Development of diagnostic SNP markers for identification of rye 1RS translocations in wheat

Wheat (Triticum aestivum L.) wild relatives are rich genetic resources for genetic improvement of wheat. The short arm of rye (Secale cereale L.) chromosome 1 (1RS) contains many beneficial genes for resistance to drought, insects, and diseases, therefore the 1RS wheat translocations have been widely used in wheat breeding programs worldwide. To facilitate marker-assisted identification of 1RS in wheat breeding, we designed a set of Kompetitive allele-specific polymerase chain reaction (KASP) markers to detect the translocations of 1RS with long arm from wheat chromosome 1A (1RS.1AL) and 1RS with long arm from wheat chromosome 1B (1RS.1BL) based on the sequence flanking single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) between wheat and rye panels. We identified a set of three SNP markers for diagnosis and differentiation of the two 1RS translocations in wheat. Among the three KASP markers, 1AS-05056 is 1RS specific, and clearly separated the genotypes with 1RS (1RS.1AL and 1RS.1BL) from those without the two 1RS translocations; whereas 1AS-29875 clearly identified the 1RS.1AL translocation and 1BS-16654 separated 1RS.1BL from 1RS.1AL. The three new KASP markers together accurately identified the presence of 1RS translocation on either 1A or 1B chromosome in a panel of 95 representative U.S. winter wheat accessions, which were further validated in two additional U.S. hard winter wheat panels. Therefore, they can be used for routine screening of 1RS.1BL and 1RS.1AL translocation lines in wheat breeding programs.

Automated summary

Wheat wild relatives are valuable genetic resources for genetic improvement of wheat. By designing KASP markers, the presence of 1RS.1BL and 1RS.1AL translocations in wheat can be accurately identified.