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Genetic Diversity and DNA Barcoding of Yam Accessions from Southern Nigeria

American Journal of Plant Sciences 2019年第1期10卷 179-207页

作者： 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 Department of Natural Sciences Bowie State University Bowie USA Department of Biotechnology Faculty of Science Ebonyi State University Abakaliki Nigeria Godfrey Okoye University Enugu Nigeria DNA Learning Center Cold Spring Harbor NYC USA Department of Microbiology University of Nigeria Nsukka Nigeria

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 im

关键词： BLAST Kimura 2-Parameter Phylogenetic Diversity rbcL Transitional Mutation

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DNA Barcoding of Nigeria’s Forest Species Listed in CITES and Other Endangered Plant Species of National Interest

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American Journal of Plant Sciences 2022年第11期13卷 1335-1346页

作者： Christie Oby Onyia Obianuju Patience Ilo chosen Ekene obih Omokafe Ugbogu Beatrice Onyinye Ojiego Sunkanmi Saheed Rufai Paschaleen Soromtochukwu Onyemaechi Emmanuel Chukwudi Chukwuma Department of Biological Sciences/Directorate of Inter-Disciplinary Research Godfrey Okoye University Enugu Nigeria Department of Environmental Biotechnology and Bioconservation National Biotechnology Development Agency Abuja Nigeria Department of Biological Sciences Godfrey Okoye University Enugu Nigeria Forestry Research Institute of Nigeria Ibadan Nigeria National Environmental Standards Regulations and Enforcement Agency Ibadan Nigeria

Illegal trade is considered one of the greatest threats to the loss of biodiversity of endangered plants. Some of these plant species are often trafficked in processed forms, making it extremely difficult for taxonomic experts to identify them. In the past, illegal traders of endangered species have been arrested and prosecuted but eventually cleared due to a lack of conclusive evidence. DNA barcoding is a veritable tool to protect these endangered species from illegal trade. It identifies all stages of the species’ life forms including processed products (milled or powdered animal and plant parts). The study utilised the rbcL gene as a single barcode region in the identification/authentication of 19 Nigeria’s endangered forest species legislated under the CITES and other endangered species of national interest. The generated sequence barcodes were used to query NCBI-GenBank and BOLD databases. 57.89% of the samples were identified down to species level and 42.11% to genus level. Amongst the 19 samples, sample (S7) yielded a high-quality sequence for a single sequencing read (forward), sufficient to identify the sample with a 99.81% identity match on NCBI-GenBank and BOLD. The results reveal that the rbcL single barcode efficiently identified most of the sampled plants;this supports the potential utilisation of DNA barcoding in the accurate detection and conservation of CITES-listed plants in Nigeria. The study documented the CITES-listed plants and other essential plants endangered or threatened plants in Nigeria and provided the first chloroplast DNA reference dataset to support the utilisation of DNA barcoding to identify CITES-listed plant species in Nigeria, which is significant for future studies.

关键词： Annonaceae Apocynaceae BOLD CITES DNA Barcoding NCBI rbcL

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