摘要
【目的】旨在全面了解叶色多彩明亮、抗逆性强的美国红枫SSR位点信息及序列特征,为开发新的功能基因相关且多态性良好的SSR标记提供依据。【方法】以美国红枫不同叶色的叶片为试验材料,经转录组测序后,利用MISA软件对美国红枫1 kb以上的Unigene进行SSR位点搜索;通过Excel软件进行SSR分布和序列特征分析并用Prime 3软件设计引物。【结果】从美国红枫转录组测序数据中共获得Unigene 78 571条,其中长度≥1 kb的Unigene共23 278条。对长度≥1 kb的Unigene进行SSR位点搜索和分析,共获得12 974个SSR位点,出现频率为55.75%,平均约3.7 kb出现1个SSR位点;美国红枫转录组SSR重复碱基类型共有7种,其中单碱基为主要重复类型,占总SSR的54.12%,其次为双碱基和三碱基重复类型,分别占总SSR的20.64%和16.19%,其他的碱基重复类型较低,仅占总SSR的9.05%。A/T、AT/TA与GAA/TTC分别为单碱基到三碱基的优势重复基元,分别占总SSR的53.95%、8.00%与1.65%,而四碱基的重复基元均较低,在0.05%以下;单碱基到六碱基各基元重复次数集中在5~22次之间,序列长度变化在10~48 bp之间,平均长度为18.43 bp;筛选出10751个SSR符合引物设计要求,共设计出32253对引物,占总SSR的82.87%。【结论】根据转录组测序结果,美国红枫转录组中SSR位点分布频率高,基序类型丰富,具有较高的多态性,在美国红枫遗传多样性和分子标记辅助育种中具有较大的应用潜力。
【Objective】The aim is to comprehensively understand the SSR loci information and sequence characteristics in American red maple with colorful and bright leaves and strong resistance,and provide a basis for the development of new functional gene-related SSR markers with good polymorphism.【Method】The different color leaves of American red maple were used as test materials.After transcriptome sequencing,the MSR software was used to search for SSR loci of unigenes with more than 1 kb of American red maple;SSR distribution and sequence characteristics were analyzed by Excel software,and Prime 3 software was used to design primers.【Result】A total of 78 571 unigenes were obtained from American red maple transcriptome sequencing data,of which 23 278 unigenes with a length≥1 kb.SSR loci were searched and analyzed for unigene with length≥1 kb,and a total of 12 974 SSRs were obtained,with a frequency of 55.75%,and an average of 1 SSR loci appeared at about 3.7 kb;there are 7 SSR repeating base types in transcriptome of the American red maple,of which the Mononucleotide is the main repeating type,accounting for 54.12%of the total SSR,followed by the Dinucleotide and Trinucleotide repeating types,accounting for 20.64%and 16.19%of the total SSR,the other base repeating types are lower,accounting for only 9.05%of the total SSR.A/T,AT/TA and GAA/TTC are the dominant repeating motifs from Mononucleotide to Trinucleotide,accounting for 53.95%,8.00%and 1.65%of the total SSR,respectively,while the repeating motifs of the Tetranucleotide are all Low,all below 0.05%;the number of repetitions of each primitive from Mononucleotide to Hexanucleotide is concentrated between 5-22 times,the sequence length varies between 10 and 48 bp,and the average length is 18.43 bp;10751 SSRs were screened for primer design requirements,and a total of 32253 primers were designed,accounting for 82.87%of the total SSRs.【Conclusion】According to the results of transcriptome sequencing,SSRs in transcriptome of American red maple have a hig
作者
郭聪
陈燕
王莹
谈峰
柯裴蓓
沙文锋
李玉娟
GUO Cong;CHEN Yan;WANG Ying;TAN Feng;KE Peibei;SHA Wenfeng;LI Yujuan(Institute of Agricultural Sciences of Jiangsu Changjiang River Bank District,Nantong 226541,Jiangsu,China)
出处
《中南林业科技大学学报》
CAS
CSCD
北大核心
2021年第7期132-141,共10页
Journal of Central South University of Forestry & Technology
基金
江苏省农业自主创新资金项目(CX[19]3121)
南通市应用基础研究项目(JC2019046)
江苏沿江地区农业科学研究所青年科技基金项目(YJ[2019]005)。
关键词
美国红枫
SSR
转录组
序列分析
American red maple
SSR
transcriptome
sequence analysis
