Analysis of genetic diversity in farmers' rice varieties in Sierra Leone using morphological and AFLP® markers

Genetic Resources and Crop Evolution

Volumn 60, Issue 4, 2013, Pages 1237-1250

  Chakanda, Robert ^a   van Treuren, Rob ^a   Visser, Bert ^a   van den Berg, Ronald ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

AFLP; Genetic variation; Landraces; Oryza; Rice; Sierra Leone; Variety names

Indexed keywords

CULTIVAR; CULTIVATION; GENETIC MARKER; GENETIC RESOURCE; GENETIC VARIATION; MORPHOLOGY; NOMENCLATURE; RICE;

GUINEA; SIERRA LEONE;

ORYZA; ORYZA GLABERRIMA; ORYZA SATIVA;

EID: 84876873752     PISSN: 09259864     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10722-012-9914-7     Document Type: Article

References (48)

1. Almekinders C (2001) Management of crop genetic diversity at the community level. Deutsche Gesellschaft für Technische Zusammenarbeit (GTZ) GmbH. Eschborn, Germany.
2. Appa Rao S, Bounphanousay C, Schiller JM, Alcantara AP, Jackson MT (2002) Naming of traditional rice varieties by farmers in the Lao PDR. Genet Resour Crop Evol 49: 83-88.
3. Barry MB, Pham JL, Noyer JL, Billot C, Courtois B, Ahmadi N (2007) Genetic diversity of the two cultivated rice species (O. sativa & O. glaberrima) in Maritime Guinea. Evidence for interspecific recombination. Euphytica 154: 127-137.
4. Bertuso AR, van Treuren R, van Eeuwijk FA, Visser L (2005) Characterisation of red rice Oryza sativa varieties developed under on-farm dynamic management on Bohol, Philippines. FAO/IPGRI Plant Genet Resour Newsl 142: 1-5.
5. Bezançon G, Diallo S (2006) Oryza glaberrima Steud. Plant resources of tropical Africa (PROTA). Wageningen, The Netherlands. http://database. prota. org/search. htm. Accessed 20 April 2009.
6. Bos D, Grigoras I, Ndiaye A (2006) Land cover and avian biodiversity in rice fields and mangroves of West Africa. A& W-report 824. Altenburg & Wymenga, ecological research, Veenwouden. Wetlands International, Dakar.
7. Brown WL (1983) Genetic diversity and genetic vulnerability-an appraisal. Econ Bot 37: 4-12.
8. Busso CS, Devos KM, Ross G, Mortimore M, Adams WM, Ambrose MJ, Alldrick S, Gale MD (2000) Genetic diversity within and among landraces of Pearl Millet (Pennisetum glaucum) under farmer management in West Africa. Genet Resour Crop Evol 47: 561-568.
9. Caicedo AL, Caitan E, Duque MC, Chica OT, Debouck DG, Tohme J (1999) AFLP fingerprinting of Phaseolus lunatus L. and related wild species form South America. Crop Sci 39: 1497-1509.
10. Clawson DL (1985) Harvest security and intraspecific diversity in traditional tropical agriculture. Econ Bot 39: 56-67.
11. Darwin CR (1859) On the origin of species by means of natural selection, 1st edn. John Murray, London, UK.
12. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
13. Federer WT, Reynolds M, Crossa J (2001) Combining results from augmented designs over sites. Agron J 93: 389-395.
14. Fulton TM, Chunwongse J, Tanksley SD (1995) Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol Biol Rep 13: 207-209.
15. Geerlings H, van Oeveren AJ, Pot JE, Jansen RC, van Schaik RV (2003) AFLP Quantar Pro: codominant and expression analysis software. http://www. keygene-products. com.
16. Havinden MA (1970) The history of crop cultivation in West Africa: a bibliographical guide. The Econ Hist Rev 23: 532-555.
17. IRRI (1980) Descriptors for rice Oryza sativa (L). International Rice Research Institute, Los Banos.
18. Jusu MS (1999) Management of genetic variability in rice (Oryza sativa L. and O. glaberrima Steud.) by breeders and farmers in Sierra Leone. PhD thesis. Wageningen University and Research Centre, Wageningen, The Netherlands.
19. Kamara SI, Jackson IJ (1997) Identification of agro-hydrologic regions in Sierra Leone. Theor Appl Climatol 57: 49-63.
20. Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35: 25-34.
21. Ko HL, Cowan DC, Henry RJ, Graham GC, Blakeney AB, Lewin LG (1994) Random amplified polymorphic DNA analysis of Australian rice (Oryza sativa L.) varieties. Euphytica 80: 179-189.
22. Longley C, Jusu MS (1999) Farmers' management of genetic variability in rice. ILEIA Newsl 15(3-4): 16-17.
