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Agronomy
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Breeding of Horticulture Plants: High-Throughput Sequencing Strategies in an Omics...
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Breeding of Horticulture Plants: High-Throughput Sequencing Strategies in an Omics Era

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

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 11442

Special Issue Editors

Dr. Xanthopoulou Aliki

E-Mail Website
Guest Editor
Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), 57001 Thermi, Greece
Interests: horticultural crops; high-throughput sequencing; breeding; phenomics; transcriptomics; metabolomics; epigenetics; proteomics and genomics
Dr. Mellidou Ifigeneia

E-Mail Website
Co-Guest Editor
Institute of Plant Breeding and Genetic Resources- ΗΑΟ DEMETER, 1st km Thesaloniki-Poligiros, PO Box 60458 Thermi, 57001 Thessaloniki, Greece
Interests: metabolic pathways of ascorbic acid in plants; fruit genetics and genomics; plant growth promoting rhizobacteria and abiotic stress
Special Issues, Collections and Topics in MDPI journals
Dr. Georgia Tanou

E-Mail Website
Co-Guest Editor
Institute of Soil Science and Water Resources, Hellenic Agricultural Organization-Demeter, Thermi, GR-57001 Thessaloniki, Greece
Interests: fruit tree physiology and nutrition; abiotic stress physiology; proteomics; metabolomics; transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticultural crops are an important source of fruits and vegetables in human nutrition. They are also used as herbal medicines and ornaments. Breeding of horticultural plants is of paramount importance and constitutes a high-interest chapter in the scientific community. In order to reach the demands of modern breeding strategies, technologies such as high-throughput sequencing, omics technologies, and genome editing combined with bioinformatics play a key role, contributing to the invention of a new breeding viewpoint. High-throughput sequencing is one of the most popular sequencing strategies and generates large data sets, thus revealing important information at genetic, transcriptomic, and epigenetic level. In addition, omics technologies can contribute to the connection of the phenotype with the genetic background in order to facilitate breeding of horticultural plants. Recently, genome editing has atrracted an increasing amount of interest from plant scientists. The rate of publication of articles related to genome editing in horticultural crops has been growing steadily, with CRISPR-based systems dominating.

In this Special Issue, we intend to enrich the scientific community with original research, reviews, and mini reviews about the breeding of horticulture plants using modern technologies such as high-throughput sequencing. Potential topics include but are not limited to:

  • High-throughput sequencing strategies in horticultural crops
  • Omics technologies and horticultural plants breeding
  • Genome editing in horticultural crops
  • Next-generation sequencing and differential expression
  • RNA seq
  • ChIP seq
  • Sequencing applications
  • Epigenomics
  • Proteomics
  • miRNAs and horticultural crop traits
  • Whole genome resequencing

We strongly believe that this collection of high quality publications can constitute the springboard for the evolution of breeding of horticultural plants.

Dr. Xanthopoulou Aliki
Dr. Mellidou Ifigeneia
Dr. Georgia Tanou
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

  • Horticultural crops
  • Breeding
  • High-throughput sequencing
  • Genome editing
  • Omics technologies
  • Bioinformatics
  • Epigenetics
  • Transcriptomics

Published Papers (4 papers)

