A single-nucleotide polymorphism that accounts for allelic variation in the Lr34 gene and leaf rust reaction in hard winter wheat

Abstract

Leaf rust, caused by Puccinia triticina Eriks, is one of the most common and persistent wheat diseases in the US Great Plains. We report that the Lr34 gene was mapped in the center of a QTL for leaf rust reaction and explained 18-35% of the total phenotypic variation in disease severity of adult plants in a Jagger x 2174 population of recombinant inbred lines (RILs) field-tested for 3 years. The sequence of the complete Lr34 gene was determined for the susceptible Jagger allele and for the resistant 2174 allele. The two alleles had exactly the same sequence as the resistant allele reported previously in Chinese Spring at three polymorphic sites in intron 4, exon 11, and exon 12. A G/T polymorphism was found in exon 22, where a premature stop codon was found in the susceptible Jagger allele (Lr34E22s), confirming a previous report, due to a point mutation compared with the resistant 2174 allele (Lr34E22r). We have experimentally demonstrated a tight association between the point mutation at exon 22 of Lr34 and leaf rust susceptibility in a segregating biparental population. A PCR marker was developed to distinguish between the Lr34E22r and Lr34E22s alleles. A survey of 33 local hard winter wheat cultivars indicated that 7 cultivars carry the Lr34E22s allele and 26 cultivars carry the Lr34E22r allele. This study significantly improves our genetic understanding of allelic variation in the Lr34 gene and provides a functional molecular tool to improve leaf rust resistance in a major US wheat gene pool.

Molecular genetics of race non-specific rust resistance in wheat

“…Derived cultivars of Jagger that also carry the Lr34/Yr18d haplotype have been reported in six North American wheat genotypes, viz. Fuller, Jagalene, Ok Bullet, Protection CL, Santa Fe, and Shocker (Cao et al 2010). …”

“…A rare haplotype ( Fig. 2) was also found in introns 4 and 6 in some plants of line '2174' based on additional sequencing (Cao et al 2010) and this haplotype was designated Lr34/Yr18e. From the studies of Dakouri et al (2010) on 700 wheat genotypes sourced from a germplasm pool referred to as a 'world collection' and 'North American collection' two new haplotypes with sequence variants in exons were identified.…”

“…The cultivar Jagger retains all the polymorphic sequences found in Lr34/Yr18a but is susceptible to leaf rust (Kolmer et al 2008;Lagudah et al 2009). Complete sequencing of the ABC transporter in Jagger showed that the encoding gene carried a G/T SNP in exon 22 resulting in a premature stop codon and therefore causing a truncation in the gene product rendering it non-functional Cao et al 2010). The Jagger haplotype is designated Lr34/Yr18d (Fig.…”

“…2). Cosegregation of the defective (susceptible) Lr34/Yr18d haplotype was documented in a recombinant inbred line family derived from Jagger/Line '2174' from which the Lr34/Yr18a haplotype inherited from '2174' was associated with leaf rust resistance in field studies over 3 years (Cao et al 2010). A rare haplotype ( Fig.…”

“…However, the challenges posed by parental germplasm sources such as H45 and haplotypes such as Lr34/Yr18d in Jagger means that caution needs to be exercised in using the perfect markers where these genotypes are an integral component of a breeding program. In the case of Jagger, specific markers were developed to detect and therefore select against the Lr34/Yr18d haplotype Cao et al 2010). Derived cultivars of Jagger that also carry the Lr34/Yr18d haplotype have been reported in six North American wheat genotypes, viz.…”