Assessment of Genetic Diversity in Secale cereale Based on SSR Markers

Abstract

The primary aim of this study was to estimate genetic diversity among Secale cereale L. accessions using 22 previously published simple sequence repeat (SSR) markers. The plant material included 367 rye accessions comprising historical and contemporary cultivars, cultivated materials, landraces, and breeding strains from the Polish breeding company Danko. The studied accessions represented a wide geographical diversity. Several methods were employed to analyze genetic diversity among the Secale cereale L. accessions and to determine population structure: principal coordinate analysis (PCoA), neighbor-joining (NJ), and Bayesian clustering. We also defined a core collection of 25 rye accessions representing over 93 % of SSR alleles. The results of these analyses showed that accessions from the rye gene bank are clearly divergent in comparison with materials received directly from European breeding companies. Our findings suggest also that the genetic pool of current rye cultivars is becoming narrower during breeding processes. The selected panel of SSR markers performed well in detection of genetic diversity patterns and can be recommended for future germplasm characterization studies in rye.Electronic supplementary materialThe online version of this article (doi:10.1007/s11105-015-0896-4) contains supplementary material, which is available to authorized users.

DArT Markers Effectively Target Gene Space in the Rye Genome

“…The percentage of primer pairs producing polymorphic product was lower but comparable to those obtained for EST derived SSR markers [47.2% (Hackauf and Wehling, 2002) and 39.4% (Martis et al, 2013)] but markedly higher than in the case of SSRs from genomic libraries [12% (Saal and Wricke, 1999)]. The average PIC value and the average number of alleles obtained in our study are comparable with those observed in a recent assessment of genetic diversity and population structure of 367 rye accessions by Targońska et al (2016), who used a set of 22 preselected, genomic library- and EST-derived SRRs – 0.66 and 4.65, respectively. We present here only the results of a preliminary experimental validation of the newly developed markers, and their suitability for large germplasm characterization studies is to be determined.…”

“…Each accession was represented by a pooled DNA sample obtained from several plants. Amplification, visualization and scoring of SSR markers as well as PIC value calculations were done as previously described (Targońska et al, 2016). …”

Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)

“…According to their location on the genome, microsatellite regions may be distinguished into genomic neutral simple sequence repeat (SSR) markers and transcript-tagged SSRs, located on expressed sequence tags (ESTs), with a potential functional value (Bradbury et al 2013;Hinchliffe et al 2011). SSR markers show significant advantages, such as reproducibility, locus specificity and low quantity of template required; nevertheless, several disadvantages have also been recorded, which are mainly due to stutter products, allele binning and allele miscalling, as a consequence of the wide use of di-nucleotide microsatellites (Cabezas et al 2011;Kaur et al 2015;Targońska et al 2015;This et al 2004). The majority of discrepancies among laboratories in scoring di-nucleotide microsatellites are due to the binning process in which raw allele lengths are converted into allele classes whose size is then expressed by an integer (Baldoni et al 2009;Weeks et al 2002).…”

The genetic polymorphism between the wild species and cultivars of rye Secale cereale L.

“…Dopierała et al [10] informed that intensive selection in the process of hybrid rye breeding narrows genetic diversity and KWS Lochow Polska studied collections of inbred lines from ancient Polish varieties (over 70 years old), old Polish and Russian varieties (over 40 years old), and local populations. Identical conclusions were made by Targońska et al [11] who suggest that the genetic pool of current rye cultivars is becoming narrower during breeding processes. The reconstruction of progress in the breeding of rye, which is a common cereal in Poland, will largely depend on the enrichment of domestic cultivars with the genes from specimens bred as a result of interspecies crossbreeding between cultivars and wild species [12,13].…”