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BackgroundTrichomes are excellent model systems for the analysis of cell differentiation and play essential roles in plant protection. From cucumber inbred line ‘WD1’, we identified an EMS-induced trichome abnormally developing mutant,nps, which exhibited smaller, denser and no pyramid-shaped head trichomes.ResultsUsing F2and BC1populations constructed from a cross betweennpsand ‘9930’, the genetic analysis showed that thenpstrait is controlled by a single recessive nuclear gene. We identifiedCsNpsby map-based cloning with 576 individuals of the F2population generated from the cross ofnpsand inbred line ‘9930’. TheCsNpswas located at a 13.4-kb genomic region on chromosome 3, which region contains three predicted genes. Sequence analysis showed that only one single nucleotide mutation (C → T) between 9930 andnpswas found in the second exon ofCsa3G748220, a plant-specific class I HD-Zip gene. The result of allelism test also indicated thatnpsis a novel allelic mutant ofMict(Micro-trichome). Thus,npswas renamedmict-L130F. By comparing the transcriptome ofmict-L130Fvs WD1 and 06–2 (mict) vs 06–1 (wildtype, near-isogenic line of 06–2), several potential target genes that may be related to trichome development were identified.ConclusionsOur results demonstrate thatMict-L130Fis involved in the morphogenesis of trichomes. Map-based cloning of theMict-L130Fgene could promote the study of trichome development in cucumber.

Sex determination is a crucially important developmental event that is pervasive throughout nature and enhances the adaptation of species. Among plants, cucumber (Cucumis sativus L.) can generate both unisexual and bisexual flowers, and the sex type is mainly controlled by several 1-aminocyclopropane-1-carboxylic acid synthases (CsACSs). However, the regulatory mechanism of these synthases remains elusive. Here, we used gene expression analysis, protein–DNA interaction assays, and transgenic plants to study the function of a gynoecium-specific gene, ETHYLENE RESPONSE FACTOR31 (CsERF31), in female flower differentiation. We found that in a predetermined female flower, ethylene signaling activates CsERF31 by CsEIN3, and then CsERF31 stimulates CsACS2, which triggers a positive feedback loop to ensure female rather than bisexual flower development. A similar interplay is functionally conserved in melon (Cucumis melo L.). Knockdown of CsERF31 by RNAi causes defective bisexual flowers to replace female flowers. Ectopic expression of CsERF31 suppresses stamen development and promotes pistil development in male flowers, demonstrating that CsERF31 functions as a sex switch. Taken together, our data confirm that CsERF31 represents the molecular link between female–male determination and female–bisexual determination, and provide mechanistic insight into how ethylene promotes female flowers, rather than bisexual flowers, in cucumber sex determination.

An unusual flower and tendril (uft) mutant in cucumber was caused by a mutation in Csa1G056950 encoding an F-box protein. Flowers and tendrils are important agronomic and yield traits of cucumber (Cucumis sativus L.). In this study, we identified an unusual flower and tendril (uft) mutant from an ethyl methanesulfonate (EMS) mutagenesis population. Genetic analysis revealed that the phenotype of the uft mutant was regulated by a single recessive nuclear gene. Map-based cloning and MutMap+ results demonstrated that Csa1G056950 (CsUFO), encoding an F-box protein, was the causal gene for the uft mutant phenotype of cucumber. A single nucleotide polymorphism (SNP) mutation (C to T) in the second exon of CsUFO resulted in premature translation termination. The expression level of CsUFO was significantly decreased in apical buds of the uft mutant compared with the wild-type (WT) WD1. Transcriptome analysis indicated that many genes for organ development were down-regulated in uft plants, suggesting CsUFO-associated networks that regulate flower and tendril development. These findings provide a new insight into understanding the molecular mechanisms of flower organogenesis in cucumber.

