications for disease control. Annu. Rev. Phytopathol. 56, 67–87 (2018).
pubmed: 30149791
doi: 10.1146/annurev-phyto-080516-035419
Steuernagel, B. et al. Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat. Biotechnol. 34, 652–655 (2016).
pubmed: 27111722
doi: 10.1038/nbt.3543
Bariana, H. S. et al. Mapping of durable adult plant and seedling resistances to stripe rust and stem rust diseases in wheat. Aust. J. Agric. Res. 52, 1247–1255 (2001).
doi: 10.1071/AR01040
Chemayek, B. et al. Tight repulsion linkage between Sr36 and Sr39 was revealed by genetic, cytogenetic and molecular analyses. Theor. Appl. Genet. 130, 587–595 (2017).
pubmed: 27913833
doi: 10.1007/s00122-016-2837-5
Cruz, C. D. et al. The 2NS translocation from Aegilops ventricosa confers resistance to the Triticum pathotype of Magnaporthe oryzae. Crop Sci. 56, 990–1000 (2016).
pubmed: 27814405
pmcid: 5087972
doi: 10.2135/cropsci2015.07.0410
Helguera, M. et al. PCR assays for the Lr37-Yr17-Sr38 cluster of rust resistance genes and their use to develop isogenic hard red spring wheat lines. Crop Sci. 43, 1839–1847 (2003).
doi: 10.2135/cropsci2003.1839
Li, Y. & Wei, K. Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize. BMC Plant Biol. 20, 93 (2020).
pubmed: 32122306
pmcid: 7052972
doi: 10.1186/s12870-020-2288-7
Gunupuru, L. R. et al. A wheat cytochrome P450 enhances both resistance to deoxynivalenol and grain yield. PLoS ONE 13, e0204992 (2018).
pubmed: 30312356
pmcid: 6185721
doi: 10.1371/journal.pone.0204992
Li, B. et al. Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure. Plant J. 73, 952–965 (2013).
pubmed: 23253213
doi: 10.1111/tpj.12086
Gent, J. I., Wang, K., Jiang, J. & Dawe, R. K. Stable patterns of CENH3 occupancy through maize lineages containing genetically similar centromeres. Genetics 200, 1105–1116 (2015).
pubmed: 26063660
pmcid: 4574241
doi: 10.1534/genetics.115.177360
Koo, D. H., Sehgal, S. K., Friebe, B. & Gill, B. S. Structure and stability of telocentric chromosomes in wheat. PLoS ONE 10, e0137747 (2015).
pubmed: 26381743
pmcid: 4575054
doi: 10.1371/journal.pone.0137747
Schneider, K. L., Xie, Z., Wolfgruber, T. K. & Presting, G. G. Inbreeding drives maize centromere evolution. Proc. Natl Acad. Sci. USA 113, E987–E996 (2016).
pubmed: 26858403
doi: 10.1073/pnas.1522008113
pmcid: 4776452
Saxena, R. K., Edwards, D. & Varshney, R. K. Structural variations in plant genomes. Brief. Funct. Genomics 13, 296–307 (2014).
pubmed: 24907366
pmcid: 4110416
doi: 10.1093/bfgp/elu016
Harewood, L. et al. Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours. Genome Biol. 18, 125 (2017).
pubmed: 28655341
pmcid: 5488307
doi: 10.1186/s13059-017-1253-8
Himmelbach, A. et al. Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species. Plant J. 96, 1309–1316 (2018).
pubmed: 30256471
doi: 10.1111/tpj.14109
Fradgley, N. et al. A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders. PLoS Biol. 17, e3000071 (2019).
pubmed: 30818353
pmcid: 6413959
doi: 10.1371/journal.pbio.3000071
Martín, A. C., Rey, M. D., Shaw, P. & Moore, G. Dual effect of the wheat Ph1 locus on chromosome synapsis and crossover. Chromosoma 126, 669–680 (2017).
pubmed: 28365783
pmcid: 5688220
doi: 10.1007/s00412-017-0630-0
Bevan, M. W. et al. Genomic innovation for crop improvement. Nature 543, 346–354 (2017).
pubmed: 28300107
doi: 10.1038/nature22011
Luján Basile, S. M. et al. Haplotype block analysis of an Argentinean hexaploid wheat collection and GWAS for yield components and adaptation. BMC Plant Biol. 19, 553 (2019).
pubmed: 31842779
pmcid: 6916457
doi: 10.1186/s12870-019-2015-4
Fox, S. L. et al. Unity hard red spring wheat. Can. J. Plant Sci. 90, 71–78 (2010).
doi: 10.4141/CJPS09024
Hanks, S. K., Quinn, A. M. & Hunter, T. The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science 241, 42–52 (1988).
pubmed: 3291115
doi: 10.1126/science.3291115
Brueggeman, R. et al. The stem rust resistance gene Rpg5 encodes a protein with nucleotide-binding-site, leucine-rich, and protein kinase domains. Proc. Natl Acad. Sci. USA 105, 14970–14975 (2008).
