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Agronomy
Special Issues
Breeding, Genetics, and Genomic of the Genus Cucumis
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Breeding, Genetics, and Genomic of the Genus Cucumis

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Horticultural and Floricultural Crops".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 14607

Special Issue Editors

Dr. Sara Sestili

E-Mail Website
Guest Editor
CREA, Research Centre for Vegetable and Ornamental Crops, Via Salaria 1, 63030 Monsampolo del Tronto, AP, Italy
Interests: molecular biology; in vitro culture; gene expression; genetic transformation; novel breeding techniques (cisgenesis and gene editing); genetic resources; plant biotic stress resistance; horticultural plant breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Nadia Ficcadenti

E-Mail Website
Guest Editor
CREA Research Centre for Vegetable and Ornamental crops, Via Salaria 1, 63077 Monsampolo del Tronto (AP), Italy
Interests: agricultural plant science; horticulture; plant breeding and genetics; genetic transformation; in vitro tissue culture; germplasm conservation; genetic diversity
Special Issues, Collections and Topics in MDPI journals
Dr. Mehtap Yıldız

E-Mail Website
Guest Editor
Department of Agricultural Biotechnology, Faculty of Agriculture, Van Yuzuncu Yil University, 65080 Van, Turkey
Interests: molecular characterization; in vitro culture; germplasm conservation; genetics; vegetable growing and breeding; carrot; melon

Special Issue Information

Dear Colleagues,

The genus Cucumis belongs to the family Cucurbitaceae and is considered the most important genus worldwide. The taxonomy of Cucumis, as well as the Cucurbitaceae family, is complex due to the high number of species involved. Being an economically important horticultural species (C. sativus and C. melo), it includes ornamental (C. dipsaceus, C. myriocarpus) and innovative plants (C. anguria and C. metuliferus) that could be commercially explored. Cucumber and melon are considered model species and are largely used to study important biological processes (sex determination, plant vascular biology, fruit quality, pest, and disease resistance) due to their highly polymorphism and the availability of the complete genome sequence. The wide Cucumis germplasm, mostly represented by wild or less known species, is a powerful starting point to shed light on important processes, such as domestication, of which the genetic basis is still poorly understood and could allow a correct taxonomical ranging. Deep investigation of the genetic diversity within the genus will help us to discover morphological and biological features that are useful for genetic resources conservation, valorization, and utilization. Cucumis represent an important genes reservoir for applying new breeding techniques, such as gene editing and cisgenesis, to study gene functions and improve important agronomic and quality traits.

This Special Issue on the “Breeding, Genetics, and Genomic of the Genus Cucumis” invites research and review articles on the advanced genetic and genomics tools to be applied in Cucumis breeding.

Dr. Sara Sestili
Dr. Nadia Ficcadenti
Dr. Mehtap Yıldız
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. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • Cucumis
  • biotechnology
  • genomic
  • genetic improvement
  • molecular markers
  • transformation
  • resistance
  • quality
  • breeding

Published Papers (6 papers)

