Related Experiment Video
Updated: Aug 20, 2025
09:55
Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
Published on: May 2, 2018
27.1K
Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing
Shingo Fujimoto1,2,3, Hajime Yaguchi4,5, Taijun Myosho6
1Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 903-0125, Japan. fujimoto.s@outlook.com.
Scientific Reports
|November 21, 2022
Summary
New primers improve multiple arbitrary amplicon sequencing (MAAS) for cost-effective genotyping. This method accurately analyzed medaka fish populations and identified genetic contributions to a mutant strain, aiding in assessing genetic disturbance.
Area of Science:
- Genomics
- Population Genetics
- Aquatic Biology
Background:
- Cost-effective genotyping is crucial for genetic studies.
- Multiple arbitrary amplicon sequencing (MAAS) offers a promising approach.
- Improving MAAS efficiency can enhance its utility.
Purpose of the Study:
- To develop and evaluate novel primers for enhanced MAAS efficiency.
- To apply the improved MAAS method for genotyping medaka (Oryzias latipes).
- To investigate the population structure and genetic origins of medaka strains.
Main Methods:
- Designed and tested new short primers (3-10 base pairs) for arbitrary PCR amplification.
- Applied MAAS to genotype 67 medaka individuals from wild and artificial populations.
- Utilized admixture analysis to reconstruct genetic backgrounds.
Main Results:
- Successfully obtained 2987 informative single nucleotide variants (SNVs) with complete genotype data.
- Confirmed the accuracy of the genotyping method by aligning with previous medaka population studies.
- Identified at least two wild populations contributing to the Himedaka mutant strain's genome.
Conclusions:
- The novel primers and MAAS approach provide efficient and cost-effective genotyping.
- The method accurately resolves population genetic structures and identifies genetic introgression.
- This technique is valuable for assessing genetic disturbance caused by commercial strains.