CsSh5.1, which controls hypocotyl elongation under high temperature conditions in cucumber, was mapped to a 57.1 kb region on chromosome 5 containing a candidate gene encoding a xyloglucan galactosyltransferase. Hypocotyl growth is a vital process in seedling establishment. Hypocotyl elongation after germination relies more on longitudinal cell elongation than cell division. Cell elongation is largely determined by the extensibility of the cell wall. Here, we identified a spontaneous mutant in cucumber (Cucumis sativus L.), sh5.1, which exhibits a temperature-insensitive short hypocotyl phenotype. Genetic analysis showed that the phenotype of sh5.1 was controlled by a recessive nuclear gene. CsSh5.1 was mapped to a 57.1 kb interval on chromosome 5, containing eight predicted genes. Sequencing analysis revealed that the Csa5G171710 is the candidate gene of CsSh5.1, which was further confirmed via co-segregation analysis and genomic DNA sequencing in natural cucumber variations. The result indicated that hypocotyl elongation might be controlled by this gene. CsSh5.1 encodes a xyloglucan galactosyltransferase that specifically adds galactose to xyloglucan and forms galactosylated xyloglucans, which determine the strength and extensibility of the cell walls. CsSh5.1 expression in wild-type (WT) hypocotyl was significantly higher than that in sh5.1 hypocotyl under high temperature, suggesting its important role in hypocotyl cell elongation under high temperature. The identification of CsSh5.1 is helpful for elucidating the function of xyloglucan galactosyltransferase in cell wall expansion and understanding the mechanism of hypocotyl elongation in cucumber.

Plants monitor environmental cues to balance growth by optimizing their inflorescence architecture. TERMINAL FLOWER 1 (TFL1) and its orthologues regulate the inflorescence structure in cucumber, yet the mechanisms underlying their responses to environmental factors and the formation of terminal flowers remain elusive. Here, we performed map-based cloning to identify the gene that controls a season-dependent determinate growth phenotype and found that it was caused by the complete deletion of CsTFL1 in the genome of cucumber line WI1983Hde. In the CsTFL1 deletion plants (CsTFL1del ), determinate growth could be partially rescued by high-temperature and long-day conditions. The expressions of CsTFL1 and its orthologue CsTFL1d could be upregulated by long-day and high-temperature signals. Knockdown of CsTFL1d resulted in determinate growth and the formation of terminal flowers in WT. These results indicate that the induction of CsTFL1d expression by long-day and high- temperature might partially rescue determinate growth of CsTFL1del . Furthermore, biochemical analyses showed that CsTFL1d interacts directly with CsNOT2a, which indicated that CsTFL1d and CsTFL1 function via similar regulatory mechanism. Our data suggest that CsTFL1 and CsTFL1d co-contribute to inhibit determinate growth by responding to temperature and photoperiod signals. It provides mechanistic insights into how environmental cues sculpt the inflorescence architecture of cucumber. This article is protected by copyright. All rights reserved.

Trichomes that cover the epidermis of aerial plant organs play multiple roles in plant protection. Compared with a unicellular trichome in model plants, the development mechanism of the multicellular trichome is largely unclear. Notably, variations in trichome development are often accompanied by defects in the biosynthesis of cuticle and secondary metabolites; however, major questions about the interactions between developmental differences in trichomes and defects in metabolic pathways remain unanswered. Here, we characterized the glabrous mutantmict/csgl1/cstbhvia combined metabolomic and transcriptomic analyses to extend our limited knowledge regarding multicellular trichome development and metabolism in cucumber.Mictwas found to be explicitly expressed within trichome cells. Transcriptomic analysis indicated that genes involved in flavonoid and cuticle metabolism are significantly downregulated inmictmutants. Further metabolomic analysis confirmed that flavonoids, lipids, and cuticle compositions are dramatically altered inmictmutants. Additional studies revealed thatMictregulates flavonoid, lipid, and cuticle biosynthesis by likely directly binding to downstream functional genes, such asCsTT4,CsFLS1,CsCER26, andCsMYB36. These findings suggest that specific metabolic pathways (e.g., flavonoids and cuticle components) are co-regulated byMictand provide insights into transcriptional regulation mechanisms of multicellular trichome development and its specific metabolism in cucumber.

