Development of SNP-based dCAPS markers linked to major head smut resistance quantitative trait locus qHS2.09 in maize

Head smut is a disease caused severely yield losses both in commercial maize and seed production in the spring maize growing region in northeastern China. In previous study, we located the major QTL qHS2.09 between SNP PZE-102187486 and PZE-102188421 by combined linkage and association mapping within an interval of ≈1.00 Mb. In this study, we report the development of six derived cleaved amplified polymorphic sequence (dCAPS) markers based on discovered single nucleotide polymorphisms (SNPs) closely linked to the major QTL qHS2.09. There was consistent allele pattern produced by SNPs and dCAPS for the same base mutation. The dCAPS marker for head smut resistance trait could be assayed by PAGE gel electrophoresis and be efficient in identification of maize inbred line Mo17, Qi319 and their derivatives. New markers were validated in fine mapping and evaluated the efficiency in 56 maize inbred lines. These dCAPS markers will facilitate as marker-assisted selection for maize breeding program.