DNA Sequence Patterns in PAX3 and BMP4 for Differential Identification of Idoma and Igede Ethnic Groups in Benue State, Nigeria

Background: Genes involved in craniofacial development may provide useful molecular markers for forensic identification and population studies. PAX3 and BMP4 regulate neural crest migration, facial morphogenesis, and skeletal patterning. This study evaluated sequence variation in these genes and their potential to differentiate the Idoma and Igede ethnic groups of Benue State, Nigeria. Methods: Buccal-swab genomic DNA samples from 300 Idoma and Igede participants were analyzed for each gene. Target regions of PAX3 exon 8 and BMP4 exon 3 were amplified by polymerase chain reaction, producing expected fragments of 311 bp and 586 bp, respectively. The amplified products were sequenced using the Sanger method and aligned with National Center for Biotechnology Information reference sequences to identify synonymous and non-synonymous variations. Observed genetic variants were also assessed in relation to craniofacial measurements. Participants included males and females aged 15–29 years from the Idoma and Igede ethnic groups. All 300 samples were successfully amplified and sequenced. Successful amplification and sequencing were obtained for both target regions. In PAX3, 34 of the 300 samples analyzed exhibited synonymous sequence variations, representing a variant frequency of 11.3%. In BMP4, 22 of the 300 samples exhibited synonymous and non-synonymous variations, corresponding to a frequency of 7.3%. Selected participants carrying functionally relevant variants showed measurable deviations from population means in craniofacial dimensions, particularly nasal width, interendocanthal width, facial height, bizygomatic width, ear dimensions, and nasal index. However, sequence alignment and phylogenetic patterns showed substantial genetic homology between the Idoma and Igede groups, with no clear population-specific clustering at either locus. discriminatory ability for differentiating the Idoma and Igede populations as distinct ethnic groups.