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A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 20914

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Prof. Dr. Yuyang Zhang

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National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
Interests: the vegetable quality (nutrition, flavor) formation and its regulation; molecular biology and biotechnology applied in vegetable crops; vegetable germplasm enhancement and molecular breeding
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Dear Colleagues,

Tomato is widely cultivated and is one of the most important vegetable crops in the world, with great economic significance. During the past two decades, tomato production has increased two-fold, which is largely the result of genetic improvement toward high yield and adaptation. Over the years, the goals of the genetic breeding of tomatoes have targeted productivity and tolerance to pests and diseases. Consumers demand high nutritional and taste quality and producers demand tomato fruit that is easy to cultivate with high adaptation to stress or disease.

Fortunately, tomato is a vegetable crop that is rich in genetic resources and could serve as a model for fruit biology and plant genetics. Great progress has been made on the genes and genetics underlying the important traits, e.g., fruit development, yield, quality, abiotic stress adaptation, and disease resistance. These genes facilitate tomato improvement by molecular approaches. Indeed, molecular breeding technology has been widely applied in tomato improvement. For this reason, the proposed Special Issue on “Genes, Genetics and Breeding of Tomato” will present advances in gene mining, genetic mechanism, and molecular breeding of tomato. We look forward to receiving your manuscripts (reviews and research articles) and are eager to share your results with the research and industry community.

Prof. Dr. Yuyang Zhang
Guest Editor

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Keywords

genes
genetics
breeding
tomato
improvement
yield
quality
disease resistance
stress tolerance

Published Papers (11 papers)

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Editorial

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4 pages, 199 KiB

Open AccessEditorial

Genes, Genetics and Breeding of Tomato

by Pingfei Ge and Yuyang Zhang

Horticulturae 2023, 9(11), 1208; https://doi.org/10.3390/horticulturae9111208 - 07 Nov 2023

Viewed by 791

Abstract

Tomato (Solanum lycopersicum) is widely cultivated and is one of the most important vegetable crops in the world, with great economic significance [...] Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

Research

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18 pages, 5508 KiB

Open AccessEditor’s ChoiceArticle

Comparative Transcriptome Analysis Reveals Potential Genes Conferring Resistance or Susceptibility to Bacterial Canker in Tomato

by Shuozhen Deng, Ziyan Li, Xinyu Liu, Wencai Yang and Yuqing Wang

Horticulturae 2023, 9(2), 242; https://doi.org/10.3390/horticulturae9020242 - 10 Feb 2023

Cited by 1 | Viewed by 1843

Abstract

Bacterial canker of tomato is a systemic disease caused by Clavibacter michiganensis (Cm), which poses a grave threat to tomato production worldwide. Towards the identification of genes underlying resistance to Cm infection, the transcriptome of the resistant inbred backcross line IBL2353 carrying the Rcm2.0 locus derived from Solanum habrochaites LA407 and the susceptible Solanum lycopersicum line Ohio88119 was comparatively analyzed after Cm inoculation, and the analysis focused on the genes with different expression patterns between resistant and susceptible lines. Gene ontology (GO) analysis revealed that top terms of differentially expressed genes comprised ubiquitin protein ligases, transcription factors, and receptor kinases. Then we screened out some genes which are potentially associated with the defense response against Cm infection in IBL2353 including the wall-associated receptor kinase-like 20 (WAKL20), and virus-induced gene silencing showed it contributes resistance to Cm infection. In addition to Cm-induced genes related to resistance, the expression of eight homologs from six susceptibility (S) gene families was analyzed. These putative resistance and susceptibility genes are valuable resources for molecular resistance breeding and contribute to the development of new control methods in tomato. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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13 pages, 1160 KiB

Open AccessFeature PaperArticle

Development of BC₃F₂ Tomato Genotypes with Arthropod Resistance Introgressed from Solanum habrochaites var. hirsutum (PI127826)

by Flávia Cristina Panizzon Diniz, Juliano Tadeu Vilela de Resende, Renato Barros de Lima-Filho, Laura Pilati, Gabriella Correia Gomes, Sergio Ruffo Roberto and Paulo Roberto Da-Silva

Horticulturae 2022, 8(12), 1217; https://doi.org/10.3390/horticulturae8121217 - 19 Dec 2022

