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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: 30 June 2024 | Viewed by 7763

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Prof. Dr. Stefano La Malfa

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Guest Editor

Department of Agriculture, Food and Environment, University of Catania Via Valdisavoia, 5-9123 Catania, Italy
Interests: breeding; germplasm characterization; minor fruit tree species; citrus; molecular characterization
Special Issues, Collections and Topics in MDPI journals

Dr. Stefania Bennici

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Guest Editor

Department of Agriculture, Food and Environment, University of Catania Via Valdisavoia, 5-9123 Catania, Italy
Interests: molecular breeding; citrus; grape; pear; almond

Special Issue Information

Dear Colleagues,

The world demand for horticultural crops showing enhanced agricultural traits (e.g., fruit quality, yield, resistance to biotic and abiotic stress) is continuously increasing. To this extent, a deep understanding of the genetic basis of agronomic traits represents a fundamental prerequisite both for understanding the trait regulatory mechanisms and for breeding. Genetic studies and the conventional breeding of fruit trees are hampered by several disadvantages such as the long juvenile period, the large plant size, and high heterozygosity. Advances in biotechnology and the advent of genomics have opened new opportunities to overcome the limits of conventional breeding in fruit tree breeding.

The availability of high-throughput genetic platforms, the release of whole genome sequence resources, omics (e.g., transcriptomics, proteomics, metabolomics, hormonomics), and genome-wide association studies have demonstrated a tremendous leap forward in the understanding of the genetic basis underlying traits of agronomical interest.

Furthermore, ongoing advances in biotechnology strategies such as the use of molecular markers and marker-assisted selection or the advent of new plant breeding techniques (e.g., cisgenesis and genome editing) greatly accelerated progress in functional trait characterization and the breeding process in fruit trees.

This Special Issue of Horticulturae aims to cover the recent findings related to the genetics and molecular breeding of fruit trees for the definition of novel cultivars with superior characteristics.

Prof. Dr. Stefano La Malfa
Dr. Stefania Bennici
Guest Editors

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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

genome-wide association analysis
quantitative-trait locus
new plant breeding techniques
fruit quality
biotic/abiotic stress

Published Papers (6 papers)

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Research

13 pages, 5786 KiB

Open AccessArticle

Cytogenetics Study of Four Edible and Ornamental Zingiber Species (Zingiberaceae) from Thailand

by Piyaporn Saensouk, Surapon Saensouk, Rattanavalee Senavongse, Duangkamol Maensiri and Phetlasy Souladeth

Horticulturae 2024, 10(4), 409; https://doi.org/10.3390/horticulturae10040409 - 18 Apr 2024

Viewed by 329

Abstract

A cytological study was carried out on four Zingiber species from Thailand, namely, Z. chrysostachys, Z. isanense, Z. junceum, and Z. niveum, which are edible and beautiful ornamental plants. They all have somatic chromosomal numbers of 2n = 22. This research contributes to karyological knowledge regarding this species. The somatic chromosomal counts of Z. niveum and Z. isanense are reported for the first time, as are the NFs of all species, which were all discovered to be 44. All four edible and ornamental species had their karyotypes: 16m + 6sm for Z. chrysostachys, 4m + 18sm for Z. isanense, 12m + 10sm for Z. junceum, and 14m + 4sm + 4st for Z. niveum. The dominant characteristics of these four Zingiber species are as follows: Z. chrysostachys has yellow bracts, pale yellow flowers, and a red labellum with white dots; Z. isanensis has red-brown bracts, white flowers, and a white labellum; Z. junceum has green bracts, yellow flowers, and a yellow labellum; and Z. niveum has white bracts, yellow flowers, and a yellow labellum. Additionally, principal component analysis (PCA) of the karyotype formula was used to divide the four Zingiber species into two groups via various points using the chromosome indexes (CIs): Z. niveum (D) with Z. chrysostachys (A), and Z. junceum (C) with Z. isanensis (B). This finding implies that, while being in the same stage, the CIs of these four Zingiber species can be used to distinguish them, revealing their resemblance at unique stages and close relationship. Accordingly, the chromosomal structure, karyotype formulae, and CIs can be used to distinguish these four edibles and ornamental Zingiber species from Thailand. Full article

(This article belongs to the Special Issue Genetics and Molecular Breeding of Fruit Tree Species)

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20 pages, 2733 KiB

Open AccessFeature PaperArticle

Decoding the Genomic Landscape of Pomegranate: A Genome-Wide Analysis of Transposable Elements and Their Structural Proximity to Functional Genes

by Samuel Simoni, Gabriele Usai, Alberto Vangelisti, Marco Castellacci, Tommaso Giordani, Lucia Natali, Flavia Mascagni and Andrea Cavallini

Horticulturae 2024, 10(2), 111; https://doi.org/10.3390/horticulturae10020111 - 24 Jan 2024

