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  • MDPI AG  (8)
  • Lou, Qunfeng  (8)
  • 1
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    A SNP Mutation in Homeodomain-DDT (HD-DDT) Transcription Factor Results in Multiple Trichomes (mt) in Cucumber (Cucumis sativus L.)
    MDPI AG ; 2021
    In:  Genes Vol. 12, No. 10 ( 2021-09-23), p. 1478-
    Details
    In: Genes, MDPI AG, Vol. 12, No. 10 ( 2021-09-23), p. 1478-
    Abstract: Trichome is a natural physical barrier protecting plants against environmental stresses, natural infestations, ultraviolet rays and pathogenicity. Trichome also helps plants in maintaining appropriate water content by reducing transpiration rate. The molecular mechanism regulating unicellular trichome development in Arabidopsis has been extensively elucidated, but the molecular mechanism regulating multicellular trichome development remains unclear. In this study, we identified a multiple trichomes (mt) mutant from a cucumber EMS (Ethylmethylsulfone) mutagenesis population. Genetic analysis indicated that an incomplete dominant gene controls the mt trait. Using a combination of map-based cloning and BSA-seq (Bulked Segregant Analysis -Sequencing), we identified the candidate gene, CsaV3_6G050410, responsible for the mt mutation. Sequence alignment revealed one base substitution in gene CsaV3_6G050410, resulting in an amino acid substitution. The deduced amino acid sequence of CsaV3_6G050410 encodes a HD-DDT (homeodomain-DDT) transcriptional regulatory protein containing a conserved homeobox domain and a DDT domain. Gene expression analysis revealed that the expression level of CsaV3_6G050410 in the mt mutant was similar to that in the WT (wild type). Transcriptome analysis indicated that the mt gene may regulate the development of the epidermis by influencing plant hormone signaling pathways or participating in several transcription factor pathways. The results of this study are fundamental for a better understanding of the function of the HD-DDT transcription factor in the trichome development of cucumber.
    Type of Medium: Online Resource
    ISSN: 2073-4425
    URL: Article
    DOI: 10.3390/genes12101478
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
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  • 2
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    Genome-Wide Identification of the B-Box Gene Family and Expression Analysis Suggests Their Potential Role in Photoperiod-Mediated β-Carotene Accumulation in the Endocarp of Cucumber (Cucumis sativus L.) Fruit
    MDPI AG ; 2022
    In:  Genes Vol. 13, No. 4 ( 2022-04-08), p. 658-
    Details
    In: Genes, MDPI AG, Vol. 13, No. 4 ( 2022-04-08), p. 658-
    Abstract: Carotenoids are indispensable to plants and essential for human nutrition and health. Carotenoid contents are strongly influenced by light through light-responsive genes such as B-Box (BBX) genes. BBX proteins, a class of zinc-finger transcription factors, mediate many light-signaling pathways, leading to the biosynthesis of important metabolites in plants. However, the identification of the BBX gene family and expression analysis in response to photoperiod-mediated carotenoid accumulation in cucumber remains unexplored. We performed a genome-wide study and determined the expression of cucumber BBX genes (hereafter referred to as CsaBBXs genes) in the endocarp of Xishuangbanna cucumber fruit (a special type of cucumber accumulating a high level of β-carotene in the endocarp) using an RNA-seq analysis of plants previously subjected to two photoperiodic conditions. Here, 26 BBX family genes were identified in the cucumber genome and named serially CsaBBX1 through CsaBBX26. We characterized CsaBBX genes in terms of their phylogenetic relationships, exon-intron structures, cis-acting elements, and syntenic relationships with Arabidopsis thaliana (L.) Heynh. RNA-seq analysis revealed a varied expression of CsaBBX genes under photoperiod treatment. The analysis of CsaBBXs genes revealed a strong positive correlation between CsaBBX17 and carotenoid biosynthetic pathway genes (phytoene synthase, ζ-carotene desaturase, lycopene ε-cyclase, β-carotene hydroxylase-1), thus suggesting its involvement in β-carotene biosynthesis. Additionally, nine CsaBBX genes (CsaBBX 4,5,7,9,11, 13,15,17 and 22) showed a significant positive correlation with β-carotene content. The selected CsaBBX genes were verified by qRT-PCR and confirmed the validity of RNA-seq data. The results of this study established the genome-wide analysis of the cucumber BBX family and provide a framework for understanding their biological role in carotenoid accumulation and photoperiodic responses. Further investigations of CsaBBX genes are vital since they are promising candidate genes for the functional analysis of carotenoid biosynthesis and can provide genetic tools for the molecular breeding of carotenoids in plants.
