On-farm dynamic management of genetic diversity: The impact of seed diffusions and seed saving practices on a population-variety of bread wheat

Evolutionary Applications

Volumn 5, Issue 8, 2012, Pages 779-795

  Thomas, Mathieu ^a   Demeulenaere, Elise ^b   Dawson, Julie C ^a   Khan, Abdul Rehman ^a   Galic, Nathalie ^a   Jouanne Pin, Sophie ^a   Remoue, Carine ^a   Bonneuil, Christophe ^b   Goldringer, Isabelle ^a  

^a INRA Institut National de la Recherche Agronomique   (France)

^b CNRS   (France)

Author keywords

in situ conservation; Interdisciplinary study; Network theory; Seed exchange network

Indexed keywords

EID: 84863631429     PISSN: 17524563     EISSN: 17524571     Source Type: Journal    
DOI: 10.1111/j.1752-4571.2012.00257.x     Document Type: Article

References (84)

1. Adamcsek, B., G. Palla, I. J. Farkas, I. Derenyi, and T. Vicsek. 2006. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics22:1021-1023.
2. Almekinders, C. J. M., N. P. Louwaars, and G. H. Bruijn. 1994. Local seed systems and their importance for an improved seed supply in developing countries. Euphytica78:207-216.
3. Alvarez, N., E. Garine, C. Khasah, E. Dounias, M. Hossaert-McKey, and D. McKey. 2005. Farmers' practices, metapopulation dynamics, and conservation of agricultural biodiversity on-farm: a case study of sorghum among the Duupa in sub-sahelian Cameroon. Biological Conservation121:533-543.
4. Aw-Hassan, A., A. Mazid, and H. Salahieh. 2008. The role of informal farmer-to-farmer seed distribution in diffusion of new barley varieties in Syria. Experimental Agriculture44:413-431.
5. Badstue, L. B., M. R. Bellon, J. Berthaud, A. Ramirez, D. Flores, and X. Juarez. 2007. The dynamics of farmers' maize seed supply practices in the central valleys of Oaxaca, Mexico. World Development35:1579-1593.
6. Barnaud, A., H. I. Joly, D. McKey, M. Deu, C. Khasah, S. Monné, and E. Garine. 2008. Management of sorghum (Sorghum bicolor) genetic resources among Duupa farmers (northern Cameroon). Cahiers Agricultures17:178-182.
7. Batagelj, V., and A. Mrvar. 2003. Pajek - analysis and visualization of large networks. In Jünger, M., Mutzel, P., ed. Graph Drawing Software, pp. 77-103. Springer, Berlin, Germany.
8. Belkhir, K., P. Borsa, L. Chikhi, N. Raufaste, and F. Bonhomme. 2000. GENETIX 4.02, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France.
9. Bonneuil, C. 2008. Producing identity, industrializing purity: elements for a cultural history of genetics. In S. Müller-Wille, and H.-J. Rheinberger, eds. A Cultural History of Heredity, pp. 81-110. MPIWGM, Berlin, Germany.
10. Bonneuil, C., and E. Demeulenaere. 2007. Vers une génétique de pair à pair? L'émergence de la sélection participative. In F. Charvolin, A. Micoud, and L. K. Nyhart, eds. Des sciences citoyennes? La question de l'amateur dans les sciences naturalistes, pp. 122-147. Edition de l'Aube, La Tour-d'aigues, France.
11. Bonneuil, C., E. Demeulenaere, F. Thomas, P.-B. Joly, G. Allaire, and I. Goldringer. 2006. Innover autrement? La recherche face à l'avènement d'un nouveau régime de production et de régulation des savoirs en génétique végétale. Quelles variétés et semences pour des agricultures paysannes durables?Dossiers de l'environnement de l'INRA30:29-51.
12. Boutin-Ganache, I., M. Raposo, M. Raymond, and C. F. Deschepper. 2001. M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. BioTechniques31:24-28.
13. Brétignière, L. 1912. Essai sur la répartition des variétés de blés cultivés en France. 10 p, Renouard, Paris, France.
14. Bustarret, J. 1944. Variétés et variations. Annales agronomiques14:336-362.
15. Carpenter, D. 2005. The in situ conservation of rice plant genetic diversity: a case study from a Philippine Barangay. Agriculture and Human Values22:421-434.
16. Delaunay, S., R. P. Tescar, A. Oualbego, K. vom Brocke, and J. Lançon. 2008. Growing cotton does not disrupt traditional sorghum seed exchange. Cahiers Agricultures17:189-194.
