Development And Application Of EST-SSR Markers In Phyllostachys Edulis

The availability of cDNAs in GenBank became an alternative source of mining simple sequence repeat (SSR). We analyzed 10608 Phyllostachys edulis cDNA sequences available in NCBI, and found 2330 simple sequence repeat (SSR) loci comprising repeats of one or two or more nucleotides in 2014 cDNA sequences. The frequency of cDNA sequences that containing SSR loci in the total sequence is 18.99%. SSRs consisted of 16.8% mononucleotide repeats, 30.3% dinucleotide repeats, 48.9% trinucleotide repeats, and 4.1% higher-number repeats in non-redundant cDNA-SSRs. The most frequent SSR motif in cDNA sequences was (CCG/CGG)n and the second one was (AG/CT)n. The result showed that bamboo had similar SSRs composition with rice than other cereals.One hundred SSR loci were selected for marker development, out of those 67 primer pairs resulted in PCR products of the expected size and SSR motif. 68 EST-SSR markers were developed and were used to assess the transferability and polymorphism of the bamboo collection consisting of 41 species classified in 6 separate tribes. Transferability of EST-SSR was the best at the level of intra-genus (Phyllostachys), Polymorphisms were evident at the level of sympodial versus monopodial bamboo species. Ph. kwangsiensis has the cloest relationship with Ph. edulis. These results show that our developed EST-SSR markers can be used in bamboo genetic diversity analyzing. SSRs in the coding region (CDS) were more transferable than those in untranslated region (3′UTR and 5′UTR). On the contrary, SSRs in the untranslated region (3′UTR and 5′UTR) were more polymorphic than in coding sequence (CDS).Our study also showed that some of EST-SSRs derived from monopodial Ph. edulis can be applied for identification of caespitose hybrid bamboo. It is further illustrates the EST-SSR markers developed here have good transferability and polymorphism.