SNP Sites Development Based on SLAF-seq Technology in Raspberry

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

Abstract

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,

CLC Number:

S663.2

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