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Horticulturae
Special Issues
Genetics and Molecular Breeding in Fruit Tree Orchards
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Genetics and Molecular Breeding in Fruit Tree Orchards

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 (29 February 2024) | Viewed by 6057

Special Issue Editors

Dr. John Matthew Chater

E-Mail Website
Guest Editor
Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32603, USA
Interests: breeding and bioinformatics for citrus variety improvement; identification and evaluation of advanced selections in scion and rootstock field trials for the Florida citrus industry and other stakeholders; fruit quality; effects of rootstock-scion combinations
Special Issues, Collections and Topics in MDPI journals
Dr. Zhenyu (Arthur) Jia

E-Mail Website
Guest Editor
Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
Interests: breeding; citrus; genetics; genomics; bioinformatics

Special Issue Information

Dear Colleagues，

The breeding of horticultural crops has changed immensely over the last few decades with technological advancements. Enhanced understanding of genetics, genomics, and bioinformatics has led to a new era of using molecular markers for selection in breeding. For many annual crops, marker-assisted selection is ongoing and has proven to be a highly effective and efficient method for meeting research objectives. Marker-assisted selection for tree fruit can be a challenge due to several factors ranging from life cycle length to the degree of heterozygosity in a fruit tree crop species, as is seen with citrus.

This Special Issue, “Genetics and Molecular Breeding in Fruit Tree Orchards”, seeks to present the current methods used for breeding and understanding the genetics of tree crops, with an emphasis on genomics and methods in marker-assisted selection. Special consideration will be given to manuscripts covering national or other germplasm collections or accessions. Manuscripts relating to deciduous and evergreen fruit and nut trees will be considered as will those which use multi-omics methods.

Dr. John Matthew Chater
Dr. Zhenyu (Arthur) Jia
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. Horticulturae 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 2200 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

  • breeding
  • genomics
  • GWAS
  • marker-assisted selection
  • tree fruit crop

Published Papers (4 papers)

