A robust molecular marker for the stem rust resistance gene, Sr22, effective against the Ug99 strain and derived lineages as well as Indian and Australian isolates was tested on a wide range of Indian and Australian wheat genotypes being used in cultivar development. The marker previously described in the SRA preceding the current project, proved to be highly diagnostic for the presence or absence of the Sr22 resistance. Following on from validating the utility of the marker, the information required for utilisation in "marker assisted wheat breeding" has been disseminated to participating scientists/institutions in the India-Australia wheat improvement program.
As part of the ongoing effort to identify additional stem rust resistance genes that interact with the durable adult plant leaf and stripe rust resistance gene (Lr34/Yr18) to provide enhanced stem rust resistance against Ug99 and other strains, F2 families derived from RL6058 and Chris were scored for stem rust resistance at Cobbitty in the 2009 field season. The wheat genotypes, Chris and RL6058, carry Lr34/Yr18 and an unknown number of stem rust resistance genes. To ensure reliable stem rust infection and rust scores, the F3 progeny will be tested in Wellington (India) and Cobbitty (Australia) in 2010. Preliminary efforts to identify the unknown stem rust resistance genes using molecular marker-genetic linkage analysis pointed to a region on wheat chromosome 2B as harbouring the stem rust resistance gene(s).
Objective 3 of the project was aimed at making comparisons of variability in the stem rust pathogen between India and Australia. These studies are expected to contribute to the overall project aim of developing more durable resistance to stem rust by improving our ability to pre-empt pathogen change by gaining a deeper understanding of how P. graminis f. sp. tritici (Pgt) generates genetic variability. Discussions were held with Dr Mohinder Prashar (Directorate of Wheat Research Regional Station at Flowerdale) in India during March 2010 on the methods used in wheat stem rust surveillance and identification of pathotypes of stem rust in India and Australia. Although delays to the start of the project slowed progress in some activities, planning is well advanced and at this stage, no foreseeable problems are expected in delivering the contracted milestones under objective 3 by project completion.

Two types of stem rust resistance to the Ug99 stem rust pathotype and other isolates from India and Australia are investigated as through the ACIAR-ICAR project. The resistance genes Sr13 and Sr22 are of the seedling resistance category. We previously reported on a diagnostic marker for Sr22 distributed to Indian and Australian wheat breeding programs. In keeping with a commitment to the wider wheat rust research community to ensure that the type and source of resistance in cultivars and breeding materials are well characterised the marker information from the ACIAR project has now been disseminated widely through publication in an international journal.
The other category of stem rust resistance is the post seedling resistance commonly referred to as adult plant resistance (APR). New sources of stem rust APR continues to be the focus of the project using germplasm collected in the early 1900's, which are referred to as the Watkins collection. Two wheat genotypes AUS28082 and AUS27856 from the collection were established to carry adult plant stem rust resistance. However, inheritance of the APR is not known. F3 populations from two crosses AUS28082/Yitpi and AUS27856/Yitpi were screened during the cropping season in 2009. Marker genotyping using known APR genes, Sr2 and Lr34-linked markers, suggested that these genotypes carry adult plant resistance gene(s) different to these known genes. Two F3 families showing putatively single gene segregation from the respective population were identified. Up to 200 F3 seeds of each of these families were space-planted to generate F3 equivalent of monogenically segregating populations (MSPs) during the crop season 2010. These progenies will be screened against stem rust at Cobbitty during the 2011 cropping season. Phenotypic results will be used to pool DNA samples from putative homozygous resistant and susceptible plants to determine chromosomal location of APR to stem rust. AUS28082/Yitpi-derived F5 population will be planted in Wellington, India and Cobbitty Australia during 2011 crop season.
Another component of the APR work is based on additional stem rust resistance genes that interact with the durable adult plant leaf and stripe rust resistance gene (Lr34/Yr18) to provide enhanced stem rust resistance against Ug99, found in wheat genotypes such as Chris and the Thatcher derivative, RL6058. Field trials in 2010 at Cobbitty and Wellington in India failed to provide reliable stem rust scores for APR in RL6058 and Chris crosses. Some of the lines showed differences in flowering time and appeared to be a confounding factor in the stem rust phenotype evaluations. We selected a subset with similar flowering time for subsequent rust phenotyping. We are phenotyping lines in three locations (Kenya, Minnesota and Australia) in 2011 to ensure that we receive reliable rust scores from at least one of these locations.
A region on wheat chromosome 2B that is linked to stem rust resistance was identified in Thatcher background and more SSR markers were mapped to the linkage group. We also identified additional SSRs which are polymorphic between parental lines to help facilitate the process of identifying other genomic regions involved in the improved stem rust resistance..