RadishDB:Samples

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Four R. sativus cultivars

We will use samples of the three major convarieties (groups of varieties) according to Specht (cited in Snow and Campbell 2005). Within convar. sativus, which contains all the edible root varieties, we will use one Asian (large root: daikon) and one European (small root: Early Scarlet Globe) cultivar. The other two convarieties are rat tail radish, grown for edible seedpods (convar. caudatus) and one of the oilseed radishes (convar. oleifera) used as a cover crop and green manure; this has been studied by extension researchers at KBS.

Four R. raphanistrum populations pooled, one weedy and three native

The weedy population will be the well-studied NY population from North America (e.g., 1, 2, 3, 4, 5, 6, 7). The three native populations will be from France and Spain and represent the three major subspecies raphanistrum, landra and maritimus.

We chose this sampling scheme so that we would uncover ample genetic variation both within and among libraries, but the plant material included in both libraries is closely related enough that we will have a high frequency of sequence matching. Although the libraries are constructed from different named species, recall from the Overview that several authors have proposed that R. sativus and R. raphanistrum are actually one species and that R. sativus was domesticated from R. raphanistrum. This means that there should be a low percentage of sequence divergence between our libraries. The libraries will contain ample genetic variation, as each plant sampled will be highly heterozygous (since Raphanus is self-incompatible), the cultivars chosen will be divergent (see above), and there is substantial marker differentiation among the weedy and native R. raphanistrum subspecies (Sahli and Conner, in prep.).

Sequence variation expected

The variation in our libraries represents natural variation (among the three native populations), variation due to domestication (among cultivars of R. sativus and between the two species, because R. sativus was likely domesticated from R. raphanistrum), and variation due to the evolution of a serious agricultural pest (among the R. raphanistrum libraries). The use of the three convarieties of R. sativus and three subspecies of R. raphanistrum means that the cDNA sequences we will generate will be more representative of the genus Raphanus in general, and of the crop and weedy radishes specifically. By sequencing separate libraries for the eight populations sampled, we will be able to assign sequence variants unambiguously to each. It will be straightforward for researchers in future work to assign variation within libraries to the different cultivars, populations, or subspecies by simply designing PCR primers to amplify the variable regions and screen the plant populations in question.

References

  1. Karoly, K. and J.K. Conner, Heritable variation in a family-diagnostic trait. Evolution, 2000. 54(4): p. 1433-1438.
  2. Agrawal, A.A., et al., Ecological genetics of an induced plant defense against herbivores: additive genetic variance and costs of phenotypic plasticity. Evolution, 2002. 56(11): p. 2206-2213.
  3. Conner, J.K., Genetic mechanisms of floral trait correlations in a natural population. Nature, 2002. 420: p. 407-410.
  4. Conner, J.K., R. Franks, and C. Stewart, Expression of additive genetic variances and covariances for wild radish floral traits: comparison between field and greenhouse environments. Evolution, 2003. 57(3): p. 487-495.
  5. Conner, J. and S. Via, Patterns of phenotypic and genetic correlations among morphological and life history traits in wild radish, Raphanus raphanistrum. Evolution, 1993. 47(2): p. 704-711.
  6. Agrawal, A.A., J.K. Conner, and J.R. Stinchcombe, Evolution of plant resistance and tolerance to frost damage. Ecology Letters, 2004. 7: p. 1199–1208.
  7. Strauss, S.Y., J.K. Conner, and K.P. Lehtila, Effects of Foliar Herbivory by Insects on the Fitness of Raphanus raphanistrum: Damage Can Increase Male Fitness. American Naturalist, 2001. 158(5): p. 496-504.


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