Qureshi, M and Guden, B and Tosun, H S and Kordrostami, M and Gangurde, S S and Uzun, B and Yol, E (2024) Selective InDel Marker Identification Across the Peanut (Arachis hypogaea L.) Genome Using ddRADSeq. Turkish Journal of Botany, 48 (SI-1). pp. 441-453. ISSN 1300-008X
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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.
Item Type: | Article |
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Divisions: | Global Research Program - Accelerated Crop Improvement |
CRP: | UNSPECIFIED |
Uncontrolled Keywords: | Groundnut, peanut, InDel markers, ddRADSeq, genetic diversity, marker-assisted breeding |
Subjects: | Mandate crops > Groundnut Others > Genetics and Genomics |
Depositing User: | Mr Nagaraju T |
Date Deposited: | 13 Aug 2025 11:08 |
Last Modified: | 13 Aug 2025 11:08 |
URI: | http://oar.icrisat.org/id/eprint/13274 |
Official URL: | https://journals.tubitak.gov.tr/botany/vol48/iss7/... |
Projects: | UNSPECIFIED |
Funders: | Akdeniz University |
Acknowledgement: | This study was supported by the Scientific Research Projects Coordination Unit of Akdeniz University with Project FYL-2022-5981. We are grateful to the USDA and ICRISAT for supplying genetic material several times. |
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