Cucumber Inbred Line Research Articles

Assessment of Physiological and Qualitative Traits of Cucumber Genotypes under Ambient Conditions

Background: With the advancement of storage period the crispness or firmness of greenhouse cucumber gradually decreased and usually had a shelf life counting from only 3 to 5 days at the ambient conditions. Methods: This experiment was conducted to evaluate the status of quality deterioration during post-harvest handling of different genotypes of greenhouse cucumber under ambient conditions. The basis of evaluation was based on the analysis of several physiological and qualitative traits including, physiological loss in weight (%), firmness (Newton), total soluble solids (°Brix), titratable acidity (%), total chlorophyll and total carotenoid content (mg/100 mg fresh weight). Result: Among cucumber inbred lines, the genotype, BRGCU-4 was observed with minimum moisture loss and highest firmness values, while the BRPCU-8 found to be best in retaining highest TSS and acidity and BRPCU-3 exhibited highest chlorophyll content during the storage period of a week. Moreover, hybrids of BRGCU-4 × BRPCU-6, followed by BRGCU-4 × BRPCU-8 were much better in retaining moistures and firmness, while the BRPCU-3 × BRPCU-6 hybrids recorded for highest chlorophyll andcarotenoid content. Therefore, these genotypes were found to be suitable for transportation, marketing and storage at ambient conditions.

Heritable Phenotypic Variations in the Self-Pollinated Progeny from Grafted Cucumber with Pumpkin as Rootstock

This study investigated whether grafting cucumber (Cucumis sativus L.) onto pumpkin (Cucurbita moschata Duch.) rootstocks can induce phenotypic variations in the self-bred cucumber progeny. The phenotypic traits of the self-pollinated progeny of grafted ‘Zhenghuang 1409’ cucumber were significantly different from those of the naturally rooted ‘Zhenghuang 1409’ parent line. Compared with the ‘Zhenghuang 1409’ cucumber inbred line, the first self-pollinated and naturally rooted generation of grafted cucumber displayed reduced length and width of the leaf at the node of the second female flower, a tapered petiole and stem, increased internode length, shorter plants, decreased fruit diameter, longer fruit stalk, thicker pulp, decreased seed length and width, and a lower 100-grain weight. Similar changes in most of these phenotypic traits were observed in the second generation of self-pollinated plants from grafted cucumber. By observing plant phenotypic traits, two leaf phenotypic variations were observed in the first generation of selfed grafted cucumber, and these two phenotypes were inherited in the second selfed generation.

Genotypic variation in nitrogen use efficiency trait in 35 cucumber inbred lines

Genotypic variation in nitrogen use efficiency trait in 35 cucumber inbred lines

Fine genetic mapping of the Mottled Rind Color (Morc) locus reveals a 4895-bp presence-absence variation contributing to the mottled or unmottled fruit rind color in cucumber

Rind color and pattern is the crucial fruit trait that preferentially affects the commercial consumption of cucumber (Cucumis sativus L.). Knowing the genetic architecture of fruit rind color and pattern is essential for improving cucumber external qualities. However, the genetic basis of cucumber fruit rind patterns is still unclear, especially for the phenotypic variation of mottled or unmottled (uniform) fruit rind color. To explore the genetic architecture of mottled fruit rind color in cucumber, we constructed F2 segregating populations using two cucumber inbred lines WI7632 and XNS16–1 showing green mottled rind color and white uniform rind color, respectively. Inheritance analysis revealed that the mottled rind color in WI7632 is genetically controlled by a dominant locus Morc (Mottled rind color). Chlorophyll content determination and chloroplast observation show that the mottled fruit rind color in WI7632 might be due to the decrease of chlorophyll synthesis caused by abnormal chloroplast development at particular fruit rind areas. Fine genetic mapping delimited the Morc locus into a 29.5-kb physical region on chromosome 5, which included only one candidate gene CsaV3_5G028870 encoding a C2H2-type zinc finger transcription factor. Sequence alignment showed that CsaV3_5G028870 and its flanking region (4895-bp in size) were missed in unmottled XNS16–1. Transcriptome profiling revealed that Morc might regulate the biosynthesis balance of heme and chlorophyll. Furthermore, the pleiotropic effects and diverse functions of Morc locus on determining multiple cucumber fruit's external qualities were discussed.

