Skip to main content
SpringerLink
Log in

Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger’s agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976–2003). Global genetic differentiation between the two collections was very low (F st = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F st, and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers’ management has globally preserved sorghum genetic diversity in Niger.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Allinne C, Mariac C, Vigouroux Y, Bezançon G, Couturon E, Moussa D, Tidjani M, Pham JL, Robert T (2008) Role of seed flow on the pattern and dynamics of pearl millet (Pennisetum glaucum [L.] R. Br.) genetic diversity assessed by AFLP markers: a study in south-western Niger. Genetica 133:167–178

    Article  PubMed  CAS  Google Scholar 

  • 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 114:237–248

    Article  PubMed  Google Scholar 

  • Barry MB, Pham JL, Béavogui S, Ghesquière A, Ahmadi N (2008) Diachronic (1979–2003) analysis of rice genetic diversity in Guinea did not reveal genetic erosion. Genet Resour Crop Evol 55:723–733

    Article  Google Scholar 

  • 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. (Available from http://www.univ-montp2.fr/~genetix/genetix/genetix.htm)

  • Bellon MR (1996) The dynamics of crop infraspecific diversity: a conceptual framework at the farmer level. Econ Bot 50:26–39

    Google Scholar 

  • Bellon MR (2009) Do we need crop landraces for the future? Realizing the global option value of in situ conservation. In: Kontoleon A, Pascual U, Smale M (eds) Agrobiodiversity, conservation and economic development. Routledge, New York, pp 51–61

    Google Scholar 

  • Ben Mohamed A, Van Duivenbooden N, Abdoussallam S (2002) Impact of climate change on agricultural production in the Sahel—methodological approach and case study for millet in Niger. Clim Change 54:327–348

    Article  Google Scholar 

  • Bezançon G, Pham JL, Deu M, Vigouroux Y, Sagnard F, Mariac C, Kapran I, Mamadou A, Gérard B, Ndjeunga J, Chantereau J (2009) Changes in the diversity, geographic distribution of cultivated millet (Pennisetum glaucum [L.] R. Br.), sorghum (Sorghum bicolor (L.) Moench) varieties in Niger between 1976 and 2003. Genet Resour Crop Evol 56:223–236

    Article  Google Scholar 

  • Brown AHD (2000) The genetic structure of crop landraces and the challenge to conserve them in situ on farms. In: Brush SB (ed) Genes in the field: on-farm conservation of crop diversity. IPGRI/IDRC/Lewis Publishers, Boca Raton, pp 29–48

    Google Scholar 

  • Brush SB (1989) Rethinking crop genetic resource conservation. Conserv Biol 3:19–29

    Article  Google Scholar 

  • Brush SB, Meng E (1998) Farmers’ valuation and conservation of crop genetic resources. Genet Resour Crop Evol 45:139–150

    Article  Google Scholar 

  • 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 111:23–30

    Article  PubMed  CAS  Google Scholar 

  • Comps B, Gömöry D, Letouzey J, Thiebaut B, Petit RJ (2001) Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech. Genetics 157:389–397

    PubMed  CAS  Google Scholar 

  • Costis C (2005) Diversité des mils et sorghos cultivés au Niger: facteurs agro-économiques, socio-économiques et les modes de gestion des variétés. Mémoire de DESS “Gestion des systémes agro-sylvo-pastoraux en zones tropicales”, Université Paris XII, p 51

  • Cromwel E, van Oosterhoust S (2000) On-farm conservation of crop diversity: policy and institutional lessons from Zimbabwe. In: Brush SB (ed) Genes in the field: on-farm conservation of crop diversity. IPGRI/IRDC/Lewis Publishers, Boca Raton, pp 217–238

    Google Scholar 

  • Deu M, Sagnard F, Chantereau J, Calatayud C, Hérault D, Mariac C, Pham JL, Vigouroux Y, Kapran I, Traoré PS, Mamadou A, Gérard B, Ndjeunga J, Bezançon G (2008) Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers. Theor Appl Genet 116:903–916

    Article  PubMed  CAS  Google Scholar 

  • Donini R, Law JR, Koebner RMD, Reeves JC, Cooke RJ (2000) Temporal trends in the diversity of UK wheat. Theor Appl Genet 100:912–917

    Article  Google Scholar 

  • El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theor Appl Genet 92:832–839

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • FAO-Orstom (1977) Prospections des mils pénicillaires et sorghos en Afrique de l’Ouest – Niger- Campagne 1976. Report

  • FAO (2008) FAOSTAT database. Available from http://www.fao.org/

  • Figliuolo G, Mazzeo M, Greco I (2007) Temporal variation of diversity in Italian durum wheat germplasm. Genet Resour Crop Evol 54:615–626

    Article  Google Scholar 

  • Gao H, Williamson S, Bustamante CD (2007) An MCMC approach for the joint inference of population structure and inbreeding rate from multi-locus genotype data. Genetics 176:1635–1651

    Article  PubMed  Google Scholar 

  • Goudet J (2002) FSTAT, a program to estimate and test gene diversity and fixation indices (version 2.9.3.2). Available from http://www.unil.ch/izea/softwares/fstat.html

