Monday, May 23, 2022
HomeNatureThe mosaic oat genome offers insights right into a uniquely wholesome cereal...

The mosaic oat genome offers insights right into a uniquely wholesome cereal crop


  • Vavilov, N. I. in Origin and Geography of Cultivated Vegetation (ed. Dorofeyev, V. F.) 22–135 (Cambridge Univ. Press, 1992).

  • Malzew, A. I. Wild and Cultivated Oats, Sectio Euavena Griseb. (Publ. of the All-Union Inst. of Appl. Botany and New Cultures below the Council of Folks’s Commissars of the USSR, 1930).

  • EFSA Panel on Dietetic Merchandise, Vitamin and Allergic reactions (NDA). Scientific opinion on the substantiation of a well being declare associated to oat β-glucan and reducing blood ldl cholesterol and lowered threat of (coronary) coronary heart illness pursuant to Article 14 of Regulation (EC) no. 1924/2006. EFSA J. https://doi.org/10.2903/j.efsa.2010.1885 (2010).

  • EFSA Panel on Dietetic Merchandise, Vitamin and Allergic reactions (NDA). Scientific opinion on the substantiation of well being claims associated to β-glucans from oats and barley and upkeep of regular blood LDL-cholesterol concentrations (ID 1236, 1299), enhance in satiety resulting in a discount in power consumption (ID 851, 852), discount of post-prandial glycaemic responses (ID 821, 824), and ‘digestive perform’ (ID 850) pursuant to Article 13(1) of Regulation (EC) no. 1924/2006). EFSA J. https://doi.org/10.2903/j.efsa.2011.2207 (2011).

  • Mathews, R., Kamil, A. & Chu, Y. International assessment of coronary heart well being claims for oat β-glucan merchandise. Nutr. Rev. 78, 78–97 (2020).

    PubMed 

    Google Scholar
     

  • Manni, M., Berkeley, M. R., Seppey, M. & Zdobnov, E. M. BUSCO: assessing genomic knowledge high quality and past. Curr. Protoc. 1, e323 (2021).

    PubMed 

    Google Scholar
     

  • Worldwide Wheat Genome Sequencing Consortium (IWGSC). et al. Shifting the bounds in wheat analysis and breeding utilizing a totally annotated reference genome. Science 361, eaar7191 (2018).


    Google Scholar
     

  • Monat, C. et al. TRITEX: chromosome-scale sequence meeting of Triticeae genomes with open-source instruments. Genome Biol. 20, 284 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rabanus-Wallace, M. T. et al. Chromosome-scale genome meeting gives insights into rye biology, evolution and agronomic potential. Nat. Genet. 53, 564–573 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bekele, W. A., Wight, C. P., Chao, S., Howarth, C. J. & Tinker, N. A. Haplotype-based genotyping-by-sequencing in oat genome analysis. Plant Biotechnol. J. 16, 1452–1463 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • GrainGenes: a database for Triticeae and Avena, Avena sativa, OT3098 v2, PepsiCo, https://wheat.pw.usda.gov/jb?knowledge=/ggds/oat-ot3098v2-pepsico (accessed 15 January 2022).

  • Ladizinsky, G. A brand new species of Avena from Sicily, presumably the tetraploid progenitor of hexaploid oats. Genet. Resour. Crop Evol. 45, 263–269 (1998).


    Google Scholar
     

  • Sanz, M. J. et al. A brand new chromosome nomenclature system for oat (Avena sativa L. and A. byzantina C. Koch) primarily based on FISH evaluation of monosomic strains. Theor. Appl. Genet. 121, 1541–1552 (2010).

    CAS 
    PubMed 

    Google Scholar
     

  • Maughan, P. J. et al. Genomic insights from the primary chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biol. 17, 92 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nomenclature Database, Nationwide Oat Convention E-newsletter, https://oatnews.org/nomenclature (accessed 8 March 2021).

