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Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020)

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 May 2023) | Viewed by 27114

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Prof. Dr. Shengli Du

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1. Cucumber Research Institute of Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
2. State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Key Laboratory of Vegetable Genetics and Breeding Enterprise, Tianjin 300192, China
Interests: vegetable breeding; genetic resources of cucumber; resistance breeding of cucumber; plant molecular breeding; haploid breeding

Prof. Dr. Yiqun Weng

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USDA-ARS Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
Interests: cucumber genetic and genomic resources; cucumber breeding (molecular breeding); chromosome evolution; domestication; crop evolution

Prof. Dr. Xiaolan Zhang

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Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
Interests: molecular mechanisms of fruit shape and shoot architecture regulation in cucumber; regulatory network of floral organ development and flowering time control in vegetable crops

Prof. Dr. Jinfeng Chen

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State Key Lab for Crop Gentics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Interests: cucumber genetic and germplasm innovation; cyto-molecular biology; biotechnology and cultivar improvement
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Shengping Zhang

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Guest Editor

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: cucumber germplasm resources; cucumber genetics and breeding; cucumber gene/QTL mapping; cucumber gene cloning; cucumber transgenic technology; cucumber gene editing

Special Issue Information

Dear Colleagues,

Academician Feng Hou (侯锋) (3 February 1928－7 November 2020), born in Pingdu, Shandong Province in 1928, was an academician of the Chinese Academy of Engineering, former vice president of Tianjin Academy of Agricultural Sciences, director of Tianjin Cucumber Research Institute, Chinese Cucumber Breeding expert, and the leader in the field of cucumber disease resistance breeding in China. He had many scientific accomplishments and successively won the National Science Conference Award, the second prize of the National Invention Award, the second prize of the National Science and Technology Progress Award, and the China Engineering Science and Technology Award.

Academician Feng Hou, who graduated from Beijing Agricultural University (now China Agricultural University) in 1954, was a famous vegetable breeding expert in China. He led in carrying out research on cucumber disease resistance breeding in China, conquering the disease resistance of cucumber downy mildew, powdery mildew, fusarium wilt, and other diseases. Additionally, he extensively introduced and utilized domestic and foreign variety resources, combined disease resistance, high yield, and early maturity, and released series of new cucumber varieties of Jinyan (津研), Jinza (津杂), and Jinchun (津春).The "fine cucumbers" have entered the dining table of thousands of households, and he was affectionately called "the king of cucumbers" by farmers. He took the lead in carrying out research on the inheritance of cucumber traits and promoted the development of vegetable breeding technology in China. The Tianjin Cucumber Research Institute he founded and its breeding, seed production, and industrialization engineering system have created a model for China's scientific research and system reform. The social benefits are significant.

To commemorate the outstanding contributions made by Prof. Hou to China cucumber breeding and industrialization, this Special Issue of Genes is soliciting original research, review or opinion articles from a variety of research fields under the theme ‘Cucumber Genetics and Breeding’. Manuscripts in the following topics are particularly encouraged: genetic resources, disease resistance, abiotic stress tolerance, development, trait discovery and genetics, genomics, and breeding. While we will focus on cucumber in this special issue, contributions from other cucurbitaceae crops are also welcome.

Prof. Dr. Shengli Du
Prof. Dr. Yiqun Weng
Prof. Dr. Xiaolan Zhang
Prof. Dr. Jinfeng Chen
Prof. Dr. Shengping Zhang
Guest Editors

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. Genes is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

cucumber
resistance breeding
molecular breeding
genetic resources
genomics
development
bioinformatics
cucurbits

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Published Papers (9 papers)

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Research

13 pages, 2902 KiB

Open AccessArticle

QTL Mapping for Ovary- and Fruit-Related Traits in Cucumis sativus-C. hystrix Introgression Line IL52

by Yuhui Wang, Yu Fang, Shixiong Ning, Lei Xia, Jinyi Zhan, Zhilong Yang, Chunyan Cheng, Qunfeng Lou, Ji Li and Jinfeng Chen

Genes 2023, 14(6), 1133; https://doi.org/10.3390/genes14061133 - 23 May 2023

Cited by 5 | Viewed by 1935

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 F_7:8 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. Full article

(This article belongs to the Special Issue Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020))

