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

ABSTRACT: To reduce the genome sequence representation, restriction site-associated DNA sequencing (RAD-seq) protocols is being widely used either with single-digest or double-digest methods. In this study, we genotyped the sesame population (48 sample size) in a pilot scale to compare single and double-digest RAD-seq (sd and ddRAD-seq) methods. We analysed the resulting short-read data generated from both protocols and assessed their performance impacting the downstream analysis using various parameters. The distinct k-mer count and gene presence absence variation (PAV) showed a significant difference between the sesame samples studied. Additionally, the variant calling from both datasets (sdRAD-seq and ddRAD-seq) exhibits a significant difference between them. The combined variants from both datas

SUBMITTER: Ruperao P 

PROVIDER: S-EPMC10237379 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature