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Plants
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Molecular Breeding in Horticultural Plants
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Molecular Breeding in Horticultural Plants

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

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 17421

Special Issue Editors

Dr. Hélia Cardoso

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Guest Editor
MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Escola de Ciências e Tecnologia, Departamento de Biologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
Interests: plant morphogenesis (adventitious rooting and somatic embryogenesis); in vitro plant propagation; abiotic stress response (transcriptomic/proteomic approach); plant breeding (marker-assisted selection)
Special Issues, Collections and Topics in MDPI journals
Dr. Augusto Peixe

E-Mail Website
Guest Editor
MED – Mediterranean Institute for Agriculture, Environment and Development, Fitotecnia Department, Sciences and Technology School, University of Évora, Mitra Campus, Ap. 94, 7006-554 Évora, Portugal
Interests: plant propagation and plant breeding; tissue culture techniques including micropropagation; micrografting; meristem tip culture and somatic embryogenesis; biology and physiology of adventitious rooting; breeding for resistance to biotic stress
Special Issues, Collections and Topics in MDPI journals
Dr. Eugénia de Andrade

E-Mail Website
Guest Editor
Unidade Estratégica de Investigação e Serviços de Sistemas Florestais e Agrícolas e Sanidade Vegetal, Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, 2780-159 Oeiras, Portugal
Interests: molecular markers (SSR); plant transformation and breeding; phytopathogens. Currently, I am working on the genetic control of the interaction between host and pathogen, breeding for resistance against potato cyst nematodes, molecular characterization of fruit flies (SSR), and early detection.

Special Issue Information

Dear Colleagues,

Plant molecular breeding, including marker-assisted breeding and genetic engineering, has experienced remarkable innovations and advances during the last few decades. The availability of high-throughput platforms focused on the different omics, from genomics to metabolomics, made available important information related to key genes and pathways associated with important agronomical traits. Different breeding programs are now focused on the use of that knowledge to produce new improved varieties. This Special Issue intends to report the recent advances in breeding strategies focused on innovative analysis coming from different omics approaches, including data achieved by high-throughput platforms. Approaches focused on genetics (genotyping and phenotyping), genomics (identification of genes directly linked with agronomical traits, regulatory elements, or functional polymorphisms), and transcriptomics (identification of key gene(s) and validation of its involvement in the expression of specific traits) will be considered. Data provided from proteomics (identification of enzymes and proteins from key pathways) and metabolomics (identification/quantification of metabolites that could be used as biomarkers on defined traits) will also be considered if an integrative approach is followed.

Dr. Hélia Cardoso
Dr. Augusto Peixe
Dr. Eugénia de Andrade
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

  • Biotic/abiotic stress tolerance
  • Transcriptome/genome analysis
  • Throughput analysis
  • Plant genetic improvement
  • Marker-assisted breeding
  • Functional polymorphisms
  • Quantitative trait locus (QTL)
  • Genetic transformation
  • Transgenic crops
  • Assisted selection

Published Papers (4 papers)

