Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Phylogeny and origin of pearl millet (Pennisetum glaucum [L.] R. Br) as revealed by microsatellite loci

  • 771 Accesses

  • 69 Citations


During the last 12,000 years, different cultures around the world have domesticated cereal crops. Several studies investigated the evolutionary history and domestication of cereals such as wheat in the Middle East, rice in Asia or maize in America. The domestication process in Africa has led to the emergence of important cereal crops like pearl millet in Sahelian Africa. In this study, we used 27 microsatellite loci to analyze 84 wild accessions and 355 cultivated accessions originating from the whole pearl millet distribution area in Africa and Asia. We found significantly higher diversity in the wild pearl millet group. The cultivated pearl millet sample possessed 81% of the alleles and 83% of the genetic diversity of the wild pearl millet sample. Using Bayesian approaches, we identified intermediate genotypes between the cultivated and wild groups. We then analyzed the phylogenetic relationship among accessions not showing introgression and found that a monophyletic origin of cultivated pearl millet in West Africa is the most likely scenario supported by our data set.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. Allaby RG, Brown TA (2003) AFLP data and the origins of domesticated crops. Genome 46:448–453

  2. Allouis S, Qi X, Lindup S, Gale MD, Devos KM (2000) Construction of a BAC library of pearl millet, Pennisetum glaucum. Theor Appl Genet 102:1200–1205

  3. Amblard S, Pernes J (1989) The identification of the cultivated pearl millet (Pennisetum) amongst plant impressions on pottery from Oued Chebbi (Dhar Oualata, Mauritania). Afr Archaeol Rev 7:117–126

  4. Amoukou AI, Marchais L (1993) Evidence of partial reproductive barrier between wild and cultivated pearl millet (Pennisetum glaucum). Euphytica 67:19–26

  5. Badr A, Müller K, Schäfer-Pregl R, El Rabey H, Effgen S et al (2000) On the origin and domestication history of barley (Hordeum vulgare). Mol Biol Evol 17:499–510

  6. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human trees with polymorphic microsatellites. Nature 368:455–457

  7. Brunken JN (1977) A systematic study of Pennisetum sect. pennisetum (Gramineae). Am J Bot 64:161–176

  8. Budak H, Pedraza F, Cregan PB, Baenziger PS, Dweikat I (2003) Development and utilization of SSRS to estimate the degree of genetic relationships in a collection of pearl millet germplasm. Crop Sci 43:2284–2290

  9. Chevenet F (2004) Treedyn—dynamic graphic editor for exploring phylogenetic or classification trees. Institut de recherche pour le développement, Montpellier, France (http://www/viradium.mpl.ird.fr/treedyn/)

  10. Clément JC, Bezançon G, Billard G (1993) Prospections des mils cultivés et sauvages d’Afrique de l’Ouest. In: Hamon S (eds) Le mil en Afrique diversité génétique et agrophysiologique: Potentialités et contraintes pour l’amélioration génétique et l’agriculture. Actes de la réunion thématique sur le mil (Pennisetum glaucum, L.), Montpellier du 24 au 26 novembre 1992

  11. D’Andrea AC, Casey J (2002) Pearl millet and Kintampo subsistence. Afr Archaeol Rev 19:147–173

  12. D’Andrea AC, Klee M, Casey J (2001) Archaeological evidence for pearl millet (Pennisetum glaucum) in sub-saharan West Africa. Antiquity 75:341–348

  13. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620

  14. Estoup A, Jarne P, Cornuet JM (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetic analysis. Mol Ecol 11:1591–1604

  15. Falush D, Stephens M, Pritchard JK (2003) Inferences of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

  16. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6 distributed by the author. Department of Genome Sciences, University of Washington, Seattle

  17. Fuller D, Korisettar R, Venkatasubbaiah PC, Jones MK (2004) Early plant domestications in southern India: some preliminary archaeobotanical results. Veget Hist Archaeobot 13:115–129

  18. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638

  19. Goudet J (2001) FSTAT, a program to estimate and test gene diversity and fixation indices (version Accessed on http://www.unil.ch./izea/softwares/fstat.html

