Molecular analysis of highly repeated genome fractions in Solanum and their use as markers for the characterization of species and cultivars

Abstract

Highly repeated DNA of potato (Solanum sp.) was characterized by cloning various major repeated elements of the nuclear genome. The percentage of the nuclear genome of the specific fractions and the restriction enzyme patterns were determined in order to show the distribution and organization of the respective repeats in the genome of Solanum tuberosum cultivars, dihaploid breeding lines and in wild species of Solanum. Several of the clones obtained were represented in a high copy number but showed no informative RFLP patterns. More information was gained from 'restriction satellite' repeats. The clone pR1T320 was found to contain satellite repeats (360 bp in length) that are proportionally present in the genome of all Solanum species at frequencies, between 0.5% and 2.6% and which are differently organized. This repeat was also found in the genera Lycopersicon, Datura and Nicotiana. With various restriction enzymes characteristic RFLP patterns were detected. A more or less genus-specific element for Solanum was the 183-bp repeat (clone pSA287; between 0.2-0.4% of the nuclear genome) that was present in the majority of the Solanum species analyzed except S. kurtzianum, S. bulbocastanum and S. pinnatisectum. In a few wild species (prominently in S. kurtzianum, S. demissum and S. acaule) a specific repeat type was detected (clone pSDT382; repeat length approximately 370 bp) that could be used to trace the wild species introduced into S. tuberosum cultivars. The repeats analyzed together with the 18S, 5.8S and 25S ribosomal DNA (1.9-5.2%, corresponding to 1800-5500 rDNA copies) comprised approximately 4-7% of the Solanum genome.

Organization, differential expression and methylation of rDNA in artificial Solanum allopolyploids

“…Additionally, to evaluate the relative amounts of parental rDNA in the allopolyploids, we have quantified the intensity of parental-specific bands after DNA blotting and hybridization. Taking together, the results showed ( Table 3) that rDNA repeats amount to approximately 7.5% of the genome of LYC, to 5% in the genomes of TUB1 and TUB4, and to 5.5% in BLB, which reasonably corresponds to the estimations recently performed for different species and varieties of Solanum (Schweizer et al, 1993).…”

Comparison of nuclear ribosomal RNA genes among Solanum species and other Solanaceae

“…Despite the great general interest in cultivated species, the origin of potato and the phylogenetic relationships among species of the genus Solanurn are not yet completely clear. Taxonomic relationships among potatoes have been based on morphological characters, interspecific hybridization behaviour, secondary compounds (Ross 1986;Hawkes 1990), and, more recently, on the restriction fragment length polymorphism (RFLP) pattern of chloroplast DNA (Hosaka 1986), single copy nuclear sequences (Debener et al 1990), and repetitive DNA components (Schweizer et al 1993). …”

Differential homogenization and amplification of two satellite DNAs in the genus Cucurbita (Cucurbitaceae)

“…The high copy number and sequence homogeneity of satellite DNA require an amplification as well as an active homogenization process (Dover 1982;Stephan 1989;Stephan and Cho 1994). Remarkably for plants, a specific satellite repeat type can be predominantly present in a genome together with other less-represented types, raising the question of the value of satellite DNA for evolutionary and taxonomical studies Schweizer et al 1993;Hemleben 1993).…”

“…However, the A-genome-specific repeat was also detected in a modified version in other species of the Poaceae (Grebenstein et al 1995). Somatic hybrids of cultivated Solanum tuberosum and Lycopersicon escuIentum or of it and wild Solanum species can be differentiated by specific satellite DNA (Schweizer et al 1988(Schweizer et al , 1993. Two satellite DNAs of Beta vulgaris have been used to classify the genus Beta and divide it in specific sections Schmidt and HeslopHarrison 1993).…”