Review. Applications of ecogeography and geographic information systems in conservation and utilization of plant genetic resources

M. Parra-Quijano, J. M. Iriondo, E. Torres

Abstract


The present paper reviews the use of ecogeographical studies in the efficient conservation and utilization of plant genetic resources. While the use of genotypic information in agrobiodiversity studies has experienced a rapid boost during the last two decades, the use of environmental information on the collecting sites of the conserved germplasm (i.e., ecogeographical characterization) has gained importance in a more gradual way. Today we know that ecogeographical characterization reveals the adaptive range of species conserved and shows the most important environmental factors or variables for adaptation. Progress in ecogeographical characterization has been helped by the development and popularization of geographic information systems (GIS) software applications and environmental data arranged in layers compatible with such applications. GIS are useful to manage and analyze georeferenced data, such as passport collection data and environmental variables. Thus, GIS have become the best tool to perform ecogeographical analyses. Other related tools such as species distribution models or gap analysis can be easily integrated in ecogeographical analysis, offering improved results. As a result, GIS, related tools and ecogeographical analysis can be useful in a wide range of applications in the collection, conservation, characterization, documentation and utilization of plant genetic resources.


Keywords


adaptation; ecogeographical analysis; environment; gap analysis; genotype; phenotype; species distribution models

Full Text:

PDF

References


Bari A, Street K, Mackay M, Endresen DTF, De Pauwe E, Amri A, 2012. Focused identificacion of germplasm strategy (FIGS) detects wheat stem rust resistance linked to environmental variables. Genet Resour Crop Evol, doi 10.1007/s10722-011-9775-5. http://dx.doi.org/10.1007/s10722-011-9775-5

Batchu AK, Zimmermann D, Schulze-Lefert P, Koprek T, 2006. Correlation between hordatine accumulation, environmental factors and genetic diversity in wild barley (Hordeum spontaneum C. Koch) accessions from the Near East Fertile Crescent. Genetica 127: 87-99. http://dx.doi.org/10.1007/s10709-005-2484-2 PMid:16850216

Benito Garzón M, Sánchez de Dios R, Sainz Ollero H, 2008. Effects of climate change on the distribution of Iberian tree species. Appl Veg Sci 11: 169-178.

Bennett SJ, Bullitta S, 2003. Ecogeographical analysis of the distribution of six Trifolium species in Sardinia. Biodivers Conserv 12: 1455-1466. http://dx.doi.org/10.1023/A:1023677726849

Berger JD, 2007. Ecogeographic and evolutionary approaches to improving adaptation of autumn-sown chickpea (Cicer arietinum L.) to terminal drought: The search for reproductive chilling tolerance. Field Crops Res 104: 112-122. http://dx.doi.org/10.1016/j.fcr.2007.03.021

Bhullar NK, Street K, Mackay M, Yahiaoui N, Keller B, 2009. Unlocking wheat genetic resources for the molecular identification of previously undescribed functional alleles at the Pm3 resistance locus. Proc Natl Acad Sci USA 106: 9519-9524. http://dx.doi.org/10.1073/pnas.0904152106 PMid:19470492    PMCid:2686639

Carwardine J, Wilson KA, Watts M, Etter A, Klein CJ, Possingham HP, 2008. Avoiding costly conservation mistakes: The importance of defining actions and costs in spatial priority setting. PLoS ONE 3: e2586. http://dx.doi.org/10.1371/journal.pone.0002586 PMid:18596914    PMCid:2440517

Ceccarelli S, 1994. Specific adaptation and breeding for marginal conditions. Euphytica 77: 205-219. http://dx.doi.org/10.1007/BF02262633

Chen G, Suprunova T, Krugman T, Fahima T, Nevo E, 2004. Ecogeographic and genetic determinants of kernel weight and colour of wild barley (Hordeum spontaneum) populations in Israel. Seed Sci Res 14: 137-146. http://dx.doi.org/10.1079/SSR2004163

Coppock JT, Rhind DW, 1991. The history of GIS. In: Geographical information systems: principles and applications (Maguire DJ, Goodchild MF, Rhind DW, eds). Longman Scientific & Technical, NY. pp: 21-43.

Decker D, 2001. GIS data sources. John Wiley & Sons, NY.

Endresen DTF, 2010. Predictive association between trait data and ecogeographic data for Nordic barley landraces. Crop Sci 50: 2418-2430. http://dx.doi.org/10.2135/cropsci2010.03.0174

Endresen DTF, 2011. Utilization of plant genetic resources, a lifeboat to the gene pool. Doctoral thesis. University of Copenhagen, Copenhagen, Denmark.