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20 pages, 7576 KiB

Open AccessArticle

Alternative Splicing of NAC Transcription Factor Gene CmNST1 Is Associated with Naked Seed Mutation in Pumpkin, Cucurbita moschata

by Qiong Shen and Yiqun Weng

Genes 2023, 14(5), 962; https://doi.org/10.3390/genes14050962 - 23 Apr 2023

Cited by 2 | Viewed by 2230

Abstract

In pumpkin (Cucurbita moschata), the naked or hull-less seed phenotype has great benefits for breeding this crop for oil or snack use. We previously identified a naked seed mutant in this crop. In this study, we report genetic mapping, identification, and characterization of a candidate gene for this mutation. We showed that the naked seed phenotype is controlled by a single recessive gene (N). The bulked segregant analysis identified a 2.4 Mb region on Chromosome 17 with 15 predicted genes. Multiple lines of evidence suggested that CmoCh17G004790 is the most probable candidate gene for the N locus which encodes a NAC transcription factor WALL THICKENING PROMOTING FACTOR 1 (CmNST1). No nucleotide polymorphism or structural variation was found in the genomic DNA sequences of CmNST1 between the mutant and the wildtype inbred line (hulled seed). However, the cDNA sequence cloned from developing seed coat samples of the naked seed mutant was 112 bp shorter than that from the wildtype which is due to seed coat-specific alternative splicing in the second exon of the mutant CmNST1 transcript. The expression level of CmNST1 in the developing seed coat was higher in the mutant than in the wildtype during early seed coat development which was reversed later. Transcriptomic profiling with RNA-Seq at different stages of seed development in the mutant and wildtype revealed a critical role of CmNST1 as a master regulator for the lignin biosynthesis pathway during seed coat development while other NAC and MYB transcription factors were also involved in forming a regulatory network for the building of secondary cell walls. This work provides a novel mechanism for the well-characterized NST1 transcription factor gene in regulating secondary cell wall development. The cloned gene also provides a useful tool for marker-assisted breeding of hull-less C. moschata varieties. Full article

(This article belongs to the Special Issue Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020))

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17 pages, 11918 KiB

Open AccessEditor’s ChoiceArticle

A Genome-Wide Association Study to Identify Novel Candidate Genes Related to Low-Nitrogen Tolerance in Cucumber (Cucumis sativus L.)

by Bowen Li, Aimin Wei, Xueqiang Tong, Yike Han, Nan Liu, Zhengwu Chen, Hongyu Yang, Huaxiang Wu, Mingjie Lv, Ning Ning Wang and Shengli Du

Genes 2023, 14(3), 662; https://doi.org/10.3390/genes14030662 - 6 Mar 2023

Cited by 1 | Viewed by 2674

Abstract

Cucumber is one of the most important vegetables, and nitrogen is essential for the growth and fruit production of cucumbers. It is crucial to develop cultivars with nitrogen limitation tolerance or high nitrogen efficiency for green and efficient development in cucumber industry. To reveal the genetic basis of cucumber response to nitrogen starvation, a genome-wide association study (GWAS) was conducted on a collection of a genetically diverse population of cucumber (Cucumis sativus L.) comprising 88 inbred and DH accessions including the North China type, the Eurasian type, the Japanese and South China type mixed subtype, and the South China type subtype. Phenotypic evaluation of six traits under control (14 mM) and treatment (3.5 mM) N conditions depicted the presence of broad natural variation in the studied population. The GWAS results showed that there were significant differences in the population for nitrogen limitation treatment. Nine significant loci were identified corresponding to six LD blocks, three of which overlapped. Sixteen genes were selected by GO annotation associated with nitrogen. Five low-nitrogen stress tolerance genes were finally identified by gene haplotype analysis: CsaV3_3G003630 (CsNRPD1), CsaV3_3G002970 (CsNRT1.1), CsaV3_4G030260 (CsSnRK2.5), CsaV3_4G026940, and CsaV3_3G011820 (CsNPF5.2). Taken together, the experimental data and identification of candidate genes presented in this study offer valuable insights and serve as a useful reference for the genetic enhancement of nitrogen limitation tolerance in cucumbers. Full article

(This article belongs to the Special Issue Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020))

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24 pages, 7083 KiB

Open AccessArticle

Improving Agrobacterium tumefaciens−Mediated Genetic Transformation for Gene Function Studies and Mutagenesis in Cucumber (Cucumis sativus L.)

by Hanqiang Liu, Jianyu Zhao, Feifan Chen, Zhiming Wu, Junyi Tan, Nhien Hao Nguyen, Zhihui Cheng and Yiqun Weng

