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Agriculture
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Breeding, Genetics, and Genomics of Fruit Crops
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Breeding, Genetics, and Genomics of Fruit Crops

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Genetics, Genomics and Breeding".

Deadline for manuscript submissions: closed (10 April 2023) | Viewed by 34019

Special Issue Editor

Prof. Dr. Gaetano Distefano

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Guest Editor
Department of Agriculture, Food and Environment, University of Catania, Via Valdisavoia 5, 95123 Catania, Italy
Interests: tree crop biotechnology; tree crop genomics; transgenics; biodiversity evaluation and analysis; fruit tree crops breeding; reproductive biology on fruit crops
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The fruit tree crop field is experiencing radical changes thanks to both technical and genetic innovations that are contributing to the production of fruits with improved characteristics (fruit quality, yield, resistance to biotic/abiotic stress). The global demand for fruit tree crops with such improved agronomical and fruit quality traits is increasing rapidly every year. However, genetic improvement by traditional breeding is slow and unpredictable due to the long juvenile phase, high degree of heterozygosity, and polygenic regulation of most agronomical traits. Traditional breeding increases its efficiency when supported by genetic and molecular information using marker-assisted selection (MAS). Advances in DNA-derived data and innovative phenotyping are bridging the genotype-to-phenotype gap in fruit tree crop selection. Developing new genomic-based tools using next-generation sequencing (NGS), high-throughput genotyping technologies (such as SNP arrays and target sequencing), and new breeding techniques (NBT) has expedited the chance for achieving important improved traits.

This Special Issue welcomes innovative research focusing on the detection and/or application of molecular markers helping breeders toward the definition of novel ideotypes characterized by superior agronomical traits.

Prof. Dr. Gaetano Distefano
Guest Editor

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Keywords

  • phenotyping
  • genotyping
  • NGS
  • NBTs
  • marker assisted selection breeding

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Published Papers (6 papers)

