Advertisement

Indicators of Genetic Diversity, Genetic Erosion, and Genetic Vulnerability for Plant Genetic Resources

  • Anthony H. D. BrownEmail author
  • Toby Hodgkin
Chapter
Part of the Sustainable Development and Biodiversity book series (SDEB, volume 7)

Abstract

This chapter surveys the conceptual basis of indicators of genetic diversity, genetic erosion, and genetic vulnerability. These are summary measures of genetic diversity in cultivated plants and their wild relatives that guide decisions, monitor progress, and warn of emerging issues of genetic resources for resilient agricultural production. Such indicators measure the genetic diversity currently present in agricultural populations on farm and held in germplasm collections, and aim to detect genetic erosion, or serious loss of diversity in time, and to warn of vulnerability due to adverse deployment of genetic diversity in space. While diversity itself encompasses many concepts, richness diversity—the number of different kinds of individuals regardless of their frequencies—is the most important theme, followed by evenness diversity—how similar the frequencies of the different variants are. Many variables are plausible as indicators of diversity. The more practical are based on number of individuals or area occupied in situ and on the number of accessions and the number of genebanks ex situ. Genetic erosion is measurable as the proportion of richness of genetic diversity no longer existing in current populations, when compared with the crop a decade previously or predicted to be lost in the next decade without remedial action. Genetic vulnerability is inversely related to richness diversity that is present locally, particularly if it is known to possess adaptation to exotic or new mutant pathotypes or insect strains or environments. Census information forms the primary data. For cultivated species, these data are based on the farmer’s unit of diversity management, most often their named varieties, their number, relative frequencies and divergence over various units of spatial and temporal scale. For wild species, the analogous units of diversity are the lowest recognized (e.g. subspecies, morphological types, ecotypes). Census data should be supplemented and validated using more direct assays at the DNA level with molecular techniques in carefully constructed samples.

Keywords

Richness and evenness diversity Population sizes Sampling Varieties Subspecies Extinction probability 

Notes

Acknowledgments

The authors are grateful to the several colleagues who have read, critiqued and edited the various versions of the study on which this chapter is based, including Drs. L. Collette and S. Diulgheroff (FAO), Dr. D.R. Marshall, L. Guarino (Global Crop Diversity Trust), Dr. E. Dulloo (Bioversity International), Dr. J.-L. Pham (Institut de recherché pour le développement [IRD]), Paul Neate and William Nuako Bandoh CSIR Forestry Research Institute, Ghana.