Genes 2023, 14(3), 601; https://doi.org/10.3390/genes14030601 - 27 Feb 2023

Cited by 10 | Viewed by 4829

Abstract

In the post−genomics era, Agrobacterium tumefaciens−mediated genetic transformation is becoming an increasingly indispensable tool for characterization of gene functions and crop improvement in cucumber (Cucumis sativus L.). However, cucumber transformation efficiency is still low. In this study, we evaluated the effects of several key factors affecting the shoot−regeneration rate and overall transformation efficiency in cucumber including genotypes, the age and sources of explants, Agrobacterium strains, infection/co−cultivation conditions, and selective agents. We showed that in general, North China cucumbers exhibited higher shoot−regeneration rate than US pickling or slicing cucumbers. The subapical ground meristematic regions from cotyledons or the hypocotyl had a similar shoot−regeneration efficiency that was also affected by the age of the explants. Transformation with the Agrobacterium strain AGL1 yielded a higher frequency of positive transformants than with GV3101. The antibiotic kanamycin was effective in selection against non−transformants or chimeras. Optimization of various factors was exemplified with the development of transgenic plants overexpressing the LittleLeaf (LL) gene or RNAi of the APRR2 gene in three cucumber lines. The streamlined protocol was also tested in transgenic studies in three additional genes. The overall transformation efficiency defined by the number of verified transgenic plants out of the number of seeds across multiple experiments was 0.2–1.7%. Screening among T₁ OE transgenic plants identified novel, inheritable mutants for leaf or fruit color or size/shape, suggesting T−DNA insertion as a potential source of mutagenesis. The Agrobacterium−mediated transformation protocol from this study could be used as the baseline for further improvements in cucumber transformation. Full article

(This article belongs to the Special Issue Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020))

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16 pages, 2713 KiB

Open AccessArticle

CsIAGLU Regulates the Angle of Leaf Petiole by Affecting Endogenous Content of Auxin in Cucumber (Cucumis sativus L.)

by Jiacai Chen, Yuxiang Huang, Xiaofeng Liu, Guangxin Chen, Liu Liu, Zhihua Cheng, Weiyuan Song, Lijie Han, Shaoyun Wang, Liming Wang, Min Li, Xiaolan Zhang and Jianyu Zhao

Genes 2022, 13(12), 2216; https://doi.org/10.3390/genes13122216 - 25 Nov 2022

Cited by 6 | Viewed by 2331

Abstract

The leaf angle is an important factor determining plant shoot architecture that may boost crop yield by increasing photosynthetic efficiency and facilitating high-density planting. Auxin is an important phytohormone involved in leaf angle regulation. Here, we identified two Single-Nucleotide Polymorphisms (SNPs) in the Indoleacetic Acid (IAA) glucosyltransferase gene CsIAGLU in 80 re-sequenced cucumber lines, of which the CsIAGLU^717G,1234T is the dominant allele associated with a small leaf pedicle angle (LPA), whereas CsIAGLU^717C,1234A is linked with a large LPA. CsIAGLU was highly expressed in leaves and petioles. In natural cucumber populations, the expression of CsIAGLU was negatively correlated with the LPA. The mutation of CsIAGLU induced by the CRISPR-Cas9 system resulted in elevated free IAA levels and enlarged cell expansion on the adaxial side of the petiole base, thus producing a greater LPA. Consistently, exogenous IAA treatment led to increased LPA and cell size. Therefore, our findings suggest that CsIAGLU functions as a negative regulator of LPA development via auxin-mediated cell expansion in cucumber, providing a valuable strategy for cucumber breeding with small LPAs. Full article

(This article belongs to the Special Issue Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020))

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17 pages, 5255 KiB

Open AccessArticle

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

by Xueting Wang, Qiming Hu, Jiaxi Wang, Lina Lou, Xuewen Xu and Xuehao Chen

Genes 2022, 13(10), 1903; https://doi.org/10.3390/genes13101903 - 19 Oct 2022

Cited by 5 | Viewed by 2711

Abstract

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. Full article

(This article belongs to the Special Issue Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020))

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11 pages, 1526 KiB

Open AccessArticle

Epidermal Patterning Factor 2-like (McEPFL2): A Putative Candidate for the Continuous Ridge (cr) Fruit Skin Locus in Bitter Gourd (Momordica charantia L.)