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Research

12 pages, 1233 KiB  
Article
The Genetic Diversity and Population Structure of Different Geographical Populations of Bottle Gourd (Lagenaria siceraria) Accessions Based on Genotyping-by-Sequencing
by Rodrigo Contreras-Soto, Ariel Salvatierra, Carlos Maldonado and Jacob Mashilo
Agronomy 2021, 11(8), 1677; https://doi.org/10.3390/agronomy11081677 - 23 Aug 2021
Cited by 9 | Viewed by 2557
Abstract
Lagenaria siceraria (Molina) Standl is an important horticultural and medicinal crop grown worldwide in the food and pharmaceutical industries. The crop exhibits extensive phenotypic and genetic variation useful for cultivar development targeting economic traits; however, limited genomic resources are available for effective germplasm [...] Read more.
Lagenaria siceraria (Molina) Standl is an important horticultural and medicinal crop grown worldwide in the food and pharmaceutical industries. The crop exhibits extensive phenotypic and genetic variation useful for cultivar development targeting economic traits; however, limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd derived from Chile, Asia, and South Africa by using single-nucleotide polymorphism (SNP) markers and mining of simple sequence repeat (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs classified as moderate to highly informative, with a mean polymorphic information content of 0.29. The mean gene diversity of 0.16 indicated a low genetic differentiation of the accessions. Analysis of molecular variance revealed less differentiation between (36%) as compared to within (48%) bottle gourd accessions, suggesting that a random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising South African accessions and an admixed group with accessions of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding. Full article
(This article belongs to the Special Issue Breeding of Horticulture Plants: High-Throughput Sequencing Strategies in an Omics Era)
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11 pages, 20137 KiB  
Article
Two User-Friendly Molecular Markers Developed for the Identification of Hybrid Lethality Genes in Brassica oleracea
by Zhiliang Xiao, Congcong Kong, Fengqing Han, Limei Yang, Mu Zhuang, Yangyong Zhang, Yong Wang, Jialei Ji, Zhansheng Li, Zhiyuan Fang and Honghao Lv
Agronomy 2021, 11(5), 982; https://doi.org/10.3390/agronomy11050982 - 14 May 2021
Cited by 2 | Viewed by 1763
Abstract
Cabbage (Brassica oleracea) is an important vegetable crop that is cultivated worldwide. Previously, we reported the identification of two dominant complementary hybrid lethality (HL) genes in cabbage that could result in the death of hybrids. To avoid such losses in the [...] Read more.
Cabbage (Brassica oleracea) is an important vegetable crop that is cultivated worldwide. Previously, we reported the identification of two dominant complementary hybrid lethality (HL) genes in cabbage that could result in the death of hybrids. To avoid such losses in the breeding process, we attempted to develop molecular markers to identify HL lines. Among 54 previous mapping markers closely linked to BoHL1 or BoHL2, only six markers for BoHL2 were available in eight cabbage lines (two BoHL1 lines; three BoHL2 lines; three lines without BoHL); however, they were neither universal nor user-friendly in more inbred lines. To develop more accurate markers, these cabbage lines were resequenced at an ~20× depth to obtain more nucleotide variations in the mapping regions. Then, an InDel in BoHL1 and a single-nucleotide polymorphism (SNP) in BoHL2 were identified, and the corresponding InDel marker MBoHL1 and the competitive allele-specific PCR (KASP) marker KBoHL2 were developed and showed 100% accuracy in eight inbred lines. Moreover, we identified 138 cabbage lines using the two markers, among which one inbred line carried BoHL1 and 11 inbred lines carried BoHL2. All of the lethal line genotypes obtained with the two markers matched the phenotype. Two markers were highly reliable for the rapid identification of HL genes in cabbage. Full article
(This article belongs to the Special Issue Breeding of Horticulture Plants: High-Throughput Sequencing Strategies in an Omics Era)
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8 pages, 861 KiB  
Communication
Induction of Promoter DNA Methylation Upon High-Pressure Spraying of Double-Stranded RNA in Plants
by Athanasios Dalakouras and Ioannis Ganopoulos
Agronomy 2021, 11(4), 789; https://doi.org/10.3390/agronomy11040789 - 16 Apr 2021
Cited by 14 | Viewed by 3006
Abstract
Exogenous application of RNA molecules is a potent method to trigger RNA interference (RNAi) in plants in a transgene-free manner. So far, all exogenous RNAi (exo-RNAi) applications have aimed to trigger mRNA degradation of a given target. However, the issue of concomitant epigenetic [...] Read more.
Exogenous application of RNA molecules is a potent method to trigger RNA interference (RNAi) in plants in a transgene-free manner. So far, all exogenous RNAi (exo-RNAi) applications have aimed to trigger mRNA degradation of a given target. However, the issue of concomitant epigenetic changes was never addressed. Here, we report for the first time that high-pressure spraying of dsRNAs can trigger de novo methylation of promoter sequences in plants. Full article
(This article belongs to the Special Issue Breeding of Horticulture Plants: High-Throughput Sequencing Strategies in an Omics Era)
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15 pages, 5630 KiB  
Article
Phenotypic, Genetic, and Epigenetic Variation among Diverse Sweet Cherry Gene Pools
by Evangelia V. Avramidou, Theodoros Moysiadis, Ioannis Ganopoulos, Michail Michailidis, Christos Kissoudis, Dimitrios Valasiadis, Konstantinos Kazantzis, Eirini Tsaroucha, Athanasios Tsaftaris, Athanassios Molassiotis, Filippos A. Aravanopoulos and Aliki Xanthopoulou
Agronomy 2021, 11(4), 680; https://doi.org/10.3390/agronomy11040680 - 02 Apr 2021
Cited by 6 | Viewed by 3302
Abstract
Sweet cherry germplasm contains a high variety of phenotypes which are associated with fruit size and shape as well as sugar content, etc. High phenotypic variation can be a result of genetic or epigenetic diversity that may interact through time. Recent studies have [...] Read more.
Sweet cherry germplasm contains a high variety of phenotypes which are associated with fruit size and shape as well as sugar content, etc. High phenotypic variation can be a result of genetic or epigenetic diversity that may interact through time. Recent studies have provided evidence that besides allelic variation, epiallelic variation can establish new heritable phenotypes. Herein we conducted a genetic and an epigenetic study (using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) markers, respectively), accompanied by phenotypic traits correlation analysis in sweet cherry gene pools. The mean genetic diversity was greater than the epigenetic diversity (hgen = 0.193; hepi = 0.185), while no significant relationship was found between genetic and epigenetic distance according to a Mantel test. Furthermore, according to correlation analyses our results provided evidence that epigenetic diversity in predefined populations of sweet cherry had a stronger impact on phenotypic traits than their rich genetic diversity. Full article
(This article belongs to the Special Issue Breeding of Horticulture Plants: High-Throughput Sequencing Strategies in an Omics Era)
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