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

Ruperao, Pradeep; Bajaj, Prasad; Subramani, Rajkumar; Yadav, Rashmi; Reddy Lachagari, Vijaya Bhaskar; Lekkala, Sivarama Prasad; Rathore, Abhishek; Archak, Sunil; Angadi, Ulavappa B.; Singh, Rakesh; Singh, Kuldeep; Mayes, Sean; Rangan, Parimalan

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 kmer 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 datasets helped in identifying the most diverse samples and possible sub-groups in the sesame population. The most diverse samples identified from each analysis (k-mer, gene PAV, SNP count, Heterozygosity, NJ and PCA) can possibly be representative samples holding major diversity of the small sesame population used in this study. The best possible strategies with suggested inputs for modifications to utilize the RAD-seq strategy efficiently on a large dataset containing thousands of samples to be subjected to molecular analysis like diversity, population structure and core development studies were discussed.

Citation

Ruperao, P., Bajaj, P., Subramani, R., Yadav, R., Reddy Lachagari, V. B., Lekkala, S. P., …Rangan, P. (2023). A pilot-scale comparison between single and double-digest RAD markers generated using GBS strategy in sesame (Sesamum indicum L.). PLoS ONE, 18(6), Article e0286599. https://doi.org/10.1371/journal.pone.0286599

• Journal Article Type: Article
• Acceptance Date: May 19, 2023
• Online Publication Date: Jun 2, 2023
• Publication Date: Jun 2, 2023
• Deposit Date: Jul 23, 2023
• Publicly Available Date: Jul 24, 2023
• Journal: PLoS ONE
• Electronic ISSN: 1932-6203
• Publisher: Public Library of Science
• Peer Reviewed: Peer Reviewed
• Volume: 18
• Issue: 6
• Article Number: e0286599
• DOI: https://doi.org/10.1371/journal.pone.0286599
• Keywords: Multidisciplinary
• Public URL: https://nottingham-repository.worktribe.com/output/23221426
• Publisher URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286599