摘要
为全面了解君迁子简单重复序列(SSR)的分布特点,开发更多的SSR分子标记,本研究对君迁子叶片转录组中Unigenes进行了SSR分析。结果表明,测序共获得93 359条Unigenes,总长度为75 880 230 bp,分析共得到13 751个SSR位点,分布在10 001条Unigenes上,发生频率为10.71%,分布频率为14.73%,平均每5.5 kb出现1个SSR位点。君迁子SSR主要以单、二核苷酸SSR为优势SSR(5 483, 5 118),所占比例分别为39.87%、37.22%,其次是三核苷酸SSR(2 010, 14.62%)。单核苷酸SSR主要以A/T类型为主(4 989,36.27%),二、三核苷酸SSR出现次数最多的分别是AG/CT(3 352, 24.38%)和AAG/CTT(842, 6.12%),四、五、六核苷酸SSR数目较少,仅占总SSR的1.6%。SSR基序长度主要位于10~20 bp之间(88.73%)。共发现181 951个SNP位点,其发生频率为0.24%,主要以同类碱基转换形式(A/G, G/A, T/C, C/T)存在,共占64.83%,碱基颠换类型共8种,占35.17%。利用Primer 3设计SSR引物,共得到11 517对引物,成功率52.24%。本研究分析了君迁子转录组SSR的分布特点,设计了大量的SSR分子标记引物,为君迁子资源的遗传多样性分析、鉴定与分类提供依据,同时为优良君迁子单株的选育与开发利用提供了科学依据。
In order to fully understand the distribution characteristics of SSR and develop more SSR primers in Diospyros lotus Linn., SSR characteristics was analyzed based on transcriptome of Diospyros lotus. The results showed that 93 359 Unigenes were obtained with a total length of 75 880 230 bp in transcriptome. A total of 13 751SSR loci were obtained from 10 001 Unigenes, with an occurrence frequency of 10.71% and the distribution frequency of 14.73%, which indicated that there was 1 SSR site per 5.5 kb on average. The SSR types of Diospyros lotus was mainly mononucleotide and dinucleotide SSR(5 483, 5 118), which account for 39.87% and 37.22%,respectively, followed by trinucleotide SSR(2 010, 14.62%). Mononucleotide SSR was dominated by A/T(4 989,36.27%), while dinucleotide and trinucleotide SSRs with the largest number of occurrences were AG/CT(3 352,24.38%) and AAG/CTT(842, 6.12%). The number of tetranucleotide, pentanucleotide, and hexanucleotide SSRs was relatively less, accounting for only 1.6% of the total SSR. The length of SSR motif was mainly between 10 bp and20 bp(88.73%). A total of 181 951 SNP sites were found with a frequency of 0.24%, and they mainly existed in the form of base transition(A/G, G/A, T/C, C/T), accounting for 64.83%. There were 8 types of base transversions,accounting for 35.17%. The Primer 3 software was applied for design primers of SSR sites, and a total of 11 517pairs of SSR primers were obtained with a success rate of 52.24%. In this study the distribution characteristics of SSR were analyzed and a large number of SSR primers were developed, which provide a basis for the genetic diversity analysis, identification and classification of Diospyros lotus, and also lay a foundation for the selection and development and utilization of excellent types of Diospyros lotus plants.
作者
张晓娜
王滢滢
周瑞金
扈惠灵
张鹏
汪显友
Zhang Xiaona;Wang Yingying;Zhou Ruijin;Hu Huiling;Zhang Peng;Wang Xianyou(College of Horticulture and Landscape Architecture,Henan Institute of Science and Technology,Xinxiang,453003;Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement,Xinxiang,453003)
出处
《分子植物育种》
CAS
北大核心
2022年第24期8170-8178,共9页
Molecular Plant Breeding
基金
河南省自然科学基金项目(162300410108)
河南省科技攻关计划项目(192102110069)共同资助。
关键词
君迁子
转录组
简单重复序列
Diospyros lotus
Transcriptome
Simple sequence repeats
