苹果基因组SSR位点分析与应用

Evaluation and Application of the SSR Loci in Apple Genome

【目的】通过对‘金冠’苹果基因组SSR位点的统计分析,为蔷薇科果树应用SSR分子标记进行高通量的遗传分析提供理论与实践基础。【方法】运用NCBI数据库中‘金冠’苹果基因组数据,分析其SSR位点分布情况,并根据SSR位点的搜索结果,设计68对引物(每条染色体设计4对),利用苹果品种对所设计引物进行应用性验证并利用梨杂交群体进行通用性检测。【结果】苹果基因组中SSR序列主要是完全重复型,17条染色体共存在163 426个SSR位点,平均每隔3.22 kb存在1个。单核苷酸至三核苷酸重复基序在染色体水平上分布较均匀,而四核苷酸至六核苷酸重复基序的分布差异较大。单核苷酸与二核苷酸重复基序所占比例最大,两者占基因组内SSR位点总数的91.67%,单核苷酸重复基序主要以A/T重复为主,二核苷酸的重复基序主要以AT/TA重复为主。在苹果品种中验证所设计的68对引物,有62对可以扩增出预期目的片段,37对存在扩增多态性。在梨杂交群体上应用所设计的68对引物,有40对具扩增目的片段,其中16对具扩增多态性。【结论】苹果基因组内SSR分布呈现一定的规律性,初步验证SSR位点在亲缘关系较近的物种间高度保守并可以通用,基于基因组数据发掘SSR位点用于后续的相关遗传研究具有可行性。

【Objective】 In order to provide a theoretical and practical foundation for the genetic analysis of Rosaceae fruit trees which based on the SSR markers,the SSR loci from apple（Malus × domestica Borkh.＇Golden Delicious＇） genome was analyzed.【Method】The genome data of apple ＇Golden Delicious＇ was downloaded from the NCBI website and the MISA software was used to analyze the distribution of genome SSR loci.We designed sixty-eight primers,which 4 primers from each chromosome according to the searching results of the SSR loci,were designed and the 10 apple cultivars and F1 progeny of pear were utilized to examine the application and transferability of designed primers,respectively.【Result】The perfect repeat sequences were found that it is the main form of the SSR sequences type and the total number of SSR loci is 163 426 in apple genome.There will be one SSR loci from every 3.22 kb on average.The distribution of the mononucleotide,dinucleotide and trinucleotide repeat motifs in the chromosome standard were stable relatively,whereas the picture of tetranucleotide,pentanucleotide and hexanucleotide repeat motifs were not.The largest proportion of the SSR loci is the mononucleotide and the dinucleotide repeat motifs,they possessed 91.67% of the total SSRs in the whole genome.As scanned for the mononucleotide repeat units,base A/T is the mainly proportion,the base pair AT/TA is the domination in the dinucleotide repeat units.There are 62 and 37 primers could amplify the predicted and polymorphic fragments in apple among 68 designed primers,separately.Whereas,in pear,there are only 16 polymorphic primers in the 40 primers which can be amplified the same size fragments as predicted.【Conclusion】Some distribution raws of SSRs in the apple genome were found.The results that SSR loci in the closer genetic relationship among species are highly conserved and can be used in the following research were demonstrated preliminarily.It is meaningful to develop SSR loci from genomic data for the application of relative genetic analysis.