Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data
Eiji Yamamoto1, Kenta Shirasawa1, Takumi Kimura2
1Kazusa DNA Research Institute, Japan.
G3 (Bethesda, Md.)
|June 3, 2020
Summary
This study introduces a cost-effective method for polyploid genetic mapping using low-coverage next-generation sequencing (NGS) data. The strategy effectively detects loci associated with traits in autohexaploid sweet potato, even with lower marker accuracy.
Area of Science:
- Plant genetics
- Genomics
- Bioinformatics
Background:
- Next-generation sequencing (NGS) enables extensive genetic marker generation for plant genetic mapping.
- High-precision genetic analysis in polyploids is challenging due to complex segregation and high-coverage data requirements.
Purpose of the Study:
- To develop a simple strategy for polyploid genetic mapping using low-coverage NGS data.
- To investigate the efficacy of allele dosage probabilities for association analyses in polyploids.
Main Methods:
- Simulated data analysis to validate the strategy.
- Utilizing allele dosage probabilities derived from read counts for association analyses.
- Application of the strategy to autohexaploid sweet potato (Ipomoea batatas) populations.
Main Results:
- Allele dosage probabilities demonstrated significant detection power for loci associated with phenotypic variations.
- Higher allele dosage estimation accuracy improved detection power, but marker number was more critical than accuracy.
- The strategy successfully identified loci associated with agronomic traits in sweet potato.
Conclusions:
- The proposed strategy offers a cost-effective approach for polyploid genetic mapping, particularly for preliminary studies.
- Utilizing a larger number of markers is beneficial, even with lower allele dosage estimation accuracy.
- This method simplifies genetic analysis in polyploid plants using accessible NGS data.