  • Harlan JR, de Wet JMJ (1972) Simplified classification of cultivated sorghum. Crop Sci 12:172–176

    Article  Google Scholar 

  • Hulme M (2001) Climatic perspectives on Sahelian desiccation: 1973–1998. Global Environ Change 11:19–29

    Article  Google Scholar 

  • Jarvis DI, Brown AHD, Hung Cuong P, Collado-Panduro L, Latournerie-Moreno L, Gyawali S, Tanto T, Sawadogo M, Mar I, Sadiki M, Thi-Ngoc Hue G, Arias-Reyes L, Balma D, Bajracharya J, Castillo F, Rijal D, Belqadi L, Rana R, Saidi S, Ouedraogo J, Zangre R, Rhrib K, Rhrib K, Chavez JL, Schoen D, Sthapit B, De Santis P, Fadda C, Hogdkin T (2008) A global perspective of the richness and evenness of traditional crop-variety diversity maintained by farming communities. Proc Natl Acad Sci USA 105:5326–5331

    Article  PubMed  Google Scholar 

  • Kim J-S, Klein PE, Klein RR, Price HJ, Mullet JE, Stelly DM (2005) Chromosome identification and nomenclature of Sorghum bicolor. Genetics 169:955–965

    Article  PubMed  CAS  Google Scholar 

  • Kouressy M, Traoré S, Vaksmann M, Grum M, Maikano I, Soumaré M, Traoré PS, Bazile D, Dingkuhn M, Sidibé A (2008) Adaptation des sorghos du Mali à la variabilité climatique. Cah Agric 17(2):95–100

    Google Scholar 

  • Lacy SM, Cleveland DA, Soleri D (2006) Farmer choice of sorghum varieties in southern Mali. Hum Ecol 34(3):331–353

    Article  Google Scholar 

  • Le Clerc V, Bazante F, Baril C, Guiard J, Zhang D (2005) Assessing temporal changes in genetic diversity of maize varieties using microsatellite markers. Theor Appl Genet 100:294–302

    Article  CAS  Google Scholar 

  • Le Clerc V, Cadot V, Canadas M, Lallemand J, Guèrin D, Boulineau F (2006) Indicators to assess temporal genetic diversity in the French catalogue: no losses for maize and peas. Theor Appl Genet 113:1197–1209

    Article  PubMed  CAS  Google Scholar 

  • Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data. Available from http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php

  • Malysheva-Otto L, Ganal MW, Law JR, Reeves JC, Röder MS (2007) Temporal trends of genetic diversity in European barley cultivars (Hordeum vulgare L.). Mol Breed 20:309–322

    Article  Google Scholar 

  • Martos V, Royo C, Rharrabti Y, Garcia del Moral LF (2005) Using AFLPs to determine phylogenetic relationships and genetic erosion in durum wheat cultivars released in Italy and Spain throughout the 20th century. Fields Crop Res 91:107–111

    Article  Google Scholar 

  • Mekbib F (2007) Infra-specific folk taxonomy in sorghum (Sorghum bicolor (L.) Moench) in Ethiopia: folk nomenclature, classification and criteria. J Ethnobiol Ethnomed 3:38

    Article  PubMed  Google Scholar 

  • Mekbib F (2008) Genetic erosion of sorghum (Sorghum bicolor (L.) Moench) in the centre of diversity, Ethiopia. Genet Resour Crop Evol 55:351–364

    Article  Google Scholar 

  • Morin SR, Calibo M, Garcia-Belen M, Pham JL, Palis F (2002) Natural hazards and genetic diversity in rice. Agric Hum Values 19:133–149

    Article  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University press, New York

    Google Scholar 

  • Nersting LG, Andersen SB, Von Bothmer R, Gullord M, Jørgensen RB (2006) Morphological and molecular diversity of Nordic oat through one hundred years of breeding. Euphytica 150:327–337

    Article  Google Scholar 

  • Nicholson S (2005) On the question of the ‘‘recovery’’ of the rains in the West African Sahel. J Arid Environ 63:615–641

    Article  Google Scholar 

  • Olsson L, Eklundh L, Ardö J (2005) A recent greening of the Sahel—trends, patterns and potential causes. J Arid Environ 63:556–566

    Article  Google Scholar 

  • Ostrowski MF, David J, Santoni S, McKhann H, Reboud X, Le Corre V, Camilleri C, Brunel D, Bouchez D, Faure B, Bataillon T (2006) Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium. Mol Ecol 15:1507–1517

    Article  PubMed  CAS  Google Scholar 

  • Peroni N, Hanazaki N (2002) Current and lost diversity of cultivated varieties, especially cassava, under swidden cultivation systems in the Brazilian Atlantic Forest. Agric Ecosyst Environ 92:171–183

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Pritchard JK, Wen W (2002) Documentation for Structure software: version 2 (http://pritch.bsd.uchicago.edu)

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

    PubMed  CAS  Google Scholar 

  • Rana RB, Garforth C, Stapith B, Jarvis D (2007) Influence of socio-economic and cultural factors in rice varietal diversity management on-farm in Nepal. Agric Hum Values 24:461–472

