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.
References
[1]
Wilkin, P., Schols, P., Chase, M.W., Chayamarit, K., Furness, C.A., Huysmans, S., Rakotonasolo, F., Smets, E., Thapyai, C. and Meerow, A.W. (2005) A Plastid Gene Phylogeny of the Yam Genus, Dioscorea: Roots, Fruits and Madagascar. Systematic Botany, 30, 736-749. https://doi.org/10.1600/036364405775097879
[2]
Govaerts, R., Wilkin, P. and Saunders, R.M.K. (2007) World Checklist of Dioscoreales. Yams and Their Allies. Kew Publisher, Royal Botanic Gardens, Kew.
[3]
Norman, P.E., Tongoona, P. and Shanahan, P.E. (2011) Diversity of the Morphological Traits of Yam (Dioscorea spp.) Genotypes from Sierra Leone. Journal of Applied Bioscience, 45, 3045-3058.
[4]
Scarcelli, N., Tostain, S., Mariac, C., Agbangla, C., Ogoubi, D., Julien, B. and Pharm, J.L. (2006) Genetic Nature of Yams (Dioscorea sp.) Domesticated by Farmers in Benin (West Africa). Genetic Resource and Crop Evolution, 53, 121-130. https://doi.org/10.1007/s10722-004-1950-5
[5]
Lebot, V. (2009) Tropical Root and Tuber Crops: Cassava, Sweet Potato, Yams and Aroids. CABI Publishers, Wallingford, UK.
[6]
FAO (2012) Food and Agricultural Organization. FAOSTATDATA. FAO, Rome. http://faostat.fao.org/
[7]
Arnau, G., Abraham, K., Sheela, M. N., Chair, H., Sartie, A. and Asiedu, R. (2010) Yams. In: Bradshaw, J.E., Ed., Root and Tuber Crops, Springer, New York, 127-148. https://doi.org/10.1007/978-0-387-92765-7_4
Nweke, F.I., Ugwu, B.O., Asadu, C.L.A. and Ay, P. (1991) Production Costs in the Yam-Based Cropping Systems of South-Western Nigeria. Resource and Crop Management Division. Research Monograph No 6, IITA Ibadan, 29 p.
[10]
Degras, L. (1993) The Yam, a Tropical Root Crop. London, 40 p.
[11]
Asiedu, R. and Sartie, A. (2010) Crops That Feed the World Yams. Food Security, 2, 305-315. https://doi.org/10.1007/s12571-010-0085-0
[12]
Zhou, Y., Zhou, C., Yao, H., Liu, Y. and Tu, R. (2008) Application of ISSR Markers in Detection of Genetic Variation among Chinese Yam (Dioscorea opposita Thunb) Cultivars. Life Science Journal, 5, 4.
[13]
Djeri, B., Tchobo, P.F., Adjrah, Y., Karou, D.S., Ameyapoh, Y., Soumanou, M.M. and Souza, C. (2015) Nutritional Potential of Yam Chips (Dioscorea cayenensis and Dioscorea rotundata Poir) Obtained Using Two Methods of Production in Togo. African Journal of Food Science, 9, 278-284. https://doi.org/10.5897/AJFS2014.1207
[14]
Mahalakshmi, V., Ng, Q. and Atalobhor, K. (2007) Development of West African Yam Dioscorea spp. Core Collection. Genetic Resource and Crop Evolution, 54, 1817-1825. https://doi.org/10.1007/s10722-006-9203-4
[15]
Kenyon, L., Lebas, B.S.M. and Seal, S.E. (2008) Yams (Dioscorea spp.) from the South Pacific Islands Contain Many Novel Badnaviruses: Implications for International Movement of Yam Germplasm. Archives of Virology, 153, 877-889. https://doi.org/10.1007/s00705-008-0062-5
[16]
IITA (2009) ITTA Annual Report. International Institute of Tropical Agriculture, Ibadan.
