A pilot-scale comparison between single and double-digest RAD markers generated using GBS strategy in sesame (Sesamum...

Area of Science:

• Genomics
• Population Genetics
• Bioinformatics

Background:

• Restriction site-associated DNA sequencing (RAD-seq) is crucial for genome representation.
• Single-digest (sdRAD-seq) and double-digest (ddRAD-seq) are common RAD-seq methods.
• Evaluating RAD-seq protocol performance is vital for downstream genetic analyses.

Purpose of the Study:

• To compare the efficacy of sdRAD-seq and ddRAD-seq methods in sesame genotyping.
• To assess the impact of both protocols on downstream genetic analyses.
• To identify optimal strategies for large-scale RAD-seq applications in sesame.

Main Methods:

• Pilot-scale genotyping of a 48-sample sesame population using sdRAD-seq and ddRAD-seq.
• Analysis of short-read data, including k-mer counts and gene presence-absence variation (PAV).
• Variant calling and comparative analysis between sdRAD-seq and ddRAD-seq datasets.

Main Results:

• Significant differences observed in k-mer counts and gene PAV between sesame samples.
• Distinct variant calling results obtained from sdRAD-seq and ddRAD-seq protocols.
• Combined variants effectively identified the most diverse sesame samples and potential subgroups.

Conclusions:

• Combining sdRAD-seq and ddRAD-seq data enhances the identification of diverse samples.
• The most diverse samples identified can serve as representative individuals for population studies.
• Strategies for efficient large-scale RAD-seq implementation in sesame were discussed.