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Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana
Xuewen Wang1,2, Shuai Yang3, Yongdui Chen4
1Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, People's Republic of China.
BMC Genomics
|June 28, 2018
Summary
This study characterized simple sequence repeats (SSRs) across seven Nicotiana genomes, developing over a million novel SSR markers (NIX markers) for plant research and breeding. A new database and genotyping protocol enhance marker utility.
Area of Science:
- Genomics
- Molecular Biology
- Plant Science
Background:
- Simple sequence repeats (SSRs) are crucial DNA markers for genetic studies and molecular breeding.
- Recent sequencing of multiple Nicotiana genomes enables comprehensive SSR analysis.
- This study focuses on the Nicotiana genus, including model plants like N. benthamiana.
Purpose of the Study:
- To perform a genome-wide characterization of SSRs in seven Nicotiana species.
- To develop novel SSR-based genetic markers for Nicotiana.
- To create a user-friendly database and efficient genotyping protocol for the developed markers.
Main Methods:
- Genome-wide SSR identification and characterization across seven Nicotiana genomes.
- Development of SSR markers using the GMATA® software package.
- Creation of a web-based database (Tobacco Markers & Primers Database - TMPD) for marker information and analysis.
Main Results:
- Characterized over 2.4 million SSRs, with mono-, di-, and tri-nucleotide repeats comprising 98% of the total.
- Developed 1,224,048 novel Nicotiana (NIX) markers, with 99.98% being unique.
- Established an efficient genotyping protocol and a comprehensive online database for NIX markers.
Conclusions:
- This research provides the first in-depth SSR characterization across seven Nicotiana genomes.
- The developed NIX markers and associated database significantly expand genetic resources for Nicotiana research and breeding.
- A novel, scalable protocol for SSR marker development and utilization was demonstrated, applicable to other organisms.
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