基于苦瓜转录组序列的SSR分子标记开发  

Development of SSR Molecular Markers for Momordica charantia Based on Transcriptome Sequences

作　　者：周银慧 洪宇 曹毅 程蛟文[2] 胡开林[2] 崔竣杰 Zhou Yinhui;Hong Yu;Cao Yi;Cheng Jiaowen;Hu Kailin;Cui Junjie(School of Food Science and Engineering,Foshan University,Foshan,528000;College of Horticuture,South China Agricutural University,Guangzhou,510642)

机构地区：[1]佛山科学技术学院食品科学与工程学院,佛山528000 [2]华南农业大学园艺学院,广州510642

出　　处：《分子植物育种》2021年第6期1933-1939,共7页Molecular Plant Breeding

基　　金：广东省自然科学基金面上项目(2019A1515011939);广东省普通高校省级重点科研项目(2018KZDXM016);广东省科技计划项目(2018B020202007);佛山科学技术学院高层次人才科研启动资助项目(CGG07127);佛山科学技术学院研究生自由探索基金项目共同资助。

摘　　要：为了全面了解苦瓜转录组SSR位点特征和满足苦瓜分子育种对分子标记的需求,利用MISA软件对来自苦瓜材料‘大沥-11’6个组织的59740条转录组Unigene序列进行SSR位点搜索,共检测出31066个SSR位点,出现频率(发现的SSR个数与总Unigene数之比)为52.00%,平均每2.62 kb出现1个SSR位点。在苦瓜转录组SSR位点中,基元类型主要为三核苷酸,占总SSR位点的42.17%;其次是二核苷酸,占总SSR位点的31.66%。利用Primer 3软件对搜索到的苦瓜转录组SSR位点进行引物设计,然后把获得的引物序列比对回苦瓜的参考基因组,选择上下游引物序列都是唯一比对的序列并去除重复后共获得9135对特异SSR引物。选择MC00上的232对特异SSR引物对‘谭边大顶’和‘华艺320’两个苦瓜品种基因组DNA进行PCR扩增,其中有219对特异引物可扩增出清晰的条带,有效扩增率为94.40%;有31对特异引物扩增产物表现出多态性,多态率为13.36%。本研究开发的苦瓜转录组特异SSR引物为苦瓜的种质资源分析、基因定位、分子标记辅助选择等理论与应用研究提供了引物数据参考。To fully understand the SSR site characteristics of Momordica charantia transcriptome and meet the need for molecular markers in molecular breeding,MISA software was used to search for the SSR sites in 59740 transcriptome unigenes from six tissues of Momordica charantia’Dali-11’,and 31066 SSR sites were detected with a frequency of 52.00%(ratio of number of SSRs found to total Unigene number)and an average of 1 SSR site per2.62 kb.The dominant SSR sites in the transcriptome of Momordica charantia were trinucleotide,accounting for42.17%of the total SSR sites;the second was dinucleotide,accounting for 31.66%of the total SSR sites.Primer3 software was used to design the SSR primers of the transcriptome of Momordica charantia,and then the obtained primer sequences were compared to the reference genome of the Momordica charantia.After aligning both forward and reverse primers back to the reference genome and removing the repeated,a total of 9135 pairs of unique SSR primers were obtained.232 pairs of primers on MC00 were selected for PCR amplification on the DNA of’Tanbiandading’and’Huayi320’,among them,219 pairs of specific primers can amplify clear bands with the effective amplification rate of 94.40%;31 pairs of specific primers showed polymorphism with the polymorph-ism rate of 13.36%.The transcriptome-specific SSR primers of Momordica charantia developed in this study provide a primer data reference for the theoretical and applied research on Momordica charantia about germplasm analysis,gene mapping and molecular marker-assisted selection.

关 键 词：苦瓜(Momordica charantia) 转录组 SSR 

分 类 号：S642.5[农业科学—蔬菜学]