[17]
FAO (2011) Food and Agricultural Organization. FAO, Rome. http://faostat.fao.org/
[18]
Mignouna, H.D., Dansi, A. and Zok, S. (2002) Morphological and Isozymic Diversity of the Cultivated Yams (Dioscorea cayenensis/Rotundata Complex) of Cameroun. Genetic Resource and Crop Evolution, 49, 21-29. https://doi.org/10.1023/A:1013805813522
[19]
Schwenk, K., Brede, N. and Streit, B. (2008) Introduction. Extent, Processes and Evolutionary Impact of Interspecific Hybridization in Animals. Philosophical Transactions of the Royal Society B, 363, 2805-2811.
[20]
Paun, O., Forest, F., Fay, M.F. and Chase, M.W. (2009) Hybrid Speciation in Angiosperms: Parental Divergence Drives Ploidy. New Phytologist, 182, 507-518. https://doi.org/10.1111/j.1469-8137.2009.02767.x
[21]
Whitney, K.D., Ahern, J.R., Campbell, L.G., Albert, L.P. and King, M.S. (2010) Patterns of Hybridization in Plants. Perspectives in Plant Ecology, 12, 175-182.
[22]
Primack, R.B. (2012) A Primer of Conservation Biology. 5th Edition, Edition Sinauer Assiociates, Sunderland, 363 p.
[23]
Dansi, A., Orobiyi, A., Dansi, M., Assogba, P., Sanni, A. and Akpagana, K. (2013) Sélection de sites pour la conservation in situ des ignames sauvages apparentées aux ignames Cultivées: Cas de Dioscorea praehensilis Au Bénin. International Journal of Biological and Chemical Sciences, 7, 60-74. https://doi.org/10.4314/ijbcs.v7i1.6
[24]
Ngo Ngwe, M.F.S., Omokolo, D.N. and Joly, S. (2015) Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices. PLoS ONE, 10, e0145364. https://doi.org/10.1371/journal.pone.0145364
[25]
Purvis, A., Gittleman, L. and Books, J.T. (2005) Phylogeny and Conservation. Cambridge University Press, London, 120-138. https://doi.org/10.1017/CBO9780511614927
[26]
Winter, M., Schweiger, O., Klotz, S., Nentwig, W., Andriopoulos, P., Arianoutsou, M., Basnou, C., Delipetrou, P., Didziulis, V., Hejda, M., Hulm, P.E., Lambdon, P.W., Perglh, J., Pysek, P., Royl, D.B. and Kuhn, I. (2009) Plant Extinctions and Introductions Lead to Phylogenetic and Taxonomic Homogenization of the European Flora. Proceeding of National Academy of Science, 106, 21721-21725. https://doi.org/10.1073/pnas.0907088106
[27]
Faith, D.P., Magallón, S., Hendry, A.P., Conti, E., Yahara, T. and Donoghue, M.J. (2010) Ecosystem Services: An Evolutionary Perspective on the Links between Biodiversity and Human Well-Being. Current Opinion in Environmental Sustainability, 2, 66-74. https://doi.org/10.1016/j.cosust.2010.04.002
[28]
Srivastava, D.S. and Vellend, M. (2005) Biodiversity-Ecosystem Function Research: Is It Relevant to Conservation? Annual Review of Ecology and Evolution System, 36, 267-294. https://doi.org/10.1146/annurev.ecolsys.36.102003.152636
[29]
Tamiru, M., Becker, H.C. and Maass, B.L. (2011) Comparative Analysis of Morphological and Farmers Cognitive Diversity in Yam Landraces (Dioscorea spp.) from Sothern Ethiopia. Tropical Agriculture and Development, 55, 28-43.
[30]
Girma, G., Spillane, C. and Gedil, M. (2015) DNA Barcoding of the Main Cultivated Yams and Selected Wild Species in the Genus Dioscorea. Journal of Systematic and Evolution, 9999, 1-10.
