Large-scale development of SSR markers in the genome of cacao | 可可全基因组SSR标记的开发及分析
2013
Cao Hengchun, College of Plant Protection, Tai’an (China), Department of Tobacco | Wang Yi, Shandong Agricultural University, Tai’an (China), College of Agriculture | Huang Lisha, Shandong Agricultural University, Tai’an (China), College of Agriculture
Chinese. SSR标记是一种广泛应用的分子标记技术，在可可基因组的研究中发挥了重要的作用。本研究运用生物信息学的方法，对可可全基因组进行了扫描，共得到10，4653个SSR区段。对这些sSR区段进行分析，发现含有碱基数目不同的重复单元之间具有较大的差异：含有七核苷酸的重复单元最多，为70，414个，占所有重复单元总数的67.3％；其次为二核苷酸重复单元，为23，272个，占总数的22.2％。在各类SSR单元中，不同核苷酸重复单元出现的频率有明显的差异，其中富含A／T重复单元的SSR单元数目最多，占总数的67％；而C／C重复单元的SSR单元数目较少，约占总数的0.02％。利用SSR单元的位点信息，设计出了65，861对引物，并在可可基因组中进行了电子PER扩增验证，结果显示100％的引物均能扩增出产物条带。在可可基因组中大规模开发的SSR标记，将为可可的进化、分类和遗传多样性研究提供参考。
Show more [+] Less [-]English. SSR markers are widely used as the molecular markers technology. They play an important role in the study of Cacao genome. By large-scale developing in the whole genome of Cacao, a total of 104 653 SSR’s fragments were obtained. After being analyzed with the methods of bioinformatics, there was diversity among the different motifs of SSR: the most was septemnueleotide repeat unit, and accounting for up to 67.3%, and the second was dinueleotide repeat unit, accounting for 22.2%. Besides that, the number of (A/T)n repeats (67%) were more than the (C/G)n types (0.02%). With those SSR information got in Cacao, 65,861 pairs of SSR markers were finally designed out, which were also tested in the genome by e-PCR. And the results showed that 100% of those primers could obtain the target products. With so large of SSR markers got in the Cacao genome, it can be well promote the development of evolution, classification and diversity study.
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