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Research

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15 pages, 1106 KiB  
Article
Reproductive Biology Factors Hampering Lemon [Citrus limon (L.) Burm. f.] Genetic Improvement
by Chiara Catalano, Giuseppina Las Casas, Alessio Giuffrida, Filippo Ferlito, Mario Di Guardo, Alberto Continella, Stefania Bennici, Stefano La Malfa, Alessandra Gentile and Gaetano Distefano
Agriculture 2022, 12(12), 2020; https://doi.org/10.3390/agriculture12122020 - 26 Nov 2022
Cited by 7 | Viewed by 3458
Abstract
Background: Floral sterility and nucellar embryony are peculiar traits of several Citrus species and represent an obstacle to traditional breeding. Morphological sterility mainly results in pistil abortion and anther atrophy, while polyembryony is due to a mechanism known as sporophytic apomixis, which consists [...] Read more.
Background: Floral sterility and nucellar embryony are peculiar traits of several Citrus species and represent an obstacle to traditional breeding. Morphological sterility mainly results in pistil abortion and anther atrophy, while polyembryony is due to a mechanism known as sporophytic apomixis, which consists of the presence of embryos in the seed generated from the nucellar (maternal) tissue alongside the zygotic embryo (sexual origin). Considering the growing interest in lemon [Citrus limon (L.) Burm. f.] breeding, and the lack of information on floral sterility and the polyembryony trait among different lemon cultivars, a morphological and molecular characterization of these traits of interest was performed on forty Sicilian and international lemon cultivars available in the citrus germplasm collection of Catania University (Italy). Methods: Eight traits related to the reproductive biology were assessed on the selected lemon cultivars, namely: pistil abortion and anther atrophy, number of seeds per fruit, number of embryos per seed, percentage of seeds showing polyembryony, germination, percentage of seeds resulting in more than one plantlet, and average seed weight. Moreover, seedlings recovered after the germination assay were genotyped with SNP and SSR markers for ascertaining their nucellar or zygotic origin. In addition, PCR analysis were performed to assess the allele combination of the miniature inverted-repeat transposable element (MITE) insertion in CitRKD1, a gene associated with the occurrence of apomixis in citrus. Results: All traits showed high variability among the accessions analyzed. As for polyembryony, lemon ‘Adamopoulos’ scored the highest percentage of polyembryonic seeds (67.6%), whilst lemon ‘Lunario’ showed the lowest value (8.7%). Conclusions: Insights on the level of polyembryony within lemon varieties will represent a valuable tool for breeders for the set-up of novel mating schemes. In fact, when a polyembryonic female parent is used in cross breeding, the selection of the zygotic individual is hampered by the presence of a nucellar one. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomics of Fruit Crops)
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17 pages, 8587 KiB  
Article
Genome-Wide Identification, In Silico Analysis and Expression Profiling of SWEET Gene Family in Loquat (Eriobotrya japonica Lindl.)
by Binqi Li, Muhammad Moaaz Ali, Tianxin Guo, Shariq Mahmood Alam, Shaista Gull, Junaid Iftikhar, Ahmed Fathy Yousef, Walid F. A. Mosa and Faxing Chen
Agriculture 2022, 12(9), 1312; https://doi.org/10.3390/agriculture12091312 - 26 Aug 2022
Cited by 6 | Viewed by 2275
Abstract
SWEETs (sugars will eventually be exported transporters) have various physiological and biochemical roles in plant growth, including pollen development, seed nourishment, nectar secretion, and longer-distance sugar transportation. The SWEET genes were identified in various plant species, but they have not yet been thoroughly [...] Read more.
SWEETs (sugars will eventually be exported transporters) have various physiological and biochemical roles in plant growth, including pollen development, seed nourishment, nectar secretion, and longer-distance sugar transportation. The SWEET genes were identified in various plant species, but they have not yet been thoroughly characterized. Here, we discovered 21 putative SWEET genes from the Eriobotrya japonica Lindl. genome. For further elucidation, comprehensive bioinformatics analysis was utilized to determine the physicochemical properties, gene organization, conserved motifs, cis-regulatory elements, gene duplication, and phylogenetic relationships of EjSWEET genes. Most of the SWEET proteins were predicted to be located on the plasma membrane or vacuole. Gene organization and motif analysis showed that the numbers of exons and motifs in each gene ranged strikingly, between 5 and 6 and between 5 and 8, respectively. Synteny analysis showed that the tandem or segmental duplication played a dynamic role in the evolution of SWEET genes in loquat. Likewise, we analyzed the expression patterns of EjSWEET genes in the root, stem, leaf, flower, and fruit of loquat. Some genes exhibited varying expression in loquat tissues, indicating their potential roles in plant development. The relative expression levels of EjSWEET1, EjSWEET3, and EjSWEET16 were noticeably higher in ripened fruits, suggesting their possible role in the transportation and unloading of sugars in fruits. The present study provides initial genome-wide identification and characterization of the SWEET gene family in loquat and lays the foundation for their further functional analysis. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomics of Fruit Crops)
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18 pages, 6361 KiB  
Article
Identification of the Citrus Superoxide Dismutase Family and Their Roles in Response to Phytohormones and Citrus Bacterial Canker
by Wen Yang, Jia Fu, Xin Huang, Jie Fan, Xiujuan Qin, Qiyuan Yu, Chenxi Zhang, Baohang Xian, Shanchun Chen, Yongrui He and Qiang Li
Agriculture 2022, 12(8), 1254; https://doi.org/10.3390/agriculture12081254 - 18 Aug 2022
Cited by 1 | Viewed by 1903
Abstract
Superoxide dismutases (SODs) play critical roles in plants, especially in the maintenance of redox homeostasis. The response of SODs in Citrus (Citrus sinensis (L.) Osbeck) to citrus bacterial canker (CBC) infection were investigated. The CsSODs were identified, and their gene structures, phylogeny, [...] Read more.
Superoxide dismutases (SODs) play critical roles in plants, especially in the maintenance of redox homeostasis. The response of SODs in Citrus (Citrus sinensis (L.) Osbeck) to citrus bacterial canker (CBC) infection were investigated. The CsSODs were identified, and their gene structures, phylogeny, conserved domains and motifs, predicted interactions, and chromosomal distribution were analyzed. CsSOD expression in response to stress-related plant hormones (salicylic acid, SA; methyl jasmonate, MeJA; and abscisic acid, ABA) and Xanthomonas citri subsp. citri (Xcc) infection were also investigated. Thirteen CsSODs were identified in C. sinensis, including four Fe/MnSODs and nine Cu/ZnSODs with typical functional domains. The CsSODs were distributed on chromosomes 3, 5, 7, and 8. Specific hormone-response motifs were identified in the gene promoter regions. Ten genes were induced by MeJA treatment, as shown by qRT-PCR, and were upregulated in the CBC-susceptible Wanjincheng citrus variety, while CsSOD06 and CsSOD08 were upregulated by ABA in both the Wanjincheng and the CBC-resistant Kumquat varieties. Xcc infection significantly altered the levels of most CsSODs. The overexpression of CsSOD06 and CsSOD08 resulted in increased hydrogen peroxide levels and SOD activity. Our findings highlight the significance of SOD enzymes in the plant response to pathogen infection and have a potential application for breeding CBC-tolerant citrus varieties. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomics of Fruit Crops)
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Review

