Tropical Environments, Biodiversity, and the Origin of Crops

  • P. Gepts
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 1)


Plants play an important, but often insufficiently recognized. role in human societies, chiefly as providers of food, feed, and fiber, but for other uses as well such as drugs and building materials. In those cases where demand for a particular plant product exceed natural supply, humans initiated cultivation of those plants 10,000 years ago, resulting in the domestication of a limited number of species in several areas of the world, generally located in tropical and subtropical areas. Tropical and subtropical areas consist of several ecozones defined by climate, soil, and vegetation and fauna. One of the major factors distinguishing tropical ecozones is the distribution of rainfall and particularly the length of the dry season, if any. From a biological standpoint, most of biodiversity is concentrated in tropical areas. This may explain in part why the majority of crops discussed in this volume originated in either tropical or subtropical ecozones with summer rains or in the tropical ecozone with year-round rains. The fundamental contribution of genomics to plant breeding is to provide information on the genotypic basis of phenotypic variation. Based on this information, marker-assisted selection systems can be developed that can increase the efficiency at identifying agronomically useful diversity and transferring it into improved cultivars. In turn, marker-assisted selection is expected to increase the efficiency of plant breeding. To achieve this goal, however, genomic resources have to be developed, not only in model species, but especially in target species as illustrated in this volume. Having access to a diverse set of improved crops is a critical element of strategies to alleviate food insecurity and poverty, which affect disproportionately rural populations. Recently, the goal of increasing crop productivity has taken added urgency because of the combined impact of the focus on biofuels and global warming. Genomics is a crucial tool in raising crop productivity for the foreseeable future.


Food Insecurity Tropical Environment Serpentine Soil Summer Rain Global Food Security 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Altschul SF, Gish W (1996) Local alignment statistics. Computer Methods for Macromolecular Sequence Analysis, pp. 460–480Google Scholar
  2. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  3. Balick MJ, Cox PA (1996) Plants, people, and culture: the science of ethnobotany. Freeman, New YorkGoogle Scholar
  4. Barker G (2006) The agricultural revolution in prehistory. Oxford University Press, OxfordGoogle Scholar
  5. Bellwood P (2005) First farmers: the origins of agricultural societies. Blackwell, Malden, MAGoogle Scholar
  6. Brady KU, Kruckeberg AR, Bradshaw HD (2005) Evolutionary ecology of plant adaptation to serpentine soils. Annual Review of Ecology Evolution and Systematics 36:243–266CrossRefGoogle Scholar
  7. Bramwell D (2002) How many plant species are there? Plant Talk (Verified June 8, 2007)Google Scholar
  8. Carlborg Ö, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nature Rev Genetics 5:618–U614CrossRefGoogle Scholar
  9. Cassman KG (2007) Climate change, biofuels, and global food security. Environ Res Lett 2:,011002CrossRefGoogle Scholar
  10. Clarke A, Gaston KJ (2006) Climate, energy and diversity. Proc Royal Soc B-Biol Sci 273:2257–2266CrossRefGoogle Scholar
  11. Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196CrossRefGoogle Scholar
  12. Crane PR, Lidgard S (1989) Angiosperm diversification and paleolatitudinal gradients in Cretaceous floristic diversity. Science 246:675–678PubMedCrossRefGoogle Scholar
  13. Currie DJ, Paquin V (1987) Large-scale biogeographical patterns of species richness of trees. Nature 329:326–327CrossRefGoogle Scholar
  14. Davies J, Berzonsky WA, Leach GD (2006) A comparison of marker-assisted and phenotypic selection for high grain protein content in spring wheat. Euphytica 152:117–134CrossRefGoogle Scholar
