Sr42

The stem rust fungus, particularly race TTKSK (Ug99), poses a serious threat to world wheat production. Gene Sr42 or SrCad (which could be the same gene or an allele of Sr42) is effective against race TTKSK. However, known genetic markers for Sr42 are mostly SSR markers which are generally labor intensive to use. In this study, we mapped a race TTKSK resistance gene derived from PI 595667 at the same locus as Sr42 on chromosome 6DS. Based on position, pedigree and infection-type information, we propose that this gene is SrCad (Sr42). We enriched the genetic map for the Sr42 region using genotyping by sequencing (GBS) and array-derived SNP markers. In total, 21 SNP markers were discovered, spanning a genetic distance of 27.2 cM. Nine of them are derived from GBS and twelve from the Illumina iSelect 90K SNP assay. Ten of the twenty-one SNP markers are closely linked (<2.2 cM, or co-segregating) with Sr42. We converted five of the closely linked SNP markers into uniplex KASP assays which will better facilitate marker-assisted selection. We validated the KASP assay in a doubled haploid wheat population derived from a three-way cross between accessions PI 410954, RB07, and Faller that shared an uncharacterized resistance gene mapped at approximately the same locus as PI 595667. The development of closely linked (co-segregating), codominant, sequence-based SNP assays will aid marker-assisted selection and map-based cloning of Sr42.

Stem rust, caused by Puccinia graminis f. sp. tritici, is a devastating disease of wheat. The emergence of race TTKSK (Ug99) and new variants in Africa threatens wheat production worldwide. The best method of controlling stem rust is to deploy effective resistance genes in wheat cultivars. Few stem rust resistance (Sr) genes derived from the primary gene pool of wheat confer resistance to TTKSK. Norin 40, which carries Sr42, is resistant to TTKSK and variants TTKST and TTTSK. The goal of this study was to elucidate the inheritance of resistance to Ug99 in Norin 40 and map the Sr gene(s). A doubled haploid (DH) population of LMPG-6/Norin 40 was evaluated for resistance to the race TTKST. Segregation of 248 DH lines fitted a 1:1 ratio (χ ² 1:1= 0.58, p = 0.45), indicating a single gene in Norin 40 conditioned resistance to Ug99. This was confirmed by an independent F_2:3 population also derived from the cross LMPG-6/Norin 40 where a 1:2:1 ratio (χ ²1:2:1 = 0.69, p = 0.71) was observed following the inoculation with race TTKSK. Mapping with DNA markers located this gene to chromosome 6DS, the known location of Sr42. PCR marker FSD_RSA co-segregated with Sr42, and simple sequence repeat (SSR) marker BARC183 was closely linked (0.5 cM) to Sr42. A previous study found close linkage between FSD_RSA and SrCad, a temporarily designated gene that also confers resistance to Ug99, thus Sr42 may be the same gene or allelic. Marker FSD_RSA is suitable for marker-assisted selection (MAS) in wheat breeding programs to improve stem rust resistance, including Ug99.