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    Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL

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    Author
    Barrero, JM; Cavanagh, C; Verbyla, KL; Tibbits, JFG; Verbyla, AP; Huang, BE; Rosewarne, GM; Stephen, S; Wang, P; Whan, A; ...
    Date
    2015-05-12
    Source Title
    Genome Biology
    Publisher
    BMC
    University of Melbourne Author/s
    Rosewarne, Garry
    Affiliation
    Veterinary and Agricultural Sciences
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Barrero, J. M., Cavanagh, C., Verbyla, K. L., Tibbits, J. F. G., Verbyla, A. P., Huang, B. E., Rosewarne, G. M., Stephen, S., Wang, P., Whan, A., Rigault, P., Hayden, M. J. & Gubler, F. (2015). Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL. GENOME BIOLOGY, 16 (1), https://doi.org/10.1186/s13059-015-0665-6.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/255292
    DOI
    10.1186/s13059-015-0665-6
    Abstract
    BACKGROUND: Next-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation. However, in species with large polyploid genomes, such as bread wheat, the ability to rapidly identify genes underlying quantitative trait loci (QTL) remains non-trivial. To overcome this, we introduce a novel pipeline that analyses, by RNA-sequencing, multiple near-isogenic lines segregating for a targeted QTL. RESULTS: We use this approach to characterize a major and widely utilized seed dormancy QTL located on chromosome 4AL. It exploits the power and mapping resolution afforded by large multi-parent mapping populations, whilst reducing complexity by using multi-allelic contrasts at the targeted QTL region. Our approach identifies two adjacent candidate genes within the QTL region belonging to the ABA-induced Wheat Plasma Membrane 19 family. One of them, PM19-A1, is highly expressed during grain maturation in dormant genotypes. The second, PM19-A2, shows changes in sequence causing several amino acid alterations between dormant and non-dormant genotypes. We confirm that PM19 genes are positive regulators of seed dormancy. CONCLUSIONS: The efficient identification of these strong candidates demonstrates the utility of our transcriptomic pipeline for rapid QTL to gene mapping. By using this approach we are able to provide a comprehensive genetic analysis of the major source of grain dormancy in wheat. Further analysis across a diverse panel of bread and durum wheats indicates that this important dormancy QTL predates hexaploid wheat. The use of these genes by wheat breeders could assist in the elimination of pre-harvest sprouting in wheat.

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