17. Delêtre, M., D. B. McKey, and T. R. Hodkinson. 2011. Marriage exchanges, seed exchanges, and the dynamics of manioc diversity. Proceedings of the National Academy of Sciences108:18249-18254.
18. Demeulenaere, E., and C. Bonneuil. 2012. Des semences en partage - construction sociale et identitaire d'un collectif "paysan" autour de pratiques semencières alternatives. Techniques and Cultures. In press.
19. Diamond, J. 2002. Evolution, consequences and future of plant and animal domestication. Nature418:700-707.
20. Dyer, R. J. 2007. The evolution of genetic topologies. Theoretical Population Biology71:71-79.
21. Dyer, R. J. 2009. GeneticStudio: a suite of programs for spatial analysis of genetic-marker data. Molecular Ecology Resources9:110-113.
22. Dyer, R. J., and J. D. Nason. 2004. Population graphs: the graph theoretic shape of genetic structure. Molecular Ecology13:1713-1727.
23. Dyer, G. A., and J. E. Taylor. 2008. A crop population perspective on maize seed systems in Mexico. Proceedings of the National Academy of Sciences of the United States of America105:470-475.
24. Dyer, R. J., J. D. Nason, and R. C. Garrick. 2010. Landscape modelling of gene flow: improved power using conditional genetic distance derived from the topology of population networks. Molecular Ecology19:3746-3759.
25. Elias, M., O. Panaud, and T. Robert. 2000. Assessment of genetic variability in a traditional cassava (Manihot esculenta Crantz) farming system, using AFLP markers. Heredity85:219-230.
26. Elias, M., L. Penet, P. Vindry, D. McKey, O. Panaud, and T. Robert. 2001. Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system. Molecular Ecology10:1895-1907.
27. Emperaire, L., P. de Robert, J. Santilli, L. Eloy, L. van Velthem, E. Katz, C. M. Lopes et al.2008. Diversité agricole et patrimoine dans le moyen Rio Negro (Amazonie brésilienne). Actes du BRG7:139-153.
28. Enjalbert, J., and J. L. David. 2000. Inferring recent outcrossing rates using multilocus individual heterozygosity: application to evolving wheat populations. Genetics156:1973-1982.
29. Enjalbert, J., I. Goldringer, J. L. David, and P. Brabant. 1998. The relevance of outcrossing for the dynamic management of genetic resources in predominantly selfing Triticum aestivum L. (bread wheat). Genetics, Selection, Evolution30:S197.
30. Excoffier, L., and H. E. L. Lischer. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources10:564-567.
31. Excoffier, L., P. E. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics131:479-491.
32. Farkas, I., D. Ábel, G. Palla, and T. Vicsek. 2007. Weighted network modules. New Journal of Physics9:180.
33. Fu, D., P. Szucs, L. Yan, M. Helguera, J. S. Skinner, J. von Zitzewitz, P. M. Hayes et al.2005. Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Molecular Genetics and Genomics273:54-65.
34. Gao, H., S. Williamson, and C. D. Bustamante. 2007. A Markov Chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics176:1635-1651.
35. Garrick, R., P. Sunnucks, and R. J. Dyer. 2010. Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evolutionary Biology10:118.
36. Goldringer, I., and T. Bataillon. 2004. On the distribution of temporal variations in allele frequency: consequences for the estimation of effective population size and the detection of loci undergoing selection. Genetics168:563-568.
37. Goldringer, I., J. Enjalbert, J. David, S. Paillard, J.-L. Pham, and P. Brabant. 2001. Dynamic management of genetic resources: a 13-year experiment on wheat. In H. D. Cooper, C. Spillane, and T. Hodgkin, eds. Broadening the Genetic Base of Crop Production, pp. 452. CABI Publishing, Rome, Italy.
38. Goldringer, I., C. Prouin, M. Rousset, N. Galic, and I. Bonnin. 2006. Rapid differentiation of experimental populations of wheat for heading time in response to local climatic conditions. Annals of Botany98:805-817.
39. Guyomarc'h, H., P. Sourdille, G. Charmet, K. Edwards, and M. Bernard. 2002. Characterisation of polymorphic microsatellite markers from Aegilops tauschii and transferability to the D-genome of bread wheat. Theoretical and Applied Genetics104:1164-1172.