  20. Harlan JR (1975) Crops and man. American Society of Agronomy and Crop Science Society of America, Madison, Wisconsin, p 295

  21. Hampton JO, Spencer PBS, Alpers DL (2004) Molecular techniques, wildlife management and importance of genetic population structure and dispersal: a case study with feral pigs. J Appl Ecol 41:735–743

  22. Heun M, Schäfer-Pregl R, Klawan D, Castagna R, Accerbi M, Borghi B, Salamini F (1997) Site of einkorn wheat domestication identified by DNA fingerprinting. Science 278:1312–1314

  23. Klee M, Zach B, Stika H-P (2004) Four thousand years of plant exploitation in the lake Chad basin (Nigeria), part III: plant impressions in postherds from the final stone age Gajiganna culture. Veget Hist Archaeobot 13:131–142

  24. Kuleung C, Baenziger PS, Kachmanand SD, Dweikat I (2006) Evaluating the genetic diversity of triticale with wheat and rye SSR Markers. Crop Sci 46:1692–1700

  25. Kuper R, Kröpelin S (2006) Climate-controlled Holocene occupation in the Sahara: motor of Africa’s evolution. Science 313:803–807

  26. Liu K, Muse S (2005) PowerMarker: new genetic data analyis software. Version 3.25. free program distributed by author over the internet from http://www.powerMarker.net

  27. Londo JP, Chiang Y-C, Hung K-H, Chiang T-Y, Schall BA (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci USA 103:9578–9583

  28. Marchais L, Tostain S (1993) Evaluation de la diversité génétique des Mils (Pennisetum glaucum, (L.) R. BR.) au moyen de marqueurs enzymatiques et relation entre formes sauvages et cultivées. In: Hamon S (eds) Le mil en Afrique diversité génétique et agrophysiologique: Potentialités et contraintes pour l’amélioration génétique et l’agriculture. Actes de la réunion thématique sur le mil (Pennisetum glaucum, L.), Montpellier du 24 au 26 novembre 1992

  29. Mariac C, Luong V, Kapran I, Mamadou A, Sagnard F, Deu M, Chantereau J, Gerard B, Ndjeunga J, Bezancon G, Pham JL, Vigouroux Y (2006a) Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Theor Appl Genet 114:49–58

  30. Mariac C, Robert T, Allinne C, Remigereau MS, Luxereau A, Tidjani M, Seyni O, Bezancon G, Pham JL, Sarr A (2006b) Genetic diversity and gene flow among pearl millet crop/weed complex: a case study. Theor Appl Genet 113:1003–1014

  31. Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler E, Doebley J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci U S A 99:6080–6084

  32. Miura R, Terauchi R (2005) Genetic control of weediness traits and the maintenance of sympatric crop-weed polymorphism in pearl millet (Pennisetum glaucum). Mol Ecol 14:1251–1261

  33. Morrell PL, Clegg MT (2007) Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent. Proc Natl Acad Sci U S A 104:3289–3294

  34. Nesbitt M, Samuel D (1996) From staple crop to extinction ? The archeology and history of the hulled wheats. In: Padulosi S, Hammer K, Heller J (eds) hulled wheats. Proceeding of the 1st international workshop on hulled wheats, pp 41–100

  35. Ozkan H, Brandolini A, Schafer-Pregl R, Salamini F (2002) AFLP analysis of a collection of tetraploid wheats indicates the origin of emmer and hard wheat domestication in southeast Turkey. Mol Biol Evol 19:1797–1801

  36. Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. Plos Genetics 2(12):e190

  37. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Cons Biol 12:844–855

  38. Porteres R (1976) African cereals: eleusine, fonio, black fonio, teff, Brachiaria, Paspalum, Pennisetum and African rice. In: Harlan J, De Wet J, Stemler A (eds) Origins of African plant domestication. Mouton Publishers, La Hague

  39. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

  40. Qi X, Lindup S, Pittaway TS, Allouis S, Gale MD, Devos KM (2001) Development of simple sequence repeat markers from bacterial artificial chromosome without sub-cloning. Biotechniques 31:355–362

