A Family of Differentially Amplified Repetitive DNA Sequences in the Genus Beta Reveals Genetic Variation in Beta vulgaris Subspecies and Cultivars

Abstract

Members of a highly abundant restriction satellite family have been isolated from the wild beet species Beta nana. The satellite DNA sequence is characterized by a conserved RsaI restriction site and is present in three of four sections of the genus Beta, namely Nanae, Corollinae, and Beta. It was not detected in species of the evolutionary old section Procumbentes, suggesting its amplification after separation of this section. Sequences of eight monomers were aligned revealing a size variation from 209 to 233 bp and an AT content ranging from 56.5% to 60.5%. The similarity between monomers in B. nana varied from 77.7% to 92.2%. Diverged subfamilies were identified by sequence analysis and Southern hybridization. A comparative study of this repetitive DNA element by fluorescent in situ hybridization and Southern analyses in three representative species was performed showing a variable genomic organization and heterogeneous localizations along metaphase chromosomes both within and between species. In B. nana the copy number of this satellite, with some 30,000 per haploid genome, is more than tenfold higher than in Beta lomatogona and up to 200 times higher than in Beta vulgaris, indicating different levels of sequence amplification during evolution in the genus Beta. In sugar beet (B. vulgaris), the large-scale organization of this tandem repeat was examined by pulsed-field gel electrophoresis. Southern hybridization to genomic DNA digested with DraI demonstrated that satellite arrays are located in AT-rich regions and the tandem repeat is a useful probe for the detection of genetic variation in closely related B. vulgaris cultivars, accessions, and subspecies.

Evaluation of rhizomania-resistance segregating sequences and overall genetic diversity pattern among selected accessions of Beta and Patellifolia. Potential implications of breeding for genetic bottlenecks in terms of rhizomania resistance

“…In a broader phylogenetic background, our results show that the level of genetic variation expressed as the percentage of polymorphic loci in sugar beet cultivars may be as low as the case of Patellifolia, which is currently ascribed to the separate genus and the representatives of which are believed to approach their final evolutionary state (Frese 1989from Jung et al 1993. Besides, we confirm here that a considerable part of biodiversity may still be exploited from the sections Beta and especially Corollinae with the latter constituting most probably the driving force of ongoing speciation, as it was previously reported (Kubis et al 1997). These results are also in agreement with the observations made by Jung et al (1993), according to which sugar beet cultivars manifest low values of genetic diversity and a close relationship to B. vulgaris ssp.…”

“…Limited genetic diversity, as well as separate clustering in the dendrogram of genetic distance in case of Patellifolia in this study may indicate their early separation event from the putative common ancestry of the sections Beta and Corollinae as also previously reported (Kubis et al 1997;Kadereit et al 2006). Being restricted in their distribution pattern to the regions of Canary Islands, Madeira and Southern Iberian coast, Patellifolia display actually a closer relationship with the representatives of other genera grouping to Hablitzieae, therefore their classification into the Beta-independent taxonomic unit has been suggested (Scott et al 1977;Jung et al 1993;Kubis et al 1997;Kadereit et al 2006).…”

“…Nevertheless, some differences in banding patterns between individual genotypes belonging to the same cultivar were observed by us, and may be found more often for materials representing different breeding lines, which was documented earlier for instance using satellite DNA repeats (Kubis et al 1997). It seems that the differences in banding patterns observed within the same cultivar result most probably from segregation for a trait that was not among the selection criteria for the development of this particular cultivar.…”

“…Thus, we believe that comparison of wild, weed and cultivated beets using different molecular markers' categories may give us a more comprehensive insight into the scale and direction of genetic bottlenecks inevitably accompanying progress in breeding this crop. Previously, neutral molecular markers were also broadly employed for characterization of Beta and Patellifolia genetic resources (Reamon-Büttner et al 1996; Kubis et al 1997;Smulders et al 2010). These techniques allowed precise assessment of the genetic diversity existing in cultivated and wild beet relatives and suggested that a considerable pool of alleles was lost during the domestication process as compared to wild sea beets which probably bear more resemblance to sugar beet ancestors, eventually leaving as low as one third to one fourth of the available natural variation (Richards et al 2004;Fénart et al 2008;Saccomani et al 2009;Biancardi et al 2010).…”

“…Being restricted in their distribution pattern to the regions of Canary Islands, Madeira and Southern Iberian coast, Patellifolia display actually a closer relationship with the representatives of other genera grouping to Hablitzieae, therefore their classification into the Beta-independent taxonomic unit has been suggested (Scott et al 1977;Jung et al 1993;Kubis et al 1997;Kadereit et al 2006). The lowest frequency of polymorphisms found for P. patellaris may be explained by the fact that this is a self-fertile tetraploid form.…”