Genomic regions under selection in crop-wild hybrids of lettuce: implications for crop breeding and environmental risk assessment

The results of this thesis show that the probability of introgression of a putative transgene to wild relatives indeed depends strongly on the insertion location of the transgene. The study of genomic selection patterns can identify crop genomic regions under negative selection in multiple environments and in several cultivar-wild crosses, which could be applicable to TM strategies. For lettuce, a fitness QTL region was identified on LG7 where the crop allele conferred a selective disadvantage through delayed flowering, lower survival, and a lower fitness and possibly through a lower competitive ability. This crop genomic background is likely deleterious in the wild habitat, especially in environments with high density competition and a seasonal flowering period. However, QTL results were also (partly) cultivar specific, so that implementation in ERA will still need to be on a case-by-case basis, which decreases its general applicability. In addition, our results show that it is more informative to identify specific genomic regions under selection than to estimate average hybrid fitness. Fitness distributions indicated there is a high likelihood in lettuce for novel crop-wild hybrids to arise that have a higher fitness than the wild parent even though the average fitness of the hybrid offspring was lower. This provides an avenue for introgression of crop alleles into the wild population. A mitigation strategy based solely on placing a transgene close to a major negatively selected crop gene could have a huge quantitative effect by reducing the chances of introgression, but it would be difficult to design a strategy that would prevent it with certainty. It is commendable to evaluate the remaining risk in the perspective of the potential consequences an escape would have for the recipient environment, as well as the foreseen benefits of the GM crop