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

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ID: 338933
2026
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Abstract
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.
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Authors Yanling Wang, Mengzhuo Zhang, Tongxu Xin, Zhenzhen Wang, Min Ni, Han Zhang, Yuhong Li, Juan Xu, Xue Yong Yang
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Journal The Plant cell
Year 2026
DOI
10.1093/plcell/koag341
URL
https://doi.org/10.1093/plcell/koag341
Keywords Keywords not found

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