Identification and Mapping of Simple Sequence Repeat Markers from Common Bean (Phaseolus vulgaris L.) Bacterial Artificial Chromosome End Sequences for Genome Characterization and Genetic-Physical Map Integration
Identification and Mapping of Simple Sequence Repeat Markers from Common Bean (Phaseolus vulgaris L.) Bacterial Artificial Chromosome End Sequences for Genome Characterization and Genetic-Physical Map Integration
复制标题
DOI：
10.3835/plantgenome2010.06.0013
复制
发表时间：
2010-11-01
期刊：
影响因子：
4.2
通讯作者：
Blair, Matthew W.
中科院分区：
文献类型：
--
作者：
Cordoba, Juana M.;Chavarro, Carolina;Blair, Matthew W.
微卫星标记或简单重复序列（SSR）位点是有用的多样性表征和遗传物理作图。不同的计算机微卫星搜索方法已被开发用于挖掘细菌人工染色体（BAC）末端序列的SSR。本研究的总体目标是基于来自G19833普通菜豆（Phaseolus vulgaris L.）图书馆另一个目的是鉴定新的SSR，同时考虑到三个串联基序鉴定程序（自动微卫星标记开发[AMMD]，串联重复序列[TRF]和SSRSTs [SSRL]）。在微卫星搜索引擎中，SSRL识别出的SSR数量最多;然而，当尝试引物设计时，由于引物设计区域较差，SSR数量下降。自动微卫星标记开发软件鉴定出许多具有有价值的AT/TA或AG/TC基序的SSR，而TRF发现的SSR较少，并且没有产生引物。从AMMD结果中选择了323个富含AT的二核苷酸和三核苷酸SSR的亚组，并用于DOR 364和G19833的亲本调查，其中75个可以在相应的群体中定位;这些代表4052个BAC克隆。连同92个先前映射的BES-和114个非BES-衍生的标记，总共280个SSR被包括在基于聚合酶链反应（PCR）的地图，整合了总共8232个BAC克隆在162个重叠群从物理地图。
Microsatellite markers or simple sequence repeat (SSR) loci are useful for diversity characterization and genetic-physical mapping. Different in silico microsatellite search methods have been developed for mining bacterial artificial chromosome (BAC) end sequences for SSRs. The overall goal of this study was genome characterization based on SSRs in 89,017 BAC end sequences (BESs) from the G19833 common bean (Phaseolus vulgaris L.) library. Another objective was to identify new SSR taking into account three tandem motif identification programs (Automated Microsatellite Marker Development [AMMD], Tandem Repeats Finder [TRF], and SSRLocator [SSRL]). Among the microsatellite search engines, SSRL identified the highest number of SSRs; however, when primer design was attempted, the number dropped due to poor primer design regions. Automated Microsatellite Marker Development software identified many SSRs with valuable AT/TA or AG/TC motifs, while TRF found fewer SSRs and produced no primers. A subgroup of 323 AT-rich, di-,and trinucleotide SSRs were selected from the AMMD results and used in a parental survey with DOR364 and G19833, of which 75 could be mapped in the corresponding population; these represented 4052 BAC clones. Together with 92 previously mapped BES- and 114 non-BES-derived markers, a total of 280 SSRs were included in the polymerase chain reaction (PCR)-based map, integrating a total of 8232 BAC clones in 162 contigs from the physical map.