Endresen DTF, Street K, Mackay M, Bari A, De Pauwe E, 2011. Predictive association between biotic stress traits and ecogeographic data for wheat and barley landraces. Crop Sci 51: 2036-2055. http://dx.doi.org/10.2135/cropsci2010.12.0717

Falconer DS, Mackay TFC, 1996. Introduction to quantitative genetics. Longman, Harlow, UK.

FAO, 1996. Global plan of action for the conservation and sustainable utilization of plant genetic resources for food and agriculture and the Leipzig declaration. FAO, Rome.

Ferguson ME, Jarvis A, Stalker HT, Williams DE, Guarino L, Valls JFM, Pittman RN, Simpson CE, Bramel PJ, 2005. Biogeography of wild Arachis (Leguminosae): distribution and environmental characterisation. Biodivers Conserv 14: 1777-1798. http://dx.doi.org/10.1007/s10531-004-0699-7

Ferreira ME, 2006. Molecular analysis of gene banks for sustainable conservation and increased use of crop genetic resources. In: The role of biotechnology in exploring and protecting agricultural genetic resources (Ruane J, Sonnino A, eds). FAO, Rome. pp: 121-127.

Fisher RA, 1918. The correlation between relatives on the supposition of Mendelian inheritance. Trans Roy Soc Edinb 52: 399-433.

Frankel OH, Bennett E, 1970. Genetic resources in plants: their exploration and conservation. Blackwell Scientific Publications, Oxford, UK.

Ghamkhar K, Snowball R, Bennett SJ, 2007. Ecogeographical studies identify diversity and potential gaps in the largest germplasm collection of bladder clover (Trifolium spumosum L.). Aust J Agric Res 58: 728-738. http://dx.doi.org/10.1071/AR06359

Ghamkhar K, Snowball R, Wintle BJ, Brown AHD, 2008. Strategies for developing a core collection of bladder clover (Trifolium spumosum L.) using ecological and agro-morphological data. Aust J Agric Res 59: 1103-1112. http://dx.doi.org/10.1071/AR08209

Gonzalo J, 2010. Diagnosis fitoclimática de la España peninsular. Hacia un modelo de clasificación funcional de la vegetación y de los ecosistemas peninsulares españoles. Organismo Autónomo de Parques Nacionales, Madrid, Spain. [In Spanish].

Greene SL, Hart TC, Afonin A, 1999a. Using geographic information to acquire wild crop germplasm for ex situ collections: I. Map development and field use. Crop Sci 39: 836-842. http://dx.doi.org/10.2135/cropsci1999.0011183X003900030037x

Greene SL, Hart TC, Afonin A, 1999b. Using geographic information to acquire wild crop germplasm for ex situ collections: II. Post-collection analysis. Crop Sci 39: 843-849. http://dx.doi.org/10.2135/cropsci1999.0011183X003900030038x

Greene SL, Afonin AA, Dzyubenko E, Dzyubenko N, 2012. Effective conservation of Medicago crop wild relatives in Russia and neighbouring countries: Gap analysis points the way forward. In: Agrobiodiversity conservation. Securing the diversity of crop wild relatives and landraces (Maxted N, Dulloo E, Ford-Lloyd BV, Frese L, Iriondo JM, Pinheiro de Carvalho MAA, eds). CAB Int, Wallingford, UK. pp: 82-90. http://dx.doi.org/10.1079/9781845938512.0082

Gregory IA, Ell PS, 2007. Historical GIS. Technologies, methodologies and scholarship. Cambridge Univ Press, Cambridge, UK. http://dx.doi.org/10.1017/CBO9780511493645

Grenier C, Bramel-Cox PJ, Hamon P, 2001. Core collection of sorghum: I. Stratification based on eco-geographical data. Crop Sci 41: 234-240. http://dx.doi.org/10.2135/cropsci2001.411234x

Guarino L, 1995. Geographic information systems and remote sensing for plant germplasm collectors. In: Collecting plant genetic diversity. Technical guidelines (Guarino L, Ramanatha Rao V, Reid R, eds). CAB Int, Wallingford, UK. pp: 315-327.

Guarino L, Maxted N, Sawkins M, 1999. Analysis of georeferenced data and the conservation and use of plant genetic resources. In: Linking genetic resources and geography: Emerging strategies for conserving crop biodiversity (Greene SL, Guarino L, eds). Am Soc Agron Crop Sci Soc, Madison, WI, USA. pp: 1-24.