Additional file 5 File S1 Amino acid sequence alignment of Mict between 10 cucumber natural lines and mutant nps.

Additional file 1 Figure S1 Partical results of linkage analysis with dcaps-M demonstrating that this marker is co-segregated with the phenotype.

Additional file 3 Figure S3 qRT-PCR confirmation of differentially expressed genes identified by transcriptome analysis.

Additional file 4 Figure S4 Mict-L130F activates the expression of CsTT4, CsFLS1, CsCER26, and CsMYB36.

Fruit tumor is one of the importantly external quality traits affected to the economic value of cucumber fruit. In order to obtain the paraffin section technology and study the cytological mechanism of morphological formation for fruit tumor in cucumber, we used the samples of warty fruit line (S52) and non-warty fruit lines (S42 with big fruit spine and S06 with small fruit spine) as materials, and improved some key links such as dehydration, dyeing and dewaxing etc., based on traditional paraffin section technology. Results demonstrated that increasing ethanol concentration gradient during dehydration can shorten the treatment time of each stage to 30 minutes. Samples were stained with Ehrlich's hematoxylin for three days, which was convenient for subsequent operation. Optimal thickness of the section was 8 μm. After twice pure xylene dewaxing, sections could be examined and selected by microscope, which shortened the time for obtaining high-quality section. High quality sections with complete tissue and clear structure can be obtained by the optimized paraffin section technology, which is an effective method to observe the cytological structure of fruit tumor. This study provides a set of complete and efficient operation steps of paraffin section technology for cucumber fruit tumor, which will provide technical reference for anatomical researches on other organs in cucumber and structural similar characteristics of other plants.

Additional file 2 Figure S2 Phenotype of leaves on nps, mict and F1(nps×mict).

The leaf is an important photosynthetic organ and plays an essential role in the growth and development of plants. Leaf color mutants are ideal materials for studying chlorophyll metabolism, chloroplast development, and photosynthesis. In this study, we identified an EMS-induced mutant, yl2.1, which exhibited yellow cotyledons and true leaves that did not turn green with leaf growth. The yl2.1 locus was controlled by a recessive nuclear gene. The CsYL2.1 was mapped to a 166.7-kb genomic region on chromosome 2, which contains 24 predicted genes. Only one non-synonymous single nucleotide polymorphism (SNP) was found between yl2.1 and wt-WD1 that was located in Exon 7 of Csa2G263900, resulting in an amino acid substitution. CsYL2.1 encodes a plastid isoform of triose phosphate isomerase (pdTPI), which catalyzes the reversible conversion of dihydroxyacetone phosphate (DHAP) to glyceraldehyde-3-phosphate (GAP) in chloroplasts. CsYL2.1 was highly expressed in the cotyledons and leaves. The mesophyll cells of the yl2.1 leaves contained reduced chlorophyll and abnormal chloroplasts. Correspondingly, the photosynthetic efficiency of the yl2.1 leaves was impaired. Identification of CsYL2.1 is helpful in elucidating the function of ptTPI in the chlorophyll metabolism and chloroplast development and understanding the molecular mechanism of this leaf color variant in cucumber.

The leaf is an important photosynthetic organ and plays an essential role in the growth and development of plants. Leaf color mutants are ideal materials for studying chlorophyll metabolism, chloroplast development, and photosynthesis. In this study, we identified an EMS-induced mutant, yl2.1, which exhibited yellow cotyledons and true leaves that did not turn green with leaf growth. The yl2.1 locus was controlled by a recessive nuclear gene. The CsYL2.1 was mapped to a 166.7-kb genomic region on chromosome 2, which contains 24 predicted genes. Only one non-synonymous single nucleotide polymorphism (SNP) was found between yl2.1 and wt-WD1 that was located in Exon 7 of Csa2G263900, resulting in an amino acid substitution. CsYL2.1 encodes a plastid isoform of triose phosphate isomerase (pdTPI), which catalyzes the reversible conversion of dihydroxyacetone phosphate (DHAP) to glyceraldehyde-3-phosphate (GAP) in chloroplasts. CsYL2.1 was highly expressed in the cotyledons and leaves. The mesophyll cells of the yl2.1 leaves contained reduced chlorophyll and abnormal chloroplasts. Correspondingly, the photosynthetic efficiency of the yl2.1 leaves was impaired. Identification of CsYL2.1 is helpful in elucidating the function of ptTPI in the chlorophyll metabolism and chloroplast development and understanding the molecular mechanism of this leaf color variant in cucumber.

