Assessment of genetic diversity in accessions of pearl millet (Pennisetum glaucum) and napier grass (Pennisetum purpureum) using microsatellite (ISSR) markers


1 Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, P. M. B. 1515, Ilorin -240003, Kwara State, Nigeria.

2 C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Bardoli, Surat -394 350, Gujarat, India.


Pearl millet (Pennisetum glaucum (L.) R. Br.) and napier grass (Pennisetum purpureum Schumach) are the most economically important species in the genus Pennisetum. Knowledge of genetic diversity of these two species would enhance their potentials for utilization. The present work assessed the genetic diversity and phylogenetic relationship among Nigerian and Indian accessions of pearl millet and napier grass using microsatellite markers. We extracted genomic DNA from each accession and carried out Polymerase Chain Reaction using Inter-Simple Sequence Repeat markers. Data obtained were analyzed for genetic diversity using MEGA 4.0 software. A total of 48 loci consisting of 410 bands were generated with 56.25% polymorphism. Principal Coordinates analysis revealed three principal axis contributed significantly (70.20%) to the observed variations. Accessions of napier grass from Nigeria and India were plotted on a coordinate plane while pearl millets from both countries co-existed on different quadrants. Cluster analysis, showed that Nigeria and India accessions of napier grass were similar. Consistent link of COM-CO-3 with Nigeria napier grass and millet accessions suggested a common progenitor. The polymorphism obtained in this study showed that ISSR is an effective marker for assessment of genetic diversity and the connection between most accessions indicated that they have common progenitor.


Ajibade S. R., Weeden N. F., and Michite S. (2000). Inter simple sequence repeat analysis of genetic relationships in the genus Vigna. Eupytical, 111: 47-55.
Allchin F. R. (1969). Early cultivated plants in India and Pakistan. In: P. J. Ucko and G. W. Dimbleby (eds). The domestication and exploitation of plants and animals, London. G. Duckworth and Co. 323-329.
Azevedo A. L., Costa P. P., Machado J. C., Machado M. A., Pereira A.V., and da SilavaLedo F. J. (2012). Cross species amplification of Pennisetum glaucum Microsatellite markers in Pennisetum purpureum and genetic diversity of Napier grass accessions. Crop Science, 52: 1776-1785.
Barbosa S., Davide L. C., and Pereira A. V. (2003). Cytogenetics of Pennisetum purpureum Schumack × Pennisetum glaucum L. Hybrids and their Parents. Ciência Agrotecnologia, 27: 26-35.
Bhattacharjee R., Bramel P. J., Hash C. T., Kolesnikova-Allen M. A. and Khairwal I.S. (2002). Assessment of genetic diversity within and between pearl millet landraces. Theoretical AppliedGenetics, 105: 666-673.
Brunken J.N. (1977). Systematic study of Pennisetum-sect - Pennisetum (gramineae). American Journal of Botany, 64: 161-176.
Burkill H.M. (1994). The useful plants of West Tropical Africa. Royal Butanic Gardens. Kew, UK p. 636
Cota-Stanchez J.R. Remarchuk K and Ubayasena K. (2006). Ready to use DNA extracted with CTAB method adopted for Herbarium specimensand mucilaginous plant tissue. Plant Molecular Biology Reports, 24: 161-167.
Davies O. (1968). The origins of agriculture in West Africa. Current Anthropology, 9: 479-482.
Dowling C. D., Burson B. L., and Jessup R. W. (2014). Marker-assisted verification of Kinggrass (Pennisetum purpureum Schumch. ×Pennisetum glaucum [L.] R. Br.). Plant Omics Journal, 7: 72-79
Esselink G. D., Nybom H., and Vosman B. (2004). Assignment of allelic configuration in polyploids suing the MAC-PR (Microsatellite DNA allele counting-peak ratios) method. Theoretical Applied Genetics, 109: 402-408.
Farrell G., Simons S. A., and Hillocks R. J. (2002). Pests, diseases and weeds of Napier grass, Pennisetum purpureum; a review. International Journal of Pest Management, 48: 39-48.