Guarino L, Jarvis A, Hijmans R, Maxted N, 2002. Geographic information systems (GIS) and the conservation and use of plant genetic resources. In: Managing plant genetic diversity (Engels JMM, Ramanatha Rao V, Brown AHD, Jackson MT, eds). CAB Int, Wallingford, UK. pp: 387-404.

Guisan A, Zimmermann NE, 2000. Predictive habitat distribution models in ecology. Ecol Model 135: 147-186. http://dx.doi.org/10.1016/S0304-3800(00)00354-9

Günther O, 1998. Environmental information systems. Springer, Berlin.

Guralnick RP, Wieczorek J, Beaman R, Hijmans RJ, 2006. BioGeomancer: Automated georeferencing to map the world's biodiversity data. PLoS Biol 4: 1908-1909.

Hijmans R, 2003. The effect of climate change of global potato production. Am J Potato Res 80: 271-280. http://dx.doi.org/10.1007/BF02855363

Hijmans RJ, Spooner DM, 2001. Geographic distribution of wild potato species. Am J Bot 88: 2101-2112. http://dx.doi.org/10.2307/3558435 PMid:21669641

Hijmans RJ, Garrett KA, Huamán Z, Zhang DP, Schreuder M, Bonierbale M, 2000. Assessing the geographic representativeness of genebank collections: the case of Bolivian wild potatoes. Conserv Biol 14: 1755-1765. http://dx.doi.org/10.1046/j.1523-1739.2000.98543.x

Hijmans RJ, Guarino L, Cruz M, Rojas E, 2001. Computer tools for spatial analysis of plant genetic resources data: 1. DIVA-GIS. Plant Genet Resour Newsl 127: 15-19.

Hossell JE, Riding AE, Brown I, 2003. The creation and characterisation of a bioclimatic classification for Britain and Ireland. J Nat Conserv 11: 5-13. http://dx.doi.org/10.1078/1617-1381-00033

Jarvis A, Williams K, Williams D, Guarino L, Caballero PJ, Mottram G, 2005. Use of GIS for optimizing a collecting mission for a rare wild pepper (Capsicum flexuosum Sendtn.) in Paraguay. Genet Resour Crop Evol 52: 671-682. http://dx.doi.org/10.1007/s10722-003-6020-x

Jarvis A, Lane A, Hijmans RJ, 2008. The effect of climate change on crop wild relatives. Agric Ecosyst Environ 126: 13-23. http://dx.doi.org/10.1016/j.agee.2008.01.013

Jarvis DI, Myer L, Klemick H, Guarino L, Smale M, Brown AHD, Sadiki M, Sthapit B, Hodgkin T, 2000. A training guide for in situ conservation on-farm. Version 1. IPGRI, Rome.

Johannsen W, 1911. The genotype conception of heredity. Am Nat 45: 129-159. http://dx.doi.org/10.1086/279202

Jones PG, Thornton PK, 2003. The potential impacts of climate change on maize production in Africa and Latin America in 2055. Glob Environ Change 13: 51-59. http://dx.doi.org/10.1016/S0959-3780(02)00090-0

Jones PG, Beebe SE, Tohme J, Galwey NW, 1997. The use of geographical information systems in biodiversity exploration and conservation. Biodivers Conserv 6: 947-958. http://dx.doi.org/10.1023/A:1018311513176

Kresovich S, Casa AM, Garris AJ, Mitchell SE, Hamblin MT, 2006. Improving the connection between effective crop conservation and breeding. In: Plant breeding: the Arnel R. Hallauer international symposium (Lamkey KR, Lee M, eds). Blackwell Publishing, Ames, IA, USA. pp: 90-96.

Lande R, 1980. Genetic variation and phenotypic evolution during allopatric speciation. Am Nat 116: 463-479. http://dx.doi.org/10.1086/283642

Lipow SR, Vance-Borland K, Clair JBSt, Henderson J, McCain C, 2004. Gap analysis of conserved genetic resources for forest trees. Conserv Biol 18: 412-423. http://dx.doi.org/10.1111/j.1523-1739.2004.00072.x

Liviero L, Maestri E, Gulli M, Nevo E, Marmiroli N, 2002. Ecogeographic adaptation and genetic variation in wild barley. Application of molecular markers targeted to environmentally regulated genes. Genet Resour Crop Evol 49: 133-144. http://dx.doi.org/10.1023/A:1014792509087

Lobo Burle M, Torres Cordeiro CM, Fonseca JR, Palhares de Melo M, Neves Alves R, Abadie T, 2003. Characterization of germplasm according to environmental conditions at the collecting site using GIS - two case studies from Brazil. Plant Genet Resour Newsl 135: 1-11.

