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Genetics and Molecular Breeding of Cucurbitaceous Crops
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Genetics and Molecular Breeding of Cucurbitaceous Crops

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 7106

Special Issue Editor

Dr. Younghoon Park

E-Mail Website
Guest Editor
Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea
Interests: plant genetics; plant breeding; molecular breeding; molecular markers; genomics; vegetables; tomato; cucurbits; disease resistance; horticultural traits
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cucurbitaceae stands out as one of the most economically important fruit and vegetable crop families, following the Solanaceae family. Cucurbitaceae includes diverse crop species such as cucumber, melon, watermelon, zucchini, pumpkin, and several different gourds. The agricultural value of these crops lies in the various nutritional components present in the edible parts of the fruits, such as cucurbitacin, carotenoids, vitamins, and other essential nutrients. In terms of academic significance, they serve as key models for fundamental biological research, showcasing diverse forms of flowers, sexual expression, fruit morphology, and plant architecture.

The genome assembly of most of these cucurbit crops has been completed, playing a pivotal role in the development of molecular markers and the discovery of new functional genes, essential for precision breeding. There is a wide range of breeding traits in these crops, including resistance to abiotic and biotic stress, functional components, flowering habits, fertility, taste and texture of edible parts, and fruit size and shape. Recent trends in breeding focus on genomics and bioinformatics analysis, as well as precision breeding relying on genome editing technologies for functional genes.

This Special Issue, “Genetics and Molecular Breeding of Cucurbitaceous Crops”, aims to advance the improvement of Cucurbitaceae crops by disseminating recent breeding trends and significant research achievements. We welcome innovative research articles and review papers that explore not only germplasm resources and conventional breeding but also diverse molecular and genomic approaches. These include genomics-assisted breeding involving molecular markers, genetic mapping, QTL analysis, genome-wide association studies, and genomic selection. Additionally, contributions covering transcriptomics, phenomics, mutation breeding, and genome editing, showcasing their progress and applications in Cucurbitaceae crop improvement, are highly encouraged. Papers focusing on new bioinformatics tools and databases and their potential contributions to the genetic enhancement of Cucurbitaceae are also welcomed.

Dr. Younghoon Park
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Cucurbitaceae
  • melon
  • watermelon
  • cucumber
  • pumpkins
  • zucchini
  • gourd
  • evolution
  • genetic diversity
  • genetic resources
  • conventional breeding
  • molecular breeding
  • genomics-assisted breeding
  • precison breeding
  • genome editing
  • genome selection

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Published Papers (6 papers)