  • Mascher, M. et al. Lengthy-read sequence meeting: a technical analysis in barley. Plant Cell 33, 1888–1906 (2021).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mascher, M. et al. A chromosome conformation seize ordered sequence of the barley genome. Nature 544, 427–433 (2017).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Chaffin, A. S. et al. A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial subgenome rearrangement. Plant Genome https://doi.org/10.3835/plantgenome2015.10.0102 (2016).

  • Yan, H. et al. Excessive-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat. Theor. Appl. Genet. 129, 2133–2149 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Santos, A. G., Livingston, D. P., Jellen, E. N., Wooten, D. R. & Murphy, J. P. A cytological marker related to winterhardiness in oat. Crop Sci. 46, 203–208 (2006).


    Google Scholar
     

  • Tinker, N. A. et al. Genome evaluation in Avena sativa reveals hidden breeding limitations and alternatives for oat enchancment. Commun. Biol. https://doi.org/10.1038/s42003-022-03256-5 (2022).

  • Alabdullah, A. Ok., Moore, G. & Martín, A. C. A duplicated copy of the meiotic gene ZIP4 preserves as much as 50% pollen viability and grain quantity in polyploid wheat. Biology 10, 290 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Griffiths, S. et al. Molecular characterization of Ph1 as a significant chromosome pairing locus in polyploid wheat. Nature 439, 749–752 (2006).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Rey, M.-D. et al. Exploiting the ZIP4 homologue throughout the wheat Ph1 locus has recognized two strains exhibiting homoeologous crossover in wheat–wild relative hybrids. Mol. Breed. 37, 95 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Moskal, Ok., Kowalik, S., Podyma, W., Łapiński, B. & Boczkowska, M. The professionals and cons of rye chromatin introgression into wheat genome. Agronomy 11, 456 (2021).

    CAS 

    Google Scholar
     

  • Dilkova, M., Jellen, E. N. & Forsberg, R. A. C-banded karyotypes and meiotic abnormalities in germplasm derived from interploidy crosses in Avena. Euphytica 111, 175–184 (2000).


    Google Scholar
     

  • Otto, S. P. The evolutionary penalties of polyploidy. Cell 131, 452–462 (2007).

    CAS 
    PubMed 

    Google Scholar
     

  • Jiao, Y. & Paterson, A. H. Polyploidy-associated genome modifications throughout land plant evolution. Philos. Trans. R. Soc. Lond. B 369, 20130355 (2014).


    Google Scholar
     

  • Grover, C. E. et al. Homoeolog expression bias and expression degree dominance in allopolyploids. New Phytol. 196, 966–971 (2012).

    CAS 
    PubMed 

    Google Scholar
     

  • van de Peer, Y., Mizrachi, E. & Marchal, Ok. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017).

    PubMed 

    Google Scholar
     

  • Ramírez-González, R. H. et al. The transcriptional panorama of polyploid wheat. Science 361, eaar6089 (2018).

    PubMed 

    Google Scholar
     

  • Garcia-Gimenez, G. et al. Focused mutation of barley (1,3;1,4)-β-glucan synthases reveals complicated relationships between the storage and cell wall polysaccharide content material. Plant J. 104, 1009–1022 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Nemeth, C. et al. Down-regulation of the CSLF6 gene leads to decreased (1,3;1,4)-β-d-glucan in endosperm of wheat. Plant Physiol. 152, 1209–1218 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wong, S. C. et al. Differential expression of the HvCslF6 gene late in grain growth might clarify quantitative variations in (1,3;1,4)-β-glucan focus in barley. Mol. Breed. 35, 20 (2015).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pinto-Sánchez, M. I. et al. Security of including oats to a gluten-free weight loss program for sufferers with celiac illness: systematic assessment and meta-analysis of medical and observational research. Gastroenterology 153, 395–409 (2017).

    PubMed 

    Google Scholar
     

  • Vinje, M. A., Walling, J. G., Henson, C. A. & Duke, S. H. Comparative gene expression evaluation of the β-amylase and hordein gene households within the creating barley grain. Gene 693, 127–136 (2019).

