Genetic markers for traits of interest in table grape breeding: berry cracking and bunch architecture

PROJECT TITLE:    Genetic markers for traits of interest in table grape breeding: berry cracking and bunch architecture

Project leader:       Justin Lashbrooke (Stellenbosch University)

Contact:                    jglash@sun.ac.za

Duration:                   1 January 2023 – 31 December 2026

Problem identification and project objectives:

Till now molecular markers have been only sparingly used towards the breeding of table grapes in South Africa. However an initial SATI funded project which comes to an end this year has identified markers for terpene based flavour and aroma, as well potential QTLs for bunch and berry morphology. Importantly this work has established a cross populations with a well characterised genetic linkage map, meaning that subsequent genetic marker development requires only trait scoring (phenotyping) in this population.
The project proposed here plans to score berry cracking and the gene expression underlying bunch architecture traits across this mapping population, and subsequently perform QTL analysis, in order to then develop genetic markers for these traits.
Currently markers do not exist for berry cracking, a major problem for grape growers worldwide, therefore developing markers and subsequently novel crack resistant cultivars is seen as a priority for many breeders. It is known that berry cracking has a strong genetic component (Ramteke et al., 2017; Yamamoto and Satoh, 1994), therefore development of genetic markers is theoretically possible. Such markers will greatly assist breeders to select appropriate crack resistant cultivars (Zoffoli et al, 2009).
Recent work in our group has identified novel bunch architecture QTLs, but this work needs to be expanded upon in order for reliable genetic markers to be developed. Bunch architecture is a complex trait, with several contributing parameters such as inflorescence and bunch cluster architecture, fruitfulness and berry size (Molitor et al., 2012). While environmental conditions of cultivation may impact bunch cluster compactness, it is a trait predominantly under genetic control, evidenced by the heritability of cluster compactness observed across grapevine cultivars (Tello et al., 2015). Compact bunches lead to berries that may ripen asynchronously, affecting quality at harvest, while compact bunches may trap water, or provide shelter to insects, thereby increasing susceptibility to diseases. Despite the importance of this trait, the molecular and genetic control of cluster compactness remains relatively poorly described. Gene expression QTLs are a promising approach to better understating this important morphological trait, and to develop more robust genetic markers (Grimplet et al., 2017).
The planned work will therefore involve scoring of berry crack susceptibility and of large-scale gene expression profiling of inflorescence across the mapping population. The data generated will then be used for traditional QTL and gene expression based QTL analysis respectively. Genomic regions identified will be interrogated, and candidate genetic markers identified. The markers will be evaluated in existing crosses and mapping populations to determine their usability/functionality in our ongoing breeding projects. Indeed, successfully characterised markers for these traits will then be used in ongoing breeding efforts to better streamline, reduce costs, and breed in a more predictive manner novel cultivars with desirable traits.