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Research

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12 pages, 4171 KiB  
Article
Editing eIF4E in the Watermelon Genome Using CRISPR/Cas9 Technology Confers Resistance to ZYMV
by Maoying Li, Yanhong Qiu, Dongyang Zhu, Xiulan Xu, Shouwei Tian, Jinfang Wang, Yongtao Yu, Yi Ren, Guoyi Gong, Haiying Zhang, Yong Xu and Jie Zhang
Int. J. Mol. Sci. 2024, 25(21), 11468; https://doi.org/10.3390/ijms252111468 - 25 Oct 2024
Viewed by 1260
Abstract
Watermelon is one of the most important cucurbit crops, but its production is seriously affected by viral infections. Although eIF4E proteins have emerged as the major mediators of the resistance to viral infections, the mechanism underlying the contributions of eIF4E to watermelon disease [...] Read more.
Watermelon is one of the most important cucurbit crops, but its production is seriously affected by viral infections. Although eIF4E proteins have emerged as the major mediators of the resistance to viral infections, the mechanism underlying the contributions of eIF4E to watermelon disease resistance remains unclear. In this study, three CleIF4E genes and one CleIF(iso)4E gene were identified in the watermelon genome. Among these genes, CleIF4E1 was most similar to other known eIF4E genes. To investigate the role of CleIF4E1, CRISPR/Cas9 technology was used to knock out CleIF4E1 in watermelon. One selected mutant line had an 86 bp deletion that resulted in a frame-shift and the expression of a truncated protein. The homozygous mutant exhibits developmental defects in plant growth, leaf morphology and reduced yield. Furthermore, the mutant was protected against the zucchini yellow mosaic virus, but not the cucumber green mottled mosaic virus. In summary, this study preliminarily clarified the functions of eIF4E proteins in watermelon. The generated data will be useful for elucidating eIF4E-related disease resistance mechanisms in watermelon. The tissue-specific editing of CleIF4E1 in future studies may help to prevent adverse changes to watermelon fertility. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding of Cucurbitaceous Crops)
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14 pages, 2414 KiB  
Article
Identification of Powdery Mildew Resistance-Related Genes in Butternut Squash (Cucurbita moschata)
by Yiqian Fu, Yanping Hu, Jingjing Yang, Daolong Liao, Pangyuan Liu, Changlong Wen and Tianhai Yun
Int. J. Mol. Sci. 2024, 25(20), 10896; https://doi.org/10.3390/ijms252010896 - 10 Oct 2024
Viewed by 781
Abstract
Powdery mildew infection is a significant challenge in butternut squash (Cucurbita moschata) production during winter in Hainan, China. The tropical climate of Hainan promotes powdery mildew infection, resulting in substantial yield losses. By utilizing transcriptome and genome sequencing data, SNPs and [...] Read more.
Powdery mildew infection is a significant challenge in butternut squash (Cucurbita moschata) production during winter in Hainan, China. The tropical climate of Hainan promotes powdery mildew infection, resulting in substantial yield losses. By utilizing transcriptome and genome sequencing data, SNPs and potential genes associated with powdery mildew resistance in butternut squash were identified. The analysis of differentially expressed genes (DEGs) following powdery mildew infection revealed several genes involved in resistance, with particular focus on a resistance (R) gene cluster that may be linked to the observed resistance. Two MLO genes in clade V from Cucurbita moschata may not be directly associated with resistance in the two genotypes studied. These findings are expected to contribute to the development of genetic tools for improving powdery mildew resistance in Cucurbita crops, thereby reducing yield losses and enhancing the sustainability of butternut squash production in Hainan and other regions. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding of Cucurbitaceous Crops)
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19 pages, 3608 KiB  
Article
Genome-Wide Association Study of Cuticle and Lipid Droplet Properties of Cucumber (Cucumis sativus L.) Fruit
by Stephanie Rett-Cadman, Yiqun Weng, Zhangjun Fei, Addie Thompson and Rebecca Grumet
Int. J. Mol. Sci. 2024, 25(17), 9306; https://doi.org/10.3390/ijms25179306 - 28 Aug 2024
Viewed by 966
Abstract
The fruit surface is a critical first line of defense against environmental stress. Overlaying the fruit epidermis is the cuticle, comprising a matrix of cutin monomers and waxes that provides protection and mechanical support throughout development. The epidermal layer of the cucumber ( [...] Read more.
The fruit surface is a critical first line of defense against environmental stress. Overlaying the fruit epidermis is the cuticle, comprising a matrix of cutin monomers and waxes that provides protection and mechanical support throughout development. The epidermal layer of the cucumber (Cucumis sativus L.) fruit also contains prominent lipid droplets, which have recently been recognized as dynamic organelles involved in lipid storage and metabolism, stress response, and the accumulation of specialized metabolites. Our objective was to genetically characterize natural variations for traits associated with the cuticle and lipid droplets in cucumber fruit. Phenotypic characterization and genome-wide association studies (GWAS) were performed using a resequenced cucumber core collection accounting for >96% of the allelic diversity present in the U.S. National Plant Germplasm System collection. The collection was grown in the field, and fruit were harvested at 16–20 days post-anthesis, an age when the cuticle thickness and the number and size of lipid droplets have stabilized. Fresh fruit tissue sections were prepared to measure cuticle thickness and lipid droplet size and number. The collection showed extensive variation for the measured traits. GWAS identified several QTLs corresponding with genes previously implicated in cuticle or lipid biosynthesis, including the transcription factor SHINE1/WIN1, as well as suggesting new candidate genes, including a potential lipid-transfer domain containing protein found in association with isolated lipid droplets. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding of Cucurbitaceous Crops)
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27 pages, 2402 KiB  
Article
Genetic Dissection of ToLCNDV Resistance in Resistant Sources of Cucumis melo
by Clara Pérez-Moro, Cristina Sáez, Alicia Sifres, Carmelo López, Narinder P. S. Dhillon, Belén Picó and Ana Pérez-de-Castro
Int. J. Mol. Sci. 2024, 25(16), 8880; https://doi.org/10.3390/ijms25168880 - 15 Aug 2024
Viewed by 1214
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV) is a begomovirus causing significant melon (Cucumis melo) crop losses globally. This study aims to map the ToLCNDV resistance in the PI 414723 melon accession, previously identified and characterized through phenotypic studies, thereby exploring [...] Read more.
Tomato leaf curl New Delhi virus (ToLCNDV) is a begomovirus causing significant melon (Cucumis melo) crop losses globally. This study aims to map the ToLCNDV resistance in the PI 414723 melon accession, previously identified and characterized through phenotypic studies, thereby exploring shared genomic regions with the established resistant source WM-7. In the present study, WM-7 and PI 414723 were crossed with the susceptible accessions ‘Rochet’ and ‘Blanco’ respectively, to generate F1 hybrids. These hybrids were self-pollinated to generate the populations for mapping the ToLCNDV resistance region and designing markers for marker-assisted selection. Disease evaluation included visual symptom scoring, viral-load quantification and tissue printing. Genotyping-by-sequencing and SNP markers were used for quantitative trait loci (QTL) mapping. For genetic analysis, qPCR and bulked segregant RNA-seq (BSR-seq) were performed. Gene expression was assessed using RNA-seq, and qRT-PCR was used for confirmation. The research narrows the candidate region for resistance in WM-7 and identifies overlapping QTLs on chromosome 11 in PI 414723, found in the region of the DNA primase large subunit. BSR-seq and expression analyses highlight potential regulatory roles of chromosome 2 in conferring resistance. Differential expression was confirmed for six genes in the candidate region on chromosome 2. This study confirms the existence of common resistance genes in PI 414723 and WM-7. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding of Cucurbitaceous Crops)
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12 pages, 2072 KiB  
Article
Search for Expression Marker Genes That Reflect the Physiological Conditions of Blossom End Enlargement Occurrence in Cucumber
by Rui Li, Runewa Atarashi, Agung Dian Kharisma, Nur Akbar Arofatullah, Yuki Tashiro, Junjira Satitmunnaithum, Sayuri Tanabata, Kenji Yamane and Tatsuo Sato
Int. J. Mol. Sci. 2024, 25(15), 8317; https://doi.org/10.3390/ijms25158317 - 30 Jul 2024
Viewed by 750
Abstract
Blossom end enlargement (BEE) is a postharvest deformation that may be related to the influx of photosynthetic assimilates before harvest. To elucidate the mechanism by which BEE occurs, expression marker genes that indicate the physiological condition of BEE-symptomatic fruit are necessary. First, we [...] Read more.
Blossom end enlargement (BEE) is a postharvest deformation that may be related to the influx of photosynthetic assimilates before harvest. To elucidate the mechanism by which BEE occurs, expression marker genes that indicate the physiological condition of BEE-symptomatic fruit are necessary. First, we discovered that preharvest treatment with a synthetic cytokinin, N-(2-Chloro-4-pyridyl)-N’-phenylurea (CPPU), promoted fruit growth and suppressed BEE occurrence. This suggests that excessive assimilate influx is not a main cause of BEE occurrence. Subsequently, the expression levels of seven sugar-starvation marker genes, CsSEF1, AS, CsFDI1, CsPID, CsFUL1, CsETR1, and CsERF1B, were compared among symptomatic and asymptomatic fruits, combined with and without CPPU treatment. Only CsSEF1 showed a higher expression level in asymptomatic fruits than in symptomatic fruits, regardless of CPPU treatment. This was then tested using fruits stored via the modified-atmosphere packaging technique, which resulted in a lower occurrence of BEE, and the asymptomatic fruits showed a higher CsSEF1 expression level than symptomatic fruits, regardless of the packaging method. CsSEF1 codes a CCCH-type zinc finger protein, and an increase in the expression of CsSEF1 was correlated with a decrease in the fruit respiration rate. Thus, CsSEF1 may be usable as a BEE expression marker gene. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding of Cucurbitaceous Crops)
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Review

