Fine-mapping of the leaf rust Lr34 locus in Triticum aestivum (L.) and characterization of large germplasm collections support the ABC transporter as essential for gene function

Abstract

Leaf rust resistance gene Lr34 is likely the most important leaf rust gene characterized to date. It has been characterized as an adult plant resistance gene and is known to enhance the resistance of other leaf rust resistance genes and to condition resistance to a number of other diseases. Located on chromosome 7D, this gene was identified to be one of six co-located genes of which, an ABC transporter was shown to be the only valid candidate. Ten new molecular markers were developed spanning the Lr34 locus, including six novel microsatellite markers (cam), one insertion site-based polymorphism marker (caISBP), two single nucleotide polymorphisms (caSNP), and one gene-specific marker (caIND). Using these new markers and others that were previously published, a comparative fine map of the locus was constructed from five segregating populations representing 1,742 lines. Identification of a susceptible line with a recombination in the 4.9 kb interval between caSNP4 located in the ABC transporter gene and cam8 located just upstream of this gene provided further evidence to support the identity of the ABC transporter as Lr34 by ruling out four of the adjacent genes. Originally, three mutations forming two haplotypes had been described for the ABC transporter gene. A third combination of the three mutations and an additional rare mutation in exon 22 were subsequently described. We identified an additional novel mutation in exon 10 that would cause a frameshift and is likely non-functional. This mutation was only found in Lr34- lines and constituted a novel molecular haplotype. Characterization of two germplasm collections of 700 Triticum aestivum lines permitted us to gain an understanding of the frequency of the ABC haplotypes characterized to date and their distribution in germplasm from and around the world. In addition to the four haplotypes previously described, a fifth haplotype was found in two of the 700 lines from the germplasm collections. These lines displayed the deletion in indel 11 characteristic of Lr34+ lines, but are likely susceptible to leaf rust. Mapping and haplotyping data suggest that of all the markers described herein, marker caIND11 is the best diagnostic marker for marker-assisted selection of Lr34 because it is co-dominant, robust and with the exception of 2/700 lines, it is highly diagnostic. Other markers are also described to provide alternatives for laboratories with different technologies.

Distribution and haplotype diversity of WKS resistance genes in wild emmer wheat natural populations

“…Alleles of resistant (Lr34res-D) and susceptible (Lr34sus-D) cultivars are characterized by only three mutations ). Only five major Lr34 haplotypes, either representing mutated versions of Lr34res-D or variants of Lr34sus-D, were identified in the wheat gene pool (Dakouri et al 2010(Dakouri et al , 2014Lagudah et al 2009;McCallum et al 2012). A recent study of a collection of 252 accessions of the D-genome progenitor of bread wheat, Aegilops tauschii, revealed very low nucleotide variation in Lr34 (π = 0.0011; Krattinger et al 2013), similar to the results presented here for Yr36.…”

“…The characterization of nucleotide diversity of the leaf rust QR gene Lr34 revealed relatively lowsequence diversity. In the wheat gene pool, two predominant Lr34 alleles (Lr34res-D and Lr34sus-D) were found that differ by only two critical codons in exon 11 and exon 12 (Dakouri et al 2010;Krattinger et al 2009Krattinger et al , 2011Lagudah et al 2009;McCallum et al 2012). …”

Recent emergence of the wheat Lr34 multi-pathogen resistance: insights from haplotype analysis in wheat, rice, sorghum and Aegilops tauschii

“…The tyrosine residue at position 634 of LR34sus-D is highly conserved among different ABCG proteins in various plant species (Krattinger et al 2011). Several additional Lr34 alleles have been identified at lower frequencies in the wheat genepool (Dakouri et al 2010;Lagudah et al 2009;McCallum et al 2012). However, none of these were associated with disease resistance and they either represent In this study we examined Lr34 homoeologs and orthologs in a set of wheat, rice and sorghum genotypes.…”

Distribution of Leaf Tip Necrosis Genes and its Association with Expression of Lesion Mimic Genes and Resistance to Spot Blotch in Spring Wheat

“…It was reported that developmentally regulated resistance is correlated with elevated Lr34 transcript levels in flag leaves of adult plants. There are several allelic forms of the Lr34 gene that have been identified in the wheat germplasm, with two alleles occurring at a high frequency [6] . Resistance allele (Lr34res) differs by only two amino acid changes from the other allelic forms associated with susceptibility (Lr34sus) and so…”