Advertisement

Theoretical and Applied Genetics

, Volume 116, Issue 7, pp 903–913 | Cite as

Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers

  • M. Deu
  • F. Sagnard
  • J. Chantereau
  • C. Calatayud
  • D. Hérault
  • C. Mariac
  • J.-L. Pham
  • Y. Vigouroux
  • I. Kapran
  • P. S. Traore
  • A. Mamadou
  • B. Gerard
  • J. Ndjeunga
  • G. Bezançon
Original Paper

Abstract

Understanding the geographical, environmental and social patterns of genetic diversity on different spatial scales is key to the sustainable in situ management of genetic resources. However, few surveys have been conducted on crop genetic diversity using exhaustive in situ germplasm collections on a country scale and such data are missing for sorghum in sub-Saharan Africa, its centre of origin. We report here a genetic analysis of 484 sorghum varieties collected in 79 villages evenly distributed across Niger, using 28 microsatellite markers. We found a high level of SSR diversity in Niger. Diversity varied between eastern and western Niger, and allelic richness was lower in the eastern part of the country. Genetic differentiation between botanical races was the first structuring factor (Fst = 0.19), but the geographical distribution and the ethnic group to which farmers belonged were also significantly associated with genetic diversity partitioning. Gene pools are poorly differentiated among climatic zones. The geographical situation of Niger, where typical western African (guinea), central African (caudatum) and eastern Sahelian African (durra) sorghum races converge, explained the high observed genetic diversity and was responsible for the interactions among the ethnic, geographical and botanical structure revealed in our study. After correcting for the structure of botanical races, spatial correlation of genetic diversity was still detected within 100 km, which may hint at limited seed exchanges between farmers. Sorghum domestication history, in relation to the spatial organisation of human societies, is therefore key information for sorghum in situ conservation programs in sub-Saharan Africa.

Keywords

Sorghum Allelic Richness Pearl Millet Spatial Genetic Structure Seed Exchange 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We thank the different people who took part in the 2003 sampling operation, and particularly Djibo Moussa, Moussa Tidjani and H. Yahaya Bissala. We are also grateful to Claire Billot and the Montpellier Languedoc-Roussillon Genopole platform for technical assistance. This work was supported by Institut Français de la Biodiversité (IFB). We thank Seydou B. Traoré (AGRHYMET) for providing access to 1971–2000 yearly rainfall normals.

Supplementary material

122_2008_721_MOESM1_ESM.doc (224 kb)
(DOC 224 kb)