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Research

17 pages, 4306 KiB  
Article
Genome-Wide Identification and Expression Analysis of SnRK Gene Family under Abiotic Stress in Cucumber (Cucumis sativus L.)
by Yanyan Luo, Yuan Niu, Rong Gao, Chunlei Wang and Weibiao Liao
Agronomy 2022, 12(7), 1550; https://doi.org/10.3390/agronomy12071550 - 28 Jun 2022
Cited by 5 | Viewed by 1839
Abstract
Sucrose non-fermenting 1-related protein kinases (SnRKs) are a kind of plant-specific serine/threonine (Ser/Thr) protein kinase, which play an important role in plant stress resistance. However, the scale analysis of SnRK in the cucumber genome is currently unclear. In the study, a [...] Read more.
Sucrose non-fermenting 1-related protein kinases (SnRKs) are a kind of plant-specific serine/threonine (Ser/Thr) protein kinase, which play an important role in plant stress resistance. However, the scale analysis of SnRK in the cucumber genome is currently unclear. In the study, a total of 30 CsSnRK genes were identified from genomic data. They were distributed on six chromosomes, including 1 CsSnRK1, 10 CsSnRK2s and 19 CsSnRK3s. According to the analysis of gene structure and motif composition, CsSnRKs showed obvious differences among the three subfamilies. The ratio of synonymous (Ks) and nonsynonymous (Ka) nucleotide substitutions (Ka/Ks) of three paralogues indicates that the CsSnRK gene family undergoes a purifying selection. The analysis of cis-acting elements shows that the promoter region of each CsSnRK gene contained different classes of hormone and stress-related cis-acting elements. Furthermore, based on RNA-sequencing data from the Short Read Archive (SRA) database of NCBI, the expression patterns of CsSnRK genes in six tissues were investigated, indicating that the expression of multiple CsSnRK genes was prevalent in these tissues. Transcription levels of CsSnRK genes after drought, methyl jasmonate (MeJA) and abscisic acid (ABA) treatments were analyzed by quantitative RT-PCR, and the results show that most of the CsSnRK genes responded to these stresses. However, under different treatments, individual genes played a major role. For example, under ABA treatment, CsSnRK2.2 and CsSnRK2.3 played a major role in the response to ABA. These results provide clear evidence that CsSnRKs may be involved in cucumber growth, development and stress response, and provide valuable information for future functional studies of CsSnRKs. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomic of the Genus Cucumis)
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21 pages, 4941 KiB  
Article
The Melon Zym Locus Conferring Resistance to ZYMV: High Resolution Mapping and Candidate Gene Identification
by Nastacia Adler-Berke, Yitzchak Goldenberg, Yariv Brotman, Irina Kovalski, Amit Gal-On, Tirza Doniger, Rotem Harel-Beja, Christelle Troadec, Abdelhafid Bendahmane, Michel Pitrat, Catherine Dogimont, Nurit Katzir and Rafael Perl-Treves
Agronomy 2021, 11(12), 2427; https://doi.org/10.3390/agronomy11122427 - 28 Nov 2021
Cited by 6 | Viewed by 2505
Abstract
Zucchini yellow mosaic virus (ZYMV; potyviridae) represents a major pathogen of Cucurbitaceae crops. ZYMV resistance in melon PI 414723 is conditioned by a dominant allele at the Zym locus. This resistant accession restricts viral spread and does not develop mosaic symptoms, but [...] Read more.
Zucchini yellow mosaic virus (ZYMV; potyviridae) represents a major pathogen of Cucurbitaceae crops. ZYMV resistance in melon PI 414723 is conditioned by a dominant allele at the Zym locus. This resistant accession restricts viral spread and does not develop mosaic symptoms, but necrosis sometimes develops in response to inoculation. In previous studies, Zym has been mapped to linkage group II of the melon genetic map. In the present study, positional cloning of the locus was undertaken, starting from the CM-AG36 SSR marker at approximately 2 cm distance. We utilized five mapping populations that share the same resistant parent, PI 414723, and analyzed a total of 1630 offspring, to construct a high-resolution genetic map of the Zym locus. Two melon BAC libraries were used for chromosome walking and for developing new markers closer to the resistance gene by BAC-end sequencing. A BAC contig was constructed, and we identified a single BAC clone, from the ZYMV susceptible genotype MR-1, that physically encompasses the resistance gene. A second clone was isolated from another susceptible genotype, WMR 29, and the two clones were fully sequenced and annotated. Additional markers derived from the sequenced region delimited the region to 17.6 kb of a sequence that harbors a NAC-like transcription factor and, depending on the genotype, either two or three R-gene homologs with a CC-NBS-LRR structure. Mapping was confirmed by saturating the map with SNP markers using a single mapping population. The same region was amplified and sequenced also in the ZYMV resistant genotype PI 414723. Because numerous polymorphic sites were noted between genotypes, we could not associate resistance with a specific DNA polymorphism; however, this study enables molecular identification of Zym and paves the way to functional studies of this important locus. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomic of the Genus Cucumis)
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17 pages, 4414 KiB  
Article
Deciphering Codon Usage Patterns in Genome of Cucumis sativus in Comparison with Nine Species of Cucurbitaceae
by Yuan Niu, Yanyan Luo, Chunlei Wang and Weibiao Liao
Agronomy 2021, 11(11), 2289; https://doi.org/10.3390/agronomy11112289 - 12 Nov 2021
Cited by 6 | Viewed by 1840
Abstract
Cucumber is the most important vegetable crop in the Cucurbitaceae family. Condon usage bias (CUB) is a valuable character of species evolution. However, there is little research on the CUB of cucumber. Thus, this study analyzes the codon usage patterns of cucumber and [...] Read more.
