CHEN Hao,QIAN Huali,XU Zhe,et al.SSR Loci Information Analysis in Polygonatum kingianum Transcriptome[J].Northern Horticulture,2022,(22):104-109.[doi:10.11937/bfyy.20221747]
滇黄精转录组SSR位点信息分析
- Title:
- SSR Loci Information Analysis in Polygonatum kingianum Transcriptome
- Keywords:
- Polygonatum kingianum; transcriptome; SSR; loci information
- 文献标志码:
- A
- 摘要:
- 以滇黄精转录组测序所获得的53 081条Unigene为试材，采用MicroSAtellite（MISA）软件检索出滇黄精的SSR位点，研究其分布频率和重复基序类型等特征，并利用Primer 3.0软件对检索出的SSR基序设计引物，筛选出符合要求的引物对，以期为滇黄精遗传连锁图谱的绘制、优良品种的辅助育种、种间的分子鉴别等研究提供参考依据。结果表明：在滇黄精转录组中共检索出9 037个SSR位点，分布于6 960条Unigene中，SSR位点的发生频率是13.11%。单核苷酸重复是滇黄精SSR主要基序类型，其中尤以A/T基序的出现频率最高，占SSR位点总数的54.00%。通过设计与筛选，最终获得10 320个SSR引物对。滇黄精转录组中的SSR位点具有丰富的类型，较高的出现频率以及较高的多态性潜能，为滇黄精SSR分子标记的开发与应用奠定了基础。
- Abstract:
- Taking 53 081 Unigenes obtained from the sequencing group of Polygonatum kingianum transcriptome as test materials.The SSR loci of Polygonatum kingianum were searched by MicroSAtellite (MISA) software，and its distribution frequency and types of repeated motifs were studied.Primers were designed for the retrieved SSR motifs by Primer 3.0 software，and primer pairs meeting the requirements were selected，in order to provide reference for the drawing of genetic linkage map of Polygonatum kingianum，the auxiliary breeding of excellent varieties,and molecular identification between species.The results showed that a total of 9 037 SSR loci were retrieved from the transcriptome of Polygonatum kingianum，distributed in 6 960 Unigenes，and the frequency of SSR?loci was 13.11%.Single nucleotide repeat was the main type of SSR motif in Polygonatum kingianum，especially the A/T motif，accounting for 54.00% of the total SSR loci.Through design and screening，10 320 SSR primer pairs were finally obtained.The SSR loci in the transcriptome of Polygonatum kingianum had rich types，high frequency and high polymorphism potential，which laid a foundation for the development and application of SSR molecular markers of Polygonatum kingianum.
参考文献/References:
