摘要
【目的】SNPs和SSRs标记在功能基因的识别和定位等方面具有重要作用。【方法】利用GATK和MISA软件分别分析狗牙根转录组测序数据的SNPs和SSRs。【结果】基于转录组数据搜索到297542个SNP位点,主要以转换型为主;搜索到分布于18982条Unigene中的22154个SSR位点,发生频率为12.89%,SSR位点主要以单核苷酸、二核苷酸和三核苷酸重复为主,三者合计占比为94.99%,其中AG/CT和CCG/CGG分别在二核苷酸和三核苷酸重复中占比最高;基序长度在12~20 bp的SSRs数量最多,占比达78.52%。【结论】狗牙根转录组中的SNPs和SSRs位点具有数量多、类型丰富和多态性较好等特点,或可为后续遗传多样性分析、品质鉴定和抗性相关性状解析等提供参考。
【Objective】SNPs and SSRs markers play an important role in the recognition and location of functional genes.【Method】The single nucleotide polymorphisms(SNPs)and simple sequence repeats(SSRs)of transcriptome sequencing data of Cynodon dactylon were analyzed by GATK and MISA software,respectively.【Result】297542 SNPs were searched based on transcriptome data,mainly based on transformation type;22154 SSRs were found in 18982 Unigenes with a frequency of 12.89%,and SSRs was mainly composed of single nucleotide,dinucleotide and trinucleotide repeats,accounting for 94.99%of the total,of which AG/CT and CG/CGG were the highest among dinucleotide and trinucleotide repeats,respectively.The number of SSRs with a length of 12 to 20 bp was the largest,accounting for 78.52%.【Conclusion】The SNPs and SSRs of the transcriptome of Cynodon dactylon are characterized by a large number,abundant types and good polymorphism,which may provide a reference for subsequent genetic diversity analysis,quality identification and resistance-related shape analysis.
作者
李彦杰
贾洪沅
李庆天
白艺旋
刘芸杉
LI Yan-jie;JIA Hong-yuan;LI Qing-tian;BAI Yi-xuan;LIU Yun-shan(College of Biology and Food Engineering,Chongqing Three Gorges University,Chonqqing Wanzhou 404100,China;Teacher School of Education,Chongqing Three Gorges University,Chonqqing Wanzhou 404100,China)
出处
《西南农业学报》
CSCD
北大核心
2020年第3期524-528,共5页
Southwest China Journal of Agricultural Sciences
基金
重庆市教委科学技术研究项目(KJQN201801207)
重庆市人文社会科学重点研究基地三峡库区可持续发展研究中心开放基金(18sxxyjd08)
2011协同创新中心和渝东北特色生物资源开发利用工程中心。
关键词
三峡库区消落带
狗牙根
转录组数据
SNP标记
SSR标记
Fluctuation Zone in Three Gorges Reservoir Area
Cynodon dactylon
Transcriptome data
SNP markers
SSR markers