TCP proteins are plant-specific transcription factors widely implicated in leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, the relationship between the transcription pattern of TCPs and organ development in cucumber has not been systematically studied. In this study, we performed a genome-wide identification of putative TCP genes and analyzed their chromosomal location, gene structure, conserved motif, and transcript expression. A total of 27 putative TCP genes were identified and characterized in cucumber. All 27 putative CsTCP genes were classified into class I and class II. Class I comprised 12 CsTCPs and Class II contained 15 CsTCPs. The 27 putative CsTCP genes were randomly distributed in five of seven chromosomes in cucumber. Four putative CsTCP genes were found to contain putative miR319 target sites. Quantitative RT-PCR revealed that 27 putative CsTCP genes exhibited different expression patterns in cucumber tissues and floral organ development. Transcript expression and phenotype analysis showed that the putative CsTCP genes responded to temperature and photoperiod and were induced by gibberellin (GA)and ethylene treatment, which suggested that CsTCP genes may regulate the lateral branching by involving in multiple signal pathways. These results lay the foundation for studying the function of cucumber TCP genes in the future.

Background: The trichomes of cucumber fruits are also called spines. Cucumber has important commercial value, and its fruit spines represent a classical tissue with which to study the cell division and differentiation mode of multicellular trichomes. Although there have been many studies on the development of unicellular trichomes in model plants, the molecular mechanism of multicellular trichome formation remains elusive. In this study, we used a pair of cucumber materials defined as having hard (Ts, wild type) or tender (ts, mutant) spines in a previous study. The whole developmental process of fruit spines was continuously observed by microscopy and SEM. In an attempt to define the developmental stages of fruit spines, transcriptome profiles at different stages were determined to explore the molecular mechanisms underlying the process of spine development. Results: According to significant phenotypic differences, the developmental process of fruit spines was clearly defined as involving four stages. Comparison of transcriptome profiles showed that 803 and 722 genes were upregulated in the stalk (stage II and stage III) and base (stage IV) developmental stages of fruit spines, respectively. Functional analysis of differentially expressed genes (DEGs) showed that for all developmental stages of fruit spines, lipid metabolism, amino acid metabolism, and signal transduction were the most noticeable pathways. However, during the development of the stalk, genes related to auxin polar transport and HD-ZIP transcription factors were significantly upregulated. bHLH transcription factors and cytoskeleton-related genes were significantly upregulated during the development of the base. In addition, stage III was the key point for differentiating between the wild type and mutant. We detected 628 DEGs between the wild type and mutant at this stage. These DEGs are mainly involved in calcium signaling of the cytoskeleton and auxin polar transport, indicating that the main reason for the disorder of the fruit spine developmental pattern in the mutant was a change in cell polarity caused by blocked intercellular signal transmission.Conclusions: Our study defines in great detail the developmental stages of cucumber fruit spines. At the same time, transcriptome profiles are used to present the gene regulatory networks at different developmental stages of cucumber fruit spines. In addition, we analyzed transcriptomic data of a wild type and mutant to elucidate the biological pathways involving C-type lectin receptor-like kinase that regulate the development of fruit spines.