    Article  Google Scholar 

  • Reif JC, Hamrit S, Heckenberger M, Schipprack W, Maurer HP, Bohn M, Melchinger AE (2005) Trends in genetic diversity among European maize cultivars and their parental components during the past 50 years. Theor Appl Genet 111:838–845

    Article  PubMed  Google Scholar 

  • Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldmann MW (2002) Genetic structure of human populations. Science 298:2381–2385

    Article  PubMed  CAS  Google Scholar 

  • Roussel V, Koenig J, Beckert M, Balfourier F (2004) Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theor Appl Genet 108:920–930

    Article  PubMed  CAS  Google Scholar 

  • Roussel V, Leisova L, Exbrayat F, Stehno Z, Balfourier F (2005) SSR allelic diversity changes in 480 European bread wheat varieties released from 1840 to 2000. Theor Appl Genet 111:162–170

    Article  PubMed  CAS  Google Scholar 

  • Snowden JD (1936) The cultivated races of sorghum. Adlard, London, pp 1–274

    Google Scholar 

  • Teklu Y, Hammer K (2006) Farmers’ perception and genetic erosion of tetraploid wheat landraces in Ethiopia. Genet Resour Crop Evol 53:1099–1113

    Article  Google Scholar 

  • Teshome A, Patterson D, Asfew Z, Torrance JK, Arnason JT (2007) Changes of Sorghum bicolor landrace diversity and farmers’ selection criteria over space and time, Ethiopia. Genet Resour Crop Evol 54:1219–1233

    Article  Google Scholar 

  • Thomas DSG, Twyman C, Osbahr H, Hewitson B (2007) Adaptation to climate changes and variability: farmer responses to intra-seasonal precipitation trends in South Africa. Clim Change 83:301–322

    Article  Google Scholar 

  • Traoré SB, Reyniers FN, Vaksmann M, Koné B, Sidibé A, Yoroté A, Yattara K, Kouressy M (2000) Adaptation à la sècheresse des écotypes locaux de sorghos au Mali. Sècheresse 11:227–237

    Google Scholar 

  • Van Etten J (2006) Changes in farmers’ knowledge of maize diversity in highland Guatemala, 1927/37–2004. J Ethnobiol Ethnomed 2:12

    Article  PubMed  Google Scholar 

  • Vigouroux Y, Jaqueth JS, Matsuoka Y, Smith OS, Beavis WD, Smith JS, Doebley J (2002) Rate and pattern of mutation at microsatellite loci in maize. Mol Biol Evol 19(8):1251–1260

    PubMed  CAS  Google Scholar 

  • Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith JSC, Jaqueth J, Smith OS, Doebley J (2005) An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169:1617–1630

    Article  PubMed  CAS  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  • Willemen L, Scheldeman X, Soto Cabellos V, Rafael Salazar S, Guarino L (2007) Spatial patterns of diversity and genetic erosion of traditional cassava (Manihot esculenta Crantz) in the Peruvian Amazon: an evaluation of socio-economic and environmental indicators. Genet Resour Crop Evol 54:1599–1612

    Article  Google Scholar 

Download references

Acknowledgments

We are grateful to the farmers from Niger who contributed to this study by providing seed samples and information on their varieties. We also thank the different people who participated in the 2003 collection, and particularly Djibo Moussa, Moussa Tidjani, and Hassane Yahaya Bissala. This work was supported by Institut Français de la Biodiversité (IFB). Part of this work was carried out using the resources of the Computational Biology Service Unit from Cornell University.

Author information

Authors and Affiliations

  1. CIRAD, UMR DAP, Avenue Agropolis, TA-A 96/03, 34398, Montpellier, France

    Monique Deu, F. Sagnard & C. Calatayud

  2. International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), P.O. Box 39063, Nairobi, Kenya

    F. Sagnard

  3. CIRAD, UPR AIVA, 34398, Montpellier, France

    J. Chantereau

  4. Institut de Recherche pour le Développement (IRD), UMR DIAPC, Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France

    Y. Vigouroux & J. L. Pham

  5. Institut de Recherche pour le Développement (IRD), UMR DIAPC, BP 11416, Niamey, Niger

    C. Mariac & G. Bezançon

  6. Institut National de la Recherche Agronomique du Niger (INRAN), BP 429, Niamey, Niger

    I. Kapran & A. Mamadou

  7. International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), BP 12404, Niamey, Niger

    B. Gérard & J. Ndjeunga

Authors
  1. Monique Deu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. F. Sagnard
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. J. Chantereau
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. C. Calatayud
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Y. Vigouroux
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. J. L. Pham
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. C. Mariac
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. I. Kapran
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. A. Mamadou
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. B. Gérard
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. J. Ndjeunga
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. G. Bezançon
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Monique Deu.

Additional information

Communicated by H. H. Geiger.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Electronic Files 1 and 2 (DOC 64 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Deu, M., Sagnard, F., Chantereau, J. et al. Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger. Theor Appl Genet 120, 1301–1313 (2010). https://doi.org/10.1007/s00122-009-1257-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-009-1257-1

Keywords

Search

Navigation