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Research

14 pages, 2999 KiB  
Article
Genome-Wide Association Study Detects Loci Involved in Scab Susceptibility in Japanese Apricot
by Koji Numaguchi, Tomoaki Kashiwamoto, Ryo Ishikawa, Takashige Ishii and Yuto Kitamura
Horticulturae 2023, 9(8), 872; https://doi.org/10.3390/horticulturae9080872 - 31 Jul 2023
Cited by 1 | Viewed by 1003
Abstract
Japanese apricot (Prunus mume) is an important fruit tree in East Asia. ‘Nanko’, the primary cultivar of Japanese apricots, usually suffers from scab, a disease caused by Venturia carpophila. However, there have been few reports on the phenotypic variation in [...] Read more.
Japanese apricot (Prunus mume) is an important fruit tree in East Asia. ‘Nanko’, the primary cultivar of Japanese apricots, usually suffers from scab, a disease caused by Venturia carpophila. However, there have been few reports on the phenotypic variation in scab resistance/susceptibility and the underlying genetic factors. In this study, we investigated the severity of naturally occurring scabs based on fruit lesions in 108 Japanese apricot accessions over four consecutive years. In each year, both resistant and susceptible accessions were observed, and significant annual correlations were detected among the ratios of diseased fruits (Rt; 0.52–0.76) and among the disease severity indices (Sv; 0.55–0.79). We also conducted a genome-wide association study (GWAS) based on exon-targeted resequencing, and significant peaks were detected in the data from 2017 and 2018. The candidate genes involved in disease resistance are located near nine single-nucleotide polymorphisms. These genes may be associated with the susceptibility of ‘Nanko’ lineages to scab. These findings shed light on the phenotypic and genetic profiles of scab resistance in P. mume and will assist future breeding programs with improving scab resistance. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fruit Tree Orchards)
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14 pages, 2661 KiB  
Article
Exploring the Phylogenetic Relationship among Citrus through Leaf Shape Traits: A Morphological Study on Citrus Leaves
by Ryan C. Traband, Xuesong Wang, Jill Lui, Lei Yu, Yoko Hiraoka, Ira A. Herniter, Christian Bowman, Mariano Resendiz, Zixian Wang, Sara P. Knowles, Sassoum Lo, Daniel H. Chitwood, Louis Santiago, Tracy Kahn, Danelle Seymour, Mikeal L. Roose, John M. Chater and Zhenyu Jia
Horticulturae 2023, 9(7), 793; https://doi.org/10.3390/horticulturae9070793 - 12 Jul 2023
Viewed by 1310
Abstract
This study utilized the Fourier-based method to analyze the morphology of over 4000 leaves from more than 190 accessions selected from the Givaudan Citrus Variety Collection at the University of California Riverside, one of the world’s most diverse collections of citrus and closely [...] Read more.
This study utilized the Fourier-based method to analyze the morphology of over 4000 leaves from more than 190 accessions selected from the Givaudan Citrus Variety Collection at the University of California Riverside, one of the world’s most diverse collections of citrus and closely related genera. Our analysis revealed significant variations in leaf morphology among the major citrus species groups, and hybrid varieties produced through breeding exhibited intermediate leaf morphology compared to their parental citrus species. We found a positive correlation between leaf area in native citrus species and temperature in lower tropical latitudes, while negative/positive associations between aspect ratio and temperature/rainfall were also observed, respectively. These results suggest that citrus leaves may have evolved into larger but thinner leaves to increase their photosynthetic capacity per unit area while maintaining water balance by reducing water loss through transpiration. Our analysis also indicates that the existing biodiversity observed in citrus species can be attributed to their migrations across the foothills of the Himalayas, southward to the islands of Indonesia, and northward to the islands of Japan. Our study supports the hypothesis that citrus species have adapted to warm areas lacking extreme daily and nightly temperatures, where a large number of species of origin are found. Overall, this study presents a promising approach to investigate the morphological variation in citrus leaves, which could potentially aid in the selection and breeding of citrus cultivars with superior physiological traits and deepen our understanding of citrus diversity. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fruit Tree Orchards)
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15 pages, 1651 KiB  
Article
Using High-Density SNP Array to Investigate Genetic Relationships and Structure of Apple Germplasm in Bosnia and Herzegovina
by Almira Konjić, Mirsad Kurtović, Jasmin Grahić, Naris Pojskić, Abdurahim Kalajdžić and Fuad Gaši
Horticulturae 2023, 9(5), 527; https://doi.org/10.3390/horticulturae9050527 - 23 Apr 2023
Viewed by 1787
Abstract
Apple accessions, currently maintained within the two main ex situ collections in Bosnia and Herzegovina (B&H), have previously been genotyped using microsatellite markers. The obtained molecular data provided insight into mislabeled accessions and redundancies, as well as the overall genetic structure of the [...] Read more.
Apple accessions, currently maintained within the two main ex situ collections in Bosnia and Herzegovina (B&H), have previously been genotyped using microsatellite markers. The obtained molecular data provided insight into mislabeled accessions and redundancies, as well as the overall genetic structure of the germplasm. The available dataset enabled the creation of a core collection consisting of 52 accessions. The reliability and usefulness of microsatellites has made this low-density marker system a norm in studies on apple germplasm. However, the increased access to medium- and high-density SNP arrays, developed specifically for apples, has opened new avenues of research into apple genetic resources. In this study, 45 apple genotypes consisting of 33 diploid core collection accessions from B&H and 12 international reference cultivars were genotyped using an Axiom® Apple 480 K SNP array in order to examine their genetic relationships, population structure and diversity, as well as to compare the obtained results with those calculated on previously reported SSR profiles. The SNPs displayed a better ability to differentiate apple accessions based on their origin, as well as to cluster them according to their pedigree. Calculating identity by descent revealed 16 pairings with first-degree relationships and uncovered the introgression of ‘Delicious’ and ‘Golden Delicious’ into the core collection. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fruit Tree Orchards)
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16 pages, 2998 KiB  
Article
Transcriptomic Analysis of Anthocyanin and Carotenoid Biosynthesis in Red and Yellow Fruits of Sweet Cherry (Prunus avium L.) during Ripening
by Qinghao Wang, Luyang Jing, Yue Xu, Weiwei Zheng and Wangshu Zhang
Horticulturae 2023, 9(4), 516; https://doi.org/10.3390/horticulturae9040516 - 21 Apr 2023
Cited by 3 | Viewed by 1499
Abstract
The diversity of fruit color in sweet cherry (Prunus avium L.) has been attributed to the presence of either anthocyanin or carotenoid. We profiled the anthocyanin and carotenoid metabolites to investigate the different pigments and the underlying regulatory mechanisms of differential expression [...] Read more.
The diversity of fruit color in sweet cherry (Prunus avium L.) has been attributed to the presence of either anthocyanin or carotenoid. We profiled the anthocyanin and carotenoid metabolites to investigate the different pigments and the underlying regulatory mechanisms of differential expression genes (DEGs) between red and yellow fruits of sweet cherry. We profiled two cultivars, ‘Jiangnanhong’(JNH, red fruits) and ‘Chaoyang’(CY, yellow fruits) to establish their anthocyanin and carotenoid metabolites by LC-MS/MS and transcriptome analysis by RNA-seq to test the difference in gene expression and metabolic substances between the two varieties. Cyanidin-3-O-rutinoside was the most different pigment between two cultivars, the content of which in red fruit was significantly higher than in the yellow one during the whole ripening stage (stage 3 and stage 4). The total carotenoid content in the two color types of fruits was close, but the content in yellow fruit was shown to be more stable after harvest. Based on the transcriptome data, the heatmap of selected structural DEGs showed that all of the anthocyanin genes expressed significantly higher levels in red fruits than that in yellow fruits. Two unigenes encoding chalcone synthase (CHS) and UDP glucose-flavonoid 3-O-glucosyltransferase (UFGT) were expressed 1134.58 and 1151.24 times higher in red than in yellow fruits at stage 4, respectively. Correlation analysis showed that anthocyanin genes in JNH were negatively correlated with those in CY; by contrast, there were some strong correlations observed between the two cultivars in carotenoid genes. Thus, the coloration of sweet cherry was mainly attributed to anthocyanin-related genes. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fruit Tree Orchards)
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