基于SLAF-seq技术的古茶树SNP位点开发  

SNP sites development in old Camellia sinensis based on specific length amplification fragment sequencing(SLAF-seq) technology

作　　者：耿广东[1] 陈立杰[2] 张素勤[1] GENG Guangdong;CHEN Lijie;ZHANG Suqin(College of Agriculture,Guizhou University,Guiyang 550025,Guizhou,China;Asset Management Office,Guizhou University,Guiyang 550025,Guizhou,China)

机构地区：[1]贵州大学农学院,贵州贵阳550025 [2]贵州大学资产经营办公室,贵州贵阳550025

出　　处：《经济林研究》2019年第2期7-12,共6页Non-wood Forest Research

基　　金：中央财政农业生产发展基金(黔财农〔2015〕240号);贵州省农业攻关项目(黔科合支撑〔2016〕2603号);贵州省农业攻关项目(黔科合支撑〔2018〕2330号);贵州省科技厅重大专项计划(黔科合重大专项字〔2016〕3002号)

摘　　要：为给古茶树遗传图谱构建、分子辅助育种和物种进化等研究提供参考,以48份贵州古茶树种质为研究对象,利用SLAF-seq技术,获取大量多态性SLAF标签,进而开发一批特异性强、稳定性高的单核苷酸多态性(SNP)位点。结果表明,利用猕猴桃参考基因组进行电子酶切预测,选择HaeIII酶进行酶切,得到237773个SLAF标签,其双端比对效率为91.40%,酶切效率为96.41%,说明SLAF建库正常。测序后各样品所获得的读长数为1279534~8460233,测序质量值Q30范围为92.61%~94.88%,均值为93.84%,测序获得的GC比例为43.52%~47.18%。共开发1656258个古茶树SLAF标签,样品的平均测序深度为24.21×,其中多态性SLAF标签有462897个,根据所获得的多态性SLAF标签来统计SNP位点信息,共得到2690638个群体SNP标记,根据完整度大于0.8且次要基因频率(MAF)大于0.05的标准进行过滤,得到283376个高一致性的群体SNP标记。In order to provide some references for the researches on genetic map construction,molecular assisted breeding and species evolution in old Camellia sinensis,using 48 samples of old C.sinensis germplasm in Guizhou as research objects,a large number of polymorphic SLAF tags were obtained by using SLAF-seq technology,and a large number of single nucleotide polymorphism (SNPs) sites were developed,which had strong specificity and high stability. The results showed that kiwifruit reference genome was used for electronic digestion prediction,HaeIII endonuclease was selected,and 237 773 SLAF tags were predicted.Double-end alignment efficiency was 91.40%,and enzyme digestion efficiency was 96.41%,indicating that SLAF library was normal.Number of sequencing reads was at the range of 1 279 534-8 460 233.Average quality of sequencing Q30 was 93.84%,ranging from 92.61% to 94.88%.Based on sequencing results,GC percentage was 43.52%-47.18%.Average sequencing depth of samples was 24.21×,and total 1 656 258 SLAF tags were developed,including 462 897 polymorphic SLAF tags.Based on obtained polymorphic SLAF tags,information of SNP sites was counted,and 2 690 638 population SNP markers were obtained.Total 283 376 highly consistent population SNP markers were obtained through filtering according to integrity greater than 0.8 and minor allele frequency (MAF) greater than 0.05.

关 键 词：古茶树 SLAF-seq SNP位点 高通量测序 分子标记 

分 类 号：S603[农业科学—园艺学]