From phenotype to genotype: the case-study of a common field trial initiated through Eucarpia for promoting Festulolium breeding

Lolium x Festuca hybrids (so-called Festulolium) renews considerably grass breeding in conjunction to the development of new genomic technology, the context of the climate change and the stressing injunction towards the breeders to release better adapted cultivars. This presentation points out some of those issues from a field trial carried out across the Eucarpia network and underlines how molecular genotyping could be essential to tackle the challenge.As hybrids between parental species quite differently adapted, Festulolium enlarge extensively genetic variability for many traits simultaneously. Two genome sources of genetic variability mix their effects within Festulolium hybrids. Thanks to preferential homologous chromosome pairing, strong linkage disequilibrium between parent species is mostly preserved within amphiploid hybrids. This contributes to maintain at intermediate level many traits simultaneously, of immediate overall advantage compared to parent species. Many experimental evidences then show that the gain of amphiploids tends to decrease as the number of generations following primary hybridization increases. When going through introgression stages into either parent species, the loss of effect on the phenotype is even more pronounced. Everything happens as if early large phenotype effects would result only from initial linkage disequilibrium, essentially at chromosome level. Thus, the exceptional high rate of homeologous recombination between Lolium and Festuca could make uneasy the retention of high linkage disequilibrium through long term selection and the recovery of substantial genetic progress.On the other hand, high heterozygosity rate due to high level of interspecific recombination could be favourable per se to stabilize Festulolium performances across years and environments, in other words, for more resilience. Thus, a better evaluation of interspecific linkage disequilibrium appears to be of crucial importance both in terms of breeding methods and breeding objectives. The challenge of breeding Festulolium may return simply to how better monitor the interspecific recombination in accordance to the objectives, either promoting it for more resilience, or fixing it at a given stage of a breeding process to take advantage of optimum Lolium-Festuca linkage disequilibrium for a given forage usage or local climate conditions.The new technology of genotyping by sequencing (GBS) has clearly this ability to assist Festulolium breeding. Genotype of individual plant as well as allele frequency in population can be assigned at thousands of single nucleotide polymorphic (SNP) loci throughout the genome, giving also access to allele dosage in polyploids which are frequent in Festulolium. In addition to the estimation of the average introgression rate among various Festulolium derivatives, GBS has also the stimulating perspective to estimate the true breeding value of traits of adaptation and how each Lolium vs Festuca genome counterpart may contribute for more precise breeding.