  15. Estrada Lugo EIJ (1989) El Códice Florentino: su información etnobotánica. Colegio de Postgraduados, Chapingo, MéxicoGoogle Scholar
  16. Flint-Garcia SA, Thornsberry JM, Buckler IV ES (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357–374CrossRefGoogle Scholar
  17. Francia E, Tacconi G, Crosatti C, Barabaschi D, Bulgarelli D, et al. (2005) Marker assisted selection in crop plants. Plant Cell Tiss Organ Cult 82:317–342CrossRefGoogle Scholar
  18. Gepts P (2000) A phylogenetic and genomic analysis of crop germplasm: a necessary condition for its rational conservation and utilization. In: Gustafson J (ed) Proc Stadler Symp. Plenum, New York, pp. 163–181Google Scholar
  19. Gepts P (2004a) Domestication as a long-term selection experiment. Plant Breed Rev 24 (Part 2): 1–44Google Scholar
  20. Gepts P (2004b) Who owns biodiversity and how should the owners be compensated? Plant Physiol 134:1295–1307CrossRefGoogle Scholar
  21. Gepts P (2006) Plant genetic resources conservation and utilization: The accomplishments and future of a societal insurance policy. Crop Sci 46:2278–2292CrossRefGoogle Scholar
  22. Gepts P, Hancock J (2006) The future of plant breeding Crop Sci 46:1630–1634Google Scholar
  23. Goff SA, Ricke D, Lan T-H, Presting G, Wang R, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100PubMedCrossRefGoogle Scholar
  24. Govaerts R (2003) How many species of seed plants are there? - a response. Taxon 52:583–584CrossRefGoogle Scholar
  25. Gur A, Zamir D (2004) Unused natural variation can lift yield barriers in plant breeding. PLoS Biology 2:1610–1615CrossRefGoogle Scholar
  26. Hall N (2007) Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 210:1518–1525PubMedCrossRefGoogle Scholar
  27. Harlan JR (1971) Agricultural origins: centers and non-centers. Science 174:468–474PubMedCrossRefGoogle Scholar
  28. Harlan JR (1992) Crops and man, 2nd edn. American Society of Agronomy, Madison, WIGoogle Scholar
  29. Hawkins BA, Field R, Cornell HV, Currie DJ, Guegan JF, et al. (2003) Energy, water, and broad-scale geographic patterns of species richness. Ecology 84:3105–3117CrossRefGoogle Scholar
  30. Hawtin GC (2000) Genetic diversity and food security. UNESCO The Courier http://www.unesco. org/courier/2000_Johnson WC, Gepts P05/uk/doss23.htm (Verified July 13, 2007)Google Scholar
  31. Johnson WC, Gepts P (2002) The role of epistasis in controlling seed yield and other agronomic traits in an Andean x Mesoamerican cross of common bean (Phaseolus vulgaris L.). Euphytica 125:69–79CrossRefGoogle Scholar
  32. Kleidon A, Mooney HA (2000) A global distribution of biodiversity inferred from climatic constraints: results from a process-based modelling study. Global Change Biol 6:507–523CrossRefGoogle Scholar
  33. Knapp SJ (1998) Marker-assisted selection as a strategy for increasing the probability of selecting superior genotypes. Crop Sci 38:1164–1174CrossRefGoogle Scholar
  34. Lam AL, Pazin DE, Sullivan BA (2005) Control of gene expression and assembly of chromosomal subdomains by chromatin regulators with antagonistic functions. Chromosoma (Berlin) 114:242–251CrossRefGoogle Scholar
  35. Lewington A (2003) Plants for people. Transworld, LondonGoogle Scholar
  36. Lobell DB, Field CB (2007) global scale climate - crop yield relationships and the impacts of recent warming. Environmental Res Lett 2:014002CrossRefGoogle Scholar
  37. Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12:57–63PubMedCrossRefGoogle Scholar
  38. Marinelli J (ed) (2005) Plant. Dorling Kindersley, New YorkGoogle Scholar
  39. Mittelbach GG, Steiner CF, Scheiner SM, Gross KL, Reynolds HL, et al. (2001) What is the observed relationship between species richness and productivity? Ecology 82:2381–2396CrossRefGoogle Scholar
  40. Mittelbach GG, Schemske DW, Cornell HV, Allen AP, Brown JM, et al. (2007) Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol Lett 10:315–331PubMedCrossRefGoogle Scholar
