基于SLAF-seq技术的红心火龙果SNP位点开发及遗传分析

SNP Sites Development by Specific Length Amplification Fragment Sequencing (SLAF-seq) and Genetic Analysis in Red Pitaya

为分析不同品种红心火龙果的遗传关系,本研究采集国内14种红心火龙果品种,通过生物信息学分析进行实验方案的系统设计,将所提取基因组进行酶切,筛选特异长度的DNA片断,构建SLAF-seq文库后进行高通量测序,将获得的序列进行分析比较后得到多态SLAF标签,在此标签基础上进一步开发特异性SNP位点,最后建立14种红心火龙果品种的进化树。本研究共开发159 560个SLAF标签,样品的平均测序深度为5.26×;共得到120 294个群体SNP,其中高一致性的群体SNP 51 859个。12种红心火龙果聚类结果发现,样品1、2、6、8、10同缘关系相近;样品3、5、7、9同缘关系相近;样品4、14同缘关系相对较近。研究表明应用SLAF-seq技术开发分子标记的效率比ISSR、RAPD、AFLP等常规技术更高。12种红心火龙果的聚类结果从基因组水平揭示不同地区品种之间的遗传分化关系,为火龙果种质的保护和遗传改良提供参考。

To analyze the genetic relationship among different cultivars, 14 red pitaya varieties were collected and sequenced by SLAF-seq technology. The scheme of the experiment was designed based on bio-informaties technology. Genome was extracted and digested by enzyme, specific size of DNA were chosen to construct the SLAF-seq library. After high-throughput sequencing, a great amount of sequences were obtained and used to gain the polymorphism SLAF tags by software alignment, then found the distribution of specific SNP sites. Finally evolutionary tree of 14 red pitaya varieties was constructed. In the end, 159 560 SLAFs were produced, and the average sequencing depth was 5.26~. 51 859 high consistency SNP sites was obtained based on the analysis of total 120 294 SNP. The clustering results of 12 red pitaya varieties showed the sample 1, 2, 6, 8, 10 had a greatly close relationship between each other, the same as the sample 3, 5, 7, 9 and sample 4, 14. This paper provided results that SLAF-seq technology could be applied in developing SNP sites in red pitaya, much more efficiently than markers like SSR, RAPD and AFLP. The clustering results revealed the relationships of population genetic evolution in the genomic level among red pitaya varieties come from different area,and provided reference for the protection of red pitaya＇s germplasm and genetic improvement.