Trichomes and fruit spines are important traits that directly affect the appearance quality and commercial value of cucumber (Cucumis sativus). Tril (Trichome-less), encodes a HD-Zip IV transcription factor that plays a crucial role in the initiation of trichomes and fruit spines, but little is known about the details of the regulatory mechanisms involved. In this study, analysis of tissue expression patterns indicated that Tril is expressed and functions in the early stages of organ initiation and development. Expression of Tril under the control of its own promoter (the TrilPro::Tril-3*flag fragment) could partly rescue the mutant phenotypes of tril, csgl3 (cucumber glabrous 3, an allelic mutant of tril), and fs1 (few spines 1, a fragment substitution in the Tril promoter region), providing further evidence that Tril is responsible for the initiation of trichomes and fruit spines. In lines with dense spine, fs1-type lines, and transgenic lines of different backgrounds containing the TrilPro::Tril-3*flag foreign fragment, spine density increased in conjunction with increases in Tril expression, indicating that Tril has a gene dosage effect on fruit spine density in cucumber. Numerous Spines (NS) is a negative regulatory factor of fruit spine density. Characterization of the molecular and genetic interaction between Tril and NS/ns demonstrated that Tril functions upstream of NS with respect to spine initiation. Overall, our results reveal a novel regulatory mechanism governing the effect of Tril on fruit spine development, and provide a reference for future work on breeding for physical quality in cucumber.

Cucumber is one of the most important vegetables in the world. The C2H2 zinc finger protein (C2H2-ZFP) family plays an important role in the growth development and abiotic stress responses of plants. However, there have been no systematic studies on cucumber. In this study, we performed a genome-wide study of C2H2-ZFP genes and analyzed their chromosomal location, gene structure, conservation motif, and transcriptional expression. In total, 101 putative cucumber C2H2-ZFP genes were identified and divided into six groups (I&ndash, VI). RNA-seq transcriptome data on different organs revealed temporal and spatial expression specificity of the C2H2-ZFP genes. Expression analysis of sixteen selected C2H2-ZFP genes in response to cold, drought, salt, and abscisic acid (ABA) treatments by real-time quantitative polymerase chain reaction showed that C2H2-ZFP genes may be involved in different signaling pathways. These results provide valuable information for studying the function of cucumber C2H2-ZFP genes in the future.

Cucumber is one of the most important vegetables in the world. The C2H2 zinc finger protein (C2H2-ZFP) family plays an important role in the growth development and abiotic stress responses of plants. However, there have been no systematic studies on cucumber. In this study, we performed a genome-wide study of C2H2-ZFP genes and analyzed their chromosomal location, gene structure, conservation motif, and transcriptional expression. In total, 101 putative cucumber C2H2-ZFP genes were identified and divided into six groups (I–VI). RNA-seq transcriptome data on different organs revealed temporal and spatial expression specificity of the C2H2-ZFP genes. Expression analysis of sixteen selected C2H2-ZFP genes in response to cold, drought, salt, and abscisic acid (ABA) treatments by real-time quantitative polymerase chain reaction showed that C2H2-ZFP genes may be involved in different signaling pathways. These results provide valuable information for studying the function of cucumber C2H2-ZFP genes in the future.

The Gy14 cucumber (Cucumis sativus) is resistant to oomyceteous downy mildew (DM), bacterial angular leaf spot (ALS) and fungal anthracnose (AR) pathogens, but the underlying molecular mechanisms are unknown. Quantitative trait locus (QTL) mapping for the disease resistances in Gy14 and further map-based cloning identified a candidate gene for the resistant loci, which was validated and functionally characterized by spatial-temporal gene expression profiling, allelic diversity and phylogenetic analysis, as well as local association studies. We showed that the triple-disease resistances in Gy14 were controlled by the cucumber STAYGREEN (CsSGR) gene. A single nucleotide polymorphism (SNP) in the coding region resulted in a nonsynonymous amino acid substitution in the CsSGR protein, and thus disease resistance. Genes in the chlorophyll degradation pathway showed differential expression between resistant and susceptible lines in response to pathogen inoculation. The causal SNP was significantly associated with disease resistances in natural and breeding populations. The resistance allele has undergone selection in cucumber breeding. The durable, broad-spectrum disease resistance is caused by a loss-of-susceptibility mutation of CsSGR. Probably, this is achieved through the inhibition of reactive oxygen species over-accumulation and phytotoxic catabolite over-buildup in the chlorophyll degradation pathway. The CsSGR-mediated host resistance represents a novel function of this highly conserved gene in plants.

