基于转录组测序的油茶SSR、SNP和InDel位点特征分析  

Analysis of SSR,SNP,InDel Loci Information in the Transcriptome of Camellia oleifera Abel.

作　　者：张震[1,2] 许彦明 彭映赫[1,2] 王瑞 陈永忠 何之龙[1,2] 张英 寻成峰[1,2] 马玉申 王湘南 龙玲 杨小胡 Zhang Zhen;Xu Yanming;Peng Yinghe;Wang Rui;Chen Yongzhong;He Zhilong;Zhang Ying;Xun Chengfeng;Ma Yushen;Wang Xiangnan;Long Ling;Yang Xiaohu(Hunan Academy of Forestry,Changsha 410004,Hunan,China;National Engineering Research Center for Camellia oleifera,Changsha 410004,Hunan,China)

机构地区：[1]湖南省林业科学院,湖南长沙410004 [2]国家油茶工程技术研究中心,湖南长沙410004

出　　处：《绿色科技》2024年第18期200-204,共5页Journal of Green Science and Technology

基　　金：湖南省重点领域研发计划(编号:2023NK2005);湖南省油茶产业科研示范项目(编号:2023LYCY0017);湖南省林业科技创新资金项目(编号:XLKY202206)。

摘　　要：基于油茶转录组测序数据,利用MISA和GATK3软件对SSR、SNP和InDel位点进行搜索。结果表明:在169652条unigene序列中共发现92228个SSR位点,出现频率54.37%,平均分布距离1.61 kb。油茶转录组SSR位点中,单核苷酸和二核苷酸是主要的重复类型,A/T和AG/CT是主要的重复基元类型,基元重复次数主要集中在5~11次,基序长度主要集中在12~20 bp。共得到1912501个SNP位点,转换类型SNP数量多于颠换类型SNP数量,转换类型中A/G数量最多,而颠换类型中A/T数量最多。共筛选出298984个InDel位点。油茶转录组SSR、SNP和InDel位点数量多、类型丰富,能够为油茶分子标记开发、种质资源评价、亲缘关系鉴定等研究提供支撑。Based on the sequencing data of Camellia oleifera Abel.,the SSR,SNP,InDel loci was searched through MISA and GATK3 software.The results showed that a total of 92228 SSR were found and distributed in 169652 unigene.The distribution density and average occurrence frequency were 1.61 kb and 54.37%,respectively.In Camellin.oleifera Abel.SSR,MNRs and DNRs were the major nucleic acid repeat types;A/T and AG/CT were the dominant repetitive bases;The number of primitive repeats is mainly concentrated between 5 and 11 times.The motifs length was mainly distributed between 12 bp and 20 bp.1912501 SNP loci were obtained,and the transitions types were more than the transversion types.In transitions types and transversion types,the number of A/G and A/T were the largest,respectively.A total of 298984 InDel loci were identified.The number and types of SSR,SNP and InDel loci in the transcriptome of Camellia.oleifera are abundant,which can provide support for the development of molecular markers,germplasm resource evaluation,genetic relationship identification and other studies.

关 键 词：油茶 转录组测序 SSR SNP INDEL 

分 类 号：S794[农业科学—林木遗传育种]