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

Jose M Barrero,Matthew J Hayden,Penghao Wang,Philippe Rigault,Stuart Stephen,Klara L Verbyla,Garry M Rosewarne,Alex Whan,Josquin F.G Tibbits,Frank Gubler,B Emma Huang,Arunas P Verbyla,Colin Cavanagh

doi:10.1186/s13059-015-0665-6

Abstract

BackgroundNext-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.ResultsWe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0665-6) contains supplementary material, which is available to authorized users.

Highlights

Next-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation
Dormancy was measured by calculating the Germination Index (GI) of grain harvested at maturity
Using a wheat Multi-parent Advanced Generation Inter-Cross (MAGIC) population, we have identified several dormancy quantitative trait loci (QTL) and have targeted for genetic analysis the major one, which is located on chromosome 4AL

Summary

Introduction

Next-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation. In species with large polyploid genomes, such as bread wheat, the ability to rapidly identify genes underlying quantitative trait loci (QTL) remains non-trivial. Seed dormancy is an adaptive trait in plants that imposes a temporal block on germination even under apparent favorable conditions. Barrero et al Genome Biology (2015) 16:93 identified across multiple populations, including the major QTL which is located on chromosome 4AL [1, 4] This QTL can explain up to 40 % of the dormancy variability in some populations and, it has been a major target for scientists and breeders over the past decade, its genetic nature has remained unknown [1]. Significant challenges remain for identifying the genetic variants underlying QTL in crops that have large, polyploid and poorly sequenced genomes. The most powerful aspect of this approach is the ability to exploit the contrast between the multiple alleles carried by the MAGIC parents, which enables accurate detection of QTL-linked single nucleotide polymorphisms (SNPs) and of differential gene expression within a QTL region

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Discussion

Conclusion