基于黑莓果实转录组数据的SSR位点特征分析  

SSR Loci Mining and Feature Analysis Based on Transcriptome Data of Blackberry Fruit

作　　者：吴雅琼 张春红[1] 杨海燕[1] 闾连飞[1] 李维林 吴文龙[1] Wu Yaqiong;Zhang Chunhong;Yang Haiyan;Lü Lianfei;Li Weilin;Wu Wenlong(Research Center for Pomology,Institute of Botany,Jiangsu Province and Chinese Academy of Sciences,Nanjing,210014;Co-Innovation Center for the Sustainable Forestry in Southern China,College of Forestry,Nanjing Forestry University,Nanjing,210037)

机构地区：[1]江苏省中国科学院植物研究所,果树研究中心,南京210014 [2]南京林业大学林学院,南方现代林业协同创新中心,南京210037

出　　处：《分子植物育种》2025年第4期1132-1139,共8页Molecular Plant Breeding

基　　金：江苏省自然科学青年基金项目(BK20210165);国家自然科学基金项目(32101566);江苏省中科院植物研究所博士人才科研启动基金项目(JIBTF202105)共同资助。

摘　　要：黑莓(Rubus spp.)是蔷薇科(Rosaceae)悬钩子属(Rubus)重要经济林小浆果树种,其果实含有丰富的营养物质,具有重要的经济和药用价值。本研究以黑莓‘Chester’果实为试验材料获得转录组序列数据,基于转录组数据分析简单重复序列(SSR)位点信息、序列特征和分布特点,以期为黑莓SSR分子标记的筛选与开发、种质资源遗传改良和遗传多样性研究提供理论基础。运用MicroSAtellite(MISA)软件对全部unigenes序列的SSR位点进行检索和特征分析,结果表明,SSR位点总数为11486,SSR发生频率为13.3%。SSR基元类型中以二、三核苷酸重复最多,分别占转录组总SSR重复数量的46.54%和39.81%,其中AG/CT(30.58%)是出现频率最高的重复基元,其次为AT/AT(11.81%)和AAG/CTT(10.84%)基元类型。不同重复基元类型间SSR序列的长度也存在差异,平均长度范围为18.07~26.26 bp,总平均长度为19.11 bp。黑莓转录组SSR长度大多集中于12~16 bp和>30 bp,占SSR总数量均超过10%,而SSR序列长度>20 bp,占比32.13%。黑莓转录组SSR位点发生频率较高,平均距离较短,重复基元类型较丰富,可为悬钩子属乃至蔷薇科的遗传多样性研究、品种鉴定和分子标记辅助育种提供新思路。Blackberry(Rubus spp.)is an important economic plant species of small fruit berries within the genus Rubus.Its fruit is rich in nutrients and has important economic and medicinal value.In this study,the transcriptome sequence data were obtained from blackberry'Chester'fruit.Based on the simple sequence repeats(SSR)site information of blackberry transcriptome,the information,sequence characteristics and distribution characteristics of SSR were explored in order to provide theoretical basis for screening and development of SSR molecular markers,genetic improvement of germplasm resources and genetic diversity research of blackberry.The SSR loci of all unigenes were retrieved and analyzed by MicroSAtellite(MISA)software.The results showed that the total number of SSR loci was 11486,and the frequency of SSR was 13.3%.Among SSR motif types,dinucleotide and trinucleotide repeats were the most frequent,accounting for 46.54%and 39.81%of the total SSR repeats of the transcriptome,respectively.The AG/CT(30.58%)was the most frequent repeat motif,followed by AT/AT(11.81%)and AAG/CTT(10.84%).The length of SSR sequence was also different among different repeat motif types,the average length of SSR sequences varied from 18.07~26.26 bp,and the total average length was 19.11 bp.The SSR length of blackberry transcriptome was mostly 12~16 bp and>30 bp,accounting for more than 10%of the total SSR,while the SSR sequence length was more than 20 bp,accounting for 32.13%.The SSR loci of blackberry transcriptome had high frequency,short average distance and abundant repeat elements,which can provide new ideas for genetic diversity research,variety identification and molecular marker assisted breeding of Rubus and Rosaceae.

关 键 词：黑莓 转录组 SSR位点 

分 类 号：S663.9[农业科学—果树学]