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Fostered and left behind alleles in peanut : interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding

Fonceka et al. BMC Plant Biology 2012. Daniel Fonceka1, Hodo-Abalo Tossim2, Ronan Rivallan1, Hélène Vignes1, Issa Faye2, Ousmane Ndoye2,
Márcio C Moretzsohn3, David J Bertioli4, Jean-Christophe Glaszmann1, Brigitte Courtois1 and Jean-François Rami1*

Background : Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated
peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its
single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be
used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a
synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for
several traits involved in peanut productivity and adaptation as well as domestication.

Results : A total of 95 QTLs were mapped in the two water treatments. About half of the QTL positive effects were
associated with alleles of the wild parent and several QTLs involved in yield components were specific to the
water-limited treatment. QTLs detected for the same trait mapped to non-homeologous genomic regions,
suggesting differential control in subgenomes as a consequence of polyploidization. The noteworthy clustering of
QTLs for traits involved in seed and pod size and in plant and pod morphology suggests, as in many crops, that a
small number of loci have contributed to peanut domestication.

Conclusion : In our study, we have identified QTLs that differentiated cultivated peanut from its wild relatives as
well as wild alleles that contributed positive variation to several traits involved in peanut productivity and
adaptation. These findings offer novel opportunities for peanut improvement using wild relatives.