    Type of Medium: Online Resource
    ISSN: 2073-4425
    URL: Article
    DOI: 10.3390/genes13040658
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
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  • 3
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    Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber
    MDPI AG ; 2023
    In:  International Journal of Molecular Sciences Vol. 24, No. 10 ( 2023-05-18), p. 8943-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 24, No. 10 ( 2023-05-18), p. 8943-
    Abstract: Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616–157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339–86,883 bp), a small single copy (SSC, 18,069–18,363 bp), and two inverted repeats (IRs, 25,166–25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms24108943
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2019364-6
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  • 4
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    Transcriptomic and Physiological Analyses Reveal Potential Genes Involved in Photoperiod-Regulated β-Carotene Accumulation Mechanisms in the Endocarp of Cucumber (Cucumis sativus L.) Fruit
    MDPI AG ; 2022
    In:  International Journal of Molecular Sciences Vol. 23, No. 20 ( 2022-10-21), p. 12650-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 23, No. 20 ( 2022-10-21), p. 12650-
    Abstract: The accumulation of carotenoids in plants is a key nutritional quality in many horticultural crops. Although the structural genes encoding the biosynthetic enzymes are well-characterized, little is known regarding photoperiod-mediated carotenoid accumulation in the fruits of some horticultural crops. Herein, we performed physiological and transcriptomic analyses using two cucumber genotypes, SWCC8 (XIS-orange-fleshed and photoperiod-sensitive) and CC3 (white-fleshed and photoperiod-non-sensitive), established under two photoperiod conditions (8L/16D vs. 12L/12D) at four fruit developmental stages. Day-neutral treatments significantly increased fruit β-carotene content by 42.1% compared to short day (SD) treatments in SWCC8 at 40 DAP with no significant changes in CC3. Day-neutral condition elevated sugar levels of fruits compared to short-day treatments. According to GO and KEGG analyses, the predominantly expressed genes were related to photosynthesis, carotenoid biosynthesis, plant hormone signaling, circadian rhythms, and carbohydrates. Consistent with β-carotene accumulation in SWCC8, the day-neutral condition elevated the expression of key carotenoid biosynthesis genes such as PSY1, PDS, ZDS1, LYCB, and CHYB1 during later stages between 30 to 40 days of fruit development. Compared to SWCC8, CC3 showed an expression of DEGs related to carotenoid cleavage and oxidative stresses, signifying reduced β-carotene levels in CC3 cucumber. Further, a WGCNA analysis revealed co-expression between carbohydrate-related genes (pentose-phosphatase synthase, β-glucosidase, and trehalose-6-phosphatase), photoperiod-signaling genes (LHY, APRR7/5, FKF1, PIF3, COP1, GIGANTEA, and CK2) and carotenoid-biosynthetic genes, thus suggesting that a cross-talk mechanism between carbohydrates and light-related genes induces β-carotene accumulation. The results highlighted herein provide a framework for future gene functional analyses and molecular breeding towards enhanced carotenoid accumulation in edible plant organs.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms232012650
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2019364-6
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  • 5
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    QTL Mapping for Ovary- and Fruit-Related Traits in Cucumis sativus-C. hystrix Introgression Line IL52
    MDPI AG ; 2023
    In:  Genes Vol. 14, No. 6 ( 2023-05-23), p. 1133-
    Details
    In: Genes, MDPI AG, Vol. 14, No. 6 ( 2023-05-23), p. 1133-