Mapping and identification of CsSF4, a gene encoding a UDP-N-acetyl glucosamine-peptide N-acetylglucosaminyltransferase required for fruit elongation in cucumber (Cucumis sativus L.).

The short fruit length phenotype in sf4 is caused by a SNP in Csa1G665390, which encodes an O-linked N-acetylglucosamine (GlcNAc) transferase in cucumber. Cucumber fruit is an excellent resource for studying fruit morphology due to its fast growth rate and naturally abundant morphological variations. The regulatory mechanisms underlying plant organ size and shape are important and fundamental biological questions. In this study, a short-fruit length mutant, sf4, was identified from an ethyl methanesulfonate (EMS) mutagenesis population derived from the North China-type cucumber inbred line WD1. Genetic analysis indicated that the short fruit length phenotype of sf4 was controlled by a recessive nuclear gene. The SF4 locus was located in a 116.7-kb genomic region between the SNP markers GCSNP75 and GCSNP82 on chromosome 1. Genomic and cDNA sequences analysis indicated that a single G to A transition at the last nucleotide of Csa1G665390 intron 21 in sf4 changed the splice site from GT-AG to GT-AA, resulting in a 42-bp deletion in exon 22. Csa1G665390 is presumed to be a candidate gene, CsSF4 that encodes an O-linked N-acetylglucosamine (GlcNAc) transferase (OGT). CsSF4 was highly expressed in the leaves and male flowers of wild-type cucumbers. Transcriptome analysis indicated that sf4 had alterations in expression of many genes involved in hormone response pathways, cell cycle regulation, DNA replication, and cell division, suggesting that cell proliferation-associated gene networks regulate fruit development in cucumber. Identification of CsSF4 will contribute to elucidating the function of OGT in cell proliferation and to understanding fruit elongation mechanisms in cucumber.

A novel mutation in ACS11 leads to androecy in cucumber

Sex determination in plants gives rise to unisexual flowers. A better understanding of the regulatory mechanism underlying the production of unisexual flowers will help to clarify the process of sex determination in plants and allow researchers and farmers to harness heterosis. Androecious cucumber (Cucumis sativus L.) plants can be used as the male parent when planted alongside a gynoecious line to produce heterozygous seeds, thus reducing the cost of seed production. The isolation and characterization of additional androecious genotypes in varied backgrounds will increase the pool of available germplasm for breeding. Here, we discovered an androecious mutant in a previously generated ethyl methanesulfonate (EMS)-mutagenized library of the cucumber inbred line ‘406’. Genetic analysis, whole-genome resequencing, and molecular marker-assisted verification demonstrated that a nonsynonymous mutation in the ethylene biosynthetic gene 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 11 (ACS11) conferred androecy. The mutation caused an amino acid change from serine (Ser) to phenylalanine (Phe) at position 301 (S301F). In vitro enzyme activity assays revealed that this S301F mutation leads to a complete loss of enzymatic activity. This study provides a new germplasm for use in cucumber breeding as the androecious male parent, and it offers new insights into the catalytic mechanism of ACS enzymes.

Mutation in the GA3ox gene governs short-internode characteristic in a korean cucumber inbred line

Mutation in the GA3ox gene governs short-internode characteristic in a korean cucumber inbred line

CRISPR/Cas9 based mlo-mediated resistance against Podosphaera xanthii in cucumber (Cucumis sativus L.).

Powdery mildews (PM) are common and severe pathogen groups that threaten plants, and PM resistance is complex and polygenic in cucumbers. Previously mlo-based resistance was reported in various plants, including cucumber, with generated loss-of CsaMLO function mutants. However, mlo-based resistance in cucumber is also complex and involves additional mechanisms such as hypersensitive response (HR) and papillae formation. For this reason, we focused on determining the mlo-based powdery mildew resistance mechanism in cucumber. CRISPR/Cas9 was used in the present study to generate loss-of-function mutants for CsaMLO1, CsaMLO8, and CsaMLO11 of PM susceptible ADR27 cucumber inbred lines and CsaMLO mutants were obtained and validated. Trypan Blue and DAB staining were performed to detect Podosphaera xanthii germination/penetration rates and accumulation of Reactive Oxygen Species (ROS). Our results indicate that PM-susceptibility associated CsaMLOs in cucumber are negative regulators in different defense mechanisms against powdery mildew at early and late stages of infection. Further, the experiment results indicated that CsaMLO8 mutation-based resistance was associated with the pre-invasive response, while CsaMLO1 and CsaMLO11 could be negative regulators in the post-invasive defense response in cucumber against P. xanthii. Although the loss-of CsaMLO8 function confers the highest penetration resistance, CsaMLO1 and CsaMLO11 double mutations could be potential candidates for HR-based resistance against PM pathogen in cucumber. These results highlighted the crucial role of CRISPR/Cas9 to develop PM resistant cucumber cultivars, possessing strong pre-invasive defense with CsaMLO8 or post-invasive with CsaMLO1/CsaMLO11 mutations.