References

  1. Aldrich PR, Doebley J, Schertz KF, Stec A (1992) Patterns of allozyme variation in cultivated and wild Sorghum bicolor. Theor Appl Genet 85:451–460Google Scholar
  2. Ayana A, Bryngelsson T, Bekele E (2000) Genetic variation of Ethiopian and Eritrean sorghum (Sorghum bicolor [L.] Moench) germplasm assessed by random amplified polymorphic DNA (RAPD). Genet Resour Crop Evol 47:471–482CrossRefGoogle Scholar
  3. Ayana A, Bryngelsson T, Bekele E (2001) Geographic and altitudinal allozyme variation in sorghum (Sorghum bicolor [L.] Moench) landraces from Ethiopia and Eritrea. Hereditas 135:1–12PubMedCrossRefGoogle Scholar
  4. Barnaud A, Deu M, Garine E, McKey D, Joly H (2007) Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces. Theor Appl Genet 114:237–248PubMedCrossRefGoogle Scholar
  5. Bataillon TM, David JL, Schoen DJ (1996) Neutral genetic markers and conservation genetics: simulated germplasm collection. Genetics 144:409–417PubMedGoogle Scholar
  6. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2002) Genetix 4.04, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France. http://www.univ-montp2.fr/∼genetix/genetix/genetix.htm
  7. Bellon MR (1997) On farm conservation as a process: an analysis of its components. In: Sperling L, Loevinsohn M (eds) Using diversity: enhancing and maintaining genetic resources on-farm. IDRC, Ottawa, Canada. http://www.idrc.ca/en/ev-85109-201-1-DO_TOPIC.html
  8. Bhattramakki D, Dong J, Chhabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L. Moench). Genome 43:988–1002PubMedCrossRefGoogle Scholar
  9. Brown SM, Hopkins MS, Mitchell SE, Senior ML, Wang TY, Duncan RR, Gonzalez Candelas F, Kresovich S (1996) Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum (Sorghum bicolor [L.] Moench). Theor Appl Genet 93:190–198CrossRefGoogle Scholar
  10. Brush SB (1995) In situ conservation of landraces in centers of crop diversity: implications of germplasm conservation and utilization. Crop Sci 35:46–354CrossRefGoogle Scholar
  11. Brush SB (2000) The issue of in situ conservation of genetic resources. In: Brush SB (eds) Genes in the field: on-farm conservation of crop diversity. IPGRI/ IDRC/Lewis Publishers, Boca Raton, pp 3–26Google Scholar
  12. Casa AM, Mitchell SE, Hamblin MT, Sun H, Bowers JE, Paterson AH, Aquadro CF Kresovich S (2005) Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats. Theor Appl Genet 111:23–30PubMedCrossRefGoogle Scholar
  13. Ceccarelli S, Bailey E, Grando S, Tutwiler R (1997) Decentralized, participatory plant breeding: a link between formal plant breeding and small farmers. New frontiers in participatory research and gender analysis. In: Proceedings of the Seminar ‘Participatory Research and Gender Analysis for Technology Development’, Cali, Colombia, pp 65–74Google Scholar
  14. Cui YX, Xu GW, Magill CW, Schertz KF, Hart GE (1995) RFLP-based assay of Sorghum bicolor (L) Moench genetic diversity. Theor Appl Genet 90:787–796CrossRefGoogle Scholar
  15. de Oliveira AC, Richter T, Bennetzen JL (1996) Regional and racial specificities in sorghum germplasm assessed with DNA markers. Genome 39:579–587PubMedGoogle Scholar
  16. Deu M, Gonzalez de Leon D, Glaszmann JC, Degremont I, Chantereau J, Lanaud C, Hamon P (1994) RFLP diversity in cultivated sorghum in relation to racial differentiation. Theor Appl Genet 88:838–844CrossRefGoogle Scholar
  17. Deu M, Hamon P, Chantereau J, Dufour P, D’Hont A, Lanaud C (1995) Mitochondrial DNA diversity in wild and cultivated sorghum. Genome 38:635–645PubMedCrossRefGoogle Scholar
  18. Deu M, Rattunde F, Chantereau J (2006) A global view of genetic diversity in cultivated sorghums using a core collection. Genome 49:168–180PubMedGoogle Scholar
  19. Djè Y, Forcioli D, Ater M, Lefèbvre C, Vekemans X (1999) Assessing population genetic structure of sorghum landraces from North-western Morocco using allozyme and microsatellite markers. Theor Appl Genet 99:157–163CrossRefGoogle Scholar
