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Agronomy
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Genetics and Genomics of Tomato and Solanaceae
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Genetics and Genomics of Tomato and Solanaceae

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (30 November 2018) | Viewed by 49673

Special Issue Editor

Dr. Dilip R. Panthee

E-Mail Website
Guest Editor
Department of Horticultural Science, North Carolina State University, Raleigh, NC 27608, USA
Interests: breeding for fruit quality; differential gene expression analysis; genomic selection; GWAS; molecular breeding; plant breeding; QTL mapping; resistance breeding; stress tolerance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Solanaceae family consists of important vegetable crops, including eggplant (Solanum melongena L.), pepper (Capsicum annum L.), potato (Solanum tuberosum L.) and tomato (Solanum lycopersicum L.). Potato is also used as a staple food, next to cereals, in several parts of the world. All these member species of the Solanaceae family contribute significantly to the agriculture-based economy throughout the world. There are a lot of genomic resources that have already been developed (such as tomato and potato) or are being developed (such as eggplant and pepper) for these species. Because of its small genome size, tomato and Petunia, which is an important flower species, are also used as model plant for the analysis of genetics and genomics for various traits. With the availability of whole genome sequence and relatively smaller genome size, short life cycle and easy to make crosses, tomato is widely used as a model plant in genetics and genomic analysis. There is sequence homology between these species, which have been investigated further by researchers for in depth understanding of genetics, genomics, as well as to improve economic traits. Researchers have generated data on various aspects, including economically important traits, and are in the process of generating more data by exploiting the available genomic resources. The aim of this Special Issue is to contribute to the area of genetics and genomics of Solanaceae crop species so that newly-emerging information can further be used in our understanding of genetics and genomics of these species. Furthermore, this information can be exploited for the improvement of these crop species to make plant breeding sustainable.

Dr. Dilip R. Panthee
Guest Editor

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Keywords

  • Bioinformatics
  • Genetic transformation
  • Genome editing
  • Genomic selection
  • GWAS
  • Molecular breeding
  • Molecular markers in plant breeding
  • QTL mapping
  • RNASeq analysis

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Published Papers (7 papers)

