Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated breakinduced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.

Sex determination in plants involves a variety of mechanisms. Here, we report the map-based cloning and characterization of the unisexual-flower-controlling gene M. M was identified as a previously characterized putative 1-aminocyclopropane-1-carboxylic acid synthase gene, while the m allele that mutated at a conserved site (Gly33Cys) lost activity in the original enzymatically active allele.

Plant trichomes serve as a highly suitable model for investigating cell differentiation at the single-cell level. The regulatory genes involved in unicellular trichome development in Arabidopsis thaliana have been intensively studied, but genes regulating multicellular trichome development in plants remain unclear. Here, we characterized Cucumis sativus (cucumber) trichomes as representative multicellular and unbranched structures, and identified Micro-trichome (Mict), using map-based cloning in an F 2 segregating population of 7,936 individuals generated from a spontaneous mict mutant. In mict plants, trichomes in both leaves and fruits, are small, poorly developed, and denser than in the wild type. Sequence analysis revealed that a 2,649-bp genomic deletion, spanning the first and second exons, occurred in a plant-specific class I homeodomain-leucine zipper gene. Tissue-specific expression analysis indicated that Mict is strongly expressed in the trichome cells. Transcriptome profiling identified potential targets of Mict including putative homologs of genes known in other systems to regulate trichome development, meristem determinacy, and hormone responsiveness. Phylogenic analysis charted the relationships among putative homologs in angiosperms. Our paper represents initial steps toward understanding the development of multicellular trichomes.

Powdery mildew is a common disease in plants, and it is also one of the main diseases in the middle and final stages of cucumber (Cucumis sativus). Powdery mildew on plant leaves affects the photosynthesis, which may reduce the plant yield. Therefore, it is of great significance to automatically identify powdery mildew. Currently, most image-based models commonly regard the powdery mildew identification problem as a dichotomy case, yielding a true or false classification assertion. However, quantitative assessment of disease resistance traits plays an important role in the screening of breeders for plant varieties. Therefore, there is an urgent need to exploit the extent to which leaves are infected which can be obtained by the area of diseases regions. In order to tackle these challenges, we propose a semantic segmentation model based on convolutional neural networks (CNN) to segment the powdery mildew on cucumber leaf images at pixel level, achieving an average pixel accuracy of 96.08%, intersection over union of 72.11% and Dice accuracy of 83.45% on twenty test samples. This outperforms the existing segmentation methods, K-means, Random forest, and GBDT methods. In conclusion, the proposed model is capable of segmenting the powdery mildew on cucumber leaves at pixel level, which makes a valuable tool for cucumber breeders to assess the severity of powdery mildew.

A set of 224 recombinant inbred lines (RILs) derived from a narrow cross between two fresh eaten types (S94 (Northern China type) 9 S06 (Northern European type)) (Cucumis sativus L.) was used to construct a genetic linkage map. With the RILs a 257-point genetic map was constructed including 206 SRAPs, 22 SSRs, 25 SCARs, 1 STS, and three economically important morphological markers (small spines (ss), uniform immature fruit color (u), dull fruit skin (D)). The seven linkage groups covered 1005.9 cM with a mean marker interval of 3.9 cM.The ss locus was linked to D and u, and they were all on Linkage group 6. The RIL map contained a total of 51 sequence-specific markers, which made possible the comparison of molecular linkage maps developed in different laboratories. Using the F 6:7 derived families, a total of 78 QTLs were detected with relatively high LOD scores (2.9-84.4) for nine fruit-related traits (fruit weight, length, and diameter, fruit flesh thickness, seed-cavity diameter, fruit-stalk length, fruit pedicel length, length/diameter and length/stalk ratio) and three flower-related traits (first flower node, first female flower node and female flower ratios). Several sequence-anchor markers (CSWCT25, CS30, CMBR41, CS08 etc.) were closely linked with some QTLs for fruit weight, fruit length, fruit flesh thickness and sex expression, which can be used for the future marker-assisted selection to improve the fruit traits in cucumber breeding.

