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

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.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.Polyploidy means that two or more complete sets of chromosomes of the same (autopolyploid) or different (allopolyploid) genomes are present in the same nucleus. It is a prominent and significant process in plant evolution [1,2]. Polyploidy has been considered important in conferring adaptive value to some cultivated species by increasing the allelic diversity, maintaining genome-wide heterozygosity and allowing the emergence of novel phenotypic variation [3-6]. The stages of polyploid formation usually include reproductive isolation from the progenitors, resulting in severe genetic bottlenecks. However, as most polyploid species have been formed recurrently from their wild progenitors [7], a moderate level of polymorphism has been kept in polyploid plants. Peanut (Arachis hypogaea L.) is an allotetraploid (2n = 4x = 40) native from South America with an AB genome. In contrast to the recurrent formation of several polyploid species, the allopolyploid structure of cultivated peanut is likely derived from a single hybridization between two wild diploid species followed by