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24 pages, 7095 KiB  
Review
Sweet Orange: Evolution, Characterization, Varieties, and Breeding Perspectives
by Sebastiano Seminara, Stefania Bennici, Mario Di Guardo, Marco Caruso, Alessandra Gentile, Stefano La Malfa and Gaetano Distefano
Agriculture 2023, 13(2), 264; https://doi.org/10.3390/agriculture13020264 - 21 Jan 2023
Cited by 15 | Viewed by 14825
Abstract
Among Citrus species, the sweet orange (Citrus sinensis (L.) Osbeck) is the most important in terms of production volumes and cultivated areas. Oranges are particularly appreciated for the organoleptic characteristics and the high nutraceutical value of the fruits (thanks especially to their [...] Read more.
Among Citrus species, the sweet orange (Citrus sinensis (L.) Osbeck) is the most important in terms of production volumes and cultivated areas. Oranges are particularly appreciated for the organoleptic characteristics and the high nutraceutical value of the fruits (thanks especially to their high content of antioxidants). Recent advances in citrus genetic and genomic resources, such as the release of the reference genomes of several sweet orange cultivars, have contributed to (i) understanding the diversification of C. sinensis and its relation with other citrus species, (ii) assessing the molecular mechanisms underlying traits of interest, (iii) identifying and characterizing the candidate genes responsible for important phenotypic traits, and (iv) developing biotechnological methods to incorporate these traits into different citrus genotypes. It has been clarified that all the genetic diversity within the sweet orange species was derived from subsequent mutations starting from a single ancestor and was derived from complex cycles of hybridization and backcrossing between the mandarin (Citrus reticulata Blanco) and the pummelo (Citrus maxima (Burm.) Merr.). This paper provides an overview of the varietal panorama together with a description of the main driving forces in present and future sweet orange breeding. In fact, for the sweet orange, as well as for other citrus species, the release of novel varieties with improved characteristics is being pursued thanks to the employment of conventional and/or innovative (molecular-based) methods. The state of the art methods together with the innovations in genomics and biotechnological tools leading to the so-called new plant breeding technologies were also reviewed and discussed. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomics of Fruit Crops)
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15 pages, 5811 KiB  
Review
Scion–Rootstock Relationship: Molecular Mechanism and Quality Fruit Production
by Mukesh Shivran, Nimisha Sharma, Anil Kumar Dubey, Sanjay Kumar Singh, Neha Sharma, Radha Mohan Sharma, Narendra Singh and Rakesh Singh
Agriculture 2022, 12(12), 2036; https://doi.org/10.3390/agriculture12122036 - 28 Nov 2022
Cited by 8 | Viewed by 8045
Abstract
Most tree fruits are commercially grown on different root systems, hence called composite plants. The section provides the root system as the rootstock, and the atop ground portion is called the scion. The combination is selected based on different traits of scion varieties, [...] Read more.
Most tree fruits are commercially grown on different root systems, hence called composite plants. The section provides the root system as the rootstock, and the atop ground portion is called the scion. The combination is selected based on different traits of scion varieties, rootstock, and prevailing edaphic situations. The dated back plant propagation technique of joining two plants (grafting/budding) that directly communicates new physiological traits to the desirable scion variety from the rootstock remains unclear. In spite of this, this propagation technique continues widely applied in the multiplication of several fruit plant species. In a grafted plant, rootstocks impacted the scion variety’s growth, yield and quality attributes, physiology, nutrient accumulation as well as biotic and abiotic stress tolerance in many ways. Modern research in plant science for next-generation sequencing providing new vital information about the molecular interactions in composite plants multiplied using grafting. Now it was confirmed that genetic exchange is occurring between rootstock and scion variety through grafting joints. In this aspect, we discuss the process and the molecular mechanism of rootstock scion interactions. This review finally explains the dynamics of rootstock–scion interactions as well as their effect on physiology in terms of production, environmental stresses, and fruit quality. The morphological, physiochemical, and molecular mechanisms have been reviewed to develop an integrated understanding of this unknowable process that questions existing genetic paradigms. The present review summarizes the reported molecular mechanism between scion and rootstock and the impact of rootstocks on the production biology of scion varieties of economically important fruit crops and identifies numerous key points to consider when conducting rootstock scion interaction experiments. Rootstocks may offer a non-transgenic approach to rapidly respond to the changing environment and expand agricultural production of perennial fruit crops where grafting is possible in order to meet the global demand for fruit, food, and demands of the future. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomics of Fruit Crops)
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Other

