Comparative transcriptomics reveals a novel variant of an energy signaling regulator for lateral branch domestication in cucumber

Genetic alleles derived from wild resources are of great importance for crop breeding and improvement; however, connecting the dots between the functional variants and genetic traits is a significant challenge due to the need for precise, diverse, and large-scale phenotyping. Differential transcripts, which carry genetic variants or alternative splicing (AS) sites, may exhibit altered gene expression and protein coding, therefore influence phenotypes, showing their potential for high-throughput identification of functional genes. In this study, full-length transcripts were assembled and analyzed from eight developmental stage tissues of wild and cultivated cucumbers, utilizing PacBio Iso-seq and Illumina RNA-seq. We identified 6,980 genes underwent AS in cucumber. Approximately 66% of AS events were cultivar-specific, and genetic variants significantly increased around these divergent AS events. Based on the transcript structure of genes and variant annotation, we focused on cis-acting genetic variants that may affect gene function, in which a 21-bp insertion in the 5′ untranslated region (UTR) of SnRK-Activating Kinase1 (CsSnAK1), an energy signaling regulator, was demonstrated to inhibit lateral branch development in cultivated cucumber by promoting CsSnAK1 mRNA abundance. Our work provides a straightforward yet reliable approach for integrating transcript structure and variant annotation to identify novel functional alleles in domestication traits.