Akademik Veri Yönetim Sistemi
Tropical Plant Biology, cilt.18, sa.1, 2025 (SCI-Expanded, Scopus)
Recent breakthroughs in the genomics of Capsicum annuum have broadened molecular genetics research. Especially, marker technologies have contributed to studies of gene identification, genomic mapping, biodiversity, and gene tagging. Insertion-deletion (InDel) polymorphisms function as significant genetic markers for evaluating diversity, population structure, and marker-assisted breeding in crops. In this study, we identified and developed InDel markers in Capsicum annuum using double-digest restriction site-associated DNA sequencing (ddRADSeq) approach. A total of 82140 InDel regions were identified across 99 pepper lines, with chr 3 displaying the largest quantity of InDels (9587) and chr 5 the lowest (5765) indicating structural differences. The predominant InDels were single-nucleotide variations, with a declining number with increasing fragment size. According to these results, 88 InDel markers were developed with an indel size > 10 bp. These InDels were allocated over all 12 chromosomes of Capsicum annuum, with 75.6% located in intergenic regions and 24.4% were found within gene/transcript regions, including exons and coding sequences (CDS). Among developed InDel markers, 20 markers were chosen for validation with genetic diversity and population structure analysis. The Polymorphic Information Content (PIC) values varied from 0.048 to 0.372, underscoring their capacity to differentiate genetic diversity among lines. STRUCTURE analysis revealed three primary genetic clusters associated with certain fruit types supported by Principal Coordinate Analysis (PCoA) and phylogenetic clustering. The developed markers in this study therefore offer an extensive genetic database for the improvement of breeding and conservation studies.