Modern grapevine breeding applies marker-assisted selection (MAS). Based on this technology important traits can be tracked on genetic level very early in the breeding process. The desired traits need to be genetically mapped, candidate genes responsible for the traits need to be identified and characterized in regard to their diversity. Molecular genetics provides the tools for this purpose. The Institute develops molecular markers for MAS breeding from the genetic differences detected.
Identification of genetic loci that carry factors affecting the level of important traits requires genetic mapping. Such maps are constructed by investigating the inheritance of several hundred small genetic elements (“markers”) in the progenies of controlled crosses. In this way marker maps covering the individual chromosomes are obtained. In a second step the genetic information is combined with the level of expression of desired traits (e.g. resistance, quality). Special computation reveals genetic linkage between a marker and a trait. In case of such linkage the corresponding locus can be studied in the completely analyzed genome of a reference model grape (PN40024, a special inbred line of `Pinot noir´) and candidate genes that may be responsible for the trait can be identified.
If the corresponding loci are absent in the model genome (e.g. factors for disease resistance) candidate genes need to be investigated in the corresponding locus-carriers of grapevine. The loci need to be analyzed for their genetic constitution. This is frequently achieved by screening of libraries that contain the complete genome fragmented in large pieces that may be easily propagated under laboratory conditions. Using the trait-linked molecular markers the locus-carrying fragments can be identified and analyzed for the presence of candidate genes. In some cases the loci may also be investigated by PCR (polymerase chain reaction) amplification of smaller genomic regions. In other cases NGS (Next Gen Sequencing) methods are applied to determine the genetic material of an interesting grapevine.
Candidate genes may also be identified by studying gene activities under special conditions. This approach is taken for genes localized in trait-determining genetic loci, genes described in the context of an interesting trait in the literature, or genes deduced from the complete set of genes that were found to be differentially active e.g. in comparison of a resistant and a susceptible grapevine variety early after fungal inoculation (RNA-Seq).
Finally any candidate gene of interest for breeding of new resistant high-quality grapevine cultivars has to undergo functional analysis to confirm its impact on the desired trait.