Viewed by 890

Abstract

Transposable elements (TEs) significantly drive dynamic changes that characterize genome evolution. However, understanding the variability associated with TE insertions among different cultivars remains challenging. The pomegranate (Punica granatum L.) has yet to be extensively studied regarding the roles of TEs in the diversification of cultivars. Herein, we explored the genome distribution of TEs and its potential functional implications among four pomegranate cultivars, ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’ and ‘Tunisia’, whose genome sequences are available. A total of 8404 full-length TEs were isolated. The content of TEs varied among the cultivars, ranging from 41.67% of ‘Taishanhong’ to 52.45% of ‘Bhagwa’. In all cultivars, the Gypsy superfamily of retrotransposons accounted for a larger genome proportion than the Copia superfamily. Seventy-three full-length TEs were found at the same genomic loci in all four cultivars. By contrast, 947, 297, 311, and 874 TEs were found exclusively in ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’, and ‘Tunisia’ cultivars, respectively. Phylogenetic clustering based on the presence of TE insertions in specific loci reflected the geographic origins of the cultivars. The insertion time profiles of LTR-REs were studied in the four cultivars. Shared elements across the four cultivars exhibited, on average, a more ancient insertion date than those exclusive to three, two, or one cultivars. The majority of TEs were located within 1000 bp from the nearest gene. This localization was observed for 57% of DNA TEs and 55% of long-terminal repeat retrotransposons (LTR-RE). More than 10% of TEs resulted inserted within genes. Concerning DNA TEs, 3.91% of insertions occurred in introns, while 2.42% occurred in exons. As to LTR-REs, 4% of insertions occurred in exons and 1.98% in introns. Functional analysis of the genes lying close to TEs was performed to infer if differences in TE insertion can affect the fruit quality. Two TE insertions were found close to two genes encoding 4-coumarate--CoA ligase, an enzyme involved in the phenylpropanoid pathway. Moreover, a TIR/Mariner element was found within the exon of a gene encoding anthocyanidin reductase in the ‘Tunisia’ genotype, crucial in the biosynthesis of flavan-3-ols and proanthocyanidins, strictly correlated with the nutraceutical properties of pomegranate. Although functional and metabolomic studies are essential to elucidate the consequences of TE insertions, these results contribute to advancing our comprehension of the role of TEs in pomegranate genomics, providing insights for crop breeding. Full article

(This article belongs to the Special Issue Genetics and Molecular Breeding of Fruit Tree Species)

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14 pages, 2828 KiB

Open AccessEditor’s ChoiceArticle

Somatic Embryogenesis and Plant Regeneration from Stem Explants of Pomegranate

by Jingting Wang, Xinhui Xia, Gaihua Qin, Jingwen Tang, Jun Wang, Wenhao Zhu, Ming Qian, Jiyu Li, Guangrong Cui, Yuchen Yang and Jingjing Qian

Horticulturae 2023, 9(9), 1038; https://doi.org/10.3390/horticulturae9091038 - 14 Sep 2023

Viewed by 1080

Abstract

Plant regeneration through somatic embryogenesis provides a solution for maintaining and genetically improving crop or fruit varieties with desirable agronomic traits. For the fruit tree pomegranate (Punica granatum L.), despite some successful applications, the existing somatic embryogenesis protocols are limited by low availability of explants and susceptibility to browning. To address these problems, in this study, we developed an effective system for induction of high-vigor pomegranate somatic embryos derived from stem explants. The usage of stem explants breaks through the difficulty in obtaining material, thus making our system suitable for widespread commercial production. To enhance the performance of our system, we identified the optimal explants, subculture cycles and combination of basal media and plant growth regulators for each step. The results showed that inoculating stem explants onto a Murashige and Skoog (MS) medium supplemented with 1.0 mg/L 6-benzylaminopurine (6-BA) and 1.0 mg/L 1-naphthaleneacetic acid (NAA) achieved the best induction rate and growth status of pomegranate calli (induction rate = ~72%), and MS medium containing 0.5 mg/L 6-BA and 1.0 mg/L NAA was the optimal condition for the induction of embryogenic calli and somatic embryos (induction rate = ~74% and 79%, respectively). The optimal subculture period for embryogenic calli was found to be 30–35 days. Strong roots were then induced in the developed somatic embryo seedlings, which survived and grew well after transplantation to the natural environment, indicating the good vitality of the induced pomegranate somatic embryos. Together, our system provides a solution to mass somatic embryo induction and plant regeneration of pomegranate and lays a foundation for future genetic transformation and bioengineering improvement of pomegranate with favorable agronomic traits. Full article

(This article belongs to the Special Issue Genetics and Molecular Breeding of Fruit Tree Species)

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16 pages, 3224 KiB

Open AccessArticle

Callus Induction and Adventitious Root Regeneration of Cotyledon Explants in Peach Trees

by Lingling Gao, Jingjing Liu, Liao Liao, Anqi Gao, Beatrice Nyambura Njuguna, Caiping Zhao, Beibei Zheng and Yuepeng Han

Horticulturae 2023, 9(8), 850; https://doi.org/10.3390/horticulturae9080850 - 26 Jul 2023