23. Longley C, Richards P (1993) Selection strategies of rice farmers in Sierra Leone. In: De Boef W, Amanor K, Wellard K, Bebbington A (eds) Cultivating knowledge: genetic diversity, farmer experimentation and crop research. Intermediate Technology Publications, London, UK, pp 51-57.
24. Mackill DJ, Zhang Z, Redoña ED, Colowit PM (1996) Level of polymorphism and genetic mapping of AFLP markers in rice. Genome 39: 969-977.
25. Maughan PJ, Saghai Maroof MA, Buss GR, Huestis GM (1996) Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance and near-isogenetic line analysis. Theor Appl Genet 93: 392-401.
26. McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76: 815-829.
27. Meertens HCC (2006) Oryza sativa L. plant resources of tropical africa (PROTA), Wageningen, The Netherlands. http://database. prota. org/search. htm. Accessed 20 April 2009.
28. Miézan K, Ghesquière A (1986) Genetic structure of African traditional rice cultivars. In: Kusk G (ed) Rice genetics. International Rice Research Institute, Los Banos, pp 91-107.
29. Nuijten E, Almekinders CJM (2008) Mechanisms explaining variety naming by farmers and name consistency of rice varieties in the Gambia. Econ Bot 62: 148-160.
30. Nuijten E, van Treuren R (2007) Spatial and temporal dynamics in genetic diversity in upland rice and late millet (Pennisetum glaucum [L.] R. Br.) in The Gambia. Genet Resour Crop Evol 54: 989-1009.
31. Nuijten E, van Treuren R, Struik PC, Mokuwa A, Okry F, Teeken B, Richards P (2009) Evidence for the emergence of new rice types of interspecific hybrid origin in West African farmers' fields. PLoS ONE 4(10): e7335. doi: 10. 1371/journal. pone. 0007335.
32. Oka HI (1988) Origin of cultivated rice. Japan Scientific Societies Press, Tokyo.
33. Richards P (1986) Coping with hunger. Hazard and experiment in a West African rice farming system. UCL Press, London.
34. Rohlf FJ (2005) NTSYS-pc: numerical taxonomy and multivariate analysis system. Version 2. 2. Exeter Software. Setauket, New York.
35. RRS (1980) An overview of a decade of research activities conducted at the rice research station. Ministry of Agriculture, Fisheries and Forestry, Rokupr.
36. RRS (1991) Rice research station annual report. Rice Research Station, Ministry of Agriculture and Food Security, Rokupr.
37. RRS (1993) Rice research station annual report. Freetown, Sierra Leone.
38. RRS (1998) Annual report-research activities and technology development at Rokupr. Rice Research Station, Rokupr.
39. Sarla N, Mallikarjuna Swamy BP (2005) Oryza glaberrima: a source for the improvement of Oryza sativa. Curr Sci 89: 955-963.
40. Teshome A, Fahrig L, Torrance JK, Lambert JD, Arnason JT, Baum BR (1999) Maintenance of sorghum (Sorghum bicolor, Poaceae) landrace diversity by farmers' selection in Ethiopia. Econ Bot 53: 79-88.
41. Tin HQ, Berg T, Bjørnstad A (2001) Diversity and adaptation in rice varieties under static (ex situ) and dynamic (in situ) management. Euphytica 122: 491-502.
42. Tin HQ, De NN, van Treuren R, Visser L (2006) Analysis of spatial and temporal variation of the farmer's rice variety Tai Nhuyen under changing cropping systems in the Mekong Delta, Vietnam. Plant Genet Resour Newsl 146: 49-55.
43. van de Peer Y, De Wachter R (1994) TREECON for windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10: 569-570.
44. Vos P, Hogers R, Bleeker M, Rijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23: 4407-4414.
45. Xie JH, Zapata-Arias FJ, Shen M, Afza R (2000) Salinity tolerant performance and genetic diversity of four rice varieties. Euphytica 116: 105-110.
46. Yoon MS, Doi K, Kaga A, Tomooka N, Vaughan DA (2000) Analysis of the genetic diversity in the Vigna minima complex and related species in East Asia. J Plant Res 113: 375-386.
47. Zhu J, Gale MD, Quarrie S, Jackson MT, Bryan GJ (1998) AFLP markers for the study of rice biodiversity. Theor Appl Genet 96: 602-611.
48. Zhu Y, Chen H, Fan J, Wang Y, Li Y, Chen J, Fan J, Yang S, Hu L, Leung H, Mew TM, Teng PS, Wang Z, Mundt CC (2000) Genetic diversity and disease control in rice. Nature 406: 718-722.