Akademik Veri Yönetim Sistemi
Turkish Journal of Botany, cilt.48, sa.SI-1, ss.441-453, 2024 (SCI-Expanded)
The advent of next-generation sequencing technologies, and particularly 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 geographical regions. The bioinformatic analysis revealed 62,728 InDels across the peanut genome, predominantly between 1 and 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 the range of 150–400 bp. Approximately 9.5% of the InDels were located in coding sequences, enhancing their potential utility in genomics-led breeding. These markers’ polymorphic information content varied from 0 to 0.371, demonstrating substantial genetic diversity with an average value 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.