Molecular Characterization of Edible Aroids Growing in Parts of Rivers State

Cocoyam (Colocasia esculenta and Xanthosoma sagittifolium) plays a critical role in food security and livelihoods in many tropical regions, yet it remains a neglected and underutilized crop, facing threats from germplasm loss and limited research attention. Understanding the genetic diversity of existing cocoyam germplasm is crucial for effective conservation and breeding programs. This study aimed to assess the genetic diversity and relationships among six cocoyam accessions from three local government areas in Rivers State, Nigeria, using molecular characterization. Field experiments were carried out between June 20, 2021 and January 20, 2022, and also in June 20, 2022 and January 20, 2023, in three local government areas of Rivers State, Nigeria—Obio/Akpor, Emohua, and Ikwerre. Six different cocoyam accessions of the National Root Crop Institute (NRCRI), Umudike, were used for the study: NCe001, NCe002, NCe003, and Xanthosoma sagittifolium (NXs001, NXs002, NXs003). DNA genomic was isolated from the plant samples by Zymo Quick DNA Plant/Seed Mini PrepKit, and DNA purity and concentration were measured by NanoDrop Spectrophotometry. The target region was amplified by OneTaq® Quick-Load® 2X Master Mix and specific primers (RBCL 1 and ATP) in a Polymerase Chain Reaction (PCR). PCR products were enzymatically purified, and sequencing was carried out. Sequence analysis involved visualizing chromatograms with Chromaslite, editing with BioEdit, and performing a Basic Local Alignment Search Tool (BLAST) search against the NCBI database. Comparable sequences were downloaded and aligned using ClustalW. The evolutionary history and phylogenetic relationships among the six accessions were inferred using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Neighbor-Joining method in MEGA 7.0.26, based on nucleotide sequence data. The molecular analyses successfully amplified and sequenced target regions. The results show a phylogenetic tree with a distance scale (0–5) indicating genetic similarity among plant varieties. NXS003, NCE003, NCE002, and NCE001 form a close cluster, suggesting high relatedness. NXS003 and NCE003 are the most similar pair, while NXS001 and NXS002 are more distantly related. NXS002 appears to be the most genetically distinct variety in the group. The results from the phylogenetic trees revealed that samples RCBBR_P1, P2, P4, P5, P7, P8, P9, and P10 consistently clustered with Colocasia esculenta accessions such as cultivar lipu (MT447085.1), isolate RR (JN105690.1), and Taimo (LC767269.1). The GenBank similarity scores ranging between 97.93% and 99.05% indicate that these samples are genetically like C. esculenta, suggesting they may represent landraces, cultivars, or locally adapted variants of the species. Interestingly, samples such as RCBBR_P3, P6, P11, and P12 clustered with Xanthosoma sagittifolium, showing similarity values up to 99.47% for P3 and P12, and as low as 96.19% for P6. These findings suggest that while P3 and P12 are closely related to the known X. sagittifolium, sample P6 may represent a genetically divergent or under-characterized variant. Samples such as RCBBR_P6 and RCBBR_P11 displayed long branch lengths and formed isolated clades, indicating substantial genetic divergence.