Molecular cloning and characterization of granule-bound starch synthase I (GBSSI) alleles from potato and sequence analysis for detection of cis-regulatory motifs

Granule-bound starch synthase (GBSS), an isoform of starch synthase, is responsible for amylose synthesis in all starch containing tissues of potato (Solanum tuberosum L.), and in other plant species. In potato, the importance of GBSSI gene function is realized through a number of published reports on both basic and applied research. Here genomic DNA was isolated from six high-yielding Indian potato cultivars, and the cultivar Desiree. Polymerase chain reactions (PCR) were carried out at varying annealing temperatures using GBSSI gene-specific primers and genomic DNA from the individual potato cultivars. Analysis of PCR amplification products provided an overview of GBSSI allelic composition of these potato cultivars which was hitherto unknown. Two partial GBSSI alleles were isolated from one of the Indian potato cultivars. The distinguishing sequence features between them were shown. Multiple sequence alignment of GBSSI alleles from different potato cultivars provided a clear view for comparison between their different regions. Base composition analysis revealed a notably higher GC rich region immediately upstream of the transcription start site of the GBSSI alleles, unlike other potato genes. Preliminary sequence analysis detected a number of different cis-regulatory sequence motifs in the GBSSI alleles which were not documented in earlier reports. The GBSSI sequences from different potato cultivars reported to date were sorted out into four groups as shown in the phylogenetic tree. A promoter was isolated from one GBSSI allele of this study, and found to be strong and tuber-specific in the potato cultivar under field conditions as examined by histochemical GUS assay.