INTEGRATING MOLECULAR MARKERS in table-grape breeding

Thus far, molecular markers have been used only sparingly in the breeding of table grapes in SA. Efforts to date focused on introducing fungal resistance genes (for downy and powdery mildews) from wild grapevine relatives. However, the use of molecular markers in grapevine breeding has the potential to go beyond just disease resistance and to encompass a wider range of traits. This is particularly important when using wild non-vinifera relatives in breeding programmes.

These plants may contribute desirable traits to counteract biotic and abiotic stresses. But they may also introduce undesirable genetic material that leads to uneven and low yields, undesirable bunch and berry morphologies and certain off-flavours and aromas. Therefore, while a significant number of markers have been developed for resistance traits, there has been a major global effort over the last few years to develop markers specifically for other agronomically relevant and quality-associated traits. For example, researchers have identified molecular markers for traits such as berry colour, berry size, berry flesh development, and aroma formation.

Thus, SATI has funded research to initiate the use of genetic markers in molecular selection, breeding, and quantitative trait locus (QTL) mapping. The goal of this research is to develop and validate molecular markers that could be used for marker-assisted selection in on-going grapevine breeding efforts. As only a handful of markers currently exist for quality traits in grapevine, our initial work involved QTL analysis of a grapevine mapping population created by Phyllis Burger, at ARC Infruitec-Nietvoorbij.

This mapping population consisted of segregating individuals derived from a cross between two grapevine cultivars, each with distinct berry quality traits (Figure 1). The objective was to identify genomic regions associated with the target traits and to potentially develop molecular markers that could be used for marker-assisted selection in future breeding programmes.

This work entails constructing what is known as a genetic map first, for the population (Vervalle et al., 2022). This map can then be used to statistically associate quantifiable traits with genetic regions. The initial results identified promise associations between specific genomic regions and quality traits such as bunch and berry morphology, phenolic content, and volatile aroma production. This indicates the potential for molecular marker development for these traits. Genetic markers for flavour compound formation were then created and optimised and were able to predict the potential for grapes in our germplasm to produce muscat and/or floral flavours (Bosman et al., 2022).

The next step of this work is to develop markers for traits related to berry size and shape, and bunch architecture, so that seedlings may be selected at an early stage for desirable berry and bunch characteristics. The first results from this work demonstrates the potential of using molecular markers in grapevine breeding to enhance the selection process for desirable quality traits. The success of future work will rely on the interaction of growers, breeders, and molecular biologists, so that molecular markers are developed for the most important traits for our local industry.

Figure 1 is an illustration of the grapevine parents used in the cross to create the mapping population investigated in this work. Importantly for the quantitative genetic study performed in this work, the parent cultivars not only differed for their flesh colour, but also for several traits indicated in the figure, including bunch density, seededness, aroma/flavour, berry size and waxiness.

References

Bosman, R., J. Vervalle, D. November, P. Burger, and J. Lashbrooke. 2023. "Grapevine genome analysis demonstrates the role of gene copy number variation in the formation of monoterpenes." Frontiers in Plant Science. 14:1112214. doi: 10.3389/fpls.2023.1112214

Vervalle, J., L. Costantini, S. Lorenzi, M. Pindo, R. Mora, G. Bolognesi, M. Marini, J. Lashbrooke, K. Tobutt, M. Vivier, R. Roodt-Wilding, M. Grando, D. Bellin. 2022. "A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip." Theroretical and Applied Genetics 135, 4371-4390 (2022). https://doi.org/10.1007/s00122-022-04225-6