Development of simple sequence repeat markers in rye (<i>Secale cereale</i> L.)

Abstract

Simple sequence repeats (SSRs), also referred to as microsatellites, represent a PCR-based marker system that has been described in mammalian and plant genomes in recent years. In self-pollinating crop plants they have been shown to be superior to other DNA markers with respect to their level of polymorphism. The technical advantages compared with RFLP markers should also facilitate marker analysis in outcrossing crops like rye. In order to determine the usefulness of SSR markers in rye genetics and breeding, several genomic libraries were screened for (CT/GA)n and (GT/CA)n dinucleotide repeats. It was estimated that these motifs occur at a frequency of one per 268-519 kb. Seventy four out of 182 positive clones were sequenced, and the majority (56.8%) revealed perfect repeats, predominantly of the type (GT/CA)n (61.9%). Fifty seven primer pairs were designed and 27 (47.4%) resulted in specific SSR markers, of which 20 were genetically mapped or assigned to chromosomes or chromosome arms, respectively. The level of polymorphism of four SSR and three RFLP markers was assessed in two open-pollinated rye cultivars. On average, the SSR markers showed larger values of expected heterozygosity (0.62 vs. 0.43) and allele number (5.9 vs. 3.4) than RFLP markers in both cultivars.

Partial resistance to powdery mildew in German spring wheat ‘Naxos’ is based on multiple genes with stable effects in diverse environments

“…The resistance QTL on 1B was located to the 1B/1R translocation of SHA3/CBRD based on the rye-specific markers SCM9 (Saal and Wricke 1999) and NOR (Koebner 1995). Since Pm8 is known to be located on this translocation, we conclude that this QTL was caused by Pm8.…”

Isolation and characterization of simple sequence repeat markers in the hexaploid forage grass timothy (Phleum pratense L.)

“…Many authors have used polymorphic information content (PIC) to evaluate the polymorphism of SSR markers (Ott 1991;Saal and Wricke 1999;Jones et al 2001). In our study, PIC was not suitable because we could not distinguish homozygous and heterozygous states from the electrophoresis patterns owing to the hexaploid nature of timothy; therefore, the allele frequencies of SSRs could not be calculated.…”

Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars

“…For primers that produced the expected fragments after PCR reactions, the number of alleles was recorded and the polymorphism information content (PIC) of an SSR locus was calculated as described by Saal and Wricke (1999):…”