The genetic diversity in traditio by wuyunyi



Mapping genebank collections                                                                                                                                                                                              by Ma. Cristina Paule, Jane Girly Cuerdo, Mary Anne Reyes,
                                                                                                                                                                                                                          Arnel Rala, Jacob van Etten, Andrew Nelson, and Robert J. Hijmans

       he genetic diversity in traditional            The samples in genebanks, and
       and modern rice varieties, and in         their associated data, can also be used to
       the wild relatives of rice, is vital      further explore and discover geographic
       to agricultural development, as it        patterns in crop diversity. In fact, these
provides the basis for rice improvement.         patterns are used to reconstruct the
Sometimes, 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 down
contribute to rice production. A good            the geographical search area in finding
example of this is the short-straw gene or       samples with important traits, such as a
the SUB1 gene that confers submergence           certain type of disease resistance. The
tolerance.                                       data also serve to identify gaps in a
     Ironically, the success of rice             genebank collection, for which collecting
breeding has rapidly replaced traditional        expeditions are still needed.
varieties with modern ones, particularly              Such analyses are possible only
in Asia’s irrigated rice fields. Thus, the       if we have a decent database in
use of crop diversity bites its own tail,        which each sample is described. Crop
becoming a threat to its persistence.            descriptors can include morphological
One important approach to avoid the              characteristics, agronomic traits, and
loss of crop biodiversity, or “genetic           genetic data. For geographic analysis, it
erosion,” is the use of genebanks. A             is crucial also to know where the sample
genebank assembles a broad collection            was taken from.
of rice varieties and conserves them                  Fortunately, “passport” information
for 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 many
                                                                                                                                                                     Map of origins of georeferenced rice samples by genebank
genebanks in India and China have                samples, no geographic coordinates are
86,119 and 70,104 samples, respectively.1        available. Most samples were collected
                                                                                                                                                               *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.
                                                                                              before the global positioning system
     Georeferencing. This refers to the process of converting text descriptions of            became available. So, their locations
     locations to geographic coordinates that can be used in an analysis. This involves       were simply expressed in text format.                                 We have now almost completed                               An important question is whether          and we aim to produce a complete
     breaking down a description such as “14 kilometers north and 2 kilometers west           At IRRI, we have worked on improving                             georeferencing the IRRI collection. This                   or not there are still gaps in the results     picture of global rice diversity soon, as
     of La Paz, Tarlac, Luzon, Philippines” into its geographic components, which can         this situation to refine the Institute’s                         map illustrates the progress we have                       of this impressive collecting effort. That     it will certainly play a crucial role in the
     then be used to assign a coordinate to the record—in this case, 15.578N, 120.704E.       genebank and also other genebanks. We                            made so far. We have also included data                    is hard to say because the data presented      conservation and management of rice
     However, processing such information is not always as straightforward as this            have used tools such as biogeomancer2                            for some other rice collections.3                          were taken from just a limited number of       genetic resources for future generations.
     example. Records often struggle with variations in spellings, obsolete names, and        to assign coordinates to genebank                                     The coverage of the rice collections                  genebanks, not all, and some records did
     sometimes misspelled entries.                                                            samples, using their available text                              reflects the global distribution of rice                   not have coordinates. Further analysis
                                                                                              description as references. This is called                        cultivation and diversity, which were                      must also be done to incorporate genetic
     Dealing with inaccurate or wrong location data. Records that do have                     “georeferencing” (see box). We also cross-                       found to be highest in East, Southeast,                    and other data to include the relative         Ms. Paule, Ms. Cuerdo, and Ms. Reyes
     location data are also checked for errors. Some common errors are mistaking              checked the coordinates and corrected                            and South Asia, and in West Africa (see                    importance (contribution of additional         are researchers; Mr. Rala is an associate
     longitude for latitude (a mistake probably made from time to time); swapping             those that were found to be wrong.                               map), as well as in the regional focuses of                diversity) of new sites. Nevertheless,         scientist; and Dr. Nelson is a geographer
     east with west or north with south; missing a latitude or longitude coordinate;                                                                           the institutes with rice genebanks (most                   some gaps stand out. In the collections        in IRRI’s Geographic Information
     truncating the decimal points in a coordinate, resulting in lower precision; or                                                                           samples in the genebank of AfricaRice                      mapped here, very few samples came             Systems, Social Sciences Division. Dr.
     simply putting in the wrong data. Not all errors can easily be corrected, but we         1                                                                are from West Africa).                                     from Japan and Korea (but these                van Etten is an assistant professor,
                                                                                                  According to "The State of the World's Plant Genetic
     have corrected those coordinates that fell in an ocean, or in the wrong country.             Resources for Food and Agriculture," FAO, 2009.                                                                         countries have genebanks of their own).        School of Biology, IE University in
     Needless to say, determining the most likely location for an accession is a time-            Available at                                                                             Collections in parts of Myanmar and            Spain, and Dr. Hijmans is an assistant
     consuming task.                                                                          2                                                                                                                           Cambodia are also sparse.                      professor, Department of Environmental
                                                                                                  Guarlnick et al. 2006. PLoS Biology. www.plosbiology.        3
                                                                                                                                                                   This work was supported by the GPG2 project (World
                                                                                                  org/article/info:doi/10.1371/journal.pbio.0040381; http://       Bank/Bioversity) and by the United States Department
                                                                                                                                                                                                                               The process of georeferencing these       Science and Policy, University of
                                                                                                                                 of Agriculture.                                        key rice accession databases continues         California-Davis.

30                                                          Rice Today April-June 2010                                                                                                                                             Rice Today April-June 2010                                                           31

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