First brassinosteroid-based dwarf mutant discovered and characterized in grapevine

In this study, we investigated the genetic control of dwarfism in naturally occurring dwarf mutant lines of grapevines. Through trait-segregation and marker-trait association analyses, we identified a major locus on Chromosome 14 tightly associated with the dwarf trait. Subsequently, we conducted a bulked RNA-seq analysis, fine mapped the dwarf trait and identified VviBR6OX1, a cytochrome P450 enzyme involved in brassinosteroid synthesis, as a candidate gene for the observed dwarfism. RNA-seq sequence analyses revealed two in-frame deletions in the gene: a 12-bp deletion in exon 1 and a 9-bp deletion in exon 4. A survey of the two indels in Vitis germplasm suggested that the 9-bp deletion is most likely the cause of dwarfism in the mutant. We recreated similar dwarf grapevines by knocking out VviBR6OX1 using CRISPR/Cas9 gene editing and confirmed VviBR6OX1's role in controlling vine architecture. Additionally, we observed several vines with an extreme compact dwarf phenotype and determined that the compact dwarfing phenotype was a result of simultaneous editing of a second BR6OX gene, VviBR6OX2. The discovery of BR-related dwarfism in grapevine provides an important genetic avenue for developing desirable vine architecture for various breeding purposes.