title: Identification, cross-taxon transferability and application of full-length cDNA SSR markers in Phyllostachys pubescens.
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.
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Zhejiang Province LinAn, 31300 P R China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Lin
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Zhejiang Province LinAn, 31300 P R China.
authors.forename: Jiang-Jie
authors.initials: JJ
authors.lastname: Lu
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Zhejiang Province LinAn, 31300 P R China.
authors.forename: Miao-Dan
authors.initials: MD
authors.lastname: Wu
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Zhejiang Province LinAn, 31300 P R China.
authors.forename: Ming-Bing
authors.initials: MB
authors.lastname: Zhou
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Zhejiang Province LinAn, 31300 P R China.
authors.forename: Wei
authors.initials: W
authors.lastname: Fang
authors.affiliation: Laboratory of Forest Ecosystem Studies, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Ide
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical 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.
authors.forename: Ding-Qin
authors.initials: DQ
authors.lastname: Tang
keywords: Cross-taxon transferability /polymorphism; Hybrid identification; Microsatellite (SSR); Outcrossing-rate estimation; Phyllostachys pubescens (edulis)