Genetic analysis and development of molecular markers linked with rust resistance in wheat

The main aim of this study was to develop closely linked markers for rust resistance genes Lr48, Lr49 and Sr48. In addition, mapping of adult plant stripe rust resistance in a landrace Aus27284 was also performed. Close SNP-Lr48 associations were identified using the iSelect 90K Infinium Array. Five SNP markers co-segregated with Lr48 and IWB70147 mapped 0.3 cM proximal. Kompetitive allele-specific PCR (KASP) assays were developed for linked SNP. In contrast, the KASP markers developed from the iSelect 90K Infinium SNP array for Lr49 did not result in close marker-trait association. Sequence comparison of flow sorted chromosome 4B from parents VL404 (Lr49) and WL711 (lr49) resulted in close association of sunKASP_21 (0.4 cM) with Lr49. The Arina/Cezanne RIL population was used to develop markers linked with Sr48 using the DArTseq platform and the iSelect 90K Infinium SNP Array. DArTseq based linkage map located Sr48 on the short arm of chromosome 2D. Marker sun590 derived from a DArTseq marker mapped 0.4 cM distal to Sr48. Sr48 was earlier mapped in the long arm of chromosome 2A in the Arina/Forno RIL population based on repulsion linkage with Yr1. The detection of 2AL-2DS translocation in Forno through genomic in-situ hybridisation (GISH) appears to have resulted in pseudo-linkage to locate Sr48 in chromosome 2AL. Aus27284 was susceptible to stripe rust at the seedling stage and exhibited resistance in field experiments. Genetic analysis showed monogenic segregation and the resistance gene was temporarily designated YrAW11. YrAW11 was located on chromosome 3BS near the centromere and KASP¬_65624/KASP_58449 and KASP_53113 flanked this locus. The closely linked markers identified in this study were tested on a set of Australian and Nordic wheat genotypes to validate their suitability for marker assisted selection (MAS). The results indicated that IWB70147, sunKASP_21, sun590 and KASP-53113 can be used for MAS of Lr48, Lr49, Sr48 and YrAW11, respectively