by Jing Yang, Yiqun Weng, Huihong Li, Qiusheng Kong, Weiluan Wang, Chenghuan Yan and Liping Wang

Genes 2022, 13(7), 1148; https://doi.org/10.3390/genes13071148 - 25 Jun 2022

Cited by 3 | Viewed by 2592

Abstract

Bitter gourd (Momordica charantia L.) is an economically important vegetable and medicinal crop in many Asian countries. Limited work has been conducted in understanding the genetic basis of horticulturally important traits in bitter gourd. Bitter gourd is consumed primarily for its young, immature fruit, and fruit appearance plays an important role in market acceptability. One such trait is the ridges on the fruit skin. In the present study, molecular mapping of a locus underlying fruit ridge continuity was conducted. Genetic analysis in segregating populations, derived from the crosses between two inbred lines Y1 with continuous ridges (CR) and Z-1-4 with discontinuous ridges (DCR), suggested that CR was controlled by a single recessive gene (cr). High-throughput genome sequencing of CR and DCR bulks combined with high-resolution genetic mapping in an F₂ population delimited cr into a 108 kb region with 16 predicted genes. Sequence variation analysis and expression profiling supported the epidermal patterning factor 2-like (McEPFL2) gene as the best candidate of the cr locus. A 1 bp deletion in the first exon of McEPFL2 in Y1 which would result in a truncated McEPFL2 protein may be the causal polymorphism for the phenotypic difference between Y1 and Z-1-4. The association of this 1 bp deletion with CR was further supported by gDNA sequencing of McEPFL2 among 31 bitter gourd accessions. This work provides a foundation for understanding the genetic and molecular control of fruit epidermal pattering and development, which also facilitates marker-assisted selection in bitter melon breeding. Full article

(This article belongs to the Special Issue Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020))

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14 pages, 5056 KiB

Open AccessArticle

Genome-Wide Association Studies Reveal Candidate Genes Related to Stem Diameter in Cucumber (Cucumis sativus L.)

by Yingying Yang, Shaoyun Dong, Han Miao, Xiaoping Liu, Zhuonan Dai, Xiangsheng Li, Xingfang Gu and Shengping Zhang

Genes 2022, 13(6), 1095; https://doi.org/10.3390/genes13061095 - 19 Jun 2022

Cited by 8 | Viewed by 2752

Abstract

The stem diameter, an important agronomic trait, affects cucumber growth and yield. However, no genes responsible for cucumber stem diameter have been identified yet. In this study, the stem diameter of 88 cucumber core germplasms were measured in spring 2020, autumn 2020 and autumn 2021, and a genome-wide association study (GWAS) was carried out based on the gene sequence and stem diameter of core germplasms. A total of eight loci (gSD1.1, gSD2.1, gSD3.1, gSD3.2, gSD4.1, gSD5.1, gSD5.2, and gSD6.1) significantly associated with cucumber stem diameter were detected. Of these, five loci (gSD1.1, gSD2.1, gSD3.1, gSD5.2, and gSD6.1) were repeatedly detected in two or more seasons and were considered as robust and reliable loci. Based on the linkage disequilibrium sequences of the associated SNP loci, 37 genes were selected. By further investigating the five loci via analyzing Arabidopsis homologous genes and gene haplotypes, five genes (CsaV3_1G028310, CsaV3_2G006960, CsaV3_3G009560, CsaV3_5G031320, and CsaV3_6G031260) showed variations in amino acid sequence between thick stem lines and thin stem lines. Expression pattern analyses of these genes also showed a significant difference between thick stem and thin stem lines. This study laid the foundation for gene cloning and molecular mechanism study of cucumber stem development. Full article

(This article belongs to the Special Issue Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020))

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22 pages, 5707 KiB

Open AccessArticle

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

by Hesbon Ochieng Obel, Chunyan Cheng, Ying Li, Zhen Tian, Martin Kagiki Njogu, Ji Li, Qunfeng Lou, Xiaqing Yu, Zhengan Yang, Joshua Otieno Ogweno and Jinfeng Chen

Genes 2022, 13(4), 658; https://doi.org/10.3390/genes13040658 - 8 Apr 2022

Cited by 14 | Viewed by 3558

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. Full article

(This article belongs to the Special Issue Cucumber Genetics and Breeding - a Themed Issue in Memory of Academician Feng Hou (1928 - 2020))

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