黄皮转录组SSR挖掘及其可用性分析  

Excavation and Usablility Analysis of SSR from Transcriptome of Clausena lansium

作　　者：陆育生 陈喆 常晓晓[1] 邱继水[1] 林志雄[1] 潘建平[1] 

机构地区：[1]广东省农业科学院果树研究所,农业部南亚热带果树生物学及遗传资源利用重点实验室,广东省热带亚热带果树研究重点实验室,广州510640

出　　处：《园艺学报》2018年第1期149-158,共10页Acta Horticulturae Sinica

基　　金：国家自然科学基金项目(31501729); 广东省科技计划项目(2015A030302041,2016B020201004); 广东省优稀水果产业技术体系项目(2017LM1071); 农业部热带作物种质资源保护项目(16RZZY-20); 广东省农业科学院院长基金项目(201605)

摘　　要：利用MISA软件筛选黄皮(Clausena lansium)转录组测序获得的68 998条Unigene,共检测出单核苷酸至六核苷酸重复类型的SSR位点11 825个,分布于11 000条Unigene中,出现频率为17.14%,平均分布距离为4.41 kb。6种SSR位点类型中主要为单、二、三个核苷酸重复,分别占总SSR位点的41.48%、24.92%和27.53%。11 825个SSR位点中共发现207种重复基序,重复次数在4~24次之间,其中出现频率高的基序有A/T、AG/CT、AT/AT、AAG/CTT和AAT/ATT。位点序列长度分布在12~25 bp之间,其中12~15 bp最多,占50.95%(6 025个SSR位点)。通过Primer 3设计得到6 102对SSR引物,随机选择30对引物进行多态性验证分析,结果显示24对有效扩增引物中,13对引物在16份不同黄皮种质中表现出多态性。以上结果表明,黄皮转录组测序产生的Unigene信息可作为开发SSR标记的有效来源,开发的大批量SSR标记可为黄皮种质资源遗传多样性分析和遗传图谱构建提供更加丰富可靠的标记选择。In this study,a total of 68 998 Unigenes from transcriptome of Clausena lansium were used for screening of SSR loci using MISA software. 11 825 SSRs,including the types of 1–6 nucleotide repeats distributed in 11 000 Unigenes were identified,with occurring frequency of 17.14% and mean distance of 4.41 kb. The major types of SSR loci were 1–3 nucleotide repeats,accounting for 93.93% of the SSR loci,of which mono-,di-and tri-nucleotide repeats were 41.48%,24.92% and 27.53%,respectively. Two hundred and seven repeat motifs with iteration numbers from 4 to 24 were discovered from the 11 825 SSR loci,and the most abundant motif were A/T,AG/CT,AT/AT,AAG/CTT and AAT/ATT. The lengths of repeat nucleotide sequences for all SSR loci ranged from 12 to 25 bp,with most from 12 to 15 bp,accounting for 50.95% of all SSR loci. A total of 6 102 SSR primers were designed and 30 primers were selected randomly for PCR amplification tests,of which 24 primers amplified effective and 13 primers showed polymorphism in sixteen different wampee germplasm. The results indicated that the Unigenes generated from trasncriptome sequencing in C. lansium could be used as an effective source to develop SSR markers. The large quantities of SSR markers will provide reliable markers for map structure,genetic polymorphism analysis for wampee germplasm resource.

关 键 词：黄皮 转录组 SSR 可用性分析 

分 类 号：S667.5[农业科学—果树学]