Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata).
BACKGROUND
Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history of yam, Dioscorea rotundata. In Africa, Yam is cultivated by tuber clonal propagation.


RESULTS
We used 12 microsatellite markers to identify intra-clonal diversity in yam varieties. We then used this diversity to assess the relative ages of clones. Using simulations, we assessed how Approximate Bayesian Computation could use clonal diversity to estimate the age of a clone depending on the size of the sample, the number of independent samples and the number of markers. We then applied this approach to our particular dataset and showed that the relative ages of varieties could be estimated, and that each variety could be ranked by age.


CONCLUSIONS
We give a first estimation of clone age in an approximate Bayesian framework. However the precise estimation of clone age depends on the precision of the mutation rate. We provide useful information on agrobiodiversity dynamics and suggest recurrent creation of varietal diversity in a clonally propagated crop.
UMR DIADE, Team DYNADIV, Institut de Recherche pour le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France. nora.scarcelli@ird.fr.
Nora
N
Scarcelli
Marie
M
Couderc
Mohamed N
MN
Baco
Janvier
J
Egah
Yves
Y
Vigouroux
D000383:Agriculture; D044822:Biodiversity; D002999:Clone Cells; D003198:Computer Simulation; D027742:Dioscorea / Q000235:genetics* / Q000254:growth & development*; D056426:Genetic Loci; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D059645:Mutation Rate; D013997:Time Factors