Reduced bunch compactness in a grapevine somatic variant

Because grapevine (Vitis vinifera L.) cultivars are highly heterozygous, they must be clonally propagated to preserve their varietal attributes. Somatic variants with looser bunches – associated with more uniform berry ripening and reduced bunch rot incidence – are particularly valuable in compact-bunch cultivars. To understand the basis of this trait, we combined phenotyping, genomics, and genetic analyses to study VP11, a loose-bunch somatic variant clone of the wine grape cultivar 'Tempranillo Tinto'. Pollen viability and the number of seeds per berry were reduced by ~50% in VP11 compared to a control clone of 'Tempranillo Tinto'. Long-read whole-genome sequencing identified eleven large somatic structural variants (SVs) in VP11, including three inter-chromosomal events. These consisted of one fixed balanced reciprocal translocation (Tra1-3), with tens-of-kilobase long duplications at the translocation breakpoints, and two segmental duplications (one fixed and one L2 meristem cell layer-restricted). All three SVs were molecularly validated, including the phasing and exchange of distal chromosome segments in Tra1-3. In VP11 self-cross progeny, pollen viability was significantly reduced among individuals carrying Tra1-3, and the two translocation chromosomes were always inherited together, indicating that gametes with an unbalanced chromosomal content are non-viable. This study identifies a heterozygous balanced translocation as a mechanism causing looser bunches in grapevine by reducing gamete viability. We conclude that even if a genetic defect reduces gamete viability, it can still be useful to decrease seed and fruit set in vegetatively propagated crops where these traits are desirable.