    Abstract: IL52 is a valuable introgression line obtained from interspecific hybridization between cultivated cucumber (Cucumis sativus L., 2n = 14) and the wild relative species C. hystrix Chakr. (2n = 24). IL52 exhibits high resistance to a number of diseases, including downy mildew, powdery mildew, and angular leaf spot. However, the ovary- and fruit-related traits of IL52 have not been thoroughly investigated. Here, we conducted quantitative trait loci (QTL) mapping for 11 traits related to ovary size, fruit size, and flowering time using a previously developed 155 F7:8 RIL population derived from a cross between CCMC and IL52. In total, 27 QTL associated with the 11 traits were detected, distributed on seven chromosomes. These QTL explained 3.61% to 43.98% of the phenotypic variance. Notably, we identified a major-effect QTL (qOHN4.1) on chromosome 4 associated with the ovary hypanthium neck width and further delimited it into a 114-kb candidate region harboring 13 candidate genes. Furthermore, the QTL qOHN4.1 is co-localized with the QTL detected for ovary length, mature fruit length, and fruit neck length, all residing within the consensus QTL FS4.1, suggesting a plausible pleiotropic effect.
    Type of Medium: Online Resource
    ISSN: 2073-4425
    URL: Article
    DOI: 10.3390/genes14061133
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
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  • 6
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    Genome-Wide Identification and Expression Analysis of Heat Shock Protein 70 (HSP70) Gene Family in Pumpkin (Cucurbita moschata) Rootstock under Drought Stress Suggested the Potential Role of these Chaperones in Stress Tolerance
    MDPI AG ; 2022
    In:  International Journal of Molecular Sciences Vol. 23, No. 3 ( 2022-02-08), p. 1918-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 23, No. 3 ( 2022-02-08), p. 1918-
    Abstract: Heat shock protein 70s (HSP70s) are highly conserved proteins that are involved in stress responses. These chaperones play pivotal roles in protein folding, removing the extra amounts of oxidized proteins, preventing protein denaturation, and improving the antioxidant system activities. This conserved family has been characterized in several crops under drought stress conditions. However, there is no study on HSP70s in pumpkin (Cucurbita moschata). Therefore, we performed a comprehensive analysis of this gene family, including phylogenetic relationship, motif and gene structure analysis, gene duplication, collinearity, and promoter analysis. In this research, we found 21 HSP70s that were classified into five groups (from A to E). These genes were mostly localized in the cytoplasm, chloroplast, mitochondria, nucleus, and endoplasmic reticulum (ER). We could observe more similarity in closely linked subfamilies in terms of motifs, the number of introns/exons, and the corresponding cellular compartments. According to the collinearity analysis, gene duplication had occurred as a result of purifying selection. The results showed that the occurrence of gene duplication for all nine gene pairs was due to segmental duplication (SD). Synteny analysis revealed a closer relationship between pumpkin and cucumber than pumpkin and Arabidopsis. Promoter analysis showed the presence of various cis-regulatory elements in the up-stream region of the HSP70 genes, such as hormones and stress-responsive elements, indicating a potential role of this gene family in stress tolerance. We furtherly performed the gene expression analysis of the HSP70s in pumpkin under progressive drought stress. Pumpkin is widely used as a rootstock to improve stress tolerance, as well as fruit quality of cucumber scion. Since stress-responsive mobile molecules translocate through vascular tissue from roots to the whole plant body, we used the xylem of grafted materials to study the expression patterns of the HSP70 (potentially mobile) gene family. The results indicated that all CmoHSP70s had very low expression levels at 4 days after stress (DAS). However, the genes showed different expression patterns by progressing he drought period. For example, the expression of CmoHSP70-4 (in subgroup E) and CmoHSP70-14 (in subgroup C) sharply increased at 6 and 11 DAS, respectively. However, the expression of all genes belonging to subgroup A did not change significantly in response to drought stress. These findings indicated the diverse roles of this gene family under drought stress and provided valuable information for further investigation on the function of this gene family, especially under stressful conditions.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms23031918
