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Genome Biol. 2015 May 12;16:93. doi: 10.1186/s13059-015-0665-6.

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

Author information

1
CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. jose.barrero@csiro.au.
2
CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. colin.cavanagh@bayer.com.
3
Current address: Bayer CropScience, Technologiepark 38, 9052, Zwijnaarde (Gent), Belgium. colin.cavanagh@bayer.com.
4
CSIRO Digital Productivity & Services Flagship, GPO Box 664, Canberra, ACT 2601, Australia. klara.verbyla@csiro.au.
5
Department of Environment and Primary Industries, Agriobio Center, Bundoora, VIC, 3083, Australia. josquin.tibbits@ecodev.vic.gov.au.
6
CSIRO Digital Productivity & Services Flagship, GPO Box 780, Atherton, QLD 4883, Australia. ari.verbyla@csiro.au.
7
CSIRO Digital Productivity & Services Flagship, GPO Box 2583, Brisbane, QLD 4001, Australia. emma.huang@csiro.au.
8
CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. garry.rosewarne@depi.vic.gov.au.
9
Current address: Department of Environment and Primary Industries, 110 Natimuk Rd, Horsham, VIC, 3400, Australia. garry.rosewarne@depi.vic.gov.au.
10
CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. stuart.stephen@csiro.au.
11
CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. penghao.wang@csiro.au.
12
CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. alex.whan@csiro.au.
13
Gydle, 101-1332 Av. Chanoine Morel, Québec, QC, G1S 4B4, Canada. prigault@gydle.com.
14
Department of Environment and Primary Industries, Agriobio Center, Bundoora, VIC, 3083, Australia. matthew.hayden@ecodev.vic.gov.au.
15
CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. frank.gubler@csiro.au.

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.

PMID:
25962727
PMCID:
PMC4443510
DOI:
10.1186/s13059-015-0665-6
[Indexed for MEDLINE]
Free PMC Article

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