High-resolution mapping of genes involved in plant stage-specific partial resistance of barley to leaf rust

Abstract

Partial resistance quantitative trait loci (QTLs) Rphq11 and rphq16 against Puccinia hordei isolate 1.2.1 were previously mapped in seedlings of the mapping populations Steptoe/Morex and Oregon Wolfe Barleys, respectively. In this study, QTL mapping was performed at adult plant stage for the two mapping populations challenged with the same rust isolate. The results suggest that Rphq11 and rphq16 are effective only at seedling stage, and not at adult plant stage. The cloning of several genes responsible for partial resistance of barley to P. hordei will allow elucidation of the molecular basis of this type of plant defence. A map-based cloning approach requires to fine-map the QTL in a narrow genetic window. In this study, Rphq11 and rphq16 were fine-mapped using an approach aiming at speeding up the development of plant material and simplifying its evaluation. The plant materials for fine-mapping were identified from early plant materials developed to produce QTL-NILs. The material was first selected to carry the targeted QTL in heterozygous condition and susceptibility alleles at other resistance QTLs in homozygous condition. This strategy took four to five generations to obtain fixed QTL recombinants (i.e., homozygous resistant at the Rphq11 or rphq16 QTL alleles, homozygous susceptible at the non-targeted QTL alleles). In less than 2 years, Rphq11 was fine-mapped into a 0.2-cM genetic interval and a 1.4-cM genetic interval for rphq16. The strongest candidate gene for Rphq11 is a phospholipid hydroperoxide glutathione peroxidase. Thus far, no candidate gene was identified for rphq16.

Keywords: Barley; High resolution mapping; Puccinia; Quantitative trait locus (QTL); Resistance.

Fig. 1

Alignment of a the integrated map “Marcel 2009” and b the high-resolution map generated in this study, at the Rphq11 region on barley chromosome 2HL with c the physical map of rice chromosome 4 and d the physical map of B. distachyon chromosome Bd5. The filled grey areas inside chromosome bars indicate the position of Rphq11. The bold marker on a is the peak marker of Rphq11. The bold markers on b are the flanking markers used for recombinant screening, and the markers with an asterisk on b are synteny-based markers. The dashed lines show homologous sequences found between only two of the three species barley, rice and B. distachyon

Fig. 2

Alignment of a the integrated map “Marcel 2009” and b the high-resolution map generated in this study, at the rphq16 region on barley chromosome 5HL with c the physical map of rice chromosome 3 and d the physical map of B. distachyon Bd1. The filled grey areas inside chromosome bars indicate the position of rphq16. The bold marker on a is the peak marker of rphq16. The bold markers on b are the flanking markers used for recombinant screening, and the markers with an asterisk on b are synteny-based markers. The dashed line shows a homologous sequence between barley and B. distachyon, which was only found in rice on another chromosome

Fig. 3

Graphical genotypes and phenotype means (RLP50S) for fixed QTL recombinants of a Rphq11 and b rphq16; the phenotype means were compiled from results of the different rounds of disease test. The white bars represent homozygous SusPtrit. Black bars represent homozygous Steptoe (a) or Dom (b). Grey bars represent intervals where recombination took place. RLP50S values with an asterisk are significantly longer than the RLP50S on SusPtrit. The number between two markers on the chromosome bar indicates the recombination frequency observed. The new genetic window of Rphq11 and rphq16 is indicated between the long dashed lines