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

Theoretical and Applied Genetics

Volumn 116, Issue 7, 2008, Pages 903-913

  Deu, M ^a   Sagnard, F ^a,b   Chantereau, J ^a   Calatayud, C ^a   Herault D ^a   Mariac, C ^c   Pham, J L ^c   Vigouroux, Y ^d   Kapran, I ^e   Traore, P S ^b   Mamadou, A ^e   Gerard, B ^f   Ndjeunga, J ^f   Bezancon G ^d  

^a CIRAD   (France)

^b INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (Mali)

^c INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^d Institut de Recherche pour le Développement IRD UMR DIAPC   (Niger)

^e Institut National de Recherches Agronomiques du Niger   (Niger)

^f ICRISAT Sahelian Center   (Niger)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; GENETIC ENGINEERING;

GENETIC DIVERSITY; MICROSATELLITE MARKERS;

PLANTS (BOTANY);

PLANT DNA;

ARTICLE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; NIGER; PHYLOGENY; POPULATION GENETICS; SORGHUM; VARIABLE NUMBER OF TANDEM REPEAT;

DNA, PLANT; GENETICS, POPULATION; GEOGRAPHY; MINISATELLITE REPEATS; NIGER; PHYLOGENY; SORGHUM; VARIATION (GENETICS);

EID: 42149123797     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-008-0721-7     Document Type: Article

References (61)

1. Aldrich PR, Doebley J, Schertz KF, Stec A (1992) Patterns of allozyme variation in cultivated and wild Sorghum bicolor. Theor Appl Genet 85:451-460
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 47:471-482
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 135:1-12
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 114:237-248
5. Bataillon TM, David JL, Schoen DJ (1996) Neutral genetic markers and conservation genetics: simulated germplasm collection. Genetics 144:409-417
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 43:988-1002
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 93:190-198
10. Brush SB (1995) In situ conservation of landraces in centers of crop diversity: implications of germplasm conservation and utilization. Crop Sci 35:46-354
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 3-26
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 111:23-30
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 65-74
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 90:787-796
15. de Oliveira AC, Richter T, Bennetzen JL (1996) Regional and racial specificities in sorghum germplasm assessed with DNA markers. Genome 39:579-587
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 88:838-844
17. Deu M, Hamon P, Chantereau J, Dufour P, D'Hont A, Lanaud C (1995) Mitochondrial DNA diversity in wild and cultivated sorghum. Genome 38:635-645
18. Deu M, Rattunde F, Chantereau J (2006) A global view of genetic diversity in cultivated sorghums using a core collection. Genome 49:168-180
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 99:157-163
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 100:918-925
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 138:205-212
22. Doggett H (1988) Sorghum, 2nd edn. Longman Scientific and Technical, London, UK
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 111:399-409
24. Ghebru B, Schmidt RJ, Bennetzen JL (2002) Genetic diversity of Eritrean sorghum landraces assessed with simple sequence repeat (SSR) markers. Theor Appl Genet 105:229-236
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 101:197-202
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 2:618-620
28. Harlan JR, de Wet JMJ (1972) Simplified classification of cultivated sorghum. Crop Sci 12:172-176
29. Hulme M (2001) Climatic perspectives on Sahelian desiccation: 1973-1998. Global Environ Change 11:19-29
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 86:1032-1039
31. Kim J-S, Klein PE, Klein RR, Price HJ, Mullet JE, Stelly DM (2005) Chromosome identification and nomenclature of Sorghum bicolor. Genetics 169:955-965
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 114:49-58
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 99:6080-6084
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 49:31-46
35. Menkir A, Goldsbrough P, Ejeta G (1997) RAPD based assessment of genetic diversity in cultivated races of sorghum. Crop Sci 37:564-569
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 48:483-499
37. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590
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 50:149-156
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 231-240
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 51:471-478
42. Perales HR, Benz BF, Brush SB (2005) Maize diversity and ethnolinguistic diversity in Chiapas, Mexico. Proc Natl Acad Sci USA 102:949-954
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 31-63
44. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844-855
45. Reenberg A (2001) Agricultural land use pattern dynamics in the Sudan-Sahel towards an event-driven framework. Land Use Policy 18:309-319
46. Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res 67:175-185
47. Rousset F (2000) Genetic differentiation between individuals. J Evol Biol 13:58-62
48. Scheuring JF, Konate IM., Toure S (1980) The Malian sorghum collection. Sorghums Newsl 23:33635
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 105:912-920
50. Smouse PE, Peakall R (1999) Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity 82:561-573
51. Snowden JD (1936) The cultivated races of sorghum. Adlard, London, UK, pp 1-274
52. Sokal RR, Wartenberg DE (1983) A test of spatial autocorrelation analysis using an isolation-by-distance model. Genetics 105:219-237
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 95:66-72
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 p
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 53:79-88
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 106:1316-1325
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 43:1680-1689
58. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370
59. Wezel A, Boecker R (1998) Fallow plant communities and site characteristics in semi-arid Niger, West Africa. J Arid Environ 40:269-280
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 Coast
61. Zongo JD, Gouyon PH, Sarr A, Sandmeier M (2005) Genetic diversity and phylogenic relations among Sahelian sorghums accessions. Genet Resour Crop Evol 52:869-878