Heterotic affinity and genetic control of monoecious cucumber (Cucumis sativus L.) inbred line for economic traits and tolerance to downy mildew disease

A cucumber (Cucumis sativus L.) hybrid could be acceptable to growers of tropical and subtropical climates if it is a high yielder with good fruit quality, and has appreciable tolerance against downy mildew disease which causes significant crop loss. Seven diverse parents were crossed in half diallel fashion to determine the extent of heterobeltiosis, mode of gene action, and combining ability effects for 17 quantitative characters at Research Farm, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, Nasia, West Bengal. Preponderance of non-additive gene action as realized from the predictability ratio for all the characters under study suggested heterosis breeding could be the best strategy to improve the yield and other component traits. On the basis of GCA effects and per se performance, two parents, BCCU-3 and BCCU-12 appeared consistently superior in respect of fruit yield/plant and other important horticultural traits including tolerance against downy mildew, and could be used as potential donors in future breeding. Outstanding hybrids based on SCA effects, heterobeltiosis manifested in them and per se performances were BCCU-16 × BCCU-4 and BCCU-3 × BCCU-16, and they could be commercially exploited after critical evaluations in tropics and subtropics. Commercially exploitable cucumber hybrids tolerant to downy mildew disease could be developed with the involvement of a single parent tolerant to this disease.

Comparative Biochemical and Transcriptomic Analyses Provide New Insights into Phytoplasma Infection Responses in Cucumber.

Flat stem and witches’ broom phytoplasma-like symptoms in the cucumber inbred line C17 were observed in a greenhouse at Yangzhou University, China for three consecutive planting seasons; these symptoms resulted in a decreased yield. To better understand the cause of these symptoms, 16S rRNA PCR, plant hormones, mineral elements, and RNA-seq profiling were performed using symptomatic and normal stem samples. The results showed that the causal agent was classified as the Candidatus phytoplasma asteris strain, a plant pathogenic prokaryote that could not be cultured in vitro. Measurement of plant hormones showed that auxin, salicylic acid, and jasmonic acid contents were significantly increased, whereas that of ethylene’s immediate biosynthetic precursor, 1-aminocyclopropane-1-carboxylic acid, was decreased in the phytoplasma-infected stems compared with the healthy stems. Furthermore, measurement of mineral element composition showed that magnesium, calcium, sodium, iron, and zinc concentrations significantly changed in the phytoplasma-infected cucumber stems compared with the uninfected stems. Comparative RNA-seq identified 253 differentially expressed genes, including 179 upregulated and 74 downregulated genes. Further analyses suggested that genes related to phenylpropanoid biosynthesis, phenylalanine metabolism, and plant hormone signal transduction contributed to phytoplasma infection. Taken together, this study presents the first in-depth assessment of disease symptoms and biochemical content of cucumber stems known to be infected with phytoplasma.

Functional copy number variation of CsSHINE1 is associated with fruit skin netting intensity in cucumber, Cucumis sativus.

Fruit skin netting in cucumber (Cucumis sativus) is associated with important fruit quality attributes. Two simply inherited genes H (Heavy netting) and Rs (Russet skin) control skin netting, but their molecular basis is unknown. Here, we reported map-based cloning and functional characterization of the candidate gene for the Rs locus that encodes CsSHINE1 (CsSHN1), an AP2 domain containing ethylene-responsive transcription factor protein. Comparative phenotypic analysis in near-isogenic lines revealed that fruit with netted skin had different epidermal structures from that with smooth skin including thicker cuticles, smaller, palisade-shaped epidermal and sub-epidermal cells with heavily suberized and lignified cell walls, higher peroxidase activities, which suggests multiple functions of CsSHN1 in regulating fruit skin netting and epidermal cell patterning. Among three representative cucumber inbred lines, three haplotypes at three polymorphic sites were identified inside CsSHN1: a functional copy in Gy14 (wild type) with light fruit skin netting, a copy number variant with two tandemly arrayed functional copies in WI7120 with heavy skin netting, and a loss-of-function copy in 9930 with smooth skin. The expression level of CsSHN1 in fruit exocarp of three lines was positively correlated with the skin netting intensity. Comparative analysis between cucumber and melon revealed conserved and divergent genetic mechanisms underlying fruit skin netting/reticulation that may reflect the different selection histories in the two crops. A discussion was made on genetic basis of fruit skin netting in the context of natural and artificial selections of fruit quality-related epidermal features during cucumber breeding.

