Identification, characterisation, and chromosome locations of rye and wheat specific ISSR and SCAR markers useful for breeding purposes

Rye (Secale cereale L. and S. strictum) offers potential to increase the genetic variability and to introduce desirable characters for wheat improvements. Cytogenetic techniques have been used to screen wheat lines containing rye chromatin. These techniques are not adequate since they are highly technical and time consuming. They are not suitable for breeding programs that require rapid screening of large numbers of genotypes. The main objective of this study was to develop and characterize ISSR and SCAR markers that can distinguish wheat from rye genome. Total DNA from wheat, rye, and triticale accessions from different provenances were amplified with ISSR primers in PCR assays. Three wheat-diagnostic sequences were identified. In addition three rye-diagnostic ISSR markers of which, one marker specifically diagnostic for Secale strictum were characterized. Pairs of primers flanking these specific sequences were designed to produce SCAR markers. Two SCAR markers were rye genome-specific. One SCAR was present in all the seven rye chromosome, and another was specific to rye chromosomes two, three, four, and seven. These newly developed ISSR and SCAR markers should be useful to wheat breeders screening genotypes that may contain rye chromatins.