40. Haudry, A., A. Cenci, C. Ravel, T. Bataillon, D. Brunel, C. Poncet, I. Hochu et al.2007. Grinding up wheat: a massive loss of nucleotide diversity since domestication. Molecular Biology and Evolution24:1506-1517.
41. Hodgkin, T., J. Rana, J. Tuxill, D. Balma, I. Mar, D. Karamura, R. Valdivia et al.2007. Seed systems and crop genetic diversity in agroecosystems. In D. Jarvis, C. Padoch, and H. D. Cooper, eds. Managing Biodiversity in Agricultural Ecosystems, pp. 77-116. CABI Publishing, Rome, Italy.
42. Ingvarsson, P. K., and B. E. Giles. 1999. Kin-structured colonization and small-scale genetic differentiation in Silene dioica. Evolution53:605-611.
43. Kamada, T., and S. Kawai. 1989. An algorithm for drawing general undirected graphs. Information Processing Letters31:7-15.
44. Louette, D., A. Charrier, and J. Berthaud. 1997. In situ conservation of maize in Mexico: genetic diversity and maize seed management in a traditional community. Economic Botany51:20-38.
45. Matsuoka, Y., Y. Vigouroux, M. M. Goodman, G. J. Sanchez, E. Buckler, and J. Doebley. 2002. A single domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the National Academy of Sciences99:6080-6084.
46. McGuire, S. J. 2007. Vulnerability in farmer seed systems: farmer practices for coping with seed insecurity for sorghum in Eastern Ethiopia. Economic Botany61:211-222.
47. McGuire, S. J. 2008. Securing access to seed: social relations and sorghum seed exchange in Eastern Ethiopia. Human Ecology36:217-229.
48. Negri, V., N. Maxted, and M. Veteläinen. 2009. European landrace conservation: an introduction. In M. Veteläinene, V. Negri, and N. Maxted, eds. European Landraces: On-Farm Conservation, Management and Use, pp. 1-22. Bioversity Technical Bulletin 15, Bioversity International, Rome, Italy.
49. Nei, M. 1972. Genetic distance between populations. The American Naturalist106:283-292.
50. Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics89:583-590.
51. Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, 512p, New york.
52. Perales, H. R., S. Brush, and C. Qualset. 2003. Dynamic management of maize landraces in Central Mexico. Economic Botany57:21-34.
53. Pressoir, G., and J. Berthaud. 2003. Population structure and strong divergent selection shape phenotypic diversification in maize landraces. Heredity92:95-101.
54. Pujol, B., P. David, and D. McKey. 2005a. Microevolution in agricultural environments: how a traditional Amerindian farming practice favours heterozygosity in cassava (Manihot esculenta Crantz, Euphorbiaceae). Ecology Letters8:138-147.
55. Pujol, B., G. Mühlen, N. Garwood, Y. Horoszowski, E. J. P. Douzery, and D. McKey. 2005b. Evolution under domestication: contrasting functional morphology of seedlings in domesticated cassava and its closest wild relatives. New Phytologist166:305-318.
56. Purugganan, M. D., and D. Q. Fuller. 2009. The nature of selection during plant domestication. Nature457:843-848.
57. R Development Core Team. 2005. R: A Language and Environment for Statistical Computing. R Development Core Team, Vienna, Austria.
58. Remington, D. L., and M. D. Purugganan. 2003. Candidate genes, quantitative trait loci, and functional trait evolution in plants. International Journal of Plant Sciences164:S7-S20.
59. Rhoné, B., R. Vitalis, I. Goldringer, and I. Bonnin. 2010. Evolution of flowering time in experimental wheat populations: a comprehensive approach to detect genetic signatures of natural selection. Evolution64:2110-2125.
60. Rhoné, B., C. Remoué, N. Galic, I. Goldringer, and I. Bonnin. 2008. Insight into the genetic bases of climatic adaptation in experimentally evolving wheat populations. Molecular Ecology17:930-943.
61. Rice, E., M. Smale, and J.-L. Blanco. 1998. Farmers' use of improved seed selection practices in Mexican maize: evidence and issues from the Sierra de Santa Marta. World Development26:1625-1640.
62. Röder, M. S., V. Korzun, K. Wendehake, J. Plaschke, M. H. Tixier, P. Leroy, and M. W. Ganal. 1998. A microsatellite map of wheat. Genetics149:2007-2023.
