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

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.