Advances in Rosaceae Fruit Genomics and Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 2958

Special Issue Editor


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Guest Editor
Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100 Murcia, Spain
Interests: fruit trees; Prunus; fruit quality; postharvest; sensory quality; genomics; transcriptomics; epigenetics
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Special Issue Information

Dear Colleagues,

The Rosaceae family encompasses a wide range of plant species utilized for both agronomic and ornamental purposes, hosting significant genetic variability. Traditional genetic breeding in fruit species has historically aimed to harness this genetic diversity to address complex challenges associated with biotic and abiotic stresses, agronomic management, and evolving consumer preferences, particularly concerning sensory and fruit quality traits.

Notably, recent decades have witnessed remarkable molecular advances that underpin these genetic breeding initiatives, yielding valuable molecular markers useful for molecular-assisted selection (MAS) at the nursery level. These advancements can largely be attributed to the rapid evolution of sequencing platforms, facilitating the comprehensive sequencing of numerous plant species and fostering deeper genomic and transcriptomic studies.

The latest sequencing technologies have successfully facilitated the implementation of genotyping by sequencing, enabling the identification of thousands of single-nucleotide polymorphisms (SNPs) within sibling populations or diverse collections of varieties. This wealth of information contributes to the development of high-density genetic maps, essential for the identification of Mendelian trait loci (MTLs) or quantitative trait loci (QTLs), as well as marker-trait associations through linear or mixed models. Moreover, the data derived from these sequencing platforms, encompassing newly available plant genomes, have significantly streamlined transcriptomic studies, facilitating targeted investigations into gene expression patterns in various plant tissues or in response to specific treatments. However, this approach has primarily been effective for Mendelian traits, given the codominant inheritance of polygenic-related traits mainly associated with fruit quality.

Consequently, there is a need to adopt new strategies, such as the selection of the best genitors for the generation of new segregating populations to provide new genotypes with desired traits. To achieve this, the implementation of genomic selection is needed, utilizing meticulously designed and accurately phenotyped breeding populations to forecast the breeding values of the parent plants to facilitate the most suitable hybrid crosses specifically tailored to target traits of interest. Phenotyping and genotyping analyses are essential for conducting comprehensive genome-wide association studies (GWAS) and genomic selection (GS), integrating this knowledge with diverse genetic backgrounds in order to accelerate the efficiency of genetic breeding programs.

The aim of this Special Issue, dedicated to “Advances in Rosaceae Fruit Genomics and Breeding”, is to provide a comprehensive overview of the most recent advancements achieved through the diligent efforts of researchers. We cordially invite you to submit advanced contributions focusing on genomic studies, with the explicit aim of enhancing and fortifying genetic breeding programs.

Dr. Juan A. Salazar
Guest Editor

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

  • fruit species
  • phenotyping
  • genotyping
  • genetics
  • genomics
  • transcriptomics
  • QTL mapping
  • GWAS
  • genomic selection

Published Papers (2 papers)

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Research

15 pages, 1603 KiB  
Article
Characterization of Almond Scion/Rootstock Communication in Cultivar and Rootstock Tissues through an RNA-Seq Approach
by Álvaro Montesinos, María José Rubio-Cabetas and Jérôme Grimplet
Plants 2023, 12(24), 4166; https://doi.org/10.3390/plants12244166 - 15 Dec 2023
Viewed by 1236
Abstract
The rootstock genotype plays a crucial role in determining various aspects of scion development, including the scion three-dimensional structure, or tree architecture. Consequently, rootstock choice is a pivotal factor in the establishment of new almond (Prunus amygdalus (L.) Batsch, syn P. [...] Read more.
The rootstock genotype plays a crucial role in determining various aspects of scion development, including the scion three-dimensional structure, or tree architecture. Consequently, rootstock choice is a pivotal factor in the establishment of new almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) intensive planting systems, demanding cultivars that can adapt to distinct requirements of vigor and shape. Nevertheless, considering the capacity of the rootstock genotype to influence scion development, it is likely that the scion genotype reciprocally affects rootstock performance. In the context of this study, we conducted a transcriptomic analysis of the scion/rootstock interaction in young almond trees, with a specific focus on elucidating the scion impact on the rootstock molecular response. Two commercial almond cultivars were grafted onto two hybrid rootstocks, thereby generating four distinct combinations. Through RNA-Seq analysis, we discerned that indeed, the scion genotype exerts an influence on the rootstock expression profile. This influence manifests through the modulation of genes associated with hormonal regulation, cell division, root development, and light signaling. This intricate interplay between scion and rootstock communication plays a pivotal role in the development of both scion and rootstock, underscoring the critical importance of a correct choice when establishing new almond orchards. Full article
(This article belongs to the Special Issue Advances in Rosaceae Fruit Genomics and Breeding)
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13 pages, 2016 KiB  
Article
Susceptibility Evaluation to Fire Blight and Genome-Wide Associations within a Collection of Asturian Apple Accessions
by Belén García-Fernández, Ramon Dolcet-Sanjuan, Diego Micheletti, María José Antón-Díaz, Cristina Solsona, Mercedes Fernández, Xavier Abad and Enrique Dapena
Plants 2023, 12(23), 4068; https://doi.org/10.3390/plants12234068 - 4 Dec 2023
Cited by 2 | Viewed by 1480
Abstract
Fire blight, caused by Erwinia amylovora, is one of the most devastating apple diseases. The selection of cultivars of low susceptibility and the study of the genetic mechanisms of the disease play important roles in fire blight management. The susceptibility level to [...] Read more.
Fire blight, caused by Erwinia amylovora, is one of the most devastating apple diseases. The selection of cultivars of low susceptibility and the study of the genetic mechanisms of the disease play important roles in fire blight management. The susceptibility level to fire blight was evaluated in 102 accessions originating from Asturias, a cider-producing region located in the north of Spain with a wide apple germplasm. Evaluations took place under quarantine conditions using artificial inoculations of grafted plants. The results revealed wide variation in susceptibility responses and low-susceptible cultivars were identified. In addition, 91 cultivars were genotyped using the Affymetrix Axiom® Apple 480 K SNP array to conduct genome-wide association studies (GWAS). A statistically significant signal was detected on chromosome 10 using the multi-locus mixed model (MLMM). Two genes were identified as major putative candidate genes: a TIR-NBS-LRR class disease protein and a protein containing a development and cell death (DCD) domain. The outcomes of this study provide a promising source of information, particularly in the context of cider apples, and set a starting point for future genetic and breeding approaches. Full article
(This article belongs to the Special Issue Advances in Rosaceae Fruit Genomics and Breeding)
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