Development of SNP Marker Sets for Marker-Assisted Background Selection in Cultivated Cucumber Varieties

Marker-assisted background selection is a powerful molecular tool that can enhance breeding efficiency through the analysis of a large number of markers representing the entire genomic background for precise selection. In the present study, the transcriptomes of 38 cucumber inbred lines with diverse traits were sequenced for single nucleotide polymorphism (SNP) mining for practical application to commercial cucumber breeding. A total of 62,378 high-quality SNPs were identified, of which 2462 SNPs were chosen based on the stringent filtering parameters. Finally, 363 evenly distributed common background selection markers (BMs) were developed and validated through polymorphism analysis and phylogenetic analysis using breeding materials with different genetic backgrounds; 327 out of 363 common BMs were useful for background selection. Moreover, the results of the phylogenetic analysis carried out using 50 selected core BMs were consistent with those for 327 common BMs. However, when the genotypes of breeding materials belonging to only the Baekdadagi-type were analyzed, the 327 common BMs showed a significant reduction in polymorphisms within the biased genomic locations. To address this issue, 59 highly polymorphic markers were selected as Baekdadagi BMs, as they showed better selection ability for the Baekdadagi-type. The 327 common BMs developed in the present study will enable efficient marker-assisted background selection in cucumber. Additionally, to reduce the genotyping cost, we suggested an alternative background selection strategy using both evenly distributed core BMs and biased Baekdadagi BMs for the improvement of commercial cucumber breeding programs.

Quantitative trait locus mapping of fruit aroma compounds in cucumber (Cucumber sativus L.) based on a recombinant inbred line population.

The fresh and unique flavor of cucumber fruits, mainly composed of aldehydes and alcohols, is one of its most important fruit qualities. However, little is known about the genetic basis of aroma compounds in cucumber fruit and the related quantitative trait loci (QTLs). In this study, genomic screening of QTLs underlying aroma compounds was performed based on the genetic linkage map constructed using 1301 single-nucleotide polymorphism (SNP) markers from genotyping-by-sequencing of a recombinant inbred line (RIL) population developed from Q16 × Q24. Significant genetic variations of aroma compounds in the RIL population were observed, and a total of 28 QTLs were screened. A major QTL (qol8-2.1) related to (E,Z)-2,6-nonadien-1-ol was detected with a markedly high LOD score (10.97 in 2020 and 3.56 in 2019) between mk190 and mk204 on chromosome 2. Genome scans identified a cluster of nine lipoxygenase genes in this region. A significant positive correlation was detected between CsaV3_2G005360 (CsLOX08) and (E,Z)-2,6-nonadien-1-ol, and five amino acid variations were detected between the CsLOX08 protein sequences of the two parental lines. Based on the genome variation of CsLOX08, we developed an InDel marker. Genotyping of InDel markers was consistent with the content of (E,Z)-2,6-nonadien-1-ol in RILs, which were also verified in nine cucumber inbred lines. The results will give breeders guidance for obtaining better flavor in cucumber.

Marker-Assisted Evaluation of Two Powdery Mildew Resistance Candidate Genes in Korean Cucumber Inbred Lines

