Identification, cross-taxon transferability and application of full-length cDNA SSR markers in Phyllostachys pubescens.
Identification, cross-taxon transferability and application of full-length cDNA SSR markers in Phyllostachys pubescens.
复制标题
DOI：
10.1186/2193-1801-3-486
复制
发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Tang DQ
中科院分区：
文献类型：
--
作者：
Lin Y;Lu JJ;Wu MD;Zhou MB;Fang W;Ide Y;Tang DQ
现有的毛竹全长cDNAs数据库(FL-cDNAs)为开发潜在的FL-cdna简单序列重复(SSR)标记提供了丰富的序列来源。我们筛选了10,608个毛白杨的cDNA，在1382个含有SSR的FL-cDNA中发现了1614个SSR。转座元件(TES)中的SSR比表达序列标签(EST)和基因组调查序列(GSSS)中的SSR更丰富，特定的二核苷酸重复序列往往与特定的TE家族相关：(Ta)n与EN/SPM相关，(CT)n与突变子相关。筛选出100个含有I型SSR的FL-cDNAs，共获得68个功能SSR标记，平均多态信息含量(PIC)值为0.12，其中22个座位具有多态现象。随着系统发育距离(intra-genus → intra-subtribe → intra-family).的增加，这些标记的可传递性变差(83.1% → 69.9% → 49.3%)，但多态(79.4% → 92.3% → 92.8%)变得更多可转移性和多态也取决于标记的位置，位于编码区的标记的可转移性(69.1%)和多态程度(89.4%)高于5‘-非编码区(63.4%，多态)和3’-非编码区(61.8%，多态)。作为原理的证明，我们能够利用我们的FL-cDNASSR标记来鉴定毛竹内外毛竹种间杂交种的亲本种群，并估计毛竹的异交率。我们的研究应该有助于在原始遗传标记稀缺的竹子物种中进行分子育种。本文的在线版本(DOI：10.1186/2193-1801-3-486)包含补充材料，可供授权用户使用。
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. The online version of this article (doi:10.1186/2193-1801-3-486) contains supplementary material, which is available to authorized users.
登录
查看更多内容
影响因子：
2.8
作者：
Kitamura, Keiko;Kawahara, Takayuki
通讯作者：
Kawahara, Takayuki
影响因子：
1.9
作者：
Lin, Xin Chun;Ruan, Xiao Sai;Fang, Wei
通讯作者：
Fang, Wei
影响因子：
3.7
作者：
Higa JK;Liang Z;Williams PG;Panee J
通讯作者：
Panee J
影响因子：
5.2
作者：
Cordeiro, GM;Casu, R;Henry, RJ
通讯作者：
Henry, RJ
DOI：
10.1590/s0100-84042001000200011
发表时间：
2001-01-01
期刊：
Revista Brasileira de Botanica
影响因子：
--
作者：
Guilherme, Frederico Augusto G.;Ressel, Kaila
通讯作者：
Ressel, Kaila