Cucumber is the most important vegetable crop in the Cucurbitaceae family. Condon usage bias (CUB) is a valuable character of species evolution. However, there is little research on the CUB of cucumber. Thus, this study analyzes the codon usage patterns of cucumber and its relatives within Cucurbitaceae on the genomic level. The analysis of fundamental indicators of codon characteristics shows that it was slightly GC poor, and there was weak codon usage bias in cucumber. We conduct the analysis of neutrality plot, ENC plot, P2 index, and COA indicates that the nucleotide composition, mutation pressure, and translational selection might play roles in CUB in cucumber and its relatives. Among these factors, nucleotide composition might play the most critical role. Based on these analyses, 30 optimal codons were identified in cucumber, most of them ending with U or A. Meanwhile, based on the RSCU values of species, a cluster tree was constructed, in which the situation of cucumber is consistent with the current taxonomic and evolutionary studies in Cucurbitaceae. This study systematically compared the CUB patterns and shaping factors of cucumber and its relatives, laying a foundation for future research on genetic engineering and evolutionary mechanisms in Cucurbitaceae. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomic of the Genus Cucumis)
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10 pages, 1431 KiB  
Article
Marker-Assisted Evaluation of Two Powdery Mildew Resistance Candidate Genes in Korean Cucumber Inbred Lines
by Mahdi Badri Anarjan, Ikhyun Bae and Sanghyeob Lee
Agronomy 2021, 11(11), 2191; https://doi.org/10.3390/agronomy11112191 - 29 Oct 2021
Cited by 3 | Viewed by 2506
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomic of the Genus Cucumis)
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14 pages, 600 KiB  
Article
Significant Parent-of-Origin Effects for Seed, Cotyledon, and Early Plant Growth Traits in Cucumber
by Madeline W. Oravec and Michael J. Havey
Agronomy 2021, 11(10), 1908; https://doi.org/10.3390/agronomy11101908 - 23 Sep 2021
Viewed by 1781
Abstract
Parent-of-origin effects have long been recognized and exploited in plant breeding and genetic studies. These effects can be conferred by preferential expression of an allele from one parent, organellar effects, or altered organellar-nuclear interaction. The goal of this work was to evaluate parent-of-origin [...] Read more.
Parent-of-origin effects have long been recognized and exploited in plant breeding and genetic studies. These effects can be conferred by preferential expression of an allele from one parent, organellar effects, or altered organellar-nuclear interaction. The goal of this work was to evaluate parent-of-origin effects on seed, cotyledon, and early growth traits in cucumber using a full eight-by-eight diallel from crossing two doubled haploids (DHs) extracted from each of four cucumber populations. Significant general combining ability (GCA), specific combining ability (SCA), and reciprocal effects were observed for all traits, and direction and magnitude of effects were DH rather than population specific. Transcriptome analyses of reciprocal hybrids with and without significant reciprocal effects for early plant growth revealed that different pathways were associated with the significant reciprocal differences. These findings are consistent with the DH-specific nature of combining abilities and reciprocal effects across cucumber populations. Because reciprocal effects were DH and hybrid-combination specific, cucumber breeders should generate and evaluate both hybrids from reciprocal crossing for improved hybrid development. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomic of the Genus Cucumis)
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16 pages, 3999 KiB  
Article
Genome-Wide Identification, Expression Profile, and Alternative Splicing Analysis of CAMTA Family Genes in Cucumber (Cucumis sativus L.)
by Rong Gao, Yanyan Luo, Fahong Yun, Xuetong Wu, Peng Wang and Weibiao Liao
Agronomy 2021, 11(9), 1827; https://doi.org/10.3390/agronomy11091827 - 12 Sep 2021
Cited by 14 | Viewed by 2121
Abstract
The calmodulin-binding transcription activator (CAMTA), as one of the most distinctive families of transcription factors, plays an important role in plant growth and development and in the stress response. However, it is currently unknown whether CAMTA exists in cucumbers and what [...] Read more.
The calmodulin-binding transcription activator (CAMTA), as one of the most distinctive families of transcription factors, plays an important role in plant growth and development and in the stress response. However, it is currently unknown whether CAMTA exists in cucumbers and what its function is. In this study, we first identified four CAMTA genes in the cucumber genome using a genome-wide search method. Subsequently, we analyzed their physical and chemical properties, gene structure, protein domains, and phylogenetic relationships. The results show that the structure of CsCAMTAs is similar to that of other plants, and a phylogenetic analysis divides them into three groups. The analysis of cis-acting elements shows that most CsCAMTAs contain a variety of hormones and stress-related elements. The RT-PCR analysis shows that CsCAMTAs have different expression levels in different tissues and can be induced by IAA, ABA, MeJA, NaCl, and PEG. Finally, we analyzed the expression pattern of CsCAMTAs’ alternative spliceosomes under salt and drought stress. The results show that the expression levels of the different spliceosomes are affected by the type of stress and the duration of stress. These data indicate that CsCAMTAs participate in growth and development and in the stress response in cucumbers, a finding which lays the foundation for future CsCAMTAs’ functional research. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomic of the Genus Cucumis)
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