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Research

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13 pages, 2814 KiB  
Article
Exploiting Genetic and Genomic Resources to Enhance Heat-Tolerance in Tomatoes
by Valentino Ruggieri, Roberta Calafiore, Carlo Schettini, Maria Manuela Rigano, Fabrizio Olivieri, Luigi Frusciante and Amalia Barone
Agronomy 2019, 9(1), 22; https://doi.org/10.3390/agronomy9010022 - 8 Jan 2019
Cited by 47 | Viewed by 7775
Abstract
High temperature is one of the most detrimental abiotic stresses in tomatoes. Many studies highlighted that even small increases in temperature can alter the plant reproductive system, causing a significant reduction in tomato yield. The aim of this study was to exploit the [...] Read more.
High temperature is one of the most detrimental abiotic stresses in tomatoes. Many studies highlighted that even small increases in temperature can alter the plant reproductive system, causing a significant reduction in tomato yield. The aim of this study was to exploit the phenotypic and genomic variations of a tomato landrace collection grown at high temperatures. Fifteen genotypes were selected as the best performing in two experimental fields. The selection was based on six yield-related traits, including flower earliness, number of flowers per inflorescence, fruit set, number of fruit per plant, fruit weight and yield per plant. In order to identify markers targeting traits that could be highly influenced by adverse climate conditions, such as flowering and fruit setting, an association mapping approach was undertaken exploiting a tomato high-throughput genomic array. The phenotypic variability observed allowed us to identify a total of 15 common markers associated with the studied traits. In particular, the most relevant associations co-localized with genes involved in the floral structure development, such as the style2.1 gene, or with genes directly involved in the response to abiotic stresses. These promising candidate genes will be functionally validated and transferred to a cultivated tomato to improve its performance under high temperatures. Full article
(This article belongs to the Special Issue Genetics and Genomics of Tomato and Solanaceae)
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18 pages, 2251 KiB  
Article
Cherry and Fresh Market Tomatoes: Differences in Chemical, Morphological, and Sensory Traits and Their Implications for Consumer Acceptance
by Joan Casals, Ana Rivera, Josep Sabaté, Roser Romero del Castillo and Joan Simó
Agronomy 2019, 9(1), 9; https://doi.org/10.3390/agronomy9010009 - 29 Dec 2018
Cited by 43 | Viewed by 6725
Abstract
The tomato commercial groups cherry and fresh market, mainly classified by fruit size, have clearly segregated markets. We aimed to estimate the variation within and between these groups and to analyze factors that impact consumer acceptance. To this end, we studied the chemical [...] Read more.
The tomato commercial groups cherry and fresh market, mainly classified by fruit size, have clearly segregated markets. We aimed to estimate the variation within and between these groups and to analyze factors that impact consumer acceptance. To this end, we studied the chemical profile (dry matter, sugars, acids) and fruit morphology (Tomato Analyzer) of 63 accessions grown in 2 environments (open air/soil culture; greenhouse/soilless culture). To identify traits underlying consumer preferences, we used a trained panel for quantitative descriptive sensory analyses and consumer surveys on a subset of genotypes. Our results confirm the higher content of reducing sugars (fructose, glucose), soluble solids, dry matter, and glutamic acid in the cherry group and the important effects of environment and genotype-by-environment interactions on fruit quality traits. The diversity within cherry for chemical composition is 1.4-fold to 2.1-fold that of fresh market. Differences in fruit morphological traits (weight, shoulder height, height/width relation) were highly related to fruit size, but no differences between groups were found for the internal structure of the fruit (locular relative content). Consumers value sweetness, glutamic acid, titratable acidity, and juiciness in cherry, and sweetness and taste intensity in the fresh market group. The implications for plant breeding are discussed. Full article
(This article belongs to the Special Issue Genetics and Genomics of Tomato and Solanaceae)
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13 pages, 2180 KiB  
Article
Marketability Probability Study of Cherry Tomato Cultivars Based on Logistic Regression Models
by Manuel Díaz-Pérez, Ángel Carreño-Ortega, Marta Gómez-Galán and Ángel-Jesús Callejón-Ferre
Agronomy 2018, 8(9), 176; https://doi.org/10.3390/agronomy8090176 - 9 Sep 2018
Cited by 11 | Viewed by 5748
Abstract
The purpose of this study was to demonstrate interest in applying simple and multiple logistic regression analyses to the marketability probability of commercial tomato (Solanum lycopersicum L.) cultivars when the tomatoes are harvested as loose fruit. A fruit’s firmness and commercial quality [...] Read more.
The purpose of this study was to demonstrate interest in applying simple and multiple logistic regression analyses to the marketability probability of commercial tomato (Solanum lycopersicum L.) cultivars when the tomatoes are harvested as loose fruit. A fruit’s firmness and commercial quality (softening or over-ripe fruit, cracking, cold damage, and rotting) were determined at 0, 7, 14, and 21 days of storage. The storage test simulated typical conditions from harvest to purchase-consumption by the consumer. The combined simple and multiple analyses of the primary continuous and categorical variables with the greatest influence on the commercial quality of postharvest fruit allowed for a more detailed understanding of the behavior of different tomato cultivars and identified the cultivars with greater marketability probability. The odds ratios allowed us to determine the increase or decrease in the marketability probability when we substituted one cultivar with a reference one. Thus, for example, the marketability probability was approximately 2.59 times greater for ‘Santyplum’ than for ‘Angelle’. Overall, of the studied cultivars, ‘Santyplum’, followed by ‘Dolchettini’, showed greater marketability probability than ‘Angelle’ and ‘Genio’. In conclusion, the logistic regression model is useful for studying and identifying tomato cultivars with good postharvest marketability characteristics. Full article
(This article belongs to the Special Issue Genetics and Genomics of Tomato and Solanaceae)
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15 pages, 2963 KiB  
Article
Diallel Analysis for Morphological and Biochemical Traits in Tomato Cultivated under the Influence of Tomato Leaf Curl Virus
by Prashant Kaushik and Major Singh Dhaliwal
Agronomy 2018, 8(8), 153; https://doi.org/10.3390/agronomy8080153 - 19 Aug 2018
Cited by 24 | Viewed by 8005
Abstract
Eloquent information about the genetic basis of inheritance is important for any breeding program. Therefore, a diallel study was conducted under the influence of tomato leaf curl virus (TLCV) disease, using the eleven advanced lines of tomato. Firstly, information regarding percent disease index [...] Read more.
Eloquent information about the genetic basis of inheritance is important for any breeding program. Therefore, a diallel study was conducted under the influence of tomato leaf curl virus (TLCV) disease, using the eleven advanced lines of tomato. Firstly, information regarding percent disease index (PDI) was determined via artificial screening with viruliferous whiteflies. Later, these lines were crossed in a half diallel mating design to produce fifty-five one-way hybrids. These hybrids and parental genotypes were evaluated for morphological and biochemical traits under open field conditions. Using the Griffing approach (Method II and Model I), the basis of the inheritance of traits was determined. Furthermore, a Bayesian model was applied to the total yield descriptor. Correlation data indicated that total yield was not correlated with any other trait. The significant general combining ability (GCA) and specific combining ability (SCA) values indicate exploitable genetic variation. The broad-sense heritability values were larger than narrow-sense heritability, showing that selection will be efficient for the improvement of these traits. Hybrid combinations H23, H42 and H49 can be considered efficient for the selection of multiple traits, including yield. Overall, this study provides useful information regarding the genetics of important traits of tomato under TLCV infestation. Full article
(This article belongs to the Special Issue Genetics and Genomics of Tomato and Solanaceae)
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25 pages, 4630 KiB  
Article
Microbial Endophytes that Live within the Seeds of Two Tomato Hybrids Cultivated in Argentina
by Silvina Marianela Yanil López, Graciela Noemi Pastorino, Mario Emilio Ernesto Franco, Rocio Medina, César Gustavo Lucentini, Mario Carlos Nazareno Saparrat and Pedro Alberto Balatti
Agronomy 2018, 8(8), 136; https://doi.org/10.3390/agronomy8080136 - 3 Aug 2018
Cited by 27 | Viewed by 5969
Abstract
Tomato (Solanum lycopersicum L.) is probably the most important vegetable consumed around the world, and like other produce is affected by stresses and diseases that reduce the yield and production. The purpose of this work was to study the phytobiome of the [...] Read more.
Tomato (Solanum lycopersicum L.) is probably the most important vegetable consumed around the world, and like other produce is affected by stresses and diseases that reduce the yield and production. The purpose of this work was to study the phytobiome of the tomato seeds of two hybrids in order to understand first of all whether tomato cultivars host similar groups of organisms, as well as their effect on the community structure, particularly of those microbes with the potential to promote growth and/or control plant pathogens. Different cultivars of tomato (genotypes) host significantly different endophytic communities, which is also reflected at the order level. These communities are particularly rich in spore-forming bacteria that have the ability either to promote plant growth or synthetize antimicrobial compounds that deter plant pathogens. We conclude that the seeds of the tomato cultivars Elpida and Silverio are sources of endophytic bacteria capable of synthetizing antifungal substances that could potentially be used for biocontrol against plant-pathogenic fungi. Full article
(This article belongs to the Special Issue Genetics and Genomics of Tomato and Solanaceae)
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12 pages, 269 KiB  
Article
Response of Bell Pepper to Rootstock and Greenhouse Cultivation in Coconut Fiber or Soil
by Neymar Camposeco-Montejo, Valentín Robledo-Torres, Francisca Ramírez-Godina, Rosalinda Mendoza-Villarreal, Miguel Ángel Pérez-Rodríguez and Marcelino Cabrera-de la Fuente
Agronomy 2018, 8(7), 111; https://doi.org/10.3390/agronomy8070111 - 4 Jul 2018
Cited by 10 | Viewed by 5644
Abstract
Vegetable production in greenhouses is preferred when soil quality is degraded by high salinity or incidence of pests and diseases. In these soils with abiotic and biotic issues, it is a challenge to increase the yield and quality of fruits. The use of [...] Read more.
Vegetable production in greenhouses is preferred when soil quality is degraded by high salinity or incidence of pests and diseases. In these soils with abiotic and biotic issues, it is a challenge to increase the yield and quality of fruits. The use of rootstocks and organic substrates are effective and environmentally friendly techniques to solve that challenge. The objective was to study the effect of rootstocks on yields and quality in bell peppers (Capsicum annuum L.) grown in either soil or coconut fiber substrate, in greenhouses. Using a randomized block design with three repetitions, the resulting treatment groups consisted of three rootstocks (Foundation-F1, Yaocali-F1, CLX-PTX991-F1 (Ultron), and non-grafted controls) with four hybrids as scions (Lamborghini, Bambuca, DiCaprio, and Ucumari). The yield of fruit per plant (YFP) and number of fruit per plant (NFP) obtained in coconut fiber were 85% and 55% greater, respectively, than in soil. The CLX-PTX991-F1 rootstock was superior to the hybrids without rootstock (p ≤ 0.05) in YFP and NPF (30% and 19.5%, respectively). The Lamborghini hybrid had significantly greater YFP and NFP than the Ucumari. We concluded that the use of coconut fiber significantly improves the yields of bell pepper and that the use of rootstock improves plant vigor and plant yield. Full article
(This article belongs to the Special Issue Genetics and Genomics of Tomato and Solanaceae)

