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Type: Journal article
Title: Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL
Author: Barrero, J.
Cavanagh, C.
Verbyla, K.
Tibbits, J.
Verbyla, A.
Huang, B.
Rosewarne, G.
Stephen, S.
Wang, P.
Whan, A.
Rigault, P.
Hayden, M.
Gubler, F.
Citation: Genome Biology, 2015; 16(1):93-1-93-18
Publisher: BioMed Central
Issue Date: 2015
ISSN: 1474-7596
Statement of
Jose M. Barrero, Colin Cavanagh, Klara L. Verbyla, Josquin F.G. Tibbits, Arunas P. Verbyla, B. Emma Huang, Garry M. Rosewarne, Stuart Stephen, Penghao Wang, Alex Whan, Philippe Rigault, Matthew J. Hayden, and Frank Gubler
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.
Keywords: Chromosomes, Plant; Triticum; Plant Proteins; Chromosome Mapping; Gene Expression Profiling; Sequence Analysis, RNA; Germination; Gene Expression Regulation, Plant; Gene Silencing; Genotype; Polyploidy; Multigene Family; Quantitative Trait Loci; Plant Dormancy
Rights: © 2015 Barrero et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
RMID: 0030029714
DOI: 10.1186/s13059-015-0665-6
Appears in Collections:Agriculture, Food and Wine publications

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