Isolation, characterization and RFLP linkage mapping of a DNA repeat family ofSolanum spegazziniiby which chromosome ends can be localized on the genetic map of potato

Abstract

SummaryIn a random sample of 2263 cloned genomic DNA fragments of the wild potato species Solanum spegazzinii six related, highly repetitive fragments (SPG repeat family) were identified that were present in much higher copy numbers in S. spegazzinii when compared with the closely related cultivated potato S. tuberosum. The SPG repeat family was organized in long arrays of multiple copies. Cross hybridization experiments with 29 wild and cultivated Solanum species and with the related tomato showed specificity of the SPG repeat family for tuber-bearing Solanum species. Among tuber bearing Solanum species a high degree of variation was observed for restriction fragment length and copy number. The variation in copy number was not correlated with established taxonomic relationships between tuber-bearing Solanum species. DNA sequence analysis revealed a subrepeat structure of 120–140 base pairs embedded in longer repeat units of variable length. Length polymorphisms between highly repeated restriction fragments detected by the SPG probes were used for segregation- and linkage analysis in four mapping populations of potato, for which RFLP maps had been constructed. Twelve loci were identified, eleven of which mapped to the distal ends of nine linkage groups. All the evidence suggested that the SPG repeat family represents a satellite repeat members of which are localized in the subtelomeric region of potato chromosomes. The SPG repeat family could be used, therefore, for completing the genetic map of potato.

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

“…More strikingly, the repetitive sequence content and composition of potato and tomato have diverged with impacts seen on genome architecture at both the macro- and the micro-level as evidenced through differences in telomeric-repetitive sequences and rDNA content and in interruption of synteny through transposition of retrotransposons. Our data are consistent with previous reports on repetitive sequences [ 36 - 42 ] which show divergence of this fraction of the genome within the Solanaceae. These data clearly suggest that while these two solanaceous genomes can be cross-leveraged for analysis of gene content and order, they are not interchangeable with respect to all genomic features.…”

“…While the cultivated species have been bred for these diverse agronomic traits, genome sequence analysis has indicated that these species share to a large extent not only genes [ 30 ] but also gene order (synteny) between their genomes [ 31 - 35 ]. While major classes of repetitive sequences are conserved among some Solanaceae species [ 36 , 37 ], lineage-specific repetitive sequences have been reported, suggesting divergence of this fraction of the genome has occurred through evolution [ 36 - 42 ]. With the availability of large genomic datasets for two Solanaceae species, tomato and potato, the extent of sequence conservation as well as synteny can be addressed in a more robust manner.…”

Characterization of telomere-subtelomere junctions in Silene latifolia

“…The DNA sequences that make up subtelomeres are able to substitute, at least to some extent, for the protective role of telomeric DNA sequences in case of telomere loss (Palladino and Gasser 1994). In subtelomeric regions in plants, both tandem and dispersed repeated sequences are found in large excess over single-copy or low-copynumber sequences, and are frequently used as markers for identifying genomic components of hybrid organisms in plant breeding and in taxonomic studies (Gebhardt et al 1995;Vershinin et al 1996). In subtelomeric regions in plants, both tandem and dispersed repeated sequences are found in large excess over single-copy or low-copynumber sequences, and are frequently used as markers for identifying genomic components of hybrid organisms in plant breeding and in taxonomic studies (Gebhardt et al 1995;Vershinin et al 1996).…”

Isolation, characterisation and mapping of simple sequence repeat loci in potato

“…Only a few of the >400 RFLP loci mapped on this population are shown. The markers designated PSTR are sub-telomeric repeats indicating the ends of linkage groups(Gebhardt et al 1995). The maps on the right show the position of the SSRs on the Germicopa population.…”