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Research

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18 pages, 5166 KiB  
Article
Carrot AOX2a Transcript Profile Responds to Growth and Chilling Exposure
by Maria Doroteia Campos, Catarina Campos, Amaia Nogales and Hélia Cardoso
Plants 2021, 10(11), 2369; https://doi.org/10.3390/plants10112369 - 03 Nov 2021
Cited by 6 | Viewed by 1642
Abstract
Alternative oxidase (AOX) is a key enzyme of the alternative respiration, known to be involved in plant development and in response to various stresses. To verify the role of DcAOX1 and DcAOX2a genes in carrot tap root growth and in response to cold [...] Read more.
Alternative oxidase (AOX) is a key enzyme of the alternative respiration, known to be involved in plant development and in response to various stresses. To verify the role of DcAOX1 and DcAOX2a genes in carrot tap root growth and in response to cold stress, their expression was analyzed in two experiments: during root growth for 13 weeks and in response to a cold challenge trial of 7 days, in both cases using different carrot cultivars. Carrot root growth is initially characterized by an increase in length, followed by a strong increase in weight. DcAOX2a presented the highest expression levels during the initial stages of root growth for all cultivars, but DcAOX1 showed no particular trend in expression. Cold stress had a negative impact on root growth, and generally up-regulated DcAOX2a with no consistent effect on DcAOX1. The identification of cis-acting regulatory elements (CAREs) located at the promoters of both genes showed putative sequences involved in cold stress responsiveness, as well as growth. However, DcAOX2a promoter presented more CAREs related to hormonal pathways, including abscisic acid and gibberellins synthesis, than DcAOX1. These results point to a dual role of DcAOX2a on carrot tap root secondary growth and cold stress response. Full article
(This article belongs to the Special Issue Molecular Breeding in Horticultural Plants)
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12 pages, 2071 KiB  
Article
Tissue-Specific RNA-Seq Analysis and Identification of Receptor-Like Proteins Related to Plant Growth in Capsicum annuum
by Won-Hee Kang, Boseul Park, Junesung Lee and Seon-In Yeom
Plants 2021, 10(5), 972; https://doi.org/10.3390/plants10050972 - 13 May 2021
Cited by 5 | Viewed by 2803
Abstract
Receptor-like proteins (RLPs) are a gene family of cell surface receptors that are involved in plant growth, development, and disease resistance. In a recent study, 438 pepper RLP genes were identified in the Capsicum annuum genome (CaRLPs) and determined to be present in [...] Read more.
Receptor-like proteins (RLPs) are a gene family of cell surface receptors that are involved in plant growth, development, and disease resistance. In a recent study, 438 pepper RLP genes were identified in the Capsicum annuum genome (CaRLPs) and determined to be present in response to multiple biotic stresses. To further understand the role of CaRLPs in plant growth and development, we analyzed expression patterns of all CaRLPs from various pepper tissues and developmental stages using RNA-seq. Ten CaRLP genes were selected for further analysis according to transcript levels with hierarchical clustering. The selected CaRLP genes displayed similarity of motifs within the same groups and structures typical of RLPs. To examine RLP function in growth and development, we performed loss-of-function analysis using a virus-induced gene silencing system. Three of the ten tested CaRLPs (CaRLP238, 253, and 360) in silenced plants exhibited phenotypic alteration with growth retardation compared to controls. All three gene-silenced peppers showed significant differences in root dry weight. Only CaRLP238 had significant differences in both root and shoot dry weight. Our results suggest that CaRLPs may play important roles in regulation of plant growth and development as well as function in defense responses to biotic stresses in the RLP gene family. Full article
(This article belongs to the Special Issue Molecular Breeding in Horticultural Plants)
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16 pages, 2643 KiB  
Article
Identification and Expression Analysis of Stress-Associated Proteins (SAPs) Containing A20/AN1 Zinc Finger in Cucumber
by Wei Lai, Yong Zhou, Rao Pan, Liting Liao, Juncheng He, Haoju Liu, Yingui Yang and Shiqiang Liu
Plants 2020, 9(3), 400; https://doi.org/10.3390/plants9030400 - 24 Mar 2020
Cited by 25 | Viewed by 3473
Abstract
Stress-associated proteins (SAPs) are a class of zinc finger proteins that confer tolerance to a variety of abiotic and biotic stresses in diverse plant species. However, in cucumber (Cucumis sativus L.), very little is known about the roles of SAP gene family [...] Read more.
Stress-associated proteins (SAPs) are a class of zinc finger proteins that confer tolerance to a variety of abiotic and biotic stresses in diverse plant species. However, in cucumber (Cucumis sativus L.), very little is known about the roles of SAP gene family members in regulating plant growth, development, and stress responses. In this study, a total of 12 SAP genes (named as CsSAP1-CsSAP12) were identified in the cucumber genome, which were unevenly distributed on six chromosomes. Gene duplication analysis detected one tandem duplication and two segmental duplication events. Phylogenetic analysis of SAP proteins from cucumber and other plants suggested that they could be divided into seven groups (sub-families), and proteins in the same group generally had the same arrangement of AN1 (ZnF-AN1) and A20 (ZnF-A20) domains. Most of the CsSAP genes were intronless and harbored a number of stress- and hormone-responsive cis-elements in their promoter regions. Tissue expression analysis showed that the CsSAP genes had a broad spectrum of expression in different tissues, and some of them displayed remarkable alteration in expression during fruit development. RT-qPCR results indicated that all the selected CsSAP genes displayed transcriptional responses to cold, drought, and salt stresses. These results enable the first comprehensive description of the SAP gene family in cucumber and lay a solid foundation for future research on the biological functions of CsSAP genes. Full article
(This article belongs to the Special Issue Molecular Breeding in Horticultural Plants)
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Review

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14 pages, 868 KiB  
Review
Accelerating Tomato Breeding by Exploiting Genomic Selection Approaches
by Elisa Cappetta, Giuseppe Andolfo, Antonio Di Matteo, Amalia Barone, Luigi Frusciante and Maria Raffaella Ercolano
Plants 2020, 9(9), 1236; https://doi.org/10.3390/plants9091236 - 18 Sep 2020
Cited by 25 | Viewed by 8298
Abstract
Genomic selection (GS) is a predictive approach that was built up to increase the rate of genetic gain per unit of time and reduce the generation interval by utilizing genome-wide markers in breeding programs. It has emerged as a valuable method for improving [...] Read more.
Genomic selection (GS) is a predictive approach that was built up to increase the rate of genetic gain per unit of time and reduce the generation interval by utilizing genome-wide markers in breeding programs. It has emerged as a valuable method for improving complex traits that are controlled by many genes with small effects. GS enables the prediction of the breeding value of candidate genotypes for selection. In this work, we address important issues related to GS and its implementation in the plant context with special emphasis on tomato breeding. Genomic constraints and critical parameters affecting the accuracy of prediction such as the number of markers, statistical model, phenotyping and complexity of trait, training population size and composition should be carefully evaluated. The comparison of GS approaches for facilitating the selection of tomato superior genotypes during breeding programs is also discussed. GS applied to tomato breeding has already been shown to be feasible. We illustrated how GS can improve the rate of gain in elite line selection, and descendent and backcross schemes. The GS schemes have begun to be delineated and computer science can provide support for future selection strategies. A new promising breeding framework is beginning to emerge for optimizing tomato improvement procedures. Full article
(This article belongs to the Special Issue Molecular Breeding in Horticultural Plants)
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