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

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; Frank Gubler

doi:10.1186/s13059-015-0665-6

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

Journal article

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

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, …

Genome biology, Vol.16(1), 93

2015

DOI: https://doi.org/10.1186/s13059-015-0665-6

PMCID: PMC4443510

PMID: 25962727

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Abstract

Chromosome Mapping

Chromosomes, Plant - genetics

Gene Expression Profiling

Gene Expression Regulation, Plant

Gene Silencing

Genotype

Germination

Multigene Family

Plant Dormancy - genetics

Plant Proteins - genetics

Polyploidy

Quantitative Trait Loci

Sequence Analysis, RNA

Triticum - classification

Triticum - genetics

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.

Details

Title: Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL
Authors/Creators: Jose M Barrero - Commonwealth Scientific and Industrial Research Organisation
Colin Cavanagh - Commonwealth Scientific and Industrial Research Organisation
Klara L Verbyla - Commonwealth Scientific and Industrial Research Organisation
Josquin F G Tibbits - Department of Environment, Land, Water and Planning
Arunas P Verbyla - Commonwealth Scientific and Industrial Research Organisation
B Emma Huang - CSIRO Digital Productivity & Services Flagship, GPO Box 2583, Brisbane, QLD 4001, Australia. emma.huang@csiro.au
Garry M Rosewarne - Commonwealth Scientific and Industrial Research Organisation
Stuart Stephen - Commonwealth Scientific and Industrial Research Organisation
Penghao Wang - Commonwealth Scientific and Industrial Research Organisation
Alex Whan - Commonwealth Scientific and Industrial Research Organisation
Philippe Rigault - Gydle, 101-1332 Av. Chanoine Morel, Québec G1S 4B4, QC, Canada
Matthew J Hayden - Department of Environment, Land, Water and Planning
Frank Gubler - Commonwealth Scientific and Industrial Research Organisation
Publication Details: Genome biology, Vol.16(1), 93
Publisher: Springer Nature
Identifiers: 991005569355207891
Murdoch Affiliation: School of Medical, Molecular and Forensic Sciences
Language: English
Resource Type: Journal article

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Collaboration types: International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biotechnology & Applied Microbiology; Genetics & Heredity
ESI research areas: Molecular Biology & Genetics