Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species
Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species
复制标题
已测序芸苔属作物物种的全基因组微卫星表征和标记开发
DOI：
10.1093/dnares/dsu011
复制
发表时间：
2014-04-03
期刊：
影响因子：
--
通讯作者：
Wang H
中科院分区：
文献类型：
--
作者：
Shi J;Huang S;Zhan J;Yu J;Wang X;Hua W;Liu S;Liu G;Wang H
尽管已经开展了大量的研究，但由于缺乏基因组序列，芸苔属植物的微卫星分布模式仍然不明确，微卫星标记的开发利用仍然受到限制/效率低下。鉴于此，我们对最近测序的三种芸苔属植物（油菜、甘蓝和甘蓝型芸苔）进行了全基因组微卫星鉴定和标记开发。所分析的这些芸苔属植物的微卫星特征高度相似或几乎相同，表明芸苔属植物的微卫星分布模式可能是保守的。微卫星的基因组分布高度不均匀，分别与基因或转座因子呈正相关或负相关。在115 869、185 662和3556 522个高频率SSR标记（每Mb分别为408.2、343.8和356.2个，分别为2.45、2.91和2.81 kb）中，大多数是新的SSR标记，大多数是确定的物理位置，大量是基因或推测的单位点SSR标记。我们还构建了一个完整的SSR标记数据库，将新开发的SSR标记与publicBrassicaSSR标记和注释的基因组成分进行整合。本研究开发的全基因组SSR标记为将已测序的芸苔种基因组资源扩展到不同芸苔种的遗传研究和育种提供了有用的工具。
Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient inBrassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequencedBrassicacrops:Brassica rapa,Brassica oleraceaandBrassica napus. The analysed microsatellite characteristics of theseBrassicaspecies were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative inBrassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with publicBrassicaSSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequencedBrassicaspecies to genetic study/breeding in differentBrassicaspecies.
DOI：
10.1093/dnares/dst040
发表时间：
2014-02
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Shi J;Huang S;Zhan J;Yu J;Wang X;Hua W;Liu S;Liu G;Wang H
通讯作者：
Wang H