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

Ruperao, P and Bajaj, P and Subramani, R and Yadav, R and Lachagari, V B R and Lekkala, S P and Rathore, A and Archak, S and Angadi, U B and Singh, R and Singh, K and Mayes, S and 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). 01-19. ISSN 1932-6203

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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 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.

Item Type: Article
Divisions: Genebank
Global Research Program - Accelerated Crop Improvement
Uncontrolled Keywords: RAD markers, GBS strategy, sesame
Subjects: Others > Plant Breeding
Others > Genetics and Genomics
Depositing User: Mr Nagaraju T
Date Deposited: 19 Jun 2023 03:32
Last Modified: 19 Jun 2023 03:32
URI: http://oar.icrisat.org/id/eprint/12114
Official URL: https://journals.plos.org/plosone/article?id=10.13...
Funders: Department of Biotechnology, Government of India
Acknowledgement: The authors are grateful to the Department of Biotechnology, Government of India for funding (16113200037-1012166). The URL of the funder is www.dbtindia.gov.in. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors are thankful to AgriGenomics Pvt Ltd (Hyderabad, India) for generating the RAD sequencing data using both sdRAD and ddRAD protocols.
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