Mackay M, 2011. Surfing the genepool, the effective and efficient use of plant genetic resources. Doctoral thesis. Swedish University of Agricultural Sciences, Alnarp, Sweden.

Maxted N, van Slagerem MW, Rihan JR, 1995. Ecogeographic surveys. In: Collecting plant genetic diversity. Technical guidelines (Guarino L, Rao VR, Reid R, eds). CAB Int, Wallingford, UK.

Maxted N, Iriondo JM, Dulloo E, Lane A, 2008. Introduction: The integration of PGR conservation with protected area management. In: Conserving plant genetic diversity in protected areas. Population management of crop wild relatives (Iriondo JM, Maxted N, Dulloo E, eds). CAB Int, Wallingford, UK. pp: 1-22. http://dx.doi.org/10.1079/9781845932824.0001

Montesano V, Negro D, Sarli G, Logozzo G, Spagnoletti Zeuli P, 2012. Landraces in Inland areas of the Basilicata region, Italy: monitoring and perspectives for on farm conservation. Genetics Resources and Crop Evolution, doi 10.1007/s10722-011-9712-7. http://dx.doi.org/10.1007/s10722-011-9712-7

Ober ES, Luterbacher MC, 2002. Genotypic variation for drought tolerance in Beta vulgaris. Ann Bot 89: 917-924. http://dx.doi.org/10.1093/aob/mcf093 PMid:12102517

Parra-Quijano, M., 2009. Diseño de colecta de tres especies de interés agrícola del género Annona para Colombia. Proyecto: Establecimiento del banco de germoplasma colombiano de anón (Annona squamosa L.). Universidad Nacional de Colombia, sede Bogotá. Available in http://www.agrobiodiversidad.org/ProyectoAnnonaColombia2009.pdf. [In Spanish].

Parra-Quijano M, Draper D, Iriondo JM, 2003. Assessing in situ conservation of Lupinus spp. in Spain through GIS. Crop Wild Relative 1: 8-9.

Parra-Quijano M, Draper D, Iriondo JM, 2007. GIS-based evaluation of the in situ conservation of a crop wild relative: the case of Spanish lupins. Bocconea 21: 105-116.

Parra-Quijano M, Draper D, Torres E, Iriondo JM, 2008. Ecogeographical representativeness in crop wild relative ex situ collections. In: Crop wild relative conservation and use (Maxted N, Ford-Lloyd BV, Kell SP, Iriondo JM, Dulloo ME, Turok J, eds). CAB International, Wallingford, UK. pp: 249-273.

Parra-Quijano M, Iriondo JM, De la Cruz M, Torres E, 2011a. Strategies for the development of core collections based on ecogeographical data. Crop Sci 51: 656-666. http://dx.doi.org/10.2135/cropsci2010.04.0191

Parra-Quijano M, Iriondo JM, Torres E, De la Rosa L, 2011b. Evaluation and validation of ecogeographical core collections using phenotypic data. Crop Sci 51: 694-703. http://dx.doi.org/10.2135/cropsci2010.05.0273

Parra-Quijano M, Iriondo JM, Torres E, 2012a. Ecogeographical land characterization maps as a tool for assessing plant adaptation and their implications in agrobiodiversity studies. Genet Resour Crop Evol 59: 205-217. http://dx.doi.org/10.1007/s10722-011-9676-7

Parra-Quijano M, Iriondo JM, Torres E, 2012b. Efficient method to improve representativeness of ex situ plant genetic resources conservation based on GIS and ecogeographic data. Biodivers Conserv 21: 79-96. http://dx.doi.org/10.1007/s10531-011-0167-0

Peeters JP, Wilkes HG, Galwey NW, 1990. The use of ecogeographical data in the exploitation of variation from gene banks. Theor Appl Genet 80: 110-112. http://dx.doi.org/10.1007/BF00224023

Ramírez-Villegas J, Khoury C, Jarvis A, Debouck DG, Guarino L, 2010. A gap analysis methodology for collecting crop genepools: a case study with Phaseolus beans. PLoS ONE 5: e13497. http://dx.doi.org/10.1371/journal.pone.0013497 PMid:20976009    PMCid:2958131

Ravikanth G, Ganeshaiah KN, Shaanker U, 2002. Identification of hot spots of species richness and genetic variability in rattans: an approach using geographical information systems (GIS) and molecular tools. Plant Genet Resour Newsl 132: 17-21.

