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Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1and A2as candidates for a major dormancy QTL
Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1and A2as candidates for a major dormancy QTL
- Source :
- Genome Biology; December 2015, Vol. 16 Issue: 1 p1-18, 18p
- Publication Year :
- 2015
-
Abstract
- 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. 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 19family. 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 PM19genes are positive regulators of seed dormancy. 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
- Language :
- English
- ISSN :
- 14747596 and 1474760X
- Volume :
- 16
- Issue :
- 1
- Database :
- Supplemental Index
- Journal :
- Genome Biology
- Publication Type :
- Periodical
- Accession number :
- ejs36073036
- Full Text :
- https://doi.org/10.1186/s13059-015-0665-6