基于SLAF-seq技术的闽楠SNP标记开发及遗传多样性分析

Marker Development and Analysis of Genetic Diversity of Phoebe bournei Germplasms Using SLAF-seq Technology

利用简化基因组测序技术SLAF-seq,对广泛分布在长江以南地区8个省份的33份闽楠种质进行SNP标记开发、指纹图谱构建和遗传多样性分析。本研究对各样品的测序数据进行统计,共获得107.52 Mb Clean Reads数据,每个样品的SNP标记数目介于309012-540030之间,样本平均测序质量值Q30为93.78%,平均GC含量为40.90%。共获得1072115个SLAF标签,其中多态性SLAF标签275389个。通过序列分析,获得121352个有效的单核苷酸多态性标记(SNP);经过指纹图谱严格的过滤条件,筛选出3452个SNP位点作为指纹图谱SNP。利用开发的SNP分子标记,将33份闽楠种质资源分为3个亚群,这3个亚群分别包含材料为Q1:17个,Q2:11个,Q3:5个。通过进一步过滤,获得270个核心SNP标记作为指纹图谱的核心标记,可用于品种种质的鉴定。研究结果表明,简化基因组测序技术SLAF-seq能高效、低廉地开发出大量SNP标记,是一种适用于闽楠种质资源遗传分析的有效工具;利用筛选出的核心SNP分子标记构建闽楠DNA指纹图谱,为SNP分子标记应用于闽楠种质鉴定、闽楠品种改良与优质品种选育提供依据,也有利于闽楠种质的高效利用及杂种优势群的建立。

In this study,a specific locus amplified fragment sequencing(SLAF-Seq)technology was used to develop SNP markers,construct fingerprint maps,and analyze the genetic diversity of 33 Phoebe bournei germplasms distributed in 8 provinces south of the Yangtze River.In this study,sequencing data of each sample was statistically analyzed,and 107.52 Mb Reads data were obtained.The Reads data of each sample ranged from 309012 to540030.The average sequencing quality value(Q30)and GC content of samples was 93.78%and 40.90%,the total of 1072115 SLAF tags and 275389 polymorphic SLAF tags were obtained.A total of 121352 single nucleotide polymorphisms(SNPs)were obtained through sequences analysis,and 3452 SNP loci were treated as markers of DNA fingerprinting.Population structure and phylogenetic relationship of 33 germplasms of Phoebe bournei were analyzed using the SNP dataset.The population was significantly divided into three different groups.These three subgroups contained germplasm resources:Q1(17),Q2(11),Q3(5).Then,in accordance with strict filter criteria,270 SNPs were obtained as core markers of DNA fingerprinting.It suggests that SLAF-seq can be used to develop large-scale SNPs for population genetic analysis,effectively and economically.SNP molecular marker is an effective tool for genetic analysis of Phoebe bournei germplasm resources.The DNA fingerprinting of Phoebe bournei is constructed by using the selected core SNP molecular markers,which provide the basis for the application of SNP molecular markers in germplasm identification,variety improvement and high-quality variety breeding of Phoebe bournei.It is beneficial for promoting effective utilization of Phoebe bournei,breeding new cultivars and building of heterotic groups.