Rodrigues ASL, Andelman SJ, Bakarr MI, Boitani L, Brooks TM, Cowling RM, Fishpool LDC, da Fonseca GAB, Gaston KJ, Hoffmann M et al., 2004. Effectiveness of the global protected area network in representing species diversity. Nature 428: 640-643. http://dx.doi.org/10.1038/nature02422 PMid:15071592

Ruiz Corral JA, Durán Puga N, Sánchez González JJ, Ron Parra J, González Eguiarte DR, Holland JB, Medina García G, 2008. Climatic adaptation and ecological descriptors of 42 Mexican maize races. Crop Sci 48: 1502-1512. http://dx.doi.org/10.2135/cropsci2007.09.0518

Savitsky BG, 1998. GIS. In: GIS methodologies for developing conservation strategies: tropical forest recovery and wildlife management in Costa Rica (Savitsky BG, Lacher TE, eds). Columbia Univ Press, NY. pp: 41-47.

Steiner JJ, Greene SL, 1996. Proposed ecological descriptors and their utility for plant germplasm collections. Crop Sci 36: 439-451. http://dx.doi.org/10.2135/cropsci1996.0011183X003600020037x

Sunil N, Varaprasad KS, Sivaraj N, Suresh Kumar T, Abraham B, Prasad RBN, 2008. Assessing Jatropha curcas L. germplasm in situ – A case study. Biomass Bioenergy 32: 198-202. http://dx.doi.org/10.1016/j.biombioe.2007.09.003

Tohme J, Jones P, Beebe S, Iwanaga M, 1995. The combined use of agroecological and characterisation data to establish the CIAT Phaseolus vulgaris core collection. In: Core collections of plant genetic resources (Hodgkin T, Brown AHD, van Hintum ThJL, Morales EAV, eds). John Wiley & Sons, Chichester, UK. pp: 95-107.

Upadhyaya HD, Reddy KN, Ahmed MI, Gowda CLL, Haussmann BIG, 2009. Identification of geographical gaps in the pearl millet germplasm conserved at ICRISAT genebank from West and Central Africa. Plant Genet Resour 8: 45-51. http://dx.doi.org/10.1017/S147926210999013X

Vallejo FA, Estrada EI, 2002. Mejoramiento genético de plantas. Universidad Nacional de Colombia, Palmira, Colombia.

Vinocur B, Altman A, 2005. Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations. Curr Opin Biotechnol 16: 123-132. http://dx.doi.org/10.1016/j.copbio.2005.02.001 PMid:15831376

Vogel KP, Schmer MR, Mitchell RB, 2005. Plant adaptation regions: Ecological and climatic classification of plant materials. Rangel Ecol Manag 58: 315-319. http://dx.doi.org/10.2111/1551-5028(2005)58[315:PAREAC]2.0.CO;2

Volis S, Yakubov B, Shulgina I, Ward D, Zur V, Mendlinger S, 2001. Tests for adaptive RAPD variation in population genetic structure of wild barley, Hordeum spontaneum Koch. Biol J Linn Soc 74: 289-303.

Walsh B, 2002. Quantitative genetics, genomics and the future of plant breeding. In: Quantitative genetics, genomics and plant breeding (Kang MS, ed). CAB Int, Wallingford, UK. pp: 23-32.

Williams CL, Hargrove WW, Liebman M, James DE, 2008. Agro-ecoregionalization of Iowa using multivariate geographical clustering. Agric Ecosyst Environ 123: 161-174. http://dx.doi.org/10.1016/j.agee.2007.06.006

Witcombe JR, Hollington PA, Howarth CJ, Reader S, Steele KA, 2008. Breeding for abiotic stresses for sustainable agriculture. Philos Trans R Soc Lond B Biol Sci 363: 703-716. http://dx.doi.org/10.1098/rstb.2007.2179 PMid:17761467    PMCid:2610105

Yawen Z, Shiquan S, Zichao L, Zhongyi Y, Xiangkun W, Honglian Z, Guosong W, 2003. Ecogeographic and genetic diversity based on morphological characters of indigenous rice (Oryza sativa L.) in Yunnan, China. Genet Resour Crop Evol 50: 567-577. http://dx.doi.org/10.1023/A:1024436501289

Zuriaga E, Blanca JM, Cordero L, Sifres A, Blas-Cerdán WG, Morales R, Nuez F, 2009. Genetic and bioclimatic variation in Solanum pimpinellifolium. Genet Resour Crop Evol 56: 39-51. http://dx.doi.org/10.1007/s10722-008-9340-z




DOI: 10.5424/sjar/2012102-303-11