  20. Djè Y, Heuertz M, Lefèbvre C, Vekemans X (2000) Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers. Theor Appl Genet 100:918–925CrossRefGoogle Scholar
  21. Djè Y, Heuertz M, Ater M, Lefèbvre C, Vekemans X (2004) In situ estimation of outcrossing rate in sorghum landraces using microsatellite markers. Euphytica 138:205–212CrossRefGoogle Scholar
  22. Doggett H (1988) Sorghum, 2nd edn. Longman Scientific and Technical, London, UKGoogle Scholar
  23. Folkertsma RT, Rattunde FH, Chandra S, Soma Raju W, Hash CT (2005) The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers. Theor Appl Genet 111:399–409PubMedCrossRefGoogle Scholar
  24. Ghebru B, Schmidt RJ, Bennetzen JL (2002) Genetic diversity of Eritrean sorghum landraces assessed with simple sequence repeat (SSR) markers. Theor Appl Genet 105:229–236PubMedCrossRefGoogle Scholar
  25. Goudet J (2001) FSTAT, a program to estimate and test gene diversity and fixation indices (version 2.9.3). http://www.unil.ch/izea/softwares/fstat.html
  26. Grenier C, Deu M, Kresovich S, Bramel-Cox PJ, Hamon P (2000) Assessment of genetic diversity in three subsets constituted from the ICRISAT sorghum collection using random vs. non-random sampling procedures. B. Using molecular markers. Theor Appl Genet 101:197–202CrossRefGoogle Scholar
  27. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620CrossRefGoogle Scholar
  28. Harlan JR, de Wet JMJ (1972) Simplified classification of cultivated sorghum. Crop Sci 12:172–176CrossRefGoogle Scholar
  29. Hulme M (2001) Climatic perspectives on Sahelian desiccation: 1973–1998. Global Environ Change 11:19–29CrossRefGoogle Scholar
  30. Kayodé PAP, Linnemann AR, Nout RMJ, Hounhouigan JD, Stomph TJ, Smulders MJM (2006) Diversity and food quality properties of farmers’ varieties of sorghum from Benin. J Sci Food Agric 86:1032–1039CrossRefGoogle Scholar
  31. Kim J-S, Klein PE, Klein RR, Price HJ, Mullet JE, Stelly DM (2005) Chromosome identification and nomenclature of Sorghum bicolor. Genetics 169:955–965PubMedCrossRefGoogle Scholar
  32. Mariac C, Luong V, Kapran I, Mamadou A, Sagnard F, Deu M, Chantereau J, Gerard B, Ndjeunga J, Bezançon G, Pham J-L, Vigouroux Y (2006) Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Theor Appl Genet 114:49–58PubMedCrossRefGoogle Scholar
  33. 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 USA 99:6080–6084PubMedCrossRefGoogle Scholar
  34. Maxted N, Guarino L, Myer L, Chiwona EA (2002) Towards a methodology for on-farm conservation of plant genetic resources. Genet Resour Crop Evol 49:31–46CrossRefGoogle Scholar
  35. Menkir A, Goldsbrough P, Ejeta G (1997) RAPD based assessment of genetic diversity in cultivated races of sorghum. Crop Sci 37:564–569CrossRefGoogle Scholar
  36. Menz MA, Klein RR, Mullet JE, Obert JA, Unruh NC, Klein PE (2002) A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP (R), RFLP and SSR markers. Plant Mol Biol 48:483–499PubMedCrossRefGoogle Scholar
  37. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  38. Nkongolo KK, Nsapato L (2003) Genetic diversity in Sorghum bicolor (L.) Moench accessions from different ecogeographical regions in Malawi assessed with RAPDs. Genet Resour Crop Evol 50:149–156CrossRefGoogle Scholar
  39. Ollitrault O, Noyer JL, Chantereau J, Glaszmann JC (1997) Structure génétique et dynamique des variétés traditionnelles de sorgho au Burkina Faso. In: Begic A (ed) Gestion des ressources génétiques de plantes en Afrique des savanes. IER-BRG Solagral, Bamako, Mali, pp 231–240Google Scholar
  40. Oosterhout SV (1997) What does in situ conservation mean in the life of a small-scale farmer? In: Sperling L, Loevinsohn M (eds) Using diversity: enhancing and maintaining genetic resources on-farm. IRDC, Ottawa, Canada. http://www.idrc.ca/en/ev-85112-201-1-DO_TOPIC.html
  41. Parzies HK, Spoor W, Ennos RA (2004) Inferring seed exchange between farmers from population genetic structure of barley landrace Arabi Aswad from Northern Syria. Genet Resour Crop Evol 51:471–478CrossRefGoogle Scholar
