SNP‐Based Improvement of a Microsatellite Marker Associated with Karnal Bunt Resistance in Wheat

Abstract

Marker‐assisted selection (MAS) has become the technology of choice for introgressing important traits with indistinct phenotypes into agronomically elite cultivars. Karnal bunt (KB, causal agent Tilletia indica Mitra) is an economically important fungal pathogen of wheat (Triticum aestivum L.) which has caused economic losses in the USA since it was first reported in 1996. To protect U.S. wheat from this emerging disease and the losses incurred from export quarantines, genetic sources of resistance are needed by breeders to improve U.S. germplasm. Resistance to KB is difficult to score phenotypically, making MAS an ideal choice for deploying this trait into U.S. wheat. Here we describe the conversion of a codominant microsatellite marker, Xgwm538, associated with a quantitative trait locus (QTL) for KB resistance into a single nucleotide polymorphism (SNP) based marker. The SNP marker was developed to improve gel‐based resolution and amplification consistency. The gwm538 primers amplify three fragments in the KB resistant line HD29: 137‐, 147‐, and a 152‐bp fragment that maps to the long arm of chromosome 4B and is linked to the KB QTL. By cloning and sequencing all three fragments, we were able to exploit a SNP and design a new primer to selectively amplify the 152‐bp fragment of interest (gwm538snp). Amplification consistency is improved with gwm538snp since the amplification of competing nontarget fragments is eliminated, and ambiguity is reduced since heterozygous plants are easily identified among backcross progeny.