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2019364-6
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  • 7
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    Molecular Research Progress on Xishuangbanna Cucumber (Cucumis sativus L. var. Xishuangbannesis Qi et Yuan): Current Status and Future Prospects
    MDPI AG ; 2022
    In:  Agronomy Vol. 12, No. 2 ( 2022-01-25), p. 300-
    Details
    In: Agronomy, MDPI AG, Vol. 12, No. 2 ( 2022-01-25), p. 300-
    Abstract: The Xishuangbanna (XIS) cucumber is an important botanical variety, accumulating high levels of β-carotene (700 μg/100 g) in the endocarp of mature fruit compared with normal green/white flesh types (25–50 μg/100 g, fresh weight). β-carotene is an essential precursor of provitamin A synthesis required for human health, thus XIS cucumber is an appealing germplasm for vitamin A breeding programs. In this review, we highlighted the molecular research progress of XIS cucumber as well as the bottlenecks undermining its utilization in genetic breeding. The XIS cucumber was first reported in 1983; thereafter, the literature on XIS cucumber was sporadic until 2012 and 2013 following QTL mapping of the Ore gene and subsequent cloning of the CsaBCH1 gene, respectively. Whereas QTL mapping studies underlying its flowering time and fruit quality related traits have been reported, fine mapping of their candidate genes remains unknown. Cucumber fruits are mainly consumed at fresh immature stage; however, XIS cucumber accumulates β-carotene at mature fruit state, thus limiting the utilization of β-carotene derived from it. In our opinion, we believe that the production and commercialization of immature orange-fleshed cucumber would gain wider acceptance among consumers. Additionally, we highlighted a comprehensive breeding strategy, precisely for enhanced β-carotene accumulation based on prior studies of XIS cucumber coupled with those from other crops. In MAS, we proposed schematic molecular backcross breeding strategy using lines possessing both ore and fft1.1 loci. This review, therefore, provides insights of XIS cucumber research and opportunities for further genetic breeding.
    Type of Medium: Online Resource
    ISSN: 2073-4395
    URL: Article
    DOI: 10.3390/agronomy12020300
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2607043-1
    SSG: 23
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  • 8
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    Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in Cucumis
    MDPI AG ; 2020
    In:  Genes Vol. 11, No. 12 ( 2020-12-12), p. 1500-
    Details
    In: Genes, MDPI AG, Vol. 11, No. 12 ( 2020-12-12), p. 1500-
    Abstract: Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid Cucumis hytivus (S14), its diploid parents, and the F1 hybrid, to reveal the function of lncRNAs in plant-interspecific hybridization and whole genome duplication. Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in C. hytivus, 44.6% of which were from intergenic regions. Based on the expression trend in allopolyploidization, we found that a high proportion of lncRNAs (94.6%) showed up-regulated expression to varying degrees following hybridization. However, few lncRNAs (33, 2.1%) were non-additively expressed after genome duplication, suggesting the significant effect of hybridization on lncRNAs, rather than genome duplication. Furthermore, 253 cis-regulated target genes were predicted for these differentially expressed lncRNAs in S14, which mainly participated in chloroplast biological regulation (e.g., chlorophyll synthesis and light harvesting system). Overall, this study provides new insight into the function of lncRNAs during the processes of hybridization and polyploidization in plant evolution.
    Type of Medium: Online Resource
    ISSN: 2073-4425
    URL: Article
    DOI: 10.3390/genes11121500
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
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