Cited by 2 | Viewed by 1506

Abstract

Arthropod pests are among the biggest problems faced in tomato production worldwide. To overcome the losses caused by these pests, one of the most sustainable and economical strategies is the use of resistance introgressed from wild species. We aimed to develop BC₃F₂ tomato genotypes with high levels of zingiberene (ZGB) and resistance to whitefly (Bemisia tabaci biotype B), South American tomato pinworm (Tuta absoluta), and the two-spotted spider mite (Tatranychus urticae), from the wild accession of Solanum habrochaites var. hirsutum (accession PI127826). The quantification of ZGB in 520 BC₃F₂ genotypes and in the parentals yielded the selection of five genotypes with high ZGB content and three with low ZGB content, which were then infested with B. tabaci, T. absolute, and T. urticae. In these eight genotypes and in the parents, the types and amounts of trichomes on the leaves were determined. Additionally, molecular markers were used to identify the genotypes with a higher recurrent genome recovery. The results confirmed the transfer of resistance from S. habrochaites to the BC₃F₂ genotypes and showed that this resistance seems to be directly related to high concentrations of ZGB and the presence of type IV trichomes. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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14 pages, 2475 KiB

Open AccessEditor’s ChoiceArticle

HyPRP1, A Tomato Multipotent Regulator, Negatively Regulates Tomato Resistance to Sulfur Dioxide Toxicity and Can Also Reduce Abiotic Stress Tolerance of Escherichia coli and Tobacco

by Xueting Chen, Lulu Wang, Yan Liang, Xiaomeng Hu, Qianqian Pan, Yin Ding and Jinhua Li

Horticulturae 2022, 8(12), 1118; https://doi.org/10.3390/horticulturae8121118 - 28 Nov 2022

Cited by 2 | Viewed by 1247

Abstract

Abiotic stresses have led to an extensive decline in global crop production and quality. As one of the abiotic stress factors, sulfur dioxide (SO₂) causes severe oxidative damage to plant tissues. Based on our previous study, a tomato hybrid-proline-rich protein 1 (HyPRP1) was found to be involved in abiotic stress and SO₂ metabolism, though the gene functions remained largely unknown. In this study, the function analysis of the HyPRP1 gene was extended, and DNA methylation analysis, subcellular localization, and cis-element analysis were performed to investigate the features of this gene. The DNA methylation analysis implied that the HyPRP1 gene was hypermethylated and the methylation density in the leaf differed from that in the flower and fruit. Subcellular localization analysis identified HyPRP1 localized in the cytoplasm and plasma membrane in vivo. The E. coli cells harboring SlHyPRP1 showed reduced salt and drought resistance. In tomato, when SO₂ toxicity occurred, the HyPRP1 RNAi knockdown lines accumulated more sulfates and less hydrogen peroxide (H₂O₂) and showed minimal leaf necrosis and chlorophyll bleaching. In tobacco, the overexpression of HyPRP1 reduced tolerance against salt stresses exerted by NaCl. We conclude that the heterologous expression of tomato HyPRP1 in E. coli and tobacco reduces abiotic stress tolerance and negatively regulates the resistance to sulfur dioxide toxicity by scavenging H₂O₂ and sulfite in tomato. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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10 pages, 4051 KiB

Open AccessArticle

Effect of Ethylene Sletr1-2 Receptor Allele on Flowering, Fruit Phenotype, Yield, and Shelf-Life of Four F1 Generations of Tropical Tomatoes (Solanum lycopersicum L.)

by Anas Anas, Gungun Wiguna, Farida Damayanti, Syariful Mubarok, Dwi Setyorini and Hiroshi Ezura

Horticulturae 2022, 8(12), 1098; https://doi.org/10.3390/horticulturae8121098 - 22 Nov 2022

Cited by 6 | Viewed by 1641

Abstract

A longer shelf-life for tomatoes without pleiotropic effects is one of the main goals of breeding programs in tropical countries. Therefore, this study aimed to evaluate the effect of the Sletr1-2 mutant allele on flowering, fruit phenotype, shelf life, and yield-related traits in four F1 hybrids from four tropical tomato genetic backgrounds. The study consisted of four tropical strains, namely ‘Intan’, ‘Mirah’, ‘Ratna’, and ‘Mutiara’, as females crossed with wild type ‘Micro-Tom’ (WT-MT) and mutant Sletr1-2 as males. Each was given three treatments and analyzed separately using a randomized block design with four replications of five samples each. The next test used was the Tukey Alpha 0.05 test. The genetic background of tropical tomatoes affects the phenotype and shelf-life. F1 mutants ‘Intan’ and ‘Ratna’ showed significant results, with a longer shelf-life than F1 WT (10.2 and 14.6 days, respectively). In addition, there were no side effects of the Sletr1-2 mutant allele in the heterozygous form on flowering, fruit phenotype, and yield. In conclusion, the Sletr1-2 allele has the potential to be used in tomato breeding programs in tropical countries. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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11 pages, 3411 KiB

