Microsatellite markers from tea plant expressed sequence tags (ESTs) and their applicability for cross-species/genera amplification and genetic mapping
Microsatellite markers from tea plant expressed sequence tags (ESTs) and their applicability for cross-species/genera amplification and genetic mapping
复制标题
茶树表达序列标签 (EST) 的微卫星标记及其跨物种/属扩增和遗传作图的适用性
DOI：
10.1016/j.scienta.2011.10.029
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发表时间：
2012-02-01
影响因子：
4.3
通讯作者：
Chen, Liang
中科院分区：
文献类型：
--
作者：
Ma, Jian-Qiang;Ma, Chun-Lei;Chen, Liang
EST数据的生物信息学挖掘是开发功能性微卫星标记的一种经济有效的方法。本工作的目的是产生新的茶树EST-SSR标记，并评估其跨种/属扩增，特别是遗传连锁图谱的潜力。从GenBank中检索到8008条茶树EST序列，经聚类分析得到2982条非冗余的独特序列，其中鉴定出561个微卫星。在这些SSR中，二核苷酸重复是最常见的重复类型（255，45.5%），其次是三核苷酸重复（18.9%）、六核苷酸重复（14.3%）、五核苷酸重复（13.5%）、四核苷酸重复（5.3%）、七核苷酸重复（2.1%）、八核苷酸重复（0.2%）和十核苷酸重复（0.2%）。AC/CF和阿加/TCT分别在二聚体和三聚体重复基序中占优势。BLASTX同源性搜索发现，319个含有SSR的EST具有显著的拟南芥蛋白质命中（E值< 1.00E-05）。总共成功设计了一组97个引物对用于标记开发和验证。结果表明，54个引物在21个茶树基因型中均获得了重复性好、特异性强的扩增产物，但只有30个位点具有多态性，平均每个位点的等位基因数为3.4个（范围：2-6个等位基因/位点）。交叉扩增结果表明，87%（26/30）的引物在19种山茶科植物中至少有一种能扩增出可标记的产物。转移率范围为7 - 77%，平均为30%。25个SSR位点在茶树假测交作图群体的亲本中表现出多态性，可用于茶树遗传连锁分析。这些新的信息EST-SSR标记将为茶树及其近缘种的遗传分析和分子育种提供有用的补充。(C)2011 Elsevier B. V.保留所有权利。
Bioinformatic mining of EST datasets is an efficient and economical method for developing functional microsatellite markers. The aim of this work is to generate new tea plant EST-SSR markers and to evaluate their potentials for cross-species/genera amplification and in particular genetic linkage mapping. A total collection of 8008 untapped tea plant ESTs were retrieved from GenBank and then clustered into 2982 non-redundant unique sequences, in which 561 microsatellites were identified. Of these SSRs, the di-nucleotide repeats were the most common repeat types (255, 45.5%), then followed by tri- (18.9%), hexa- (14.3%), penta- (13.5%), tetra- (5.3%), hepta- (2.1%), octa- (0.2%), and deca-nucleotide repeats (0.2%). AC/CF and AGA/TCT predominated in dimeric and trimeric repeat motifs, respectively. BLASTX homology searches found that 319 SSR-containing ESTs had significant Arabidopsis protein hits (E-value < 1.00E-05). In total, a set of 97 primer pairs was successfully designed for marker development and validation. Finally, fifty-four primers yielded repeatable and distinct amplification products among 21 tea plant genotypes, however, only 30 loci were polymorphic with an average allele number of 3.4/locus (range: 2-6 alleles/locus). Cross-amplification showed that 87% (26/30) primers could yield scorable products in at least one of nineteen Theaceae species. The transferability ranged from 7 to 77% with a mean of 30%. Furthermore, twenty-five SSR loci were polymorphic for the parents of a pseudo-testcross mapping population of tea plant, indicating they could be utilized for genetic linkage mapping. These novel informative EST-SSR markers will be a useful addition to genetic analysis and molecular breeding programs in tea plant and its related species. (C) 2011 Elsevier B.V. All rights reserved.