FAO and ICRISAT (1996). The world Sorghum and millet economics; facts, trends and outlook. Food and Agricultural Organization of the United Nations: Rome, Italy and International Crops Research Institute for the Semi-Arid Tropics: Patanchera 502 324, Andhra Pradesh, India p. 23-26.
Gale M. D., Devos K. M., Zhu J. H., Allouis S., Couchman M. S., Liu H., Pittaway T. S., Qi X. Q., Kolesnikova-Allen M., and Hash C.T. (2001). New molecular marker technologies for pearl millet improvement. International Sorghum and Millets Newsletter, 42: 16-22
Galvan M. Z., Bornet B., Balatti P. A., and Branchard M. (2003). Inter sequence repeat (ISSR) markers as a tool for assessment of both genetic diversity and gene pool origin in common bean (Phaseolus vulgaris L.). Euphytical, 132: 297-301.
Hanna W. W., Baltensperger D. D., and Seetharam A. (2004). Pearl millet and millets. In: Moser (ed.) Warm season (C4) grasses. Agron. Monogr. 45. ASA, CSSA, and SSSA, Madison, W1.
Hash C. T., Bhasker Raj A.G., Lindup S., Sharma A., Beniwal C. R., Folkertsma R.T., Mahalakshmi V., Zerbini E. and Blümmel M. (2003). Opportunities for marker-assisted selection (MAS) to improve the feed quality of crop residues in pearl millet and sorghum. Field Crops Research, 84: 79-88.
HiluK.W. (1995). Evolution of finger millet: evidence from random amplified polymorphic DNA. Genome, 38: 232-238.
JauharP. P. (1998). Cytogenetics and breeding of pearl millet and related species. AR Liss, New York.
Kannan B., Sanapathy S., Raj A. G. B., Chandra S., Muthiah A., Dhanapal A. P., and Hash C. T. (2014). Association analysis of SSR markers with phenology, grain and stover-yield realted traits in pearl millet (Pennisetum glaucum (L.) R. Br.). The Scientific World Journal.  
Khairwal I. S., Rai K. N., Diwakar B., Sharma Y. K., Rajpurohit B. S., Nirwan B., and Bhattacharjee R. (2007). Pearl millet: Crop management and seed production manual.Patancheru, Andhra Pradesh, India: ICRISAT. 108 pp.
Kumari K., and Pande A. (2010). Study of genetic diversity in finger millet (EleusinecoracanaL. Gaertn) using RAPD  markers. African Journal of Biotechnology, 9: 4542-4549.
Langeland K. A., Ferrell J. A., Sellers B., MacDonald G. E., and Stocker R. K. (2008). Identification and biology of  non-native plants in Florida’s natural areas. IFAS. Sp. Island Press, Washington, DC. pp 21-37
Liu C. J., Witcombe J. R., Pittaway T. S., Nash M., Hash C. T., Busso C. S., and Gale M. D. (1994). An RFLP-based genetic map of pearl millet (Pennisetum glaucum). Theoretical Applied Genetics, 89: 481-487.
Mariac C., Luong V., Kapran I., Mamadou A., Sagnard M., Deu M., Chantereau J., Gerard B., Ndjeunga J., Bezancon G., Pham J., and Vigouroux Y. (2006). Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Theoretical Applied Genetics, 114: 49-58.
Martel E., De Nay D., Siljak-Yakovlev S., Brown S., and Sarr A. (1997). Genome size variation of basic chromosome number in pearl millet and fourteen related Pennisetum species. The Journal of Heredity, 88: 139-143.
Mignouna H. D., Abang M. M., and Fagbemi S. A. (2003). A comparative assessment of molecular markers assay (AFLP, RAPD and SSR) for white yam (Dioscorearotundata) germplasm characterization. Annals of Applied Biology, 142: 269-276. 