63. Roussel, V., J. Koenig, M. Beckert, and F. Balfourier. 2004. Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theoretical and Applied Genetics108:920-930.
64. Rousset, M., I. Bonnin, C. Remoué, M. Falque, B. Rhoné, J.-B. Veyrieras, D. Madur et al.2011. Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics123:907-926.
65. Rozenfeld, A. F., S. Arnaud-Haond, E. Hernández-García, V. M. Eguíluz, E. A. Serrão, and C. M. Duarte. 2008. Network analysis identifies weak and strong links in a metapopulation system. Proceedings of the National Academy of Sciences of the United States of America105:18824-18829.
66. Sherman, J. D., L. Yan, L. Talbert, and J. Dubcovsky. 2004. A PCR marker for growth habit in common wheat based on allelic variation at the gene. Crop Science44:1832.
67. Siol, M., J. M. Prosperi, I. Bonnin, and J. Ronfort. 2008. How multilocus genotypic pattern helps to understand the history of selfing populations: a case study in Medicago truncatula. Heredity100:517-525.
68. Slatkin, M. 1977. Gene flow and genetic drift in a species subject to frequent local extinctions. Theoretical Population Biology12:253-262.
69. Smale, M., A. Aguirre, M. R. Bellon, J. Mendoza, and I. M. Rosas. 1999. Farmer management of maize diversity in the Central Valleys of Oaxaca, Mexico. CIMMYT/INIFAP 1998 baseline socioeconomic survey.
70. Somers, D., P. Isaac, and K. Edwards. 2004. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics109:1105-1114.
71. Stephens, M., N. J. Smith, and P. Donnelly. 2001. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics68:978-989.
72. Subedi, A., D. Singh, P. Shrestha, S. R. Subedi, and B. R. Sthapit. 2004. Stability of farmers' networks and nodal farmers in terai and hill villages of Nepal: implications for agrobiodiversity management on-farm. In B. R. Sthapit, M. P. Upadhyay, P. K. Shrestha, and D. I. Jarvis, eds. On-Farm Conservation of Agricultural Biodiversity in Nepal. Volume II. Managing Diversity and Promoting its Benefits, pp. 36. Proceedings of the Second National Workshop., Nagarkot, Nepal.
73. Thomas, M., J. C. Dawson, I. Goldringer, and C. Bonneuil. 2011. Seed exchanges, a key to analyze crop diversity dynamics in farmer-led on-farm conservation. Genetic Resources and Crop Evolution58:321-338.
74. Vilmorin-Andrieux Companie. 1880. Les meilleurs blés - Description et culture des principales variétés de froments d'hiver et de printemps. 175 p, Vilmorin-Andrieux Companie, Paris, France.
75. Vitalis, R., K. Dawson, and P. Boursot. 2001. Interpretation of variation across marker loci as evidence of selection. Genetics158:1811-1823.
76. Waples, R. S. 1989. A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics121:379-391.
77. Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution38:1358-1370.
78. Whitlock, M. C., and D. E. McCauley. 1990. Some population genetic consequences of colony formation and extinction: genetic correlations within founding groups. Evolution44:1717-1724.
79. Whittaker, J. 1990. Graphical Methods in Applied Multivariate Statistics. J. Wiley and Son, New York.
80. Wright, S. 1951. The genetic structure of populations. Annals of Eugenics15:323-354.
81. Yan, L., A. Loukoianov, G. Tranquilli, M. Helguera, T. Fahima, and J. Dubcovsky. 2003. Positional cloning of the wheat vernalization gene VRN1. Proceedings of the National Academy of Sciences100:6263-6268.
82. Yan, L., M. Helguera, K. Kato, S. Fukuyama, J. Sherman, and J. Dubcovsky. 2004. Allelic variation at the VRN-1 promoter region in polyploid wheat. Theoretical and Applied Genetics109:1677-1686.
83. Zeven, A. C. 1999. The traditional inexplicable replacement of seed and seed ware of landraces and cultivars: a review. Euphytica110:181-191.
84. Zhang, P., S. Dreisigacker, A. Buerkert, S. Alkhanjari, A. E. Melchinger, and M. L. Warburton. 2006. Genetic diversity and relationships of wheat landraces from Oman investigated with SSR markers. Genetic Resources and Crop Evolution53:1351-1360.