Selective InDel Marker Identification Across the Peanut (Arachis hypogaea L.) Genome Using ddRADSeq

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
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.
Links:	Google Scholar

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