Tnt1 is an active retrotransposon originally identified in tobacco (Nicotiana tabacum L.) (Grandbastien et al., 1989), but its transposition activity could be activated through tissue culture in other plant species. The insertions are stable and inheritable in the progeny, which has made it a valuable and versatile tool for developing insertional mutagenesis libraries in several plant species. Here, we explored its utility for mutagenesis in cucumber (Cucumis sativus L.). T3 Tnt1 transgenic cucumber plants were subjected to tissue culture to regenerate self-pollinated progeny. With PCR and analyses and Southern hybridization, we found regenerated plants maintained the original Tnt1 insertion and created new insertions suggesting characteristic re-transposition activity of Tnt1 during this process. Using genome walking, some flanking sequences of Tnt1 insertions were recovered in regenerated plants. The results demonstrated that Tnt1 could be stably inherited and re-transposable during tissue culture in cucumber and that it is feasible to use for developing an insertional mutagenesis library for cucumber. Keywords: cucumber, Tnt1, retrotransposon, tissue culture, mutagenesis library

Map-based cloning identified a candidate gene for resistance to the anthracnose fungal pathogen Colletotrichum orbiculare in cucumber, which reveals a novel function for the highly conserved STAYGREEN family genes for host disease resistance in plants. Colletotrichum orbiculare is a hemibiotrophic fungal pathogen that causes anthracnose disease in cucumber and other cucurbit crops. No host resistance genes against the anthracnose pathogens have been cloned in crop plants. Here, we reported fine mapping and cloning of a resistance gene to the race 1 anthracnose pathogen in cucumber inbred lines Gy14 and WI 2757. Phenotypic and QTL analysis in multiple populations revealed that a single recessive gene, cla, was underlying anthracnose resistance in both lines, but WI2757 carried an additional minor-effect QTL. Fine mapping using 150 Gy14 × 9930 recombinant inbred lines and 1043 F2 individuals delimited the cla locus into a 32 kb region in cucumber Chromosome 5 with three predicted genes. Multiple lines of evidence suggested that the cucumber STAYGREEN (CsSGR) gene is a candidate for the anthracnose resistance locus. A single nucleotide mutation in the third exon of CsSGR resulted in the substitution of Glutamine in 9930 to Arginine in Gy14 in CsSGR protein which seems responsible for the differential anthracnose inoculation responses between Gy14 and 9930. Quantitative real-time PCR analysis indicated that CsSGR was significantly upregulated upon anthracnose pathogen inoculation in the susceptible 9930, while its expression was much lower in the resistant Gy14. Investigation of allelic diversities in natural cucumber populations revealed that the resistance allele in almost all improved cultivars or breeding lines of the U.S. origin was derived from PI 197087. This work reveals an unknown function for the highly conserved STAYGREEN (SGR) family genes for host disease resistance in plants.

Using map-based cloning of ts gene, we identified a new sort of gene involved in the initiation of multicellular tender spine in cucumber. The cucumber (Cucumis sativus L.) fruit contains spines on the surface, which is an extremely valuable quality trait affecting the selection of customers. In this study, we elaborated cucumber line NC072 with wild type (WT) hard fruit spines and its spontaneous mutant NC073, possessing tender and soft spines on fruits. The mutant trait was named as tender spines (ts), which is controlled by a single recessive nuclear gene. We identified the gene ts by map-based cloning with an F2 segregating population of 721 individuals generated from NC073 and WT line SA419-2. It was located between two markers Indel6239679 and Indel6349344, 109.7 kb physical distance on chromosome 1 containing fifteen putative genes. With sequencing and quantitative reverse transcription-polymerase chain reaction analysis, the Csa1G056960 gene was considered as the most possible candidate gene of ts. In the mutant, Csa1G056960 has a nucleotide change in the 5′ splicing site of the second intron, which causes different splicing to delete the second exon, resulting in a N-terminal deletion in the predicted amino acid sequence. The gene encodes a C-type lectin receptor-like tyrosine-protein kinase which would play an important role in the formation of cucumber fruit. This is firstly reported of a receptor kinase gene regulating the development of multicellular spines/trichomes in plants. The ts allele could accelerate the molecular breeding of cucumber soft spines.