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22 pages, 1006 KiB  
Opinion
Regionally Adapted Model of an Ideal Malus×domestica Borkh Apple Variety for Industrial-Scale Cultivation in European Russia
by Ivan M. Kulikov, Julia V. Burmenko, Natalya YU. Svistunova, Sergey N. Evdokimenko, Fedor F. Sazonov, Tatyana A. Tumaeva and Sergey N. Konovalov
Agriculture 2022, 12(12), 2124; https://doi.org/10.3390/agriculture12122124 - 10 Dec 2022
Cited by 5 | Viewed by 2406
Abstract
Apple is one of the most common fruit crops in the Russian fruit-growing industry, with huge varietal diversity and a vast cultivation area. The key regions for industrial-scale apple cultivation are the Central, Central Chernozem, and North Caucasian Districts. The main disadvantage of [...] Read more.
Apple is one of the most common fruit crops in the Russian fruit-growing industry, with huge varietal diversity and a vast cultivation area. The key regions for industrial-scale apple cultivation are the Central, Central Chernozem, and North Caucasian Districts. The main disadvantage of the relevant apple cultivars, especially the ones intended for intensified horticultural practices, is their low resistance against abiotic stresses and the fruit’s low quality and poor marketable condition. In Russia, apple is a crop of strategic importance that is consistently included in the household food basket, so fruit producers hold new varieties to higher standards and expect them to outperform their predecessors in terms of yield per plant, resistance against abiotic and biotic stresses, and quality, as well as show strong competitiveness and a more rapid return on investment, while satisfying stricter requirements. The objective of the present study was to summarize the data on the phenotypic manifestations of economically valuable traits of the apple cultivars approved for use in the Russian Federation depending on the region of cultivation; to determine the parametric characteristics of the most valuable traits in the form of a model of an “ideal” regionally adapted industrial cultivar, and to identify the sources of the traits in the regions suitable for their production. A regionally adapted model of commercial apple cultivars, characterized by 28 features and properties divided into three groups and defining the cultivar’s resistance against abiotic and biotic stresses, yield per plant, product quality, and suitability for mechanized harvesting, is presented in this paper. In the European part of Russia, the optimal parameters of a commercial apple tree cultivar are as follows: plant height on a medium-sized rootstock under 3 m; potential yield per plant of at least 25–50 kg; high fruit uniformity above 80%; winter and late-winter harvest maturity period; high storability of over 210 days and good transportability; average fruit mass from 120 g to 220 g; juicy and shattering crisp pulp; small seed cavity; fragrant fruits with taste rating of at least 4.5 points; appearance rating of 5 points and attractive, mostly red, glossy color with natural wax bloom; regular, symmetric, but diverse shapes; content of sugar above 10%, ascorbic acid above 15 mg/100 g, organic acids up to 1% (for dessert varieties); content of soluble dry solids of at least 20%. The cultivars that come closest to the regionally adapted model of an ideal variety based