Two genes, CsLRR-RPK2 (CsGy5G015660) and CsaMLO8 (Csa5G623470), have been considered as powdery mildew (PM) resistance genes in cucumbers. In this study, we evaluated the involvement of the alleles of these two genes in PM resistance in 100 commercial Korean cucumber inbred lines. To achieve this, we developed cleaved amplified polymorphic sequences (CAPS) and InDel markers from CsLRR-RPK2 and CsaMLO8. Genotyping analysis indicated that the CsLRR-RPK2-CAPS marker showed a stronger correlation with the PM-resistant phenotype, with an 84% consistency compared to the CsaMLO8-InDel marker. The use of the CsaMLO8-InDel marker showed a 70% consistency between phenotype and genotype results. It was proposed that the CsLRR-RPK2-CAPS marker successfully eliminated PM-susceptible inbred lines, since both genotype and phenotype results were 100% identical. Furthermore, the present study revealed that the introduction of one of these alleles is probably enough to confer PM resistance in cucumbers. However, seven PM-resistant inbred lines harbored either CsaMLO8 or CsLRR-RPK2 alleles, indicating that there is another PM-resistant resource(s) besides CsaMLO8- and CsLRR-RPK2–originated resistance in the commercial Korean inbred lines. Our results provide reliable evidence confirming two PM-resistant candidate genes for the detection of PM resistance resources in cucumber inbred lines.

Estimation of general combining ability (GCA) in fifteen Cucumis sativus L inbred lines of the fifth generations

The study on General Combining ability (GCA) of 15 cucumber inbred lines (I5) was carried out at the Research and Development Center for High-tech Agriculture, Ho Chi Minh City. The objective of the study was to identify the appropriate parental lines for producing F1 hybrid cucumber cultivars. Experimental materials included 15 cucumber inbred lines (I5) (L3, L9, L21, L22, L28, L32, L33, L36, L39, L61, L63, L69, L71, L74 and L78) and two test lines (T1 - TN 456 from Trang Nong Company, imported from Thailand and T2 - Cuct 1450 from Chia Tai - Thailand), forming 30 hybrid combinations by the method of topcross. The results showed that seven inbred lines including L3, L9, L21, L28, L33, L61 and L71 had high ability to combine with both T1 and T2 tester lines abby fruit yield with GCA index from + (0.8) to + (9.4). Evaluation of 30 cucumber hybrid was combinations on the growth and fruit yield characteristics showed that L28/T1 and L71/T2 hybrids were significantly different from other hybrids with high yields of 43.1 tons/ha and 41.3 tons/ha, respectively

Genomic Prediction and the Practical Breeding of 12 Quantitative-Inherited Traits in Cucumber (Cucumis sativus L.).

Genomic prediction is an effective way for predicting complex traits, and it is becoming more essential in horticultural crop breeding. In this study, we applied genomic prediction in the breeding of cucumber plants. Eighty-one cucumber inbred lines were genotyped and 16,662 markers were identified to represent the genetic background of cucumber. Two populations, namely, diallel cross population and North Carolina II population, having 268 combinations in total were constructed from 81 inbred lines. Twelve cucumber commercial traits of these two populations in autumn 2018, spring 2019, and spring 2020 were collected for model training. General combining ability (GCA) models under five-fold cross-validation and cross-population validation were applied to model validation. Finally, the GCA performance of 81 inbred lines was estimated. Our results showed that the predictive ability for 12 traits ranged from 0.38 to 0.95 under the cross-validation strategy and ranged from −0.38 to 0.88 under the cross-population strategy. Besides, GCA models containing non-additive effects had significantly better performance than the pure additive GCA model for most of the investigated traits. Furthermore, there were a relatively higher proportion of additive-by-additive genetic variance components estimated by the full GCA model, especially for lower heritability traits, but the proportion of dominant genetic variance components was relatively small and stable. Our findings concluded that a genomic prediction protocol based on the GCA model theoretical framework can be applied to cucumber breeding, and it can also provide a reference for the single-cross breeding system of other crops.

Transcriptomic and Histological Analysis of the Response of Susceptible and Resistant Cucumber to Meloidogyne incognita Infection Revealing Complex Resistance via Multiple Signaling Pathways.

The root-knot nematode (RKN), Meloidogyne incognita, is a devastating pathogen for cucumber (Cucumis sativus L.) specially in production under protected environments or continuous cropping. High level RKN resistance has been identified in African horned melon Cucumis metuliferus (CM). However, the resistance mechanism remains unclear. In this study, the comparative analysis on phenotypic and transcriptomic responses in the susceptible cucumber inbred line Q24 and the resistant CM, after M. incognita infection, was performed. The results showed that, in comparison with Q24, the CM was able to significantly reduce penetration numbers of second stage juveniles (J2), slow its development in the roots resulting in fewer galls and smaller giant cells suggesting the presence of host resistance in CM. Comparative transcriptomes analysis of Q24 and CM before and after M. incognita infection was conducted and differentially expressed genes (DEGs) associated with host resistance were identified in CM. Enrichment analyses revealed most enriched DEGs in Ca2+ signaling, salicylic acid (SA)/jamonate signaling (JA), as well as auxin (IAA) signaling pathways. In particular, in CM, DEGs in the Ca2+ signaling pathway such as those for the calmodulin and calcium-binding proteins were upregulated at the early stage of M. incognita infection; genes for SA/JA synthesis/signal transduction were markedly activated, whereas the IAA signaling pathway genes were inhibited upon infection suggesting the importance of SA/JA signaling pathways in mediating M. incognita resistance in CM. A model was established to explain the different molecular mechanisms on M. incognita susceptibility in cucumber and resistance to M. incognita infection in CM.