［1］汪毅.黔本草（二）［M］.贵阳：贵州科技出版社,2017.［2］王婧,陶爱恩,杨燕,等.滇黄精中多糖的分离与抗氧化活性研究［J］.中草药,2021,52(16):4789-4796.［3］钱华丽,赵琪,徐哲,等.不同产地黄精的皂苷和多糖含量［J］.贵州农业科学,2022,50(3):96-102.［4］李玲,黄玉玲,杨玉玲,等.滇黄精不同部位理化指标与化学成分差异性研究［J］.农学学报,2021,11(8):70-75.［5］杨建宇,刘冠军,刘白云,等.中华中医药道地药材系列汇讲（7）道地药材滇黄精的研究近况［J］.现代医学与健康研究,2020,4(7):100-103.［6］王艺.黄精、滇黄精多糖的结构表征与降血糖活性分析［D］.西安:陕西师范大学,2019.［7］魏佳迪.基于代谢组学的滇黄精抗脂代谢紊乱作用机制研究［D］.昆明:云南中医学院,2018.［8］崔於.黄精抗衰老作用研究近况［J］.科技视界,2012(29):421.［9］刘爽,胡舒婷,贾巧君,等.黄精的化学组成及药理作用的研究进展［J］.天然产物研究与开发,2021(10):1783-1796.［10］杨兴鑫,穆健康,顾雯,等.滇黄精资源的开发应用进展及前景分析［J］.生物资源,2019,41(2):138-142.［11］LIU T,ZHU S,FU L,et al.Development and characterization of 1827 expressed sequence tag-derived simple sequence repeat markers for ramie(Boehmeria nivea L.Gaud)［J］.PLoS One,2013,8(4):e60346.［12］左茜茜,宋英杰,马心妍,等.苦荞全基因组SSR位点挖掘及遗传多样性分析［J］.中国农业科技导报,2022,24(4):38-51.［13］刘玉玲,张红岩,韩雪梅,等.蚕豆农艺性状的SSR标记关联分析［J］.西南农业学报,2022(3):503-516.［14］吴梦丽.防己种质资源SSR评价及DNA条形码构建［D］.南宁:广西中医药大学,2021.［15］张景,李晓东,宗庆波,等.半夏SSR分子标记开发与遗传多样性［J］.华中农业大学学报,2021(6):19-26.［16］刘朝玉.广东省益智栽培类型SSR分子标记的遗传多样性研究［D］.广州:华南农业大学,2019.［17］郑兰兰,张旭东,姚淞元,等.药用植物鸦胆子的基因组调研及SSR分子标记开发［J］.湖北医药学院学报,2020(5):427-431.［18］姜明,马德志,周丽,等.基于EST-SSR分子标记的狼毒大戟资源遗传多样性分析［J］.广东化工,2021,48(3):138-139.［19］TEMNYKH S,DE CLERCK G,LUKASHOVA A,et al.Computational and experimental analysis of microsatellites in rice(Oryza sativa L.):Frequency,length variation,transposon associations,and genetic marker potential［J］.Genome Res,2001,11(8):1441.［20］李小白,向林,罗洁,等.转录组测序(RNA-seq)策略及其数据在分子标记开发上的应用［J］.中国细胞生物学学报,2013(5):720-726,740.［21］朱巧,邓欣,张树冰,等.黄精属6种植物的SSR遗传差异分析［J］.中国中药杂志,2018(14):2935-2943.［22］陈友吾,廖荣俊,叶碧欢,等.多花黄精转录组SSR位点分析及分子标记开发［J］.中草药,2020(1):182-189.［23］黄琼林,何瑞,詹若挺,等.南药青天葵转录组SSR位点信息分析［J］.北方园艺,2015(12):76-79.［24］黄琼林.高良姜转录组简单重复序列位点分析［J］.时珍国医国药,2022(2):386-389.［25］王东,曹玲亚,高建平.党参转录组中SSR位点信息分析［J］.中草药,2014(16):2390-2394.［26］李翠婷,张广辉,马春花,孟等.野三七转录组中SSR位点信息分析及其多态性研究［J］.中草药,2014(10):1468-1472.［27］时博,赵乐,霍常青.白花前胡转录组简单重复序列位点分析［J］.中医学报,2017(10):1954-1958.［28］富贵,刘玉萍,苏旭.基于转录组数据的密花香薷SSR位点特征分析［J］.西北植物学报,2021(4):654-663.［29］代娇,时小东,顾雨熹,等.厚朴转录组SSR标记的开发及功能分析［J］.中草药,2017(13):2726-2732.［30］李清,李标,郭顺星.金钗石斛转录组SSR位点信息分析［J］.中国中药杂志,2017(1):63-69.