[31]
Terauchi, R., Chikaleke, V.A. and Thottappilly, G. (1992) Origin and Phylogeny of Guinea Yams as Revealed by RFLP Analysis of Chloroplast DNA and Nuclear Ribosomal DNA. Theoretical and Applied Genetics, 83, 743-751. https://doi.org/10.1007/BF00226693
[32]
Mignouna, H.D., Abang, M.M. and Fagbemi, S.A. (2003) A Comparative Assessment of Molecular Marker Assays (AFLP, RAPD and SSR) for White Yam (Dioscorea rotundata) Germplasm Characterization. Annals of Applied Biology, 142, 269-276. https://doi.org/10.1111/j.1744-7348.2003.tb00250.x
[33]
Saski, C.A., Bhattacharjee, R., Scheffler, B.E. and Asiedu, R. (2015) Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST Sequences, de Novo Sequencing and GBS Libraries. PLoS ONE, 10, e0134031. https://doi.org/10.1371/journal.pone.0134031
[34]
Akakpo, R., Scarcelli, N., Chaïr, H., Dansi, A., Djedatin, G., Thuillet, A.-C., Rhoné, B., François, O., Alix, K. and Vigouroux, Y. (2017) Molecular Basis of African Yam Domestication: Analyses of Selection Point to Root Development, Starch Biosynthesis, and Photosynthesis Related Genes. BMC Genome, 18, 782. https://doi.org/10.1186/s12864-017-4143-2
[35]
Kress, W.J. and Erickson, D.L. (2007) A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region. PLoS ONE, 2, e508. https://doi.org/10.1371/journal.pone.0000508
[36]
Schaefer, J. and Strimmer, K. (2005) An Empirical Bayes Approach to Inferring Large-Scale Gene Association Networks. Bioinformatics, 21, 754-764. https://doi.org/10.1093/bioinformatics/bti062
[37]
Miller, S.E. (2007) DNA Barcoding and the Renaissance of Taxonomy. Proceeding of National Academy of Science, 104, 4775-4776. https://doi.org/10.1073/pnas.0700466104
[38]
Asahina, H., Shinozaki, J., Masuda, K., Morimitsu, Y. and Satake, M. (2010) Identification of Medicinal Dendrobium Species by Phylogenetic Analyses Using Matk and rbcL Sequences. Journal of the National Medical Association, 64, 133-138. https://doi.org/10.1007/s11418-009-0379-8
[39]
Gao, X., Zhu, Y.-P., Wu, B.-C., Zhao, Y.-M., Chen, J.-Q. and Hang, Y.Y. (2008) Phylogeny of Dioscorea Sect. Stenophora Based on Chloroplast matK, rbcL and trnL-F Sequences. Journal of Systematic Evolution, 46, 315-321.
[40]
DNA Learning Center Barcoding 101 (2011). http://www.dnabarcoding101.org/lab/protocol-2.html
[41]
Bousalem, M., Durand, O., Scarcelli, N., Lebas, B.S.M., Kenyon, L., Marchandm, J.L., Lefort, F. and Seal, S.E. (2009) Dilemmas Caused by Endogenous Pararetroviruses Regarding the Taxonomy and Diagnosis of Yam (Dioscorea spp.) Badnaviruses: Analyses to Support Safe Germplasm Movement. Archives of Virology, 154, 297-314. https://doi.org/10.1007/s00705-009-0311-2
[42]
Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y., Ma, X., Gao, T., Pang, X., Luo, K., Li, Y., Li, X., Jia, X., Lin, Y. and Leon, C. (2010) Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species. PLoS ONE, 5, e8613. https://doi.org/10.1371/journal.pone.0008613
[43]
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology Evolution, 28, 2731-2739. https://doi.org/10.1093/molbev/msr121
[44]
Steel, M. and Penny, D. (2000) Parsimony, Likelihood, and the Role of Models in Molecular Phylogenetics. Molecular Biology Evolution, 17, 839-850. https://doi.org/10.1093/oxfordjournals.molbev.a026364
[45]
Kuck, P., Mayer, C., Wagele, J.W. and Misof, B. (2012) Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model. PLoS ONE, 7, e36593. https://doi.org/10.1371/journal.pone.0036593
[46]
Felsenstein, J. (1985) Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach. Molecular Biology Evolution, 17, 368-376. https://doi.org/10.1007/BF01734359
[47]
