Finding missing links
Although the grapevine genome has been sequenced, scientists haven’t yet figured out the function of most of its estimated 35 000-40 000 genes. So, correlating a plant’s genotype (its DNA) with its phenotype (its observable and measurable characteristics) presents challenges.
One way to do this is quantitative trait locus (QTL) mapping. Fortunately for Lashbrooke, table-grape breeder Phyllis Burger from the ARC Infruitec-Nietvoorbij had laid the groundwork by crossing two cultivars with contrasting characteristics.
Burger chose Deckrot, a red-fleshed wine-grape cultivar with compact bunches, and G1-7720, a red ARC table-grape selection with loose bunches, as parent vines. “A primary reason Phyllis made this cross was to bring red flesh into table grapes, putting her ahead of her time,” comments Lashbrooke.
Burger raised about 120 of the offspring from her cross, each representing a unique recombination of the parental genomes. As a result, the offspring exhibited a range of phenotypes spanning the extremes of their parents.
“So, let’s say you rate them on a scale of one to 10 for compact to loose bunches, and then you do genotyping of this population,” explains Lashbrooke. “Then you can determine statistically which bits of the genome are more often present when the bunches are loose or when they are compact. This statistical linkage is called QTL mapping.”
The map doesn’t identify the genes influencing traits, but it does point researchers to the right gene regions. Considering that the grapevine genome has about 500 million base pairs (about the same as the number of letters in 1 000 standard novels), knowing where to focus is a good start.
Zooming in further
Identifying the gene regions linked to traits of interest is like using a table of contents to turn to the right book chapter. Despite being a tiny subset of the whole genome, these regions still contain hundreds of genes, and only a few are linked to the trait of interest.
To get from the right chapter to the right page, Lashbrooke used transcriptome analysis to quantify gene expression in developing flowers.
“The developing flower is important because that is where the genes that change the bunch shape are expressed,” he says. “Once the flower is formed, the bunch shape will be quite similar to that flower shape.”
He uncovered several genes that are differentially expressed in loose and compact bunches. Overlaying this information with the QTL maps highlighted where significant changes in gene expression co-located with regions that were statistically associated with bunch architecture.
Having narrowed his focus, Lashbrooke’s next step is to find the variants linked to bunch shape and develop markers for them. However, he cautions that bunch architecture is likely influenced by multiple genes, not all of which are necessarily present in his study population.
“All we would be able to say is that, for our population of grapevines, a particular genetic region contributes a certain percentage of the variation in bunch architecture,” he says. “But the only genetics we’re studying are those present in the two cultivars that were in the cross. Any other interesting genetics that aren’t in those cultivars are never even considered in this work.”
Nonetheless, this project adds to a growing body of research on grapevine genetics that is already informing breeding programmes.
“Marker-assisted selection is happening all over the world,” says Lashbrooke. “We just need more markers to make it more interesting, and those markers need to be linked to traits breeders want or want to avoid, like cracking.”
Moving the limits
Berry cracking is a headache for many growers in SA and abroad. Scientists have demonstrated that cracking has a strong genetic basis, and Lashbrooke has conducted extensive research (funded by SATI and the Post-Harvest Innovation Fund) on its mechanism.
Recently, he discovered that berries with more elastic skins are better able to withstand cracking, whereas those with stronger skins are not.
While searching for genetic variation related to cracking among Burger’s vines, he noticed that red-fleshed grapes appear far more crack-resistant than white-fleshed grapes. This could be because red flesh in itself relates to crack resistance, or because there are genes imparting crack resistance close to the genes for red flesh – the closer together genes are, the more likely they are to be inherited together.
“We’re investigating, but we have seen that berries with red flesh are usually not crisp at all,” says Lashbrooke. “They are also elastic, which correlates with my previous findings.”
Understanding problems such as cracking at the level of genes, biochemistry, and berry skins may seem like an academic exercise, but it’s the only way to ensure those problems aren’t bred into new cultivars.
For Lashbrooke, grasping and harnessing the full genetic potential of grapevines is critical for the future of the table-grape industry.
“Growers get better and better at growing plants using new technologies, but we’re clearly reaching a limit of what we can do, and that limit is the genetic potential,” he says. “Breeding exists to move that genetic limit.”
More on Lashbrooke’s berry-cracking research (SAFJ Feb|Mar 2026).
