黄秆乌哺鸡竹转录组EST-SSR分子标记开发与应用

娄永峰; 甘然; 朱成磊; 肖复明; 高志民

doi:10.11913/PSJ.2095-0837.2022.30355

黄秆乌哺鸡竹转录组EST-SSR分子标记开发与应用

1. 江西省林业科学院, 江西省植物生物技术重点实验室, 南昌 330032;
2. 国际竹藤中心, 国家林业和草原局/北京市竹藤科学与技术重点开放实验室, 北京 100102

基金项目:

国家林木种质资源共享服务平台(2005DKA21003)；国际竹藤中心基本科研业务费专项(1632020004)。

详细信息

作者简介:
娄永峰(1983-)，男，博士，副研究员，研究方向为林木遗传育种与森林培育(E-mail:330403612@qq.com)。

通讯作者:
高志民,E-mail:gaozhimin@icbr.ac.cn

中图分类号: Q943.2
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出版历程
- 收稿日期: 2021-11-08
- 修回日期: 2021-12-24
- 网络出版日期: 2022-10-31
- 发布日期: 2022-06-27

Development and application of EST-SSR markers based on transcriptome of Phyllostachys vivax McClure f. aureocaulis N. X. Ma

1. Jiangxi Provincial Key Laboratory of Plant Biotechnology, Jiangxi Academy of Forestry, Nanchang 330032, China;
2. State Forestry and Grassland Administration/Beijing Key Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China

Funds:

This work was supported by grants from the National Forest Genetic Resources Platform (2005DKA21003) and Fundamental Scientific Research on Professional Work Supported by the International Center for Bamboo and Rattan (1632020004).

摘要

摘要: 基于黄秆乌哺鸡竹(Phyllostachys vivax McClure f. aureocaulis N. X. Ma)转录组数据，利用生物信息学方法分析其SSR位点分布特征，同时针对“黄秆”和“绿秆”两种类型差异表达基因序列中的SSR位点设计引物，并利用刚竹属(Phyllostachys)材料验证其通用性。结果显示，从黄秆乌哺鸡竹89 874个Unigenes序列中，共鉴定出12 651个SSR位点，分布频率为14.07%；其中单核苷酸重复基序最多(51.02%)、其次为3核苷酸(25.61%)和2核苷酸(21.94%)；共发现80种重复基序，其中出现频率最高的为A/T(46.60%)，其次是AG/CT(13.97%)和CCG/CGG(9.90%)。在设计的51对引物中，44对(86.27%)能有效扩增，在刚竹属材料中平均通用性为92.41%，其中39对具有多态性，多态性EST-SSR标记能区分同属的不同种，但不能有效区分种内种质资源。
- 黄秆乌哺鸡竹 /
- 转录组 /
- EST-SSR标记 /
- 通用性
Abstract: Based on transcriptome data of Phyllostachys vivax McClure f. aureocaulis N. X. Ma, the distribution and characteristics of simple sequence repeat (SSR) loci were analyzed using bioinformatics. Primers were designed according to the SSR loci in the differentially expressed genes between the “yellow culm type” and “green culm type”. The validity and transferability of the primers within the Phyllostachys genus were determined using samples from Phyllostachys species. Results showed that 12 651 SSR loci were detected in 89 874 unigene sequences of Ph.vivax f. aureocaulis, with a frequency of 14.07%. Among the SSR loci, mononucleotide repeat motifs were the most abundant (51.02%), followed by trinucleotide and dinucleotide repeat motifs (25.61% and 21.94%, respectively). Of the 80 repeat motifs found, the most abundant was A/T (46.60%), followed by AG/CT (13.97%) and CCG/CGG (9.90%). Based on the SSR loci of differentially expressed genes between the “yellow culm type” and “green culm type”, a total of 51 primer pairs were designed, 44 (86.27%) of which were able to amplify the expected polymerase chain reaction (PCR) products. Average transferability of the 44 primers pairs in the selected Phyllostachys species was 92.41%, with 39 pairs containing interspecific polymorphisms. These polymorphic-expressed sequence tag-derived EST-SSR markers could effectively distinguish different bamboo species in Phyllostachys but could not effectively distinguish intraspecific germplasm resources.
- Phyllostachys vivax /
- Transcriptome /
- EST-SSR markers /
- Transferability

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