Morakinyo J. A., and Adebola P. O. (1991). Karyotype analysis and meiotic chromosome behaviour in Pennisetum americanum, P. purpureum and P. pedicellatum. Nigerian Journal of Botany, 4: 127-134
Nybom H. (1990). Application of DNA fingerprinting in plant breeding. Proceedings of International DNA Fingerprinting Sympossium. Bern. pp 32-45
Ogunkanmi L. A.,Oboh B., Williams O., Monu G., and Ogundipe T. O. (2009). Phylogenetic and genomic relationships in the genus Malus based on RAPD’S. Journal of Biotechnology, 8: 3387-3391
Otoo E., Akromah R., Kolesnikova-Allen M., and Asiedu R. (2009). Delineation of pona complex of yam in Ghana using SSR markers. International Journal of Genetics and Molecular Biology, 1: 006-016
Oumar I., Mariac C., Pham J. L., and Vigouroux Y. (2008). Phylogeny and origin of pearl millet (Pennisetum glaucum [L.] R. Br) as revealed by microsatellite loci. Theoretical Applied Genetics, 117: 489- 497.
Pfeiffer T., Roschanski A. M., PannellKorbecka G., and Schnitter M. (2011). Characterization of microsatellite loci and reliable genotyping in a polyploidy plant, Mercurialisperennis(Euphorbiaceae). The Journal of Heredity, 102: 479-488.
Poncet V., Lamy F., Enjalbert J., Joly H., Sarr A., and Robert T. (1998). Genetic analysis of the domestication syndrome in pearl millet (Pennisetum glaucum L., Poaceae): inheritance of the major characters. Hered, 81: 648-658.
Rai K. N., Gupta S. K., Bhattacharjee R., Kulkarni V. N. M., Singh A. K., and Rao A. S. (2009). Morphological characteristics of ICRISAT-bred pearl millet hybrid seed parent. Journal of SAT Agriculture Research, 7: 56-71
Scotti I., Paglia G., Magni F., and Morgante M. (1999). Microsatellite markers as a tool for detection of intra- and interpopulational genetic structure. In: E. D. Gillet (ed.) Which DNA marker for which purpose? Final Compendium of the Research Project Development, Oprtimization and validation of molecular tools for assessment of biodiversity in forest trees in the European Union DGXII Biotechnology. FW IV Research Programme Molecular Tools for Biodiversity.
Semagn K., Bjornstad A., and Ndjiondjop M. N. (2006). An overview of molecular marker methods for plants. African Journal of Biotechnologh, 5: 2540-2568.
Skerman P. J., and Rivers F. (1990). Tropical grasses: FAO plant production and protection series 23. Food and Agriculture Organization of the United Nations. Rome 832 p.
Stich B., Haussmann B. I. G., Pasam R., Bhosale S., Hash C. T., Melchinger E., and Parzies H. K. (2010). Patterns of molecular and phenotypic diversity in Pearl millet (Pennisetum glaucum (L.) R. Br.) from West and Central Africa and their relation to geographical and environmental parameters. BMC Plant Biology,10: 216
SupriyaS. S., Nepolean T, Hash C. T., Rajaram V., Eshwar K., Sharma R., Thakur R. P., Pandurangarao V., and Yadav R. C. (2010). Identification of quantitative trait loci associated with rust resistance in pearl millet using DArT and SSR based linkage map. National Symposium on Genomics and Crop Improvement: Relevance and Conservations, February 25-27, 2010, Acharya N.G. Ranga Agricultural University, Rajendranagar, Hyderabad.
Tchamba M. N., and Seme P. M. (1993). Diet and feeding behaviour of the forest elephant in the Santchon Reserve, Cameroon. African Journal of Ecology 31: 165-171
Techio V. H., Davide L. C., and Pereira A. V. (2006). Meiosis in elephant grass (Pennisetum purpureum) (Poaceae, Poales) and their interspecific hybrids. Genetics and Molecular Biology, 29: 415-423
Varshney R. K., Hoisington D. A., and Tyagi A. K. (2006). Advances in cereal genomics and applications in crop breeding. Trends in Biotechnology, 24: 490-499.
vom Brocke K., Christinck A., Weltzien E. R., Presterl T. and Geiger H. H. (2003). Farmer’s seed systems and management practices determine pearl millet genetic diversity patterns in semi-arid regions of India. Crop Science, 43: 1680-1689.