    CAS 
    PubMed 

    Google Scholar
     

  • Juhász, A. et al. Genome mapping of seed-borne allergens and immunoresponsive proteins in wheat. Sci. Adv. 4, eaar8602 (2018).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, Y. et al. Genome-, transcriptome- and proteome-wide analyses of the gliadin gene households in Triticum urartu. PLoS ONE 10, e0131559 (2015).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huo, N. et al. Dynamic evolution of α-gliadin prolamin gene household in homeologous genomes of hexaploid wheat. Sci. Rep. 8, 5181 (2018).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shewry, P. R. & Halford, N. G. Cereal seed storage proteins: buildings, properties and position in grain utilization. J. Exp. Bot. 53, 947–958 (2002).

    CAS 
    PubMed 

    Google Scholar
     

  • Black, M. & Derek Bewley, J. Seed Know-how and Its Organic Foundation (CRC Press, 2000).

  • Sollid, L. M. et al. Replace 2020: nomenclature and itemizing of celiac disease-relevant gluten epitopes acknowledged by CD4+ T cells. Immunogenetics 72, 85–88 (2020).

    PubMed 

    Google Scholar
     

  • Hardy, M. Y. et al. Ingestion of oats and barley in sufferers with celiac illness mobilizes cross-reactive T cells activated by avenin peptides and immuno-dominant hordein peptides. J. Autoimmun. 56, 56–65 (2015).

    CAS 
    PubMed 

    Google Scholar
     

  • Adamski, N. M. et al. A roadmap for gene useful characterisation in crops with giant genomes: classes from polyploid wheat. eLife 9, e55646 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chawade, A. et al. Growth and characterization of an oat TILLING-population and identification of mutations in lignin and β-glucan biosynthesis genes. BMC Plant Biol. 10, 86 (2010).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • von Wettstein-Knowles, P. Ecophysiology with barley eceriferum (cer) mutants: the results of humidity and wax crystal construction on yield and vegetative parameters. Ann. Bot. 126, 301–313 (2020).


    Google Scholar
     

  • Wang, X., Kong, L., Zhi, P. & Chang, C. Replace on cuticular wax biosynthesis and its roles in plant illness resistance. Int. J. Mol. Sci. 21, 5514 (2020).

    CAS 
    PubMed Central 

    Google Scholar
     

  • von Wettstein-Knowles, P. The polyketide elements of waxes and the Cer-cqu gene cluster encoding a novel polyketide synthase, the β-diketone synthase, DKS. Vegetation 6, 28 (2017).


    Google Scholar
     

  • Schneider, L. M. et al. The Cer-cqu gene cluster determines three key gamers in a β-diketone synthase polyketide pathway synthesizing aliphatics in epicuticular waxes. J. Exp. Bot. 67, 2715–2730 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hen-Avivi, S. et al. A metabolic gene cluster within the wheat W1 and the barley Cer-cqu loci determines β-diketone biosynthesis and glaucousness. Plant Cell 28, 1440–1460 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tinker, N. A. et al. A SNP genotyping array for hexaploid oat. Plant Genome 7, 1–8 (2014).


    Google Scholar
     

  • Bandi, V. & Gutwin, C. Interactive exploration of genomic conservation. In Proceedings of the forty sixth Graphics Interface Convention 2020 (GI’20) https://synvisio.github.io (2020).

  • Mascher, M. et al. Pseudomolecules and annotation of the third model of the reference genome sequence meeting of barley cv. Morex [Morex V3]. e!DAL Plant Genomics and Phenomics Analysis Information Repository (PGP) https://doi.org/10.5447/ipk/2021/3 (accessed 3 December 2020).

  • Blake, V. C. et al. GrainGenes: centralized small grain assets and digital platform for geneticists and breeders. Database 2019, baz065 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • RELATED ARTICLES

    LEAVE A REPLY

    Please enter your comment!
    Please enter your name here

    Most Popular

    Recent Comments