SUMMARYCucumber fruits that have tubercules and spines (trichomes) are known to possess a warty (Wty) phenotype. In this study, the tuberculate fruit gene Tu was identified by map-based cloning, and was found to encode a transcription factor (TF) with a single C 2 H 2 zinc finger domain. Tu was identified in all 38 Wty lines examined, and was completely absent from all 56 non-warty (nWty) lines. Cucumber plants transgenic for Tu (TCP) revealed that Tu was required for the Wty fruit phenotype. Subcellular localization showed that the fusion protein GFP-Tu was localized mainly to the nucleus. Based on analyses of semi-quantitative and quantitative reverse transcription polymerase chain reaction (RT-PCR), and mRNA in situ hybridization, we found that Tu was expressed specifically in fruit spine cells during development of fruit tubercules. Moreover, cytokinin (CTK) content measurements and cytological observations in Wty and nWty fruits revealed that the Wty fruit phenotype correlated with high endogenous CTK concentrations. As a result of further analyses on the transcriptomic profile of the nWty fruit epidermis and TCP fruit warts, expression of CTKassociated genes, and hormone content in nWty fruit epidermis, Wty fruit warts and epidermis, and TCP fruit warts and epidermis, we found that Tu probably promoted CTK biosynthesis in fruit warts. Here we show that Tu could not be expressed in the glabrous and tubercule-free mutant line gl that contained Tu, this result that futher confirmed the epistatic effect of the trichome (spine) gene Gl over Tu. Taken together, these data led us to propose a genetic pathway for the Wty fruit trait that could guide future mechanistic studies.

A 173-point genetic linkage map of cucumber (Cucumis sativus L.), consisting of 116 SRAPs, 33 RAPDs, 11 SSRs, 9 SCARs, 3 ISSRs, and 1 STS, was constructed using 130 F 2 progeny derived from a narrow cross between line S94 (Northern China open-field type) and line S06 (greenhouse European type). The seven linkage groups spanned 1016 cM with a mean marker interval of 5.9 cM. Using the F 2 population and its F 3 derived families, a total of 38 QTLs were detected on five linkage groups with an LOD threshold of 3.0 for nine fruit-related traits: fruit weight, length, and diameter, fruit flesh thickness, seed-cavity diameter, fruit-stalk length, fruit pedicel length, length/diameter and length/stalk ratio. Of the identified QTLs, fsl4.3 for fruit-stalk length explained the largest portion of phenotypic variation (r 2 ¼ 30%). Several QTLs were detected in the same linkage region in different generations and different seasons. Additionally, several QTLs for various fruit traits were mapped to the same or neighbouring marker intervals, suggesting they are possible character associations for controlling cucumber fruit development.

Fruit spines are a special type of trichome that impacts the quality and appearance of cucumber (Cucumis sativus L.) fruit. Scanning electron microscopy revealed that the trichome-less (tril) mutant originating from European greenhouse cucumber has a completely glabrous phenotype on cotyledons, hypocotyls, young leaves, fruits, and fruit stalks. Genetic analysis revealed that tril was inherited as a recessive allele at a single locus. Using 1058 F2 individuals derived from a cross between cucumber tril mutant CGN19839 and the micro-trichome (mict) mutant 06-2, tril was mapped to chromosome 6, and narrowed down to a 37.4 kb genomic region which carries seven predicted genes. Genetic and molecular analyses revealed that gene Cucsa.045360 is a possible candidate gene for the differentiation of epidermal cells to trichomes. It is a member of the class IV homeodomain-leucine zipper (HD-Zip IV) family and encodes homeodomain and START domain, sharing 66.7% predicted amino acid sequence identity to PROTODERMAL FACTOR2 (PDF2) and 35.0% to GLABRA2 (GL2) of Arabidopsis. The homeobox domain had changed amino acid sequence because of an insertion in tril mutant. The results of genetic analysis and transcriptome profiling indicated that the Tril gene had an epistatic effect on the Mict gene in trichome development. Phenotypes of the tril mutant such as glabrous fruits and female flowers at every node could be used in developing new cultivars.