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Turkish Journal of Botany

Author ORCID Identifier

MOIN QURESHI: 0000-0003-0032-5799

BİRGÜL GUDEN: 0000-0002-7375-6533

HİLAL TOSUN: 0000-0001-8360-2610

MOJTABA KORDROSTAMI: 0000-0003-0314-1354

SUNIL GANGURDE: 0000-0001-7119-8649

BÜLENT UZUN: 0000-0001-6228-9629

ENGİN YOL: 0000-0002-3152-6078

DOI

10.55730/1300-008X.2826

Abstract

The advent of next-generation sequencing technologies, mainly double digest restriction site-associated DNA sequencing (ddRADSeq), has significantly advanced the development of molecular markers for crop genetics. This study used ddRADSeq to identify and develop insertion-deletion (InDel) markers in 25 peanut genotypes from diverse geographic regions. The bioinformatic analysis unveiled 62728 InDels across the peanut genome, predominantly between 1-5 bp, which constituted 96% of the total, while InDels of ≥ 6 bp accounted for 3.96%. We focused on 1013 InDels of at least 10 bp for further analysis, representing 1.61% of the total reads, with a distribution of 832 insertions and 181 deletions. Of those, 21 InDels were selected for primer design and successfully amplified to produce markers within a 150-400 bp range. Approximately 14% of InDels were located in coding sequences enhancing their potential utility in genomics-led breeding. These markers' polymorphic information content (PIC) varied from 0 to 0.371, demonstrating substantial genetic diversity with an average of 0.163. These findings confirm the effectiveness of ddRADSeq for InDel marker development in peanuts, illustrating its potential to enhance marker-assisted breeding programs by providing robust tools for assessing genetic diversity.

Keywords

Groundnut, ddRADSeq, genetic diversity, marker-assisted breeding

First Page

441

Last Page

453

Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

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