相似文献/References:
[1]黄琼林,何 瑞,詹若挺,等.南药青天葵转录组SSR位点信息分析[J].北方园艺,2015,39(12):76.[doi:10.11937/bfyy.201512021]
HUANG Qiong-lin,HE Rui,ZHAN Ruo-ting,et al.SSR Loci Information Analysis in Nervilia fordii Transcriptome[J].Northern Horticulture,2015,39(22):76.[doi:10.11937/bfyy.201512021]
[2]苏秀红,李庆磊,陈随清,等.冬凌草转录组SSR位点分析及多态性初步评价[J].北方园艺,2016,40(04):93.[doi:10.11937/bfyy.201604025]
SU Xiuhong,LI Qinglei,CHEN Suiqing,et al.Analysis of SSR Loci Information in Transcriptome of Rabdosia rubescens (Henmsl.) Hara and Its Polymorphism[J].Northern Horticulture,2016,40(22):93.[doi:10.11937/bfyy.201604025]
[3]刘慧敏,乌云塔娜,杜红岩.杜仲转录组基因密码子使用偏好性分析[J].北方园艺,2016,40(13):85.[doi:10.11937/bfyy.201613023]
LIU Huimin,WUYUN Tana,DU Hongyan.Analysis of Characteristic of Codon Usage of Eucommia ulmoides Transcriptome[J].Northern Horticulture,2016,40(22):85.[doi:10.11937/bfyy.201613023]
[4]王云生,文光琴,聂飞.矮丛蓝莓品种“美登”叶片转录组测序和生物信息学分析[J].北方园艺,2017,41(01):101.[doi:10.11937/bfyy.201701023]
WANG Yunsheng,WEN Guangqin,NIE Fei.Leaf Transcriptome Sequencing and Bioinformatics Analysis of Lowbush Blueberry Variety ‘Blomidon’[J].Northern Horticulture,2017,41(22):101.[doi:10.11937/bfyy.201701023]
[5]姚娜,刘秀明,董园园,等.转录组的测序方法及应用研究概述[J].北方园艺,2017,41(12):192.[doi:10.11937/bfyy.201712043]
YAO Na,LIU Xiuming,DONG Yuanyuan,et al.Advances in Application and Seguencing Methods of Transcriptome[J].Northern Horticulture,2017,41(22):192.[doi:10.11937/bfyy.201712043]
[6]龙月红,宋菊,国红玉,等.刺五加转录因子基因的挖掘[J].北方园艺,2017,41(20):153.[doi:10.11937/bfyy.20170195]
LONG Yuehong,SONG Ju,GUO Hongyu,et al.Exploring Transcription Factors in Eleutherococcus senticosus[J].Northern Horticulture,2017,41(22):153.[doi:10.11937/bfyy.20170195]
[7]刘洋,卢凯政,卞少杰,等.田间自然温度调控下核桃根系差异表达基因分析[J].北方园艺,2020,44(17):30.[doi:10.11937/bfyy.20194278]
LIU Yang,LU Kaizheng,BIAN Shaojie,et al.Analysis of Differentially Expressed Gene Profile in the Root of Walnut Under Natural Temperature Regulation in the Field[J].Northern Horticulture,2020,44(22):30.[doi:10.11937/bfyy.20194278]
[8]廖绪红,沙秀芬,廖雪梅,等.藁本属药用植物分子生物学研究进展[J].北方园艺,2021,(12):133.[doi:10.11937/bfyy.20203322]
LIAO Xuhong,SHA Xiufen,LIAO Xuemei,et al.Research Progress on Molecular Biology of Ligusticum[J].Northern Horticulture,2021,(22):133.[doi:10.11937/bfyy.20203322]
[9]王一清,王安琪,冯钧婷,等.亚洲百合糖代谢相关基因的表达与代谢分析[J].北方园艺,2022,(06):60.[doi:10.11937/bfyy.20213255]
WANG Yiqing,WANG Anqi,FENG Junting,et al.Analysis of Gene Expression and Metabolism Related to Sugar Metabolism of Lilium Asiatica Hybrida[J].Northern Horticulture,2022,(22):60.[doi:10.11937/bfyy.20213255]
[10]王小敏,张春红,胡丽超,等.基于高通量测序的蓝莓果实转录组[J].北方园艺,2022,(13):49.[doi:10.11937/bfyy.20214714]
WANG Xiaomin,ZHANG Chunhong,HU Lichao,et al.SSR Information Analysis of Blueberry Fruit Transcriptome Based on High Throughput Sequencing[J].Northern Horticulture,2022,(22):49.[doi:10.11937/bfyy.20214714]
备注/Memo
第一作者简介：陈浩（1997-），男，硕士研究生，研究方向为中药资源开发与利用。E-mail：ch1746751160@163.com.责任作者：季鹏章（1975-），男，博士，研究员，现主要从事中药资源开发与利用等研究工作。E-mail：pengzhji@126.com.基金项目：国家自然科学基金资助项目(31760347)；云南省科技厅-云南中医药大学中医联合专项重点资助项目(202001AZ070001-010)；云南中医药大学高层次人才科学研究资助项目(30270104868)；云南省创新人才培养资助项目(2018HB085)。收稿日期：2022-04-27