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22 pages, 336 KiB  
Review
Molecular Markers for Marker-Assisted Breeding for Biotic and Abiotic Stress in Melon (Cucumis melo L.): A Review
by Durre Shahwar, Zeba Khan and Younghoon Park
Int. J. Mol. Sci. 2024, 25(12), 6307; https://doi.org/10.3390/ijms25126307 - 7 Jun 2024
Viewed by 1502
Abstract
Melon (Cucumis melo L.) is a globally grown crop renowned for its juice and flavor. Despite growth in production, the melon industry faces several challenges owing to a wide range of biotic and abiotic stresses throughout the growth and development of melon. [...] Read more.
Melon (Cucumis melo L.) is a globally grown crop renowned for its juice and flavor. Despite growth in production, the melon industry faces several challenges owing to a wide range of biotic and abiotic stresses throughout the growth and development of melon. The aim of the review article is to consolidate current knowledge on the genetic mechanism of both biotic and abiotic stress in melon, facilitating the development of robust, disease-resistant melon varieties. A comprehensive literature review was performed, focusing on recent genetic and molecular advancements related to biotic and abiotic stress responses in melons. The review emphasizes the identification and analysis of quantitative trait loci (QTLs), functional genes, and molecular markers in two sections. The initial section provides a comprehensive summary of the QTLs and major and minor functional genes, and the establishment of molecular markers associated with biotic (viral, bacterial, and fungal pathogens, and nematodes) and abiotic stress (cold/chilling, drought, salt, and toxic compounds). The latter section briefly outlines the molecular markers employed to facilitate marker-assisted backcrossing (MABC) and identify cultivars resistant to biotic and abiotic stressors, emphasizing their relevance in strategic marker-assisted melon breeding. These insights could guide the incorporation of specific traits, culminating in developing novel varieties, equipped to withstand diseases and environmental stresses by targeted breeding, that meet both consumer preferences and the needs of melon breeders. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding of Cucurbitaceous Crops)
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