Soininen, E.M., Valentini, A., Coissac, E., Miquel, C., Gielly, L., Brochmann, C., Brysting, A.K., Sønstebø, J.H., Ims, R.A., Yoccoz, N.G. and Taberlet, P. (2009) Analysing Diet of Small Herbivores: The Efficiency of DNA Barcoding Coupled with High-Throughput Pyrosequencing for Deciphering the Composition of Complex Plant Mixtures. Frontier Zoology, 6, 16. https://doi.org/10.1186/1742-9994-6-16
[48]
Fazekas, A.J., Burgess, K.S., Kesanakurti, P.R., Graham, S.W., Newmaster, S.G., Husband, B.C., Percy, D.M., Hajibabaei, M. and Barrett, S.C. (2008) Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well. PLoS ONE, 3, e2802. https://doi.org/10.1371/journal.pone.0002802
[49]
Hollingsworth, P.M., Graham, S.W. and Little, D.P. (2011) Choosing and Using a Plant DNA Barcode. PLoS ONE, 6, e19254. https://doi.org/10.1371/journal.pone.0019254
[50]
Clement, W.L. and Donoghue, M.J. (2012) Barcoding Success as a Function of Phylogenetic Relatedness in Viburnum, a Clade of Woody Angiosperms. BMC Evolutionary Biology, 12, 73. https://doi.org/10.1186/1471-2148-12-73
[51]
Li, X.W., Yang, Y., Henry, R.J., Rosetto, M., Wang, Y.T. and Chen, S.L. (2014) Plant DNA Barcoding, from Gene to Genome. Biological Reviews, 90, 157-166. https://doi.org/10.1111/brv.12104
[52]
Dong, W., Xu, C., Li, C., Sun, J., Zuo, Y., Shi, S., Cheng, T., Guo, J. and Zhou, S. (2015) ycf1, the Most Promising Plastid DNA Barcode of Land Plants. Scientific Reports, 5, Article No. 8348. https://doi.org/10.1038/srep08348
[53]
CBOL Plant Working Group (2009) A DNA Barcode for Land Plants. Proceedings of the National Academy of Sciences, 106, 12794-12797. https://doi.org/10.1073/pnas.0905845106
[54]
Sun, X.Q., Zhu, Y.J., Guo, J.L., Peng, B., Bai, M.M. and Hang, Y.Y. (2012) DNA Barcoding the Dioscorea in China, a Vital Group in the Evolution of Monocotyledon: Use of matK Gene for Species Discrimination. PLoS ONE, 7, e32057. https://doi.org/10.1371/journal.pone.0032057
[55]
Faith, D.P. and Baker, A.M. (2006) Phylogenetic Diversity (PD) and Biology Conservation: Some Bioinformatics Challenges. Evolutionary Bioinformatics, 2, 70-77. https://doi.org/10.1177/117693430600200007
[56]
Mooers, A.O., Heard, S.B. and Chrostowski, E. (2005) In Phylogeny and Conservation. Oxford University Press, Oxford, 333.
[57]
Faith, D.P. (2016) The Phylogenetic Diversity Framework: Linking Evolutionary History to Feature Diversity for Biodiversity Conservation. Biodiversity Conservation and Phylogenetic Systematics, Topics in Biodiversity and Conservation, 14. https://doi.org/10.1007/978-3-319-22461-9_3
[58]
Cadotte, M.W. (2013) Experimental Evidence That Evolutionarily Diverse Assemblages Result in Higher Productivity. PNAS, 110, 8996-9000. https://doi.org/10.1073/pnas.1301685110
[59]
Pearson, W.R. (2014) BLAST and FASTA Similarity Searching for Multiple Sequence Alignment. Methods Molecular Biology, 1079, 75-101. https://doi.org/10.1007/978-1-62703-646-7_5
[60]
Maloukh, L., Kumarappan, A., Jarrar, M., Salehi, J., El-waki, H. and Lakshmi, T.V.R. (2017) Discriminatory Power of rbcL Barcode Locus for Authentication of Some of United Arab Emirates (UAE) Native Plants. 3 Biotech, 7, 144. https://doi.org/10.1007/s13205-017-0746-1
[61]
Elansary, O.H., Ashfaq, M., Ali, H.M. and Yessoufou, K. (2017) The First Initiative of DNA Barcoding of Ornamental Plants from Egypt and Potential Applications in Horticulture Industry. PLoS ONE, 12, e0172170. https://doi.org/10.1371/journal.pone.0172170
[62]
Sikic, K. and Carugo, O. (2010) Protein Sequence Redundancy Reduction: Comparison of Various Methods. Bioinformatics, 5, 234-239. https://doi.org/10.6026/97320630005234