References

  1. Barry MB, Pham JL, Beavogui S, Ghesquiere A, Ahmadi N (2008) Diachronic (1979–2003) analysis of rice genetic diversity in Guinea did not reveal genetic erosion. Genet Resour Crop Evol 55:723–733CrossRefGoogle Scholar
  2. Bezancon G, Pham J-L, Deu M et al (2009) Changes in the diversity and geographic distribution of cultivated millet (Pennisetumglaucum (L.) R. Br.) and sorghum (Sorghum bicolor (L.) Moench) varieties in Niger between 1976 and 2003. Genet Resour Crop Evol 56:223–236CrossRefGoogle Scholar
  3. Bisht IS, Mehta PS, Bhandari DC (2007) Traditional crop diversity and its conservation on-farm for sustainable agricultural production in Kumaon Himalaya of Uttaranchal state: a case study. Genet Res Crop Evol 54:345–357CrossRefGoogle Scholar
  4. Bonneuil C, Goffaux R, Bonnin I, Montalent P, Hannon C, Balfourier F, Goldringer I (2012) A new integrative indicator to assess crop genetic diversity. Ecol Ind 23:280–289CrossRefGoogle Scholar
  5. Brown AHD (2008) Indicators of genetic diversity, genetic erosion and genetic vulnerability for plant genetic resources for food and agriculture. Thematic Background Study, FAO Report State of the World PGRFA, 26 pGoogle Scholar
  6. Brown AHD, Weir BS (1983) Measuring genetic variation in plant populations. In: Tanksley SD, Orton TJ (eds) Isozymes in plant genetics and breeding, part A. Elsevier, New York, pp 219–239Google Scholar
  7. Brown AHD, Hardner CM (2000) Sampling the gene pools of forest trees and ex situ conservation. In: Young A, Boyle TJB, Boshier D (eds) Forest conservation genetics principles and practices. CSIRO, Collingwood, pp 185–196Google Scholar
  8. Brown AHD, Brubaker CL (2002) Indicators for sustainable management of plant genetic resources: how well are we doing? In: Engels JMM, Ramanatha Rao V, Brown AHD, Jackson MT (eds) Managing plant genetic diversity. CABI, Wallingford, pp 249–262Google Scholar
  9. Brown AHD, Hodgkin T (2007) Measuring, managing, and maintaining crop genetic diversity on farm. In: Jarvis DI, Padoch C, Cooper HD (eds) Managing biodiversity in agricultural ecosystems. Columbia University Press, New York, pp 13–33Google Scholar
  10. Crozier RH (1997) Preserving the information content of species: genetic diversity, phylogeny and conservation worth. Annu Rev Ecol Syst 28:243–268CrossRefGoogle Scholar
  11. Deu M, Sagnard F, Chanterwau J et al (2010) Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger. Theor Appl Genet 120:1301–1313CrossRefPubMedGoogle Scholar
  12. Diulgheff S (2006) A global overview of assessing and monitoring genetic erosion of crop wild relatives and local varieties using WIEWS and other elements of the FAO global system of PGR. In: Ford-Lloyd BV, Dias SR, Bettencourt E (eds) Genetic erosion and pollution assessment methodologies. Proceedings of PGR forum workshop 5, Bioversity International, Rome, pp 6–14. Available at http://www.bioversityinternational.org/fileadmin/bioversity/publications/pdfs/1171.pdf
  13. FAO, IPGRI (1994) Genebank standards. FAO/IPGRI, RomeGoogle Scholar
  14. Figliuolo G, Mazzeo M, Greco I (2007) Temporal variation of diversity in Italian durum wheat germplasm. Genet Resour Crop Evol 54:615–626CrossRefGoogle Scholar
  15. Flor A, Bettencourt E, Arriegas PI, Dias SR (2006) European crop wild relative conservation criteria—indicators for the CWR species’ list prioritization. In: Ford-Lloyd BV, Dias SR, Bettencourt E (eds) Genetic erosion and pollution assessment methodologies. Bioversity International, Rome, pp 83–87Google Scholar
  16. Ford-Lloyd BV, Brar D, Khush GS, Jackson MT, Virk PS (2008) Genetic erosion over time of rice landrace Agrobiodiversity. Plant Genet Resour Charact Util 7:163–168CrossRefGoogle Scholar
  17. Frankel OH, Brown AHD, Burdon JJ (1995) The conservation of plant biodiversity. Cambridge University Press, CambridgeGoogle Scholar
  18. Gómez-Mendoza L, Arriaga L (2007) Modeling the effect of climate change on the distribution of oak and pine species of Mexico. Conserv Biol 21:1545–1555CrossRefPubMedGoogle Scholar
  19. Gonzalez-Orozco CE, Brown AHD, Knerr N, Miller JT, Doyle JJ (2012) Hotspots of diversity of wild Australian soybean relatives and their conservation in situ. Conserv Genet 13:1269–1281CrossRefGoogle Scholar
