TITLE:
Genetic Diversity and DNA Barcoding of Yam Accessions from Southern Nigeria
AUTHORS:
George N. Ude, David O. Igwe, Julian McCormick, Onyinye Ozokonkwo-Alor, Jonathan Harper, Daniel Ballah, Cecille Aninweze, Obih Chosen, Michael Okoro, Christabel Ene, Venatus Chieze, Mariam Unachukwu, Christie Onyia, George Acquaah, James Ogbonna, Aditi Das
KEYWORDS:
BLAST, Kimura 2-Parameter, Phylogenetic Diversity, rbcL, Transitional Mutation
JOURNAL NAME:
American Journal of Plant Sciences,
Vol.10 No.1,
January
22,
2019
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.