Genetic Diversity and DNA Barcoding of Yam Accessions from Southern Nigeria

George N Ude,Daniel Ballah,Cecille Aninweze,Onyinye Ozokonkwo-Alor,Michael Okoro,Venatus Chieze,Mariam Unachukwu,David O Igwe,Jonathan Harper,Aditi Das,Christie Onyia,George Acquaah,Christabel Ene,James Ogbonna,Julian Mccormick,Obih Chosen

doi:10.4236/ajps.2019.101015

Abstract

Knowledge of genetic diversity and barcoding of yam is lacking in Enugu and Ebonyi States of southern Nigeria. Therefore, DNA barcoding was used to facilitate identification and biodiversity studies of yam species from Southern Nigeria. Seventy five yam accessions were collected from Enugu and Ebonyi States, including International Institute of Tropical Agriculture for DNA extraction and amplification using a chloroplast DNA (cpDNA) ribulose-1,5-bisphosphate carboxylase (rbcL) marker. There was high level of similarity among the accessions and presence of 534 conserved and 7 variable sites. A transversional mutation of G/T at a consensus position of 335 was identified followed by transitions at 362 (A/G), 368 (A/G), 371 (C/T) and 391 (C/T) within the accessions. Phylogeny resolved the yam accessions into ten major groups with their bootstrap values ranging from 0 - 100. Phylogenetic diversity was highest in group X, followed by VII, VI and IX. The inter-group genetic distance based on Kimura 2-parameter model ranged from 0.5000 ± 0.4770 - 5.0560 ± 2.5760, while the intra-group had 0.5250 ± 0.5000 - 2.0103 ± 1.2579. The mean genetic diversity within the entire population was 0.7970 ± 0.06910. BLAST analysis of total bit score, query coverage, and percentage identity were in the ranges of 411 - 1011, 99% - 100% and 97% - 100%, respectively. However, the rbcL could not resolve the yam accessions well following the comparative assessment of some discrepancies in the detected number of species from phylogenetic groupings, genetic diversity indices and NCBI BLAST hits, thereby, exposing the inefficiency of this marker in discriminating the yam accessions. It was demonstrated that rbcL is not an effective marker; therefore, it should not be recommended as a standard-alone marker of choice for DNA barcoding of yam accessions, especially, when accurate identification, discrimination and estimation of genetic diversity of this vital crop are of paramount importance for crop improvement and germplasm conservation.

Highlights

Yam (Dioscorea spp.) is a monocotyledonous, an annual or perennial stem tuber belonging to the family Dioscoreaceae of flowering plants
The group with the lowest phylogenetic diversity (PD) value D. rotundata clustered with other species and they were collected from a given single region
The use of phylogenetic diversity (PD), which is associated with functionality in biodiversity and which was applied in the computational processes for the estimation of phylogenetic groups with lowest and largest collections in terms of diversity was of great potential

Summary

Introduction

Yam (Dioscorea spp.) is a monocotyledonous, an annual or perennial stem tuber belonging to the family Dioscoreaceae of flowering plants. Dioscorea has been described as the largest genus with an estimated 600 species, 10 of which are cultivated and of economic importance [1] [2] [3]. It is the second most important crop after cassava in West Africa [4] [5] [6]. Important and cultivatable species of this vital crop include D. cayenensis Lam., D. alata L., D. rotundata Poir., D. trifida L. f., D. bulbifera L., D. pentaphylla L., D. opposita Thunb., D. transversa R. Within Africa, the common species cultivated include D. rotundata (white yam), D. alata (water yam) and D. cayenensis (yellow yam), some of which have been reported to possess medicinal and ornamental values [8]

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Discussion

Conclusion