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MAPSMapping genebank colThe genetic diversity in traditional The samples in genebanks, andand modern rice varieties, and in their associated data, can also be used tothe wild relatives of rice, is vital further explore and discover geographicto agricultural development, as it patterns in crop diversity. In fact, theseprovides the basis for rice improvement. patterns are used to reconstruct theSometimes, a single rare gene found prehistorical origins and spread of crops.in only a few varieties can greatly These data can be used to narrow downcontribute to rice production. A good the geographical search area in findingexample of this is the short-straw gene or samples with important traits, such as athe SUB1 gene that confers submergence certain type of disease resistance. Thetolerance.data also serve to identify gaps in aIronically, the success of rice genebank collection, for which collectingbreeding has rapidly replaced traditional expeditions are still needed.varieties with modern ones, particularly Such analyses are possible onlyin Asia’s irrigated rice fields. Thus, the if we have a decent database inuse of crop diversity bites its own tail, which each sample is described. Cropbecoming a threat to its persistence. descriptors can include morphologicalOne important approach to avoid the characteristics, agronomic traits, andloss of crop biodiversity, or “genetic genetic data. For geographic analysis, iterosion,” is the use of genebanks. A is crucial also to know where the samplegenebank assembles a broad collection was taken from.of rice varieties and conserves themFortunately, “passport” informationfor breeding. In total, there are 780,551 such as name of species, common name,samples of rice in genebanks. The institute code, date of acquisition,International Rice Research Institute and location is generally available in(IRRI) has 109,136 samples, while genebank databases. However, for manygenebanks in India and China have samples, no geographic coordinates are86,119 and 70,104 samples, respectively. 1 available. Most samples were collected*Georeferencing. This refers to the process of converting text descriptions oflocations to geographic coordinates that can be used in an analysis. This involvesbreaking down a description such as “14 kilometers north and 2 kilometers westof La Paz, Tarlac, Luzon, Philippines” into its geographic components, which canthen be used to assign a coordinate to the record—in this case, 15.578N, 120.704E.However, processing such information is not always as straightforward as thisexample. Records often struggle with variations in spellings, obsolete names, andsometimes misspelled entries.Dealing with inaccurate or wrong location data. Records that do havelocation data are also checked for errors. Some common errors are mistakinglongitude for latitude (a mistake probably made from time to time); swappingeast with west or north with south; missing a latitude or longitude coordinate;truncating the decimal points in a coordinate, resulting in lower precision; orsimply putting in the wrong data. Not all errors can easily be corrected, but wehave corrected those coordinates that fell in an ocean, or in the wrong country.Needless to say, determining the most likely location for an accession is a timeconsumingtask.before the global positioning systembecame available. So, their locationswere simply expressed in text format.At IRRI, we have worked on improvingthis situation to refine the Institute’sgenebank and also other genebanks. Wehave used tools such as biogeomancer 2to assign coordinates to genebanksamples, using their available textdescription as references. This is called“georeferencing” (see box). We also crosscheckedthe coordinates and correctedthose that were found to be wrong.12According to "The State of the World's Plant GeneticResources for Food and Agriculture," FAO, 2009.Available at www.fao.org/ag/AGP/agps/PGRFA/wrlmap_e.htm.Guarlnick et al. 2006. PLoS Biology. www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040381; http://bg.berkeley.edu/latest/.30 Rice Today April-June 2010
lectionsby Ma. Cristina Paule, Jane Girly Cuerdo, Mary Anne Reyes,Arnel Rala, Jacob van Etten, Andrew Nelson, and Robert J. HijmansMap of origins of georeferenced rice samples by genebank*IRRI = International Rice Research Institute, AfricaRice = Africa Rice Center (formerly known as WARDA), CAAS = Chinese Academy of Agricultural Sciences,USDA = United States Department of Agriculture, ILRI = International Livestock Research Institute.We have now almost completedgeoreferencing the IRRI collection. Thismap illustrates the progress we havemade so far. We have also included datafor some other rice collections. 3The coverage of the rice collectionsreflects the global distribution of ricecultivation and diversity, which werefound to be highest in East, Southeast,and South Asia, and in West Africa (seemap), as well as in the regional focuses ofthe institutes with rice genebanks (mostsamples in the genebank of AfricaRiceare from West Africa).3This work was supported by the GPG2 project (WorldBank/Bioversity) and by the United States Departmentof Agriculture.An important question is whetheror not there are still gaps in the resultsof this impressive collecting effort. Thatis hard to say because the data presentedwere taken from just a limited number ofgenebanks, not all, and some records didnot have coordinates. Further analysismust also be done to incorporate geneticand other data to include the relativeimportance (contribution of additionaldiversity) of new sites. Nevertheless,some gaps stand out. In the collectionsmapped here, very few samples camefrom Japan and Korea (but thesecountries have genebanks of their own).Collections in parts of Myanmar andCambodia are also sparse.The process of georeferencing thesekey rice accession databases continuesand we aim to produce a completepicture of global rice diversity soon, asit will certainly play a crucial role in theconservation and management of ricegenetic resources for future generations.Ms. Paule, Ms. Cuerdo, and Ms. Reyesare researchers; Mr. Rala is an associatescientist; and Dr. Nelson is a geographerin IRRI’s Geographic InformationSystems, Social Sciences Division. Dr.van Etten is an assistant professor,School of Biology, IE University inSpain, and Dr. Hijmans is an assistantprofessor, Department of EnvironmentalScience and Policy, University ofCalifornia-Davis.Rice Today April-June 201031
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