Fruit diameter is one of important agronomy traits that has greatly impacts fruit yield and commercial value in cucumber (Cucumis sativus L.). Hence, we preliminary mapping of fruit diameter was conducted to refine its genetic locus. In this study, to genetic mapping of QTLs that control cucumber fruit diameter, a F2 population with 120 individuals was developed by the East Asian line ‘9930’ (known as narrow fruit diameter) and the European-type cucumber ‘EU224’ (known as wide fruit diameter). Then a Genotyping-by-Sequencing (GBS)-based genetic map with 5662 markers was constructed and the total length is 656.177 cM, with average marker interval of 0.116 cM. Based on this high-density genetic map, a major QTL qfd1.1 related to fruit diameter was detected with a markedly high LOD score 4.07 located approximately 300 kb interval on Chromosome 1 (located between Chr1:1654704–1958556). To confirm qfd1.1 that detected by F2 population, we performed genetic mapping of fruit diameter with an introgression line (IL) about fruit diameter. We developed two KASP markers (FD-1 and FD-2) related to the fruit diameter. Based on this, we inserted the European cucumber EU224 into the qfd1.1 range and targeted widening the fruit diameter of the 9930 cucumber variety, further indicating that qfd1.1 is a new locus regulating the fruit diameter of cucumber. Our findings will support breeders in their research on cucumber fruit diameter.

One key post-transcriptional modification mechanism that dynamically controls a number of physiological processes in plants is alternative splicing (AS). However, the functional impacts of AS on fruit ripening remain unclear. In this research, we used RNA-seq data from climacteric (VED, Harukei 3) and non-climacteric (PI, PS) melon cultivars to explore alternative splicing (AS) in immature and mature fruit. The results revealed dramatic changes in differential AS genes (DAG) between the young and mature fruit stages, particularly in genes involved in fruit development/ripening, carotenoid and capsaicinoid biosynthesis, and starch and sucrose metabolism. Serine/arginine-rich (SR) family proteins are known as important splicing factors in AS events. From the melon genome, a total of 17 SR members were discovered in this study. These genes could be classified into eight distinct subfamilies based on gene structure and conserved motifs. Promoter analysis detected various cis-acting regulatory elements involved in hormone pathways and fruit development. Interestingly, these SR genes exhibited specific expression patterns in reproductive organs such as flowers and ovaries. Additionally, concurrent with the increase in AS levels in ripening fruit, the transcripts of these SR genes were activated during fruit maturation in both climacteric and non-climacteric melon varieties. We also found that most SR genes were under selection during domestication. These results represent a novel finding of increased AS levels and SR gene expression during fruit ripening, indicating that alternative splicing may play a role in fruit maturation.

Identification of global transcriptional events is crucial for genome annotation, as accurate annotation enhances the efficiency and comparability of genomic information across species. However, the annotation of transcripts in the cucumber genome remains to be improved, and many transcriptional events have not been well studied. We collected 1,904 high-quality public cucumber transcriptome samples from the National Center for Biotechnology Information (NCBI) to identify and annotate transcript isoforms in the cucumber genome. Over 44.26 billion Q30 clean reads were mapped to the cucumber genome with an average mapping rate of 92.75%. Transcriptome assembly identified 151,453 transcripts spanning 20,442 loci. Among these, 12.7% of transcripts exactly matched annotated genes in the cucumber reference genome. More than 80% of the transcripts were classified as novel isoforms. Approximately 96.6% of these isoforms originated from known gene loci, while around 3.3% were derived from novel gene loci. Coding potential prediction identified 4,543 long non-coding RNAs (lncRNAs) across 3,376 loci. Building on these results, we identified tissue-specific transcripts in 10 tissues. Among that, 1,655 annotated genes and 4,214 predicted transcripts were considered as tissue-specific. The root exhibited the highest number of tissue-specific transcripts, followed by shoot apex. Subsequent selective pressure analysis revealed that tissue-specific regions experienced stronger directional selection compared to non-specific regions. By analyzing thousands of published transcriptome data, we identified abundant transcriptional events and tissue-specific transcripts in cucumbers. This study presented here adds the great value to the public data and offers insights for further exploration of a more comprehensive tissue regulatory network in cucumber.