Cited by 1 | Viewed by 2321

Abstract

Callus induction is a key step in establishing plant regeneration and genetic transformation. In this study, we present a comprehensive large-scale investigation of the callus induction rate (CIR) in peach trees, which revealed significant variability within the peach germplasm. Notably, the late-maturing cultivars exhibited significantly higher levels of CIR. Moreover, cultivars characterized as having high CIR exhibited potential for the development of adventitious roots (ARs) during callus induction, and a positive correlation was observed between CIR and the ability to regenerate ARs. However, long-term subculture callus lost root regeneration capacity due to changes in cellular morphology and starch and flavonoid content. Additionally, PpLBD1 was identified as a good candidate gene involved in the regulation of callus adventitious rooting in peach trees. Our results provide an insight into the mechanisms underlying callus induction and adventitious root development and will be helpful for developing regeneration systems in peach trees. Full article

(This article belongs to the Special Issue Genetics and Molecular Breeding of Fruit Tree Species)

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17 pages, 3707 KiB

Open AccessArticle

Construction of a High-Density Genetic Linkage Map Based on Bin Markers and Mapping of QTLs Associated with Fruit Size in Jujube (Ziziphus jujuba Mill.)

by Tianfa Guo, Qianqian Qiu, Fenfen Yan, Zhongtang Wang, Jingkai Bao, Zhi Yang, Yilei Xia, Jiurui Wang, Cuiyun Wu and Mengjun Liu

Horticulturae 2023, 9(7), 836; https://doi.org/10.3390/horticulturae9070836 - 22 Jul 2023

Viewed by 1156

Abstract

Jujube (Ziziphus jujuba Mill.) is a fruit tree that is gaining increasing importance in drought-affected regions worldwide. The fruit size is an important quantitative agronomic trait that affects not only the fruit yield and attractiveness but also consumer preference. Genetic enhancement of fruit appearance is a fundamental goal of jujube breeding programs. The genetic control of jujube fruit size traits is highly quantitative, and development of high-density genetic maps can facilitate fine mapping of quantitative trait loci (QTLs) and gene identification. However, studies regarding the construction of high-density molecular linkage maps and identification of quantitative trait loci (QTLs) targeting fruit size in jujube are limited. In this study, we performed whole-genome resequencing of the jujube cultivars “JMS2” and “Xing16” and their 165 F₁ progenies to identify genome-wide single-nucleotide polymorphism (SNP) markers and constructed a high-density bin map of jujube that can be used to assist in the selection of multiple traits in jujube breeding. This analysis yielded a total of 116,312 SNPs and a genetic bin map of 2398 bin markers spanning 1074.33 cM with an average adjacent interval of 0.45 cM. A quantitative genetic analysis identified 15 QTLs related to fruit size and the observed phenotypic variation associated with a single QTL ranged from 9.5 to 13.3%. Through the screening of overlapping and stable QTL regions, we identified 113 candidate genes related to fruit size. These genes were ascertained to be involved in cell division, cell wall metabolism, synthesis of phytohormones (ABA, IAA, and auxin), and encoding of enzymes and transcription factors. These candidate genomic regions will facilitate marker-assisted breeding of fruits with different sizes and shapes and lay a foundation for future breeding and manipulation of fruit size and shape in jujube. Full article

(This article belongs to the Special Issue Genetics and Molecular Breeding of Fruit Tree Species)

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18 pages, 4426 KiB

Open AccessArticle

Genome-Wide Association Mapping of Oil Content and Seed-Related Traits in Shea Tree (Vitellaria paradoxa subsp. nilotica) Populations

by Juventine Boaz Odoi, Emmanuel Amponsah Adjei, Michael Teye Barnor, Richard Edema, Samson Gwali, Agyemang Danquah, Thomas Lapaka Odong and Prasad Hendre

Horticulturae 2023, 9(7), 811; https://doi.org/10.3390/horticulturae9070811 - 14 Jul 2023

Viewed by 984

Abstract

Shea tree (Vitellaria paradoxa) is an important fruit tree crop because of its oil used for cooking and the industrial manufacture of cosmetics. Despite its essential benefits, quantitative trait loci linked to the economic traits have not yet been studied. In this study, we performed association mapping on a panel of 374 shea tree accessions using 7530 Single-Nucleotide Polymorphisms (SNPs) markers for oil yield and seed-related traits. Twenty-three SNP markers significantly (−log10 (p) = 4.87) associated with kernel oil content, kernel length, width, and weight were identified. The kernel oil content and kernel width had the most significant marker–trait associations (MTAs) on chromosomes 1 and 8, respectively. Sixteen candidate genes identified were linked to early induction of flower buds and somatic embryos, seed growth and development, substrate binding, transport, lipid biosynthesis, metabolic processes during seed germination, and disease resistance and abiotic stress adaptation. The presence of these genes suggests their role in promoting bioactive functions that condition high oil synthesis in shea seeds. This study provides insights into the important marker-linked seed traits and the genes controlling them, useful for molecular breeding for improving oil yield in the species. Full article

(This article belongs to the Special Issue Genetics and Molecular Breeding of Fruit Tree Species)

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