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Races belonging to Ug99 lineage of stem rust fungus  Puccinia   graminis  f. sp.  tritici  ( Pgt ) continue to pose a threat to wheat ( Triticum   aestivum  L.) production in various African countries. Growing resistant varieties is the most economical and environmentally friendly control measure. Recombinant inbred line (RIL) populations from the crosses of susceptible parent ‘Cacuke’ with the resistant parents ‘Huhwa’ and ‘Yaye’ were phenotyped for resistance at the seedling stage to  Pgt  race TTKSK (Ug99) and in adult plants in field trials at Njoro, Kenya for two seasons in 2016. Using the Affymetrix Axiom breeders SNP array, two stem rust resistance genes, temporarily designated as  SrH  and  SrY , were identified and mapped on chromosome arm 2BL through selective genotyping and bulked segregant analysis (BSA), respectively. Kompetitive allele specific polymorphism (KASP) markers and simple sequence repeat (SSR) markers were used to saturate chromosome arm 2BL in both RIL populations.  SrH  mapped between markers  cim109  and  cim114  at a distance of 0.9 cM proximal, and  cim117  at 2.9 cM distal.  SrY  was flanked by markers  cim109  and  cim116  at 0.8 cM proximal, and  IWB45932  at 1.9 cM distal. Two Ug99-effective stem rust resistance genes derived from bread wheat,  Sr9h  and  Sr28 , have been reported on chromosome arm 2BL. Infection types and map position in Huhwa and Yaye indicated that  Sr28  was absent in both the parents. However, susceptible reactions produced by resistant lines from both populations against  Sr9h -virulent race TTKSF+ confirmed the presence of a common resistance locus  Sr9h  in both lines. Test of allelism is required to establish genetic relationships between genes identified in present study and  Sr9h . Marker  cim117  linked to  SrH  was genotyped on set of wheat lines with Huhwa in the pedigree and is advised to be used for marker assisted selection for this gene, however, a combination of phenotypic and genotypic assays is desirable for both genes especially for selection of  Sr9h  in breeding programs.

Identification and Validation of a Common Stem Rust Resistance Locus in Two Bi-parental Populations