Characterization of Trinucleotide Microsatellites in Eggplant

Abstract

A small insert genomic library of eggplant (Solanum melongena L.) was screened with eight trinucleotide probes. Based on the screening of approximately 108,000 plaques, the occurrence of (AAC/TTG) _n, (AAG/TTC)_n, (ACC/TGG)_n, (ACG/TGC)_n, (ACT/TGA)_n, (AGC/TCG) _n, (AGG/TCC)_n and (ATC/TAG) _n repeats was estimated to be, respectively, 1.2 × 10 ³, 1.3 × 10², 4.0 × 10², 7.6 × 10, 1.1 × 10², 5.7 × 10, 1.3 × 10² and 3.8 × 10, i. e. once every 951 kbp, 8.3 Mbp, 2.8 Mbp, 14.5 Mbp, 9.7 Mbp, 19.3 Mbp, 8.3 Mbp and 29 Mbp in the eggplant genome, respectively. Two trinucleotide repeats, (AAC/TTG)_n and (ACC/TGG) _n, predominated, accounting for 84.5 % of the isolated trinucleotide microsatellites. A total of 83.5 % of the identified trinucleotide repeats contained seven repeat units or less. Inserts of the positive clones were sequenced and 85 PCR primer sequences bordering the microsatellite repeats were designed. In order to assess the polymorphism, 11 S. melongena lines and 11 Solanum relatives were used. The mean number of alleles per polymorphic locus was 2.1 for S. melongena lines and 2.9 for Solanum relatives. Low levels of polymorphism were observed in eggplant, with the average heterozygosity being 0.31 between S. melongena lines and 0.32 between Solanum relatives. Most of the markers that detected polymorphism between S. melongena lines contained eight or more repeat units. The motif most frequently found in Solanum was (AAC/TTG)_n in this study. All the primer sets which detected PCR products in S. melongena yielded PCR products in S. incanum, which is in agreement with its very close relationship with S. melongena. Further transferability, however, was rather low, since only half of the primer sets gave products in Solanum relatives except for S. incanum. Analysis of the polymorphic loci in an eggplant F₂ population revealed a codominant mendelian segregation.