Genomic DNA Diversity in Tomato Varieties Revealed by Indel and SSR Markers

The emergency of intronic and genomic sequences in tomato (Solanum lycopersicum L.) provides a base for developing indel markers.  Some of them have been discovered to date.  However, whether these markers can be used in tomato molecular breeding remains unclear.  Therefore, indel and SSR markers were used to analyze genomic DNA diversity in 59 fresh-market tomato varieties growing in China to investigate the potential of indel markers in tomato molecular breeding.  Comparison between 59 Chinese varieties and 23 US varieties were also conducted at marker level.  The results indicated that the indel marker showed lower polymorphisms in varieties with narrowed genetic basis, suggesting that they were not suitable to detect polymorphisms in this kind of tomato lines.  At the same time, we also found that both indel and SSR markers showed lower polymorphisms in Chinese varieties than in US varieties.  Genetic difference was very small between varieties developed by Chinese breeding programs but relatively larger between Chinese and foreign varieties.