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Solanaceae Genetic Resources: Genomics, Phenomics and Breeding
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Solanaceae Genetic Resources: Genomics, Phenomics and Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetic Resources".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 8319

Image courtesy of Jaime Prohens, University of Valencia

Special Issue Editors

Prof. Dr. Ezio Portis

E-Mail Website
Guest Editor
DISAFA Plant Genetics, University of Torino, 10095 Grugliasco, Italy
Interests: association mapping; genetics; genomics; marker-assisted selection; marker–trait association; molecular breeding; next-generation sequencing; plant breeding; plant genetic resources; population genetics
Dr. Lorenzo Barchi

E-Mail Website
Guest Editor
DISAFA Plant Genetics, University of Torino, 10095 Grugliasco, Italy
Interests: genomics; bioinformatics; quantitative trait locus (QTL); next-generation sequencing (NGS); genome-wide association selection (GWAS) and mapping; genotyping-by-sequencing (GBS); molecular assisted selection (MAS)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Solanaceae are one of the largest family of vascular plants, and the Solanum genus alone, with over 1,300 species, is one of the largest plant genera. Solanum comprises three species of exceptional economic importance: tomato (S. lycopersicum), potato (S. tuberosum) and eggplant (S. melongena), which represent, together with pepper (Capsicum annum), the major Solanaceous food crops. The genomes of these crops have been sequenced and proven to be highly collinear, providing a solid basis for genomics-assisted breeding. Linking genomic information with phenotypic data on germplasm collections and ad hoc-developed segregating populations constitutes an extensively studied area. Its major application is the use of the appropriate genomic tool(s) for prediction or identification of the genotype(s) holding the trait of interest and supporting their use in breeding. This Special Issue of Plants will focus on Solanaceae genetic and genomics, genotypic and phenotypic characterization as well as QTL mapping of key breeding traits in crops, using both traditional mapping populations and genome-wide association studies (GWAS). Studies aiming at identifying candidate genes within the identified genomic regions are also welcome.

Prof. Dr. Ezio Portis
Prof. Dr. Lorenzo Barchi
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • abiotic and biotic stresses
  • genetic resources
  • genomes and phenotypes
  • genome-wide association (GWA) mapping
  • genomic selection
  • mapping studies
  • marker-assisted selection (MAS)
  • molecular breeding
  • pan-genomes
  • phenomics and metabolomics
  • quantitative trait locus (QTL), genotyping by sequencing (GBS)
  • whole-genome re-sequencing

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Published Papers (3 papers)

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Research

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19 pages, 4546 KiB  
Article
Development of Chloroplast Microsatellite Markers and Evaluation of Genetic Diversity and Population Structure of Cutleaf Groundcherry (Physalis angulata L.) in China
by Shangguo Feng, Kaili Jiao, Zhenhao Zhang, Sai Yang, Yadi Gao, Yanyun Jin, Chenjia Shen, Jiangjie Lu, Xiaori Zhan and Huizhong Wang
Plants 2023, 12(9), 1755; https://doi.org/10.3390/plants12091755 - 25 Apr 2023
Cited by 7 | Viewed by 1825
Abstract
Cutleaf groundcherry (Physalis angulata L.), an annual plant containing a variety of active ingredients, has great medicinal value. However, studies on the genetic diversity and population structure of P. angulata are limited. In this study, we developed chloroplast microsatellite (cpSSR) markers and [...] Read more.
Cutleaf groundcherry (Physalis angulata L.), an annual plant containing a variety of active ingredients, has great medicinal value. However, studies on the genetic diversity and population structure of P. angulata are limited. In this study, we developed chloroplast microsatellite (cpSSR) markers and applied them to evaluate the genetic diversity and population structure of P. angulata. A total of 57 cpSSRs were identified from the chloroplast genome of P. angulata. Among all cpSSR loci, mononucleotide markers were the most abundant (68.24%), followed by tetranucleotide (12.28%), dinucleotide (10.53%), and trinucleotide (8.77%) markers. In total, 30 newly developed cpSSR markers with rich polymorphism and good stability were selected for further genetic diversity and population structure analyses. These cpSSRs amplified a total of 156 alleles, 132 (84.62%) of which were polymorphic. The percentage of polymorphic alleles and the average polymorphic information content (PIC) value of the cpSSRs were 81.29% and 0.830, respectively. Population genetic diversity analysis indicated that the average observed number of alleles (Na), number of effective alleles (He), Nei’s gene diversity (h), and Shannon information indices (I) of 16 P. angulata populations were 1.3161, 1.1754, 0.1023, and 0.1538, respectively. Moreover, unweighted group arithmetic mean, neighbor-joining, principal coordinate, and STRUCTURE analyses indicated that 203 P. angulata individuals from 16 populations were grouped into four clusters. A molecular variance analysis (AMOVA) illustrated the considerable genetic variation among populations, while the gene flow (Nm) value (0.2324) indicated a low level of gene flow among populations. Our study not only provided a batch of efficient genetic markers for research on P. angulata but also laid an important foundation for the protection and genetic breeding of P. angulata resources. Full article
(This article belongs to the Special Issue Solanaceae Genetic Resources: Genomics, Phenomics and Breeding)
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16 pages, 2378 KiB  
Article
Geographical Patterns of Genetic Variation in Locoto Chile (Capsicum pubescens) in the Americas Inferred by Genome-Wide Data Analysis
by Nahuel E. Palombo and Carolina Carrizo García
Plants 2022, 11(21), 2911; https://doi.org/10.3390/plants11212911 - 29 Oct 2022
Cited by 7 | Viewed by 2408
Abstract
The locoto chile (Capsicum pubescens) is a regionally important food crop grown and marketed throughout the mid-highlands of South andCentral America, but little is known about its evolution and the diversity it harbours. An initial scan of genetic diversity and structure [...] Read more.
The locoto chile (Capsicum pubescens) is a regionally important food crop grown and marketed throughout the mid-highlands of South andCentral America, but little is known about its evolution and the diversity it harbours. An initial scan of genetic diversity and structure across its cultivation range was conducted, the first one using a genomic approach. The RAD-sequencing methodology was applied to a sampling of C. pubescens germplasm consisting of 67 accessions from different American countries, covering its range of distribution/cultivation on the continent. The RAD-seq SNP data obtained clustered the accessions into three major groups, with a high degree of admixture/reticulation among them. Moderate but significant differentiation and geographic structuration were found, depicting a south–north pattern in the distribution of genetic variation. The highest levels of diversity were found among central-western Bolivian individuals, while the lowest was found across Central America-Mexican germplasm. This study provides new genome-wide supported insights into the diversity and differentiation of C. pubescens, as well as a starting point for more efficient use of its genetic variation and germplasm conservation efforts. The findings also contribute to understanding the evolutionary history of C. pubescens, but further investigation is needed to disentangle its origin and diversification under domestication. Full article
(This article belongs to the Special Issue Solanaceae Genetic Resources: Genomics, Phenomics and Breeding)
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Review

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27 pages, 3274 KiB  
Review
A Compendium for Novel Marker-Based Breeding Strategies in Eggplant
by Luciana Gaccione, Matteo Martina, Lorenzo Barchi and Ezio Portis
Plants 2023, 12(5), 1016; https://doi.org/10.3390/plants12051016 - 23 Feb 2023
Cited by 7 | Viewed by 3194
Abstract
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in [...] Read more.
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant’s traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes. Full article
(This article belongs to the Special Issue Solanaceae Genetic Resources: Genomics, Phenomics and Breeding)
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