A SNP of HD-ZIP I transcription factor leads to distortion of trichome morphology in cucumber (Cucumis sativus L.)

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 F2 and BC1 populations constructed from a cross between nps and ‘9930’, the genetic analysis showed that the nps trait is controlled by a single recessive nuclear gene. We identified CsNps by map-based cloning with 576 individuals of the F2 population generated from the cross of nps and inbred line ‘9930’. The CsNps was 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 and nps was found in the second exon of Csa3G748220, a plant-specific class I HD-Zip gene. The result of allelism test also indicated that nps is a novel allelic mutant of Mict (Micro-trichome). Thus, nps was renamed mict-L130F. By comparing the transcriptome of mict-L130F vs 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 that Mict-L130F is involved in the morphogenesis of trichomes. Map-based cloning of the Mict-L130F gene could promote the study of trichome development in cucumber.

Identification and characterization of a long fruit mutant in Cucumis sativus L.

A long fruit (lf) mutant was obtained from the cucumber inbred line 'SN5' by ethyl methanesulfonate (EMS)-mediated mutagenesis. We found that plant height and internode length of lf were significantly decreased, while leaf area was significantly increased in comparison to wild type (WT) plants. Higher carbohydrate level, together with lower chlorophyll content and photosynthetic parameters, was revealed in lf leaves than those of WT. Longer fruits, as well as enhanced fruit quality, were observed for mutant plants in comparison to WT, and the difference in fruit length was continuously increased with the development of fruits. ELISA and real-time PCR analyses demonstrated the significant alterations in not only the CTK and IAA contents but also the expression of key genes related to cytokinin and auxin signalings in the fruits of lf when compared to WT plants, evidencing the involvement of cytokinin and auxin in fruit elongation of lf cucumber. Our results could benefit subsequent gene mapping and expand our knowledge about cucumber fruit length regulation.

QTL-seq analysis of powdery mildew resistance in a Korean cucumber inbred line.

QTL mapping and RT-PCR analyses identified the CsGy5G015660 as a strong powdery mildew resistance candidate gene and natural variation of CsGy5G015660 allele was observed using 115 core germplasm. Powdery mildew (PM) is among the most serious fungal diseases encountered in the cultivation of cucurbits. The development of PM-resistant inbred lines is thus of considerable significance for cucumber breeding programs. In this study, we applied bulked segregant analysis combined with QTL-seq to identify PM resistance loci using F2 population derived from a cross between two Korean cucumber inbred lines, PM-R (resistant) and PM-S (susceptible). Genome-wide SNP profiling using bulks of the two extreme phenotypes identified two QTLs on chromosomes 5 and 6, designated pm5.2 and pm6.1, respectively. The two PM resistance loci were validated using molecular marker-based classical QTL analysis: pm5.2 (30% R2 at LOD 11) and pm6.1 (11% R2 at LOD 3.2). Furthermore, reverse transcriptase-PCR analyses, using genes found to be polymorphic between PM-R and PM-S, were conducted to identify the candidate gene(s) responsible for PM resistance. We found that transcripts of the gene CsGy5G015660, encoding a putative leucine-rich repeat receptor-like serine/threonine-protein kinase (RPK2), showed specific accumulation in PM-R prior to the appearance of disease symptoms, and was accordingly considered a strong candidate gene for PM resistance. In addition, cleaved amplified polymorphic sequence markers from CsGy5G015660 were developed and used to screen 35 inbred lines. Natural variation in the CsGy5G015660 allele was also observed based on analysis of a core collection of 115 cucumber accessions. Our results provide new genetic insights for gaining a better understanding of the genetic basis of PM resistance in cucumber, and pave the way for further utilization in cucumber PM resistance breeding programs.