基于SLAF-seq技术的树莓SNP位点开发

doi:10.11924/j.issn.1000-6850.casb18030143

摘要/Abstract

摘要： 为分析树莓群体的遗传进化关系，开发特异性SNP标记。选用23 个栽培种树莓以用SLAF-seq技术测序，从树莓全基因组范围开发SNP位点，以黑树莓基因组为参考基因组，通过生物信息学分析进行电子酶切预测，筛选特异长度的DNA片断，构建SLAF-seq 文库。通过高通量测序的方式获得海量序列标签，利用软件分析比对，获得多态性SLAF标签，进而开发大量特异性SNP位点。对照水稻的测序数据与参考基因组比对结果，双端比对效率为95.60%，酶切效率为93.52%，说明SLAF建库正常。通过测序共产生59.93 Mb的读长数据，测序质量值Q30 平均为95.07%，所有样品GC含量均值为39.16%，GC含量普遍不高，说明达到测序要求。本研究共获得425402 个SLAF标签，其中多态性的SLAF标签共有121610 个。获得749811 个有效单核苷酸多态(SNP)，利用这些SNP分析了23 个树莓种质的群体结构与系统发生树。利用简化基因组测序技术SLAF-seq 可以高效地、低成本地开发出大量的可用于群体遗传结构分析的SNP标记。

关键词: 中长期天气预报, 中长期天气预报, 数值预报, 集合预报, 均值和方差, 集合预报产品

Abstract: The aims are to analyze the genetic evolution relationship of raspberry populations, and develop specific SNP markers. 23 raspberry varieties were sequenced by Specific Length Amplification Fragment Sequencing (SLAF-seq) technology. The SNP site was developed from the whole genome of raspberry. The genome of black raspberry was used as the reference genome. The electron enzyme cutting prediction was conducted by bio-informatics analysis, the specific length DNA fragments were screened and the SLAF-seq library was constructed. Mass sequence tags were obtained by high-throughput sequencing, and polymorphic SLAF tags were obtained by software analysis and comparison, and then a large number of specific SNP loci were developed. Compared with the sequencing data of rice and the comparison results of the reference genome, the results showed that the paired-end comparison rate was 95.60%, enzyme digestion efficiency was 93.52%, which indicated that the SLAF database was normal. A total of 59.93 Mb reads were obtained, the average quality value of Q30 was 95.07%, the mean value of GC content in all samples was 39.16%, and the average level of GC content was low which indicated that it met the sequencing requirement. A total of 425402 SLAF tags were obtained, of which 121610 were polymorphic SLAF tags. 749811 effective single nucleotide polymorphisms (SNP) were obtained and the population structure and phylogenetic tree of 23 raspberry germplasm were analyzed by these SNP. SLAF-seq technology can develop a large number of SNP markers,

中图分类号:

S663.2

杨光,孙兰英,李鹏举,段亚东. 基于SLAF-seq技术的树莓SNP位点开发[J]. 中国农学通报, 2018, 34(36): 58-64.

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