Open AccessEditor’s ChoiceArticle

Altered brassinolide sensitivity1 Regulates Fruit Size in Association with Phytohormones Modulation in Tomato

by Muhammad Ali Mumtaz, Fangman Li, Xingyu Zhang, Jinbao Tao, Pingfei Ge, Ying Wang, Yaru Wang, Wenxian Gai, Haiqiang Dong and Yuyang Zhang

Horticulturae 2022, 8(11), 1008; https://doi.org/10.3390/horticulturae8111008 - 31 Oct 2022

Cited by 1 | Viewed by 1396

Abstract

BRs (Brassinosteroids) regulate many essential pathways related to growth, cell elongation, cell expansion, plant architecture, and fruit development. The potential exogenous application of BR-derivatives has been proven to stimulate plant growth and development, including quality attributes of fruits, whereas its biosynthesis inhibition has shown the opposite effect. In this study, BR-insensitive tomato mutants were used to reveal the potential function of BR signaling in the regulation of fruit development to elaborate the regulatory mechanism of BR signaling in tomato fruits. The BR-signaling mutant exhibited a typical dwarf phenotype and reduced vegetative growth, fruit size, and weight. Microscopic and transcriptional evaluation of the abs1 mutant fruits implies that reduced cell size and number are responsible for the phenotypic variations. Additionally, we also found that the altered content of phytohormones, such as auxin, gibberellin, cytokinin, and ethylene levels, contributed to altered fruit development. Moreover, fruit growth and cell development-specific gene expression levels were downregulated in BR-insensitive plants; culminating in reduced cell size, cell number, and cell layers. These findings provide insight into physio-chemical changes during fruit development in response to BR-insensitivity. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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18 pages, 3925 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Identification, Cloning and Expression Profile of RanBP2-Type Zinc Finger Protein Genes in Tomato

by Yanna Gao, Ning Li, Jiaojiao Ruan, Ying Li, Xiaoli Liao and Changxian Yang

Horticulturae 2022, 8(11), 985; https://doi.org/10.3390/horticulturae8110985 - 23 Oct 2022

Cited by 1 | Viewed by 1287

Abstract

The RanBP2-type zinc finger (RBZ) protein genes, which are well-characterized in animals, are involved in the regulation of mRNA processing. Although they are diversely distributed in plants, their functions still remain largely unknown. In this study, we performed a comprehensive bioinformatic analysis of 22 RBZ genes in tomato. The gene structure analysis revealed that the SlRBZ genes have 2 to 17 exons. SlRBZ proteins contain typical conserved domains, including Motif 1 or Motif 2, or a combination of Motif 9 and Motif 4. Two paralogous pairs were identified in the tomato. Segmental duplication possibly contributed to the expansion of the SlRBZ genes in tomato. Interestingly, the SlRBZ15 gene generated four products, yielded by alternative splicing. A cis-regulatory element analysis revealed that SlRBZ genes might be involved in the complex regulatory networks during plant growth and development. The expression profiles of the SlRBZ genes were analyzed in different tissues using eight phytohormones and four abiotic stress treatments based on RNA sequencing data and qRT-PCR verification. The results showed that each gene responded differently to more than one phytohormone or abiotic stress type. This research provides a foundation for future functional research on SlRBZ genes in tomato. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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14 pages, 2617 KiB

Open AccessEditor’s ChoiceArticle

The SlSWEET12c Sugar Transporter Promotes Sucrose Unloading and Metabolism in Ripening Tomato Fruits

by Jiaqi Sun, Chaoyang Feng, Xin Liu and Jing Jiang

Horticulturae 2022, 8(10), 935; https://doi.org/10.3390/horticulturae8100935 - 12 Oct 2022

Cited by 6 | Viewed by 1804

Abstract

Sugar content is a primary determinant of taste and quality in tomato (Solanum lycopersicum) fruit. Sugar allocation from source to sink is dependent on the activity of plasma membrane sugar transporters and is a critical process in plant development. Sugar will eventually be exported transporters (SWEETs) are sugar transporters that play key roles in plant biology, including growth and development. However, few studies have been conducted on the tomato SWEET protein family to date. Through gene expression analysis, we found that SlSWEET12c had the highest expression during the red ripening stage of tomato fruits. Yeast functional complementation, subcellular localization, and GUS activity assays showed that SlSWEET12c is a plasma membrane-localized sugar transporter that accumulates in the vascular bundles, carpel, and sarcocarp. Silencing SlSWEET12c increased sucrose accumulation and reduced the number of hexoses in tomato fruits; the opposite effects were observed under SISWEET12c overexpression. Invertase activity was also decreased after silencing SISWEET12c. These results suggest that SlSWEET12c is a sugar transporter that promotes sucrose unloading and metabolism in ripening tomato fruits, offering a new target for improving tomato quality and production. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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13 pages, 977 KiB

