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.
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DOI：
10.1093/dnares/dst040
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发表时间：
2014-02
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
尽管已经进行了大量的研究，但微卫星分布模式仍然不明确，并且由于缺乏基因组序列，微卫星标记在芸苔属中的开发/利用仍然有限/效率低下。鉴于此，我们在最近测序的三种芸苔属作物：芜菁、甘蓝和甘蓝型油菜中进行了全基因组微卫星表征和标记开发。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正相关或负相关。在115 869个SSR标记中，有185 662个和356 522个SSR标记出现频率较高（408.2、343.8和356.2个/Mb或1个/2.45、2.91和2.81kb），大多数是新的SSR标记，大多数已确定物理位置，大量为基因型或推定的单位点SSR标记。我们还建立了一个综合的数据库，为新开发的SSR标记，这是集成与公共芸苔属SSR标记和注释基因组成分。本研究开发的全基因组SSR标记为将已测序芸苔属物种的注释基因组资源扩展到不同芸苔属物种的遗传研究/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 in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. 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 public Brassica SSR 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 sequenced Brassica species to genetic study/breeding in different Brassica species.
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影响因子：
5.4
作者：
Cloutier, Sylvie;Miranda, Evelyn;Ward, Kerry;Radovanovic, Natasa;Reimer, Elsa;Walichnowski, Andrzej;Datla, Raju;Rowland, Gordon;Duguid, Scott;Ragupathy, Raja
通讯作者：
Ragupathy, Raja
影响因子：
2.4
作者：
Ge, Yu;Ramchiary, Nirala;Piao, Zhong Yun
通讯作者：
Piao, Zhong Yun
影响因子：
4.4
作者：
Cavagnaro PF;Senalik DA;Yang L;Simon PW;Harkins TT;Kodira CD;Huang S;Weng Y
通讯作者：
Weng Y
DOI：
10.1111/j.1471-8286.2006.01488.x
发表时间：
2006-12-01
期刊：
MOLECULAR ECOLOGY NOTES
影响因子：
--
作者：
Burgess, Benjamin;Mountford, Hayley;Batley, Jacqueline
通讯作者：
Batley, Jacqueline
影响因子：
7
作者：
Lysak, MA;Koch, MA;Schubert, I
通讯作者：
Schubert, I