Abstract
Current databases of Phyllostachys pubescens full-length cDNAs (FL-cDNAs) provide a rich source of sequences for the development of potential FL-cDNA simple sequence repeat (SSR) markers. We screened 10,608 P. pubescens cDNAs, discovering 1614 SSRs in 1382 SSR-containing FL-cDNAs. The SSRs were more abundant within transposable elements (TEs) than expressed sequence tags (ESTs) and genome survey sequences (GSSs), and specific dinucleotide repeats tended to associate with particular TE families: (TA)n with En/Spm and (CT)n with Mutator. A selected panel of 100 FL-cDNAs containing type I SSRs yielded 68 functional SSR markers with an average polymorphism information content (PIC) value of 0.12, among which 22 loci contained polymorphisms. These markers became less transferrable (83.1% → 69.9% → 49.3%) but more polymorphic (79.4% → 92.3% → 92.8%) with increasing phylogenetic distance (intra-genus → intra-subtribe → intra-family). Transferability and polymorphism also depended on the location of the marker, with those located in the coding region being more transferrable (69.1%) and less polymorphic (89.4%) than those in the 5′-UTR (63.4% transferable, 90.7% polymorphic) and the 3′-UTR (61.8% transferable, 91.4% polymorphic). As proof of principle, we were able to use our FL-cDNA SSR markers to identify the parental stocks in interspecific hybrids of bamboo within and beyond P. pubescens, and estimate the outcrossing rate for P. pubescens. Our research should facilitate molecular breeding in bamboo species where original genetic markers are scarce.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-3-486) contains supplementary material, which is available to authorized users.
Highlights
Bambusoideae is a subfamily of the grass family Poaceae and is further divided into nine subtribes comprising more than 80 bamboo genera and about 1400 species worldwide
We investigated the distribution of simple sequence repeat (SSR) among DNA transposons, and found they were most likely to occur in En/Spm elements
We found that 32 of the selected cDNAs were unsuitable because the PCR failed to generate a product or generated products lacking SSRs (28 cDNAs), but the remaining 68 sequences allowed the development of FLcDNA SSR markers (Table 3)
Summary
Bambusoideae is a subfamily of the grass family Poaceae and is further divided into nine subtribes comprising more than 80 bamboo genera and about 1400 species worldwide. Fifty genera and more than 500 species are found in China, among which Phyllostachys pubescens (synonym: P. edulis) is commercially the most important species providing the third largest source of timber and the most predominant source of bamboo shoots. P. pubescens plantations cover an area of 3 million ha (approximately 2% of the total forest area), which has doubled over the last 30 years and taken on a more important ecological role (Fu 2001). Silviculture, Zhejiang A & F University, Zhejiang Province, LinAn 31300, P R China. Laboratory of Forest Ecosystem Studies, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. Various problems associated with P. pubescens plantations including its simultaneous flowering intervals of more than 60 years and recovers from a limited number of clones (Janzen 1976; Watanabe et al 1982). The little knowledge of its basic biology, genetics and breeding system bring about the practical difficulties associated with the identification and characterization of superior genotypes
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