  41. Qi X, Pittaway TS, Lindup S, Liu H, Waterman E, Padi FK, Hash CT, Zhu J, Gale MD, Devos KM (2004) An integrated genetic map and new set of simple sequence repeat markers for pearl millet, Pennisetum glaucum. Theor Appl Genet 109:1485–1493

  42. Renno J-F, Winkel T (1996) Phenology and reproductive effort of cultivated and wild forms of Pennisetum glaucum under experimental conditions in the Sahel: implications for the maintenance of polymorphism in the species. Can J Bot 74:959–964

  43. Robert T, Lespinasse R, Pernes J (1991) Gametophytic competition as influencing gene flow between wild and cultivated forms of pearl millet (Pennisetum typhoides). Genome 34:195–200

  44. Rosenberg NA, Woolf E, Pritchard JK, Schaap T, Gefel D, Shpirer I, Lavi U, Bonne-Tamir B, Hillel J, Feldman MW (2001) Distinctive genetic signature in the Libyan Jews. Proc Natl Acad Sci USA 98:858–863

  45. Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW (2005) Clines, clusters, and the effect of study design on the inference of human population structure. Plos Genetics 1:e70

  46. Salamini F, Heun M, Brandolini A, Özkan H, Wunder J (2004) Comment on « AFLP data and the origins of domesticated crop ». Genome 47:615–620

  47. Salzmann U, Hoelzmann P (2005) The Dahomey gap: an abrupt climatically induced rain forest fragmentation in West Africa during the late Holocene. Holocene 15:190–199

  48. Sarr A, Sandmeier M, Pernès J (1988) Gametophytic competition in pearl millet Pennisetum typhoides (Sapf. And Hubb). Genome 30:924–929

  49. Second G (1982) Origin of the genetic diversity of cultivated rice (Oryza ssp.): study of the polymorphim scored at 40 isoenzyme loci. Jpn J Genet 46:448–453

  50. Thuillet AC, Bataillon T, Poirier S, Santoni S, David JL (2005) Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data. Genetics 169:1589–1599

  51. Tostain S (1992) Enzyme diversity in pearl millet (Pennisetum glaucum) 3 Wild millet. Theor Appl Genet 83:736–742

  52. Tostain S (1998) Le mil, une longue histoire, hypothèses sur sa domestication et ses migrations. In: Chastenet N (ed) Plantes et paysages d’Afrique. Karthala, Paris, pp 461–490

  53. Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith S, Jaqueth J, Smith O, Doebley J (2005) An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169:617–1630

  54. Vilà C, Leonard JA, Göthersthröm A, Marklund S, Sandberg K, Lidén K, Wayne RK, Ellegren H (2001) Widespread origins of domestic horse lineage. Science 291:474–477

  55. Zohary D, Hopf M (2000) Domestication of plants in the old world: the origin and spread of cultivated plants in West Asia, Europe and the Nile Valley. Oxford University Press, New York

Download references


I.O. was funded by the Agence Universitaire de la Francophonie (AUF). This work was supported by the Institut de Recherche pour le Développement - IRD. We thank S. Tostain and G. Bezançon for their discussion and help in the choice of pearl millet samples, and R. Oldham for help during redaction of the article. The two anonymous reviewers significantly improved the previous version of the manuscript.

Author information

Correspondence to Yves Vigouroux.

Additional information

Communicated by H. H. Geiger.

Electronic supplementary material

Below is the link to the electronic supplementary material.

MOESM1 [Supplementary Table 1] (PDF 30 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Oumar, I., Mariac, C., Pham, J. et al. Phylogeny and origin of pearl millet (Pennisetum glaucum [L.] R. Br) as revealed by microsatellite loci. Theor Appl Genet 117, 489–497 (2008). https://doi.org/10.1007/s00122-008-0793-4

Download citation


  • Allelic Richness
  • Pearl Millet
  • Wild Accession
  • Pennisetum Glaucum
  • Hybrid Genotype