Abstract
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.