Review

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11 pages, 228 KiB  
Review
Progress in Developing Bacterial Spot Resistance in Tomato
by Sadikshya Sharma and Krishna Bhattarai
Agronomy 2019, 9(1), 26; https://doi.org/10.3390/agronomy9010026 - 9 Jan 2019
Cited by 20 | Viewed by 8915
Abstract
Bacterial spot (BS), caused by four species of Xanthomonas: X. euvesicatoria, X. vesicatoria, X. perforans and X. gardneri in tomato (Solanum lycopersicum L.) results in severe loss in yield and quality by defoliation and the appearance of lesions on fruits, [...] Read more.
Bacterial spot (BS), caused by four species of Xanthomonas: X. euvesicatoria, X. vesicatoria, X. perforans and X. gardneri in tomato (Solanum lycopersicum L.) results in severe loss in yield and quality by defoliation and the appearance of lesions on fruits, respectively. The combined industry standard for BS control (foliar applications Actigard® rotated with copper plus mancozeb) does not offer sufficient protection, especially when weather conditions favor disease spread. Development of tomato cultivars with BS resistance is thus an important measure to minimize losses. Hypersensitive and non-hypersensitive resistance has been identified in different wild accessions and cultivated tomato relatives and has been transferred to cultivated tomato. However, complete resistance is yet to be obtained. With the advent of next generation sequencing and precise genome editing tools, the genetic regions that confer resistance to bacterial spot can be targeted and enriched through gene pyramiding in a new commercial cultivar which may confer higher degree of horizontal resistance to multiple strains of Xanthomonas causing bacterial spot in tomato. Full article
(This article belongs to the Special Issue Genetics and Genomics of Tomato and Solanaceae)
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