Genetic Characterisation of the Slow Rusting Stripe Rust QTL (QYr.sgi-4A.1) of Kariega

The multi-pathogen Lr34/Yr18/Sr57/Pm38 resistance gene is one of a few genes proven to be effective against all three wheat rusts over decades. Cloning of this slow rusting gene located on 7D, revealed that it encodes a full-size ATP-binding cassette (ABC) transporter of the ABCG subfamily. Kariega was the first wheat cultivar in South Africa to be subjected to a linkage mapping approach to unravel the genetics of a quantitative trait. Using a QTL analysis approach, its adult plant stripe rust resistance components were determined and verified i.e.: Lr34/Yr18/Sr57/Pm38 (7D), QYr-sgi.2B.1 (2B) and QYr-sgi4A.1 (4A). Similar to Lr34/Yr18 (Lr34-D), the slow-rusting nature of QYr-sgi4A.1 on 4AL is of particular interest. Krattinger et al. identified and characterised homoeologous and orthologous Lr34 genes in hexaploid wheat and other grasses. The homoeologs were identified on 4AL (Lr34-B) and 7A (Lr34-A) of which the latter’s sequence is disrupted by the insertion of repetitive elements. The homoeologous LR34-B protein (97% amino acid identity with LR34-D) has the susceptible haplotype for the two critical polymorphisms that distinguish the LR34 proteins of susceptible from resistant wheat cultivars. In addition, by comparing the map location of Lr34-B with that of QYr-sgi4A.1, Krattinger concluded that the slow rusting QYr-sgi4A.1 maps distal to Lr34-B and therefore seems to be a different genetic element. In this study we report on the validation of the uniqueness of QYr-sgi4A.1 by sequencing sections of Lr34-B in Kariega and Avocet S and the analysis of the QYr-sgi4A.1 region using the Illumina iSelect 90K wheat SNP array.