Development of simple sequence repeat markers in rye (Secale cerealeL.)

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.

The identification of QTLs associated with the in vitro response of rye (Secale cereale L.)

“…Both these qualities enable the population and its map to be used for repeated phenotypic measurements and subsequent QTL analyses, comparing the localizations of the identified QTLs, and for integration with other genetic maps of rye. In most cases, the locations of the SSR markers on the L318 x L9 map were in agreement with previously published data [18,28,31,Korzun,pers. comm.…”

“…One of the major factors affecting the map quality was the relatively high number of markers with deviating segregation. Segregation distortion is a common phenomenon in rye, even in F 2 populations [18,[29][30][31][32], and is believed to be the result of selection at the gametic or zygotic stage. It can be expected that inbreeding depression causing certain lines to be lost during the development of the population resulted in a shift in the allele proportions in the remaining lines resulting in distorted segregation.…”

“…The three groups of SSR primer pairs listed below were used to screen for polymorphism between the parental lines. Group I consisted of 85 primer pairs (pp), developed from rye genomic libraries: 41 pp (WRM) by Bolibok et al [17]; 27 pp (SCM) by Saal and Wricke [18]; and 17 pp (RMS) by Lochow Petkus GmbH, Bergen, Germany, supplied as aliquots by Dr. V. Korzun. Group II consisted of 159 pp developed from EST sequences deposited in public data bases: 99 pp (SCM0) designed by Hackauf and Wehling [19]; and 60 pp (REMS) developed by Khlestkina et al [20] and provided by Dr. V. Korzun.…”

Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments

“…cerasiforme accessions, for the wild species, and for all 19 accessions combined. These values were calculated as previously described (Saal and Wricke 1999):…”

Production and cytomolecular identification of new wheat-perennial rye (Secale cereanum) disomic addition lines with yellow rust resistance (6R) and increased arabinoxylan and protein content (1R, 4R, 6R)

“…In the present study, S. cereale-specific SSR markers were applied to verify the FISH identification of 'Kriszta' chromosome in the wheat-S. cereanum addition lines. Chromosomal location of the rye chromosome-specific SSR markers were originally assigned in CS-'Imperial' disomic addition lines (Saal and Wricke 1999), but the majority of these SSR markers produced chromosome-specific amplicons in the parental 'Kriszta' rye and the 1R, 4R and 6R wheat-S. cereanum addition lines as well ( Fig. 3 and Table 2), which proves the relatively high transferability of SSR markers from S. cereale into S. cereanum.…”