Cucumber, Cucumis sativus L. (2n = 2x = 14), is an important vegetable crop worldwide. It was the first specialty crop with a publicly available draft genome. Its relatively small, diploid genome, short life cycle, and self-compatible mating system offers advantages for genetic studies. In recent years, significant progress has been made in molecular mapping, and identification of genes and QTL responsible for key phenotypic traits, but a systematic review of the work is lacking. Here, we conducted an extensive literature review on mutants, genes and QTL that have been molecularly mapped or characterized in cucumber. We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped. For each gene, detailed information was compiled including chromosome locations, allelic variants and associated polymorphisms, predicted functions, and diagnostic markers that could be used for marker-assisted selection in cucumber breeding. We also documented 322 QTL for 42 quantitative traits, including 109 for disease resistances against seven pathogens. By alignment of these QTL on the latest version of cucumber draft genomes, consensus QTL across multiple studies were inferred, which provided insights into heritable correlations among different traits. Through collaborative efforts among public and private cucumber researchers, we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber. This is the first attempt to systematically summarize, analyze and inventory cucumber mutants, cloned or mapped genes and QTL, which should be a useful resource for the cucurbit research community.

Figure S10. Alignment of promoter sequence of CsUP from WT and up. (PDF 108 kb)

Figure S8. Genomic DNA sequence alignment of Cs535790 from WT and up (PDF 67 kb)

Figure S5. Alignment of predicted protein sequences between WT and CGN19839. The amino acid highlighted in red is the acid alternation (Ile47 in WT to Val47 in CGN19839) caused by the SNP in the first exon of Csa1G535800. The amino acids highlighted in yellow are abnormal in CGN19839 and the amino acids highlighted in blue are missing in CGN19839. The DnaJ domain at the C-terminal is underlined (PDF 81 kb)

Figure S3. Pedicel orientation of B1 and CGN19839 indicating that both inbred lines have the upward-pedicel phenotype (PDF 271 kb)

Table S1. Primers used for mapping, cloning and qPCR. (PDF 186â kb) (PDF 185 kb)

Figure S7. Alignment of coding sequence of CsUP from WT and up with 19 other cucumber lines. The whole coding sequence length is 1404 bp. The 491–495 bp position of up and B1 is the 5-bp deletion highlighted in blue. The 139 bp position of CGN19839 that altered from A to G is highlighted in red, and the 1234–1237 bp position in CGN19839 is the 4-bp deletion in blue (PDF 451 kb)

Figure S2. Partial results of linkage analysis with indel-CsUp demonstrating that this marker is co-segregated with the upward-pedicel phenotype (PDF 91 kb)

Figure S4. Structure of Csa1G535800 and two mutation sites in CGN19839. a Structure of Csa1G535800. Boxes and lines indicate exons and introns, respectively. Two green boxes in Csa1G535800 indicate the 5′ UTR and the 3′ UTR. Sequencing results revealed that, compared to WT, CGN19839 has a SNP in the first exon and a 4-bp deletion in the sixth exon of Csa1G535800. The yellow box shows the deletion sequence in CGN19839. b The position of the SNP and the 4-bp deletion in the encoding sequence. Sequencing results revealed that there was a SNP (‘A’ in C-8-6 and ‘G’ in CGN19839) at 139 bp and a 4-bp deletion at 1234–1237 bp from the ATG start codon (PDF 188 kb)