大花序桉顶芽转录组SSR位点信息分析  

Bioinformatic analysis of simple sequence repeat(SSR)loci in Eucalyptus cloeziana buds transcriptome

作　　者：蒋维昕[1] 梁馨元 兰俊 王建忠 白天道[1] JIANG Weixin;LIANG Xinyuan;LAN Jun;WANG Jianzhong;BAI Tiandao(Forestry College,Guangxi University,Nanning 530000,Guangxi,China;Dongmen Forest Farm of Guangxi Zhuang Autonomous Region,Chongzuo 532108,Guangxi,China)

机构地区：[1]广西大学林学院,广西南宁530000 [2]广西壮族自治区国有东门林场,广西崇左532108

出　　处：《中南林业科技大学学报》2021年第4期148-155,共8页Journal of Central South University of Forestry & Technology

基　　金：广西重点研发计划项目(2018AB44025);广西大学科研项目(20180493)。

摘　　要：【目的】分析珍贵用材树种大花序桉转录组SSR位点信息,旨在为开发新的大花序桉功能基因相关的多态性SSR标记提供理论基础。【方法】以2年生大花序桉顶芽为试验材料,基于Illumina HiSeq X Ten高通量测序技术平台获得其转录组序列数据,利用MISA软件对全部无冗余Unigene序列进行SSR位点检索和分析,并使用Primer 3软件进行SSR引物设计,以研究大花序桉顶芽转录组中的SSR位点分布特征及多态性标记开发潜力。【结果】大花序桉26587条转录组Unigene中共获得12366个SSR位点,分布在8218条Unigene序列中,SSR位点出现频率为46.51%,分布密度为平均每2.75 kb含有1个SSR位点;大花序桉顶芽转录组全部SSR位点中共发现116种重复基元类型,其中二、三核苷酸为主要重复基元类型,各占SSR总数的46.60%和34.20%;除了单碱基重复基元类型,AG/CT和CCG/CGG为优势重复基元,分别占44.94%和12.53%;SSR基元重复次数以低重复次数(5~10次)为主(71.28%),其次为11~15次重复(21.48%);SSR基序平均长度为19.7 bp,63.75%的基序长度集中于12~20 bp之间;符合引物设计要求且重复片段长度≥20 bp以上的低重复基元(二三核苷酸重复)类型SSR序列共1993个,占总序列的16.12%;试验随机筛选合成了24对引物,可扩增出清晰且符合预期条带大小的引物共14对,扩增效率为58.33%。【结论】大花序桉顶芽转录组SSR位点发生频率高,分布密度大,重复基元类型丰富,引物扩增效率高,多态性标记开发潜力大,在大花序桉及其他桉树的群体遗传学研究、分子标记辅助育种以及遗传图谱绘制中有较大应用前景。【Objective】Simple sequence repeat(SSR)characteristics in Eucalyptus cloeziana buds transcriptome were studied so as to provide a basis for the development of new and rich polymorphic SSR markers related to functional genes of E.cloeziana.【Method】MISA software was conducted to search SSR loci in terminal bud transcriptome of two-year-old E.cloeziana,based on Illumina sequencing technology.The distribution characteristics and motif types of SSR sites in bud transcriptome of E.cloeziana were analyzed and the SSR primer was designed by using Primer 3.【Result】A total of 12366 SSRs were identified from 8218 of 26587 bud Unigene sequences of E.cloeziana,with a frequency of 46.51%and the average distribution distance of the transcriptomic SSRs was 2.75 kb.A total of 116 different repeating motifs were detected in bud Unigene sequences of E.cloeziana.Among them,the dinucleotides and trinucleotides were the most abundant repetitive types,accounting for 46.60%and 34.20%of all the SSRs of E.cloeziana,respectively.The main repeat motifs were AG/CT and CCG/CGG,accounting for 44.94%and 12.53%,respectively.Most of the repeat number of the SSRs were from 5 to 10(71.28%),followed by from 11 to 15(21.48%).The motif length of 63.75%was concentrated between 12 and 20 bp with an average length of 19.7 bp.There were a total of 1993 low-repeats(di-and tri-nucleotide)SSR sequences with fragment length≥20 bp that met the primer design requirements.Meanwhile,a total of 24 SSR primer pairs randomly selected were synthesized and verified by PCR amplification,and 14 primers with clear and expected products were detected,with an amplification efficiency of 58.33%.【Conclusion】SSR loci in the terminal bud transcriptome of E.cloeziana showed high frequency,large distribution density,abundant types of motifs and high amplification efficiency,which implied great potential in the study of genetic diversity,molecular marker-assisted breeding and genetic mapping of Eucalyptus.

关 键 词：大花序桉 转录组 SSR 顶芽 

分 类 号：S718.46[农业科学—林学]