Genetic Improvement of Apple: Breeding, Markers, Mapping and Biotechnology

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: closed (10 March 2024) | Viewed by 2045

Special Issue Editors


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Guest Editor
Institute of Horticulture, Dobele, Latvia
Interests: disease-resistant apple cultivar breeding; apple genetic resource research; apple cultivar testing; hybrid plum research and breeding

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Guest Editor
Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA 22602, USA
Interests: tree fruits genetics and biology; tree biotechnology; stress physiology; hormonal signaling and molecular plant-microbe interactions
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Special Issue Information

Dear Colleagues,

In modern fruit growing, the establishment of plantations to ensure high fruit yields that are relatively constant from one year to another, of superior quality, and economically profitable peremptorily requires adequate cultivars. The cultivar became the most important factor of production as it plays the primary role in the realization of the sustainable fruit ecosystem that adequately meets the ever-increasing demands of the market, users, processors, consumers, and producers (farmers).

Over the last few decades, researchers’ attention on this species has grown exponentially as evidenced by the increasing number of scientific publications, especially regarding its basic biology. However, there are still open questions and challenges in this fascinating field around topics such as domestic apple’s evolution in quality and stress resistance compared to that of wild apple, pome fruit development and flesh quality formation, grafting and rootstock–scion interactions, bud differentiation and dormancy, and life cycle regulation. In the post-genomic era, the analysis of gene functions in apple is required for agricultural utilization and molecular breeding.

In this Special Issue, “Genetic Improvement of Apple: Breeding, Markers, Mapping and Biotechnology”, we plan to attract articles (original research papers, reviews, opinions, perspectives and methods) that focus on Malus biology, including germplasm resources, the genome, evolution, development, genetics, stress, fruit quality, nutrition, cultivation and postharvest at all levels. Articles comprising transcriptome, proteome, metabolome and epigenome studies and studies on biochemistry, physiology, genes, proteins, metabolites, stress biology, fruit development, fruit quality, grafting biology, flower development and postharvest biology are most welcome.

Dr. Laila Ikase
Dr. Sherif M. Sherif
Guest Editors

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Keywords

  • apple cultivars
  • selection breeding
  • disease resistant apple cultivars
  • orchards
  • apple genetic resource

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Published Papers (1 paper)

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Research

16 pages, 3314 KiB  
Article
In Silico Apple Genome-Encoded MicroRNA Target Binding Sites Targeting Apple Chlorotic Leaf Spot Virus
by Muhammad Aleem Ashraf, Nimra Murtaza, Judith K. Brown and Naitong Yu
Horticulturae 2023, 9(7), 808; https://doi.org/10.3390/horticulturae9070808 - 14 Jul 2023
Cited by 1 | Viewed by 1629
Abstract
Apple chlorotic leaf spot virus (ACLSV) (genus, Trichovirus; family, Betaflexiviridae) is a widespread, deleterious, and the most damaging pathogen of pome and fruit trees including domesticated apple (Malus × domestica Borkh.), to which it is transmitted by grafting and pruning. [...] Read more.
Apple chlorotic leaf spot virus (ACLSV) (genus, Trichovirus; family, Betaflexiviridae) is a widespread, deleterious, and the most damaging pathogen of pome and fruit trees including domesticated apple (Malus × domestica Borkh.), to which it is transmitted by grafting and pruning. The positive-sense, single-stranded RNA virus is 600–700 nm long and has a genome of 74.7–7.56 kbp in size, minus the poly-A tail and 3′- and 5′-untranslated regions. The genome has three overlapping open reading frames (ORFs) that encode a replication-associated protein (Rep), movement protein (MP), and coat protein (CP). RNA interference (RNAi)-mediated antiviral defense in eukaryotes has evolved to control infections in plant viruses. The objective of this study was to analyze locus-derived microRNAs (mdm-miRNAs) in the apple genome with potential for targeting ACLSV +ssRNA-encoded mRNAs, using a predictive approach that involves four algorithms. The goal is to mobilize the in silico-predicted endogenous mdm-miRNAs and trigger the RNAi pathway experimentally in apple trees to evaluate antiviral resistance to ACLSV. Experimentally validated apple (2n = 2X = 34) mdm-miRNAs (n = 322) were obtained from the miRBase database and aligned to the ACLSV genome (KU870525). Of the 322 targeting mature locus-derived mdm-miRNAs analyzed, nine apple mdm-miRNA homologs (mdm-miR395k, mdm-miR5225c, and mdm-miR7121 (a, b, c, d, e, f, g, h) were predicted by all “four algorithms”, whereas fifty-eight mdm-miRNAs were identified as consensus binding sites by the combined results of two algorithms. The miRanda, RNA22, and TAPIR algorithms predicted binding of mdm-miR395k at nucleotide position 4691 and identified it as the most effective interacting mdm-miRNA targeting the virus ORF1 sequence. An integrated Circos plot was generated to validate the accuracy of target prediction and determine if apple mdm-miRNAs could bind to the predicted ACLSV mRNA target(s). A genome-wide in silico-predicted miRNA-mediated target gene regulatory network was implicated to validate interactions necessary to warrant in vivo analysis. The availability of validated locus-derived microRNAs (mdm-miRNAs) with predicted potential to target ACLSV in infected apple trees represents the first step toward development of ACLSV-resistant apple trees. Full article
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