  41. Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opinion Biotechnol 14:214–219CrossRefGoogle Scholar
  42. Myers N (1990) The biodiversity challenge: Expanded hot-spots analysis. The Environmentalist 10:243–256PubMedCrossRefGoogle Scholar
  43. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858PubMedCrossRefGoogle Scholar
  44. Nichols WF, Killingbeck KT, August PV (1998) The influence of geomorphological heterogeneity on biodiversity II. A landscape perspective. Conservation Biol 12:371–379Google Scholar
  45. Partel M, Laanisto L, Zobel M (2007) Contrasting plant productivity-diversity relationships across latitude: The role of evolutionary history. Ecology 88:1091–1097PubMedCrossRefGoogle Scholar
  46. Raunkiaer C (1934) The life forms of plants and statistical plant geography. Oxford University Press, OxfordGoogle Scholar
  47. Ribaut JM, Ragot M (2007) Marker-assisted selection to improve drought adaptation in maize: the backcross approach, perspectives, limitations, and alternatives. J Exp Bot 58:351–360PubMedCrossRefGoogle Scholar
  48. Rockström J, Lannerstad M, Falkenmark M (2007) Assessing the water challenge of a new green revolution in developing countries. Proc Natl Acad Sci USA 104:6253–6260PubMedCrossRefGoogle Scholar
  49. Rosegrant MW, Cline SA (2003) global food security: Challenges and policies. Science 302:1917–1919PubMedCrossRefGoogle Scholar
  50. Sarr DA, Hibbs DE, Huston MA (2005) A hierarchical perspective of plant diversity. Quart Rev Biol 80:187–212PubMedCrossRefGoogle Scholar
  51. Schultz J (2005) The ecozones of the world, 2nd edn. Springer, BerlinGoogle Scholar
  52. Singan V, Colbourne JK (2005) MicrosatDesign is a pipeline for transforming sequencer trace files into DNA markers. CGB Technical Report 2005–01. The Center for Genomics and Bioinformatics, Indiana University, Bloomington (Verified July 13, 2007)Google Scholar
  53. Smith B (1995) The emergence of agriculture. Scientific American Library, New YorkGoogle Scholar
  54. Sreenivasulu N, Sopory S.K, Kishor PBK (2007) Deciphering the regulatory mechanisms of abiotic stress tolerance in plants by genomic approaches. Gene 388:1–13PubMedCrossRefGoogle Scholar
  55. Tanksley S, McCouch S (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066PubMedCrossRefGoogle Scholar
  56. Toledo A, Burlingame B (2006) Biodiversity and nutrition: A common path toward global food security and sustainable development. J Food Composition Anal 19:477–483CrossRefGoogle Scholar
  57. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604PubMedCrossRefGoogle Scholar
  58. Valliyodan B, Nguyen HT (2006) Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Curr Opin Plant Biol 9:189–195PubMedCrossRefGoogle Scholar
  59. van Driel R, Fransz PF, Verschure PJ (2003) The eukaryotic genome: a system regulated at different hierarchical levels. J Cell Sci 116:4067–4075PubMedCrossRefGoogle Scholar
  60. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630PubMedCrossRefGoogle Scholar
  61. von Braun J, Swaminathan MS, Rosegrant MW (2003) 2003–2004 IFPRI annual report essay: Agriculture, food security, nutrition and the Millennium Development Goals. IFPRI (Verified July 13, 2007)Google Scholar
  62. Xu YB, McCouch SR, Zhang QF (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol 59:7–26PubMedCrossRefGoogle Scholar
  63. Yamaguchi K, Mayfield SP (2005) Transcriptional and translational regulation of photosystem II gene expression. Advances in Photosynthesis and Respiration:The light-driven water: Plastoquinone oxireductase, pp. 649–668Google Scholar
  64. Yu J, Hu S, Wang J, Wong GK-S, Li S, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92PubMedCrossRefGoogle Scholar
  65. Zeder MA (2006) Central questions in the domestication of plants and animals. Evolutionary Anthropology 15:105–117CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • P. Gepts
    • 1
  1. 1.Department of Plant Sciences / MS1, Section of Crop and Ecosystem SciencesUniversity of CaliforniaDavisUSA

Personalised recommendations