DNA Barcodes of the Yam Species of the genus Dioscorea in Southeastern Nigeria

Undergraduate #132
Discipline: Biological Sciences
Subcategory: Plant Research

Julian C. McCormick - Bowie State University
Co-Author(s): Daniel Ballah and Jonathan Harper, Bowie State University, Bowie, MD Onyinye Ozokonkwo, Godfrey Okoye University, Enugu State, Nigeria

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The aim of this study was to characterize the diverse accessions of yam species in the genus Dioscorea in southeastern Nigeria using the DNA barcoding technique. Our project generated species specific DNA barcodes to track yam flour types and trace the yam species from which they were produced for exportation to the United States from African countries. To reach these aims, our group followed a general DNA barcoding pipeline. We collected various yam plant samples from local Nigerian farms and villages. Following the collection of yam samples, DNA was extracted and purified using the silicia bead extraction method. Subsequently, PCR was used to amplify a specific region of the chloroplast and sent to a third party, Genewiz LLC., for sequencing. The PCR products were checked for amplicons by agarose gel electrophoresis to verify successful amplification of the desired 600bp rbcl gene segment before sequencing. Samples were analyzed using DNA Subway, an intuitive interface for genome informatics developed by the iPlant Collaborative. DNA barcodes analyzed with the “Blue Line” of DNA Subway allows students to merge biochemistry, bioinformatics, evolution, and ecology. Our results show species specific single nucleotide polymorphisms (SNPs) which can be used to put the studied yam species into expected groups for identification purposes. Clustering analysis using neighbor joining method showed unique phylogenetic relationships between the following species – Dioscorea bulbifera, Discorea dumentorum, Dioscorea esculenta, Disocorea alata and Dioscorea rotundata. The future of this research is to use the SNPs to screen unidentified yam flours sold in African food stores in USA to identify the yam species from where the flours were derived.

Funder Acknowledgement(s): The National Science Foundation: HBCU-UP inititative; Bowie State University: Student Undergraduate Research Institute (SURI).

Faculty Advisor: George Ude,