  20. Guarino L (1999) Approaches to measuring genetic erosion. In: Serwinski J, Faberova I (eds) Proceedings of the technical meeting on the methodology of the FAO world information and early warning system on plant genetic resources. Czech Republic Research Institute of Crop Production, Prague, Czech Republic and FAO, Rome, pp 26–28Google Scholar
  21. Hamrick JL, Godt MJW (1989) Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics, breeding, and genetic resources. Sinauer Associates Inc., Sunderland, pp 43–63Google Scholar
  22. Holden J, Peacock J, Williams T (1993) Genes, crops and the environment. Cambridge University Press, CambridgeGoogle Scholar
  23. 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 N, Arias-Reyes L, Balma D, Bajracharya J, Castillo F, Rijal D, Loubna B, Rana R, Saidi S, Ouedraogo J, Zangre R, Rhrib K, Chavez JL, Schoen D, Sthapit B, De Santis P, Fadda C, Hodgkin T (2008). A global perspective of the richness and evenness of traditional crop-variety diversity maintained by farming communities. Proc Natl Acad Sci USA 105:5326–5331Google Scholar
  24. Kombo GR, Dansi A, Loko LY, Orkwor GC, Vodouhe R, Assogba P, Magema JM (2012) Diversity of cassava (ManihotesculentaCrantz) cultivars and is management in the department of Bouenza in the Republic of Conga. Genet Resour Crop Evol 59:1789–1803CrossRefGoogle Scholar
  25. Le Clerc V, Cadot V, Canadas M, Lallemand J, Guerin D, Boulineau F (2006) Indicators to assess temporal genetic diversity in the French catalogue: no loss for maize and peas. Theor Appl Genet 113:1197–1209CrossRefPubMedGoogle Scholar
  26. Magurran AE (2003) Measuring biological diversity. Blackwell, OxfordGoogle Scholar
  27. Maxted N, Guarino L (2006) Genetic erosion and genetic pollution of crop wild relatives. In: Ford-Lloyd BV, Dias SR, Bettencourt E (eds) Genetic erosion and pollution assessment methodologies. Proceedings of PGR Forum Workshop 5, Terceira Island, Autonomous Region of the Azores, Portugal, Bioversity International, Rome, pp 35–45Google Scholar
  28. Nuitjen E, van Treuren R (2007) Spatial and temporal dynamics in genetic diversity in upland rice and late millet (Pennisetumglaucum (L.) R. Br.) in the Gambia. Genet Resour Crop Evol 54:989–1009CrossRefGoogle Scholar
  29. Pfeil BE, Tindale MD, Craven LA (2001) A review of the Glycine clandestina species complex (Fabaceae: Phaseolae) reveals two new species. Aust Syst Bot 14:891–900CrossRefGoogle Scholar
  30. Sadiki M, Jarvis D, Rijal D et al (2007) Variety names: an entry point to crop genetic diversity and distribution in agroecosystems. In: Jarvis DI, Padoch C, Cooper HD (eds) Managing biodiversity in agricultural ecosystems. Columbia University Press, NY, pp 34–76Google Scholar
  31. Singh RP, Hodson DP, Jin Y, Huerta-Esopino J, Kinyua M, Wanyera R, Njua P, Ward RW (2006) Current status, likely migration and strategies to mitigate the threat to wheat production from race Ug99 (TTKS) of stem rust pathogen. In: CAB reviews: perspectives in agriculture, veterinary science, nutrition and natural resources 1, No. 054Google Scholar
  32. 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. Genet Resour Crop Evol 54:1219–1233CrossRefGoogle Scholar
  33. van de Wouw M, Kik C, van Hintum T, van Treuren R, Visser B (2009) Genetic erosion in crops: concept, research results and challenges. Plant Genet Resour Charact Util 8:1–15CrossRefGoogle Scholar
  34. van de Wouw M, van Treuren R, van Hintum T (2013) A historical analysis of diversity trends in French and Dutch letter cultivars. Euphytica 190:229–239CrossRefGoogle Scholar
  35. Vigouroux Y, Mariac C, De Mita S, Pham JL, Gerard B et al (2011) Selection for earlier flowering crop associated with climatic variations in the Sahel. PLoS ONE 6(5):e19563CrossRefPubMedPubMedCentralGoogle Scholar
  36. Willemen L, Scheldeman X, Cabellos VS et al (2007) Spatial patterns of diversity and genetic erosion of traditional cassava (Manihotesculenta Crantz) in the Peruvian Amazon: an evaluation of socio-economic and environmental indicators. Genet Resour Crop Evol 54:1599–161Google Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.National Research Collections AustraliaCSIROCanberraAustralia
  2. 2.WatsonAustralia
  3. 3.Bioversity InternationalMaccarese, RomeItaly

Personalised recommendations