  42. Perales HR, Benz BF, Brush SB (2005) Maize diversity and ethnolinguistic diversity in Chiapas, Mexico. Proc Natl Acad Sci USA 102:949–954PubMedCrossRefGoogle Scholar
  43. Perrier X, Flori A, Bonnot F (2003) Methods for data analysis. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publishers, Inc. and CIRAD, Montpellier, pp 31–63Google Scholar
  44. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855CrossRefGoogle Scholar
  45. Reenberg A (2001) Agricultural land use pattern dynamics in the Sudan-Sahel towards an event-driven framework. Land Use Policy 18:309–319CrossRefGoogle Scholar
  46. Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res 67:175–185CrossRefGoogle Scholar
  47. Rousset F (2000) Genetic differentiation between individuals. J Evol Biol 13:58–62CrossRefGoogle Scholar
  48. Scheuring JF, Konate IM., Toure S (1980) The Malian sorghum collection. Sorghums Newsl 23:33635Google Scholar
  49. Schloss SJ, Mitchell SE, White GM, Kukatla R, Bowers JE, Paterson AH, Kresovich S (2002) Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench. Theor Appl Genet 105:912–920PubMedCrossRefGoogle Scholar
  50. Smouse PE, Peakall R (1999) Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity 82:561–573PubMedCrossRefGoogle Scholar
  51. Snowden JD (1936) The cultivated races of sorghum. Adlard, London, UK, pp 1–274Google Scholar
  52. Sokal RR, Wartenberg DE (1983) A test of spatial autocorrelation analysis using an isolation-by-distance model. Genetics 105:219–237PubMedGoogle Scholar
  53. Taramino G, Tarchini R, Ferrario S, Lee M, Pe ME (1997) Characterization and mapping of simple sequence repeats (SSRs) in Sorghum bicolor. Theor Appl Genet 95:66–72CrossRefGoogle Scholar
  54. Tescar RP (2004) Echanges Informels des Semences de sorgho (Sorghum bicolor L. Moench) au Burkina, études de cas: le Centre-Ouest, le Centre-Nord et la Boucle de Mouhoun, DEA Dissertation, INA P-G, Paris, 42 pGoogle Scholar
  55. Teshome A, Fahrig L, Torrance JK, Lambert JD, Arnason TJ, Baum BR (1999) Maintenance of sorghum (Sorghum bicolor, Poaceae) landrace diversity by farmers’ selection in Ethiopia. Econ Bot 53:79–88Google Scholar
  56. Uptmoor R, Wenzel W, Friedt W, Donaldson G, Ayisi K, Ordon F (2003) Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs. Theor Appl Genet 106:1316–1325PubMedGoogle Scholar
  57. vom Brocke K, Christinck A, Weltzien E, Presterl T, Geiger HH (2003) Farmers’ seed systems and management practices determine pearl millet genetic diversity patterns in semiarid regions of India. Crop Sci 43:1680–1689CrossRefGoogle Scholar
  58. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  59. Wezel A, Boecker R (1998) Fallow plant communities and site characteristics in semi-arid Niger, West Africa. J Arid Environ 40:269–280CrossRefGoogle Scholar
  60. Zongo JD (1991) Ressources génétiques des sorghos (Sorghum bicolor L. Moench) du Burkina Faso: Evaluation agromorphologique et génétique. PhD Thesis, University of Abidjan, Ivory CoastGoogle Scholar
  61. Zongo JD, Gouyon PH, Sarr A, Sandmeier M (2005) Genetic diversity and phylogenic relations among Sahelian sorghums accessions. Genet Resour Crop Evol 52:869–878CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • M. Deu
    • 1
  • F. Sagnard
    • 1
    • 2
  • J. Chantereau
    • 3
  • C. Calatayud
    • 1
  • D. Hérault
    • 1
  • C. Mariac
    • 4
  • J.-L. Pham
    • 4
  • Y. Vigouroux
    • 5
  • I. Kapran
    • 6
  • P. S. Traore
    • 2
  • A. Mamadou
    • 6
  • B. Gerard
    • 7
  • J. Ndjeunga
    • 7
  • G. Bezançon
    • 5
  1. 1.CIRADUMR DAPMontpellierFrance
  2. 2.International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)BamakoMali
  3. 3.CIRADUPR Agrobiodiversité en savaneMontpellierFrance
  4. 4.Institut de Recherche pour le Développement (IRD)MontpellierFrance
  5. 5.Institut de Recherche pour le Développement (IRD)NiameyNiger
  6. 6.Institut National de la Recherche Agronomique du Niger (INRAN)NiameyNiger
  7. 7.International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)NiameyNiger

Personalised recommendations