Abstract:

Plant genomics projects involving model species and many agriculturally important crops are resulting in a rapidly increasing database of genomic and expressed DNA sequences. The big collection of expressed sequence tags (ESTs) from Populus species is available in public database, and offers an opportunity to identify simple sequence repeats (SSR) in ESTs by data mining. These sequences may provide an estimate of diversity in the expressed portion of the genome and may be useful for comparative mapping, for tagging important traits of interest, and for additional map-based cloning of important genes. We analyzed 20 023 EST sequences from Populus deltoides and P. euramericana for their potential use in developing SSR markers. The EST sequences were clustered into contigs firstly to find dinucleotide, trinucleotide, tetranucleotide and pentanucleotide SSR. Totally, 1 604 contigs with 1 918 SSRs were identified from 10 816 contigs, and accounted for 14.8% of the total number of contigs. Dinucleotide repeats were the most abundant repeat class, and accounted for 62.3% of all found SSRs. About 90% primers out of the designed 48 pairs were able to produce an amplification product from 6 poplar cultivars, among which 58% exhibited polymorphism for at least one cultivar among the six tested ones. The number and type of repeats were also discussed. The development of new EST-SSR markers from Populus has potential important implication for genetic analysis and exploitation of genetic resources of Populus and would provide a more direct estimate of functional diversity.

Key words: Populus, expressed sequence tags (EST), simple sequence repeats (SSR)