Identification of SNP markers linked with known oat stem rust resistance genes using bulked segregant analysis

Oat stem rust, caused by Puccinia graminis f. sp. avenae Eriks. & E. Henn. (Pga), can reduce yield and quality in oat, Avena sativa L. (Roelfs and Long 1980 ). Resistance breeding has been used as a cost-effective strategy to prevent these losses. There are currently 17 numbered oat stem rust resistance genes (Pg), and one gene complex known as Pg-a. Twelve of the numbered Pg genes are used as standard differentials to identify pathogenic races of Pga (Fetch Jr. and Jin 2007). While RFLP and RAPD markers for Pg9 and Pg13 have been previously reported (O'Donoughue et al. 1996), there has been no systematic search for markers linked to all known Pg genes. Objectives of this study were to 1) generate crosses of each standard differential and the Pg-a complex in two susceptible genetic backgrounds, and 2) find SNP markers linked to resistance using bulked segregant analysis. Accessions with Pg8 (CIav 9321; with Rodney 0 background) and the Pg-a complex (CIav 9339) were crossed to the susceptible A. sativa cultivars ‘Marvellous’ and ‘Otana’. A. strigosa accession CIav 6956 with Pg6 was crossed with the susceptible A. strigosa accessions CIav 2524 and PI 573582. Populations were advanced to F2:3 and 10 seedlings from each of 70 families, parents, and F1s were inoculated with Pga race KBD (virulent to Pg2, Pg3, Pg4, and Pg15 and avirulent to Pg1, Pg6, Pg8, Pg9, Pg10, Pg12, Pg13, Pg16 and the Pg-a complex). Homozygosity in the F2:3 families was verified in the F2:4. F1s obtained from crosses with the Pg6, Pg8 and Pg-a complex were resistant, indicating dominant inheritance. A 1:1 segregation ratio of homozygous F2:3 families in the ‘Otana’/Pg6 and ‘Otana’/Pg8 crosses indicated the presence of a single dominant resistant gene. The segregation ratio of 2 resistant to 1 susceptible F2:3 families in the ‘Otana’/Pg-a was not consistent with previous work that concluded the Pg-a complex consisted of the recessive Pg12, and at least one other recessive Pg gene (Fetch Jr. 2006). The parents, F1s, and families that were homozygous for susceptibility from the ‘Otana’/Pg8, ‘Otana’/Pg-a, and PI 573582/Pg6 crosses were genotyped with the Illumina Oat Consortium 6K SNP BeadArray. Markers linked to resistance will be identified when genotyping data are available. Marker information obtained from this project can be used to identify new Pg resistance (Steinberg et al. 2005), and facilitate selection of progeny with multiple resistant genes.