pubmed: 18812501
doi: 10.1073/pnas.0807270105
pmcid: 2567477
Faris, J. D. et al. A unique wheat disease resistance-like gene governs effector-triggered susceptibility to necrotrophic pathogens. Proc. Natl Acad. Sci. USA 107, 13544–13549 (2010).
pubmed: 20624958
doi: 10.1073/pnas.1004090107
pmcid: 2922177
Luo, M. C. et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551, 498–502 (2017).
pubmed: 29143815
pmcid: 7416625
doi: 10.1038/nature24486
Borrill, P., Harrington, S. A. & Uauy, C. Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat. Plant J. 97, 56–72 (2019).
pubmed: 30407665
Dvorak, J., Mcguire, P. E. & Cassidy, B. Apparent sources of the A genomes of wheats inferred from polymorphism in abundance and restriction fragment length of repeated nucleotide-sequences. Genome 30, 680–689 (1988).
doi: 10.1139/g88-115
Watson-Haigh, N. S., Suchecki, R., Kalashyan, E., Garcia, M. & Baumann, U. DAWN: a resource for yielding insights into the diversity among wheat genomes. BMC Genomics 19, 941 (2018).
pubmed: 30558550
pmcid: 6296097
doi: 10.1186/s12864-018-5228-2
Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
pubmed: 11932250
pmcid: 187518
Slater, G. S. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).
pubmed: 15713233
pmcid: 553969
doi: 10.1186/1471-2105-6-31
Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36 (2000).
pubmed: 10592175
pmcid: 102395
doi: 10.1093/nar/28.1.33
Thornton, K. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19, 2325–2327 (2003).
pubmed: 14630667
doi: 10.1093/bioinformatics/btg316
Cheng, S. et al. Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants. Plant J. 85, 532–547 (2016).
pubmed: 26764122
doi: 10.1111/tpj.13121
Steuernagel, B. et al. Physical and transcriptional organisation of the bread wheat intracellular immune receptor repertoire. Preprint at https://doi.org/10.1101/339424 (2018).
Steuernagel, B. et al. The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire. Plant Physiol. 183, 468–482 (2020).
pubmed: 32184345
pmcid: 7271791
doi: 10.1104/pp.19.01273
Spannagl, M. et al. PGSB PlantsDB: updates to the database framework for comparative plant genome research. Nucleic Acids Res. 44 (D1), D1141–D1147 (2016).
pubmed: 26527721
doi: 10.1093/nar/gkv1130
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
pubmed: 9862982
pmcid: 148217
doi: 10.1093/nar/27.2.573
Nagaki, K. et al. Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163, 1221–1225 (2003).
pubmed: 12663558
pmcid: 1462492
doi: 10.1093/genetics/163.3.1221
Guo, X. et al. De novo centromere formation and centromeric sequence expansion in wheat and its wide hybrids. PLoS Genet. 12, e1005997 (2016).
pubmed: 27110907
pmcid: 4844185
doi: 10.1371/journal.pgen.1005997
Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907–915 (2019).
pubmed: 31375807
pmcid: 7605509
doi: 10.1038/s41587-019-0201-4
Wicker, T. et al. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol. 19, 103 (2018).
pubmed: 30115100
pmcid: 6097303
doi: 10.1186/s13059-018-1479-0
Tang, Z., Yang, Z. & Fu, S. Oligonucleotides replacing the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 for FISH analysis. J. Appl. Genet. 55, 313–318 (2014).
pubmed: 24782110
doi: 10.1007/s13353-014-0215-z
Zhao, L. et al. Cytological identification of an Aegilops variabilis chromosome carrying stripe rust resistance in wheat. Breed. Sci. 66, 522–529 (2016).
pubmed: 27795677
pmcid: 5010304
doi: 10.1270/jsbbs.16011
Komuro, S., Endo, R., Shikata, K. & Kato, A. Genomic and chromosomal distribution patterns of various repeated DNA sequences in wheat revealed by a fluorescence in situ hybridization procedure. Genome 56, 131–137 (2013).
pubmed: 23659696
doi: 10.1139/gen-2013-0003
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
pubmed: 29750242
pmcid: 6137996
doi: 10.1093/bioinformatics/bty191
Kubaláková, M., Vrána, J., Cíhalíková, J., Simková, H. & Doležel, J. Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 104, 1362–1372 (2002).
pubmed: 12582592
doi: 10.1007/s00122-002-0888-2
Brinton, J. et al. A haplotype-led approach to increase the precision of wheat breeding. Commun. Biol. https://doi.org/10.1038/s42003-020-01413-2 (2020).
Thomas, J. et al. Chromosome location and markers of Sm1: a gene of wheat that conditions antibiotic resistance to orange wheat blossom midge. Mol. Breed. 15, 183–192 (2005).
doi: 10.1007/s11032-004-5041-2
Lamb, R. J. et al. Resistance to Sitodiplosis mosellana (Diptera: Cecidomyiidae) in spring wheat (Gramineae). Can. Entomol. 132, 591–605 (2000).
doi: 10.4039/Ent132591-5
la Cour, T. et al. Analysis and prediction of leucine-rich nuclear export signals. Protein Eng. Des. Sel. 17, 527–536 (2004).
pubmed: 15314210
doi: 10.1093/protein/gzh062