Open AccessCommunication

Tomato Response to Fusarium spp. Infection under Field Conditions: Study of Potential Genes Involved

by Joana A. Ribeiro, André Albuquerque, Patrick Materatski, Mariana Patanita, Carla M. R. Varanda, Maria do Rosário Félix and Maria Doroteia Campos

Horticulturae 2022, 8(5), 433; https://doi.org/10.3390/horticulturae8050433 - 12 May 2022

Cited by 8 | Viewed by 2824

Abstract

Tomato is one of the most important horticultural crops in the world and is severely affected by Fusarium diseases. To successfully manage these diseases, new insights on the expression of plant–pathogen interaction genes involved in immunity responses to Fusarium spp. infection are required. The aim of this study was to assess the level of infection of Fusarium spp. in field tomato samples and to evaluate the differential expression of target genes involved in plant–pathogen interactions in groups presenting different infection levels. Our study was able to detect Fusarium spp. in 16 from a total of 20 samples, proving the effectiveness of the primer set designed in the ITS region for its detection, and allowed the identification of two main different species complexes: Fusarium oxysporum and Fusarium incarnatum-equiseti. Results demonstrated that the level of infection positively influenced the expression of the transcription factor WRKY41 and the CBEF (calcium-binding EF hand family protein) genes, involved in plant innate resistance to pathogens. To the best of our knowledge, this is the first time that the expression of tomato defense-related gene expression is studied in response to Fusarium infection under natural field conditions. We highlight the importance of these studies for the identification of candidate genes to incorporate new sources of resistance in tomato and achieve sustainable plant disease management. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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9 pages, 2005 KiB

Open AccessArticle

Development of a Gene-Based High Resolution Melting (HRM) Marker for Selecting the Gene ty-5 Conferring Resistance to Tomato Yellow Leaf Curl Virus

by Yinlei Wang, Liuxia Song, Liping Zhao, Wengui Yu and Tongmin Zhao

Horticulturae 2022, 8(2), 112; https://doi.org/10.3390/horticulturae8020112 - 26 Jan 2022

Cited by 4 | Viewed by 2357

Abstract

Tomato yellow leaf curl virus (TYLCV) causes serious yield reductions in China. The use of certain resistance genes in tomato varieties has alleviated the impact of the virus to a certain extent. Recently, varieties with the Ty-1, Ty-2, or Ty-3 genes lost their resistance to TYLCV in some areas in China. New genes should be introduced into tomato to maintain the resistance to TYLCV. Tomato line AVTO1227 has excellent resistance to disease due to the resistance gene ty-5. In this study, we screened different types of markers in a tomato F₂ population to compare their accuracy and efficiency. The sequencing analysis results were consistent with the high resolution melting (HRM) marker genotype and field identification results. The result confirmed that the functional marker of ty-5 was accurate and reliable. The single nucleotide polymorphism-based HRM genotyping method established in this study can be used for the selection of breeding parent material, gene correlation analysis, and molecular marker-assisted breeding. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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Review

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17 pages, 969 KiB

Open AccessReview

Advances in the Characterization of the Mechanism Underlying Bacterial Canker Development and Tomato Plant Resistance

by Yuqing Wang, Shuozhen Deng, Ziyan Li and Wencai Yang

Horticulturae 2022, 8(3), 209; https://doi.org/10.3390/horticulturae8030209 - 27 Feb 2022

Cited by 7 | Viewed by 2997

Abstract

Bacterial canker caused by the Gram-positive actinobacterium Clavibacter michiganensis is one of the most serious bacterial diseases of tomatoes, responsible for 10–100% yield losses worldwide. The pathogen can systemically colonize tomato vascular bundles, leading to wilting, cankers, bird’s eye lesions, and plant death. Bactericidal agents are insufficient for managing this disease, because the pathogen can rapidly migrate through the vascular system of plants and induce systemic symptoms. Therefore, the use of resistant cultivars is necessary for controlling this disease. We herein summarize the pathogenicity of C. michiganensis in tomato plants and the molecular basis of bacterial canker pathogenesis. Moreover, advances in the characterization of resistance to this pathogen in tomatoes are introduced, and the status of genetics-based research is described. Finally, we propose potential future research on tomato canker resistance. More specifically, there is a need for a thorough analysis of the host–pathogen interaction, the accelerated identification and annotation of resistance genes and molecular mechanisms, the diversification of resistance resources or exhibiting broad-spectrum disease resistance, and the production of novel and effective agents for control or prevention. This review provides researchers with the relevant information for breeding tomato cultivars resistant to bacterial cankers. Full article

(This article belongs to the Special Issue Genes, Genetics and Breeding of Tomato)

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