Development and validation of gene-specific KASP markers for YrAS2388R conferring stripe rust resistance in wheat

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive fungal disease with a significant economic impact. Aegilops tauschii, the D-genome progenitor of wheat (Triticum aestivum, AABBDD), offers valuable gene pool for Pst resistance. The Ae. tauschii gene YrAS2388 confers resistance to a wide range of Pst races and encodes a typical nucleotide oligomerization domain-like receptor (NLR). The functional YrAS2388R has duplicated 3′ untranslated regions (3′UTRs). In the present study, we have developed two gene-specific kompetitive allele specific PCR (KASP) markers for YrAS2388R by comparing multiple homoeologous and paralogous genomic sequences of YrAS2388 alleles from allopolyploid wheat genomes. KASP-E5 was developed based on SNP in the exon5 sequences of YrAS2388, which behaves as a co-dominant marker. KASP-E6′ was developed based on the 3′UTR sequences of YrAS2388, which behaves as a dominant marker. These markers were validated in different types of wheat populations and showed clear functional differentiation that was completely agreement with the gel based gene-specific marker for YrAS2388R. Our results indicate that KASP-E5 and KASP-E6′ are perfect diagnostic markers for YrAS2388R and would be useful for marker assisted selection in wheat resistance breeding.