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Key message  A dwarfism gene  LacDWARF1  was mapped by combined BSA-Seq and comparative genomics analyses to a 65.4 kb physical genomic region on chromosome 05.    Abstract  Dwarf architecture is one of the most important traits utilized in Cucurbitaceae breeding because it saves labor and increases the harvest index. To our knowledge, there has been no prior research about dwarfism in the sponge gourd. This study reports the first dwarf mutant WJ209 with a decrease in cell size and internodes. A genetic analysis revealed that the mutant phenotype was controlled by a single recessive gene, which is designated  Lacdwarf1  ( Lacd1 ). Combined with bulked segregate analysis and next-generation sequencing, we quickly mapped a 65.4 kb region on chromosome 5 using F 2  segregation population with InDel and SNP polymorphism markers. Gene annotation revealed that  Lac05g019500  encodes a gibberellin 3β-hydroxylase (GA3ox) that functions as the most likely candidate gene for  Lacd1 . DNA sequence analysis showed that there is an approximately 4 kb insertion in the first intron of  Lac05g019500  in WJ209.  Lac05g019500  is transcribed incorrectly in the dwarf mutant owing to the presence of the insertion. Moreover, the bioactive GAs decreased significantly in WJ209, and the dwarf phenotype could be restored by exogenous GA 3  treatment, indicating that WJ209 is a GA-deficient mutant. All these results support the conclusion that  Lac05g019500  is the  Lacd1  gene. In addition, RNA-Seq revealed that many genes, including those related to plant hormones, cellular process, cell wall, membrane and response to stress, were significantly altered in WJ209 compared with the wild type. This study will aid in the use of molecular marker-assisted breeding in the dwarf sponge gourd.    Supplementary Information  The online version contains supplementary material available at (10.1007/s00122-021-03938-4).

A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula)