基于ddGBS的桉树SNP挖掘和系统进化分析  

SNPs discovery and phylogenetic analysis in Eucalypts using ddGBS

作　　者：贾翠蓉 朱显亮 王莉 周长品[1,2] 翁启杰[1,2] 甘四明[1,2] 李发根[1,2] JIA Cuirong;ZHU Xianliang;WANG Li;ZHOU Changpin;WENG Qijie;GAN Siming;LI Fagen(Key Laboratory of the State Forestry and Grassland Administration for Tropical Forestry Research,Research Institute of Tropical Forestry,Chinese Academy of Forestry,Guangzhou 510520,Guangdong,China;College of Forestry,Nanjing Forestry University,Nanjing 210037,Jiangsu,China)

机构地区：[1]中国林业科学研究院热带林业研究所,广东广州510520 [2]中国林业科学研究院热带林业研究国家林业和草原局重点实验室,广东广州510520 [3]南京林业大学林学院,江苏南京210037

出　　处：《中南林业科技大学学报》2020年第10期101-108,共8页Journal of Central South University of Forestry & Technology

基　　金：中国林科院基本科研业务费专项(CAFYBB2017MA006);广西创新驱动发展专项(桂科AA17204087-3)。

摘　　要：【目的】利用ddGBS技术获得桉树树种间高质量SNP标记,为桉树系统分类提供新思路。【方法】通过对14个桉树树种(每个树种各两份样品)进行ddGBS建库测序分析,发掘SNP位点,开展位点注释及核苷酸多样性分析,并且通过IQ-TREE软件采用最大似然法(ML)构建系统进化树。【结果】测序共获得30.49 Gb的数据,平均每个样品的数据量为1.09 Gb;平均Q30为98%,表明测序质量好;平均GC含量(44.0%)与巨桉参考基因组接近;样品与巨桉参考基因组比对匹配率在45.0%~88.9%之间,平均为77.8%。按照数据无缺失、平均测序深度≥4 x、最小杂合比为0.05的条件筛选SNP,最终获得42 222个高质量SNP位点,其中14个桉树树种的特有SNP位点数为428~2 107不等。利用SnpEff软件进行位点注释分析后发现约有12 237个SNPs位于外显子区域。基于最终获得的42 222个高质量SNP位点构建系统进化树,14个桉树树种聚类结果与Hill和Johnson的桉属双蒴盖亚属及伞房属的分类结果一致。【结论】采用ddGBS技术高效发掘高质量SNP位点,可广泛应用于桉树SNP开发。利用开发的高质量SNP位点构建的系统进化树为桉树的进化研究提供了理论支持。通过ddGBS技术进行SNP标记开发及分型将对桉树关联遗传学研究和重要性状QTL定位具有重要意义。【Objective】High-quality SNP markers were discovered and genotyped from ddGBS(Double digest genotyping by sequencing)to provide a new idea for the research of phylogenetic lineages in eucalypts.【Method】A total of fourteen Eucalyptus species,two samples of each were used for SNP discovery and genotyping by using ddGBS.SNP variant annotation and nucleotide diversity were also analyzed.The maximum-likelihood phylogeny tree of 28 samples was constructed by using IQ-TREE.【Result】In total,30.49 Gb clean data were obtained with average 1.09 Gb for each sample and average Q30 was 98.0%resulted in high quality and reliability sequence data.The average GC content(44.0%)was similar to the reference genome of E.grandis and the mapping ratio aligning to the reference genome was 45.0%-88.9%,with an average of 77.8%.Totally 42222 high-quality SNP loci were identified with no missing data,an average sequencing depth≥4 x and a minimum heterozygosity ratio≥0.05.Only 428-2107 unique SNP loci were found in each species.About 12237 SNP markers were found in the exon region by annotation with SnpEff.The phylogeny of fourteen Eucalyptus also match Hill&Johnson’s taxonomic classification of the subgenus Symphyomyrtus.【Conclusion】ddGBS can successfully generated highly informative genome-wide SNPs and used for phylogenetic tree construction,which supports evolution research of eucalyptus.Therefor using ddGBS to discovered and genotype SNPs in Eucalyptus provides a better understanding on association genetic studies and on detection of trait-associated QTLs in the future.

关 键 词：桉树 ddGBS SNP 进化分析 

分 类 号：S722.39[农业科学—林木遗传育种]