title: Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL.
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.
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. jose.barrero@csiro.au.
authors.forename: Jose M
authors.initials: JM
authors.lastname: Barrero
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. colin.cavanagh@bayer.com.|Current address: Bayer CropScience, Technologiepark 38, 9052, Zwijnaarde (Gent), Belgium. colin.cavanagh@bayer.com.
authors.forename: Colin
authors.initials: C
authors.lastname: Cavanagh
authors.affiliation: CSIRO Digital Productivity & Services Flagship, GPO Box 664, Canberra, ACT 2601, Australia. klara.verbyla@csiro.au.
authors.forename: Klara L
authors.initials: KL
authors.lastname: Verbyla
authors.affiliation: Department of Environment and Primary Industries, Agriobio Center, Bundoora, VIC, 3083, Australia. josquin.tibbits@ecodev.vic.gov.au.
authors.forename: Josquin F G
authors.initials: JF
authors.lastname: Tibbits
authors.affiliation: CSIRO Digital Productivity & Services Flagship, GPO Box 780, Atherton, QLD 4883, Australia. ari.verbyla@csiro.au.
authors.forename: Arunas P
authors.initials: AP
authors.lastname: Verbyla
authors.affiliation: CSIRO Digital Productivity & Services Flagship, GPO Box 2583, Brisbane, QLD 4001, Australia. emma.huang@csiro.au.
authors.forename: B Emma
authors.initials: BE
authors.lastname: Huang
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. garry.rosewarne@depi.vic.gov.au.|Current address: Department of Environment and Primary Industries, 110 Natimuk Rd, Horsham, VIC, 3400, Australia. garry.rosewarne@depi.vic.gov.au.
authors.forename: Garry M
authors.initials: GM
authors.lastname: Rosewarne
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. stuart.stephen@csiro.au.
authors.forename: Stuart
authors.initials: S
authors.lastname: Stephen
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. penghao.wang@csiro.au.
authors.forename: Penghao
authors.initials: P
authors.lastname: Wang
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. alex.whan@csiro.au.
authors.forename: Alex
authors.initials: A
authors.lastname: Whan
authors.affiliation: Gydle, 101-1332 Av. Chanoine Morel, Québec, QC, G1S 4B4, Canada. prigault@gydle.com.
authors.forename: Philippe
authors.initials: P
authors.lastname: Rigault
authors.affiliation: Department of Environment and Primary Industries, Agriobio Center, Bundoora, VIC, 3083, Australia. matthew.hayden@ecodev.vic.gov.au.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Hayden
authors.affiliation: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. frank.gubler@csiro.au.
authors.forename: Frank
authors.initials: F
authors.lastname: Gubler
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D005838:Genotype; D018525:Germination; D005810:Multigene Family; D057445:Plant Dormancy / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D011123:Polyploidy; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA; D014908:Triticum / Q000145:classification / Q000235:genetics*
chemical_list: D010940:Plant Proteins