Development of sequence tagged site and cleaved amplified polymorphic sequence markers for wheat stripe rust resistance gene Yr5

The Yr5 gene confers resistance to all races of the wheat stripe rust pathogen [Puccinia striiformis Westend. f. sp. tritici Eriks. (P. s. tritici)] identified so far in the USA. Cosegregating resistance gene analog polymorphism (RGAP) markers for Yr5 are available but their use requires skills in polyacrylamide gel electrophoresis and may not be polymorphic across various varieties. To develop better markers to be used in marker-assisted selection for the Yr5 resistance, sequence tagged site (STS) primers were designed on the basis of the sequences of RGAP markers Xwgp-18 (AY167598) from the spring wheat (Triticum aestivum L.)'Avocet Susceptible' (AVS) and Xwgp-17 (AY167597) from the Yr5 near isogenic line (NIL) in the AVS background carrying the Yr5 gene from T. aestivum subsp. spelta (L.) Thell. cv. Album (TSA). Three sets of STS markers (two codominant and one dominant) were developed to amplify a region including a polymorphic 6-base pairs (bp) insertion-deletion (indel). The cosegregation of the STS markers with Yr5 was confirmed with 114 BC7:F-3 lines developed from the cross between AVS and TSA. The STS markers worked well in five out or 17 non-Yr5 wheat varieties, but the remaining varieties had a similar size of fragment to the Yr5 marker. Because the codominant STS markers were based on a 6-bp indel, they could not be separated by agarose gel electrophoresis. Cleaved amplified polymorphic sequence (CAPS) markers were then developed on the basis of a DpnII restriction site that is present in all non-Yr5 varieties and absent in the Yr5 NIL. The CAPS markers for the Yr5 NIL and non-Yr5 varieties can be separated by agarose gel electrophoresis. The codominant STS markers are easier to score than the original RGAP markers. The CAPS markers are not only easier to score, but also can be used in crosses of an Yr5 donor with a much wider range of wheat germplasms. These markers should be valuable tools to accelerate the introgression of Yr5 into commercial cultivars and to combine Yr5 with other genes for durable resistance to stripe rust.