2.2. Post-genomics and genomics-assisted breeding

The age of genomics:

Four olive genomes have been assembled so far, a development that is allowing advances in the genomics-assisted breeding. However, for an efficient use of the genomics knowledge in breeding we need to improve the quality of the assembled genomes. This goal will be probably achieved in the near future, giving way to the post-genomic era.

Furthermore, considering the high heterozygosity of the olive genome, a necessary step is also to have the two haplotypes of the genome available. In a recent Italian Project (OLGENOME) the sequencing of the Leccino genome was completed where the quality of the assembly and annotation is very high, the anchoring is complete and the haploid versions will soon be available.

QTLs for breeding: 

More and more olive varieties are currently being sequenced. This is allowing the use of GWAS analysis to find genetic markers (GM) associated to olive tree qualities. Those GM have to be confirmed by independent experiments and once this is done, we have good GM for assisted breeding. This process is underway by a number of research groups and it is reasonable to expect that in the next years we will have a number of GM to be use as QTLs in breeding.

Considering the quick linkage disequilibrium decay of olive, genome resequencing seems  to be the better technique for approaches such as GWAS than reduced-representation sequencing /GBS. The problem in olive trees is the phenotyping of a large number of varieties in different environments to consider the interaction genotype x environment and the genotypic sample which must include an adequate number of individuals and with a low level of stratification to increase the statistical power of the GWAS and reduce the possibility of spurious associations. Several works indicate very close degrees of kinship between the varieties and this can lead to spurious associations. The resequencing of genomes allows to evaluate the haplotype sharing which allows to individuate more precisely the degree of relatedness.  Genomic resequencing is also better suited for this reason. The creation of common core collections (as they did for peach), in different collections could be crucial for obtaining functional allelic variants and useful not only for GWAS but also for the application of the genome editing technique.

Efficient screening of the best genomes:

The development of new tools simplify the genetic screening of progeny plants to facilitate the work of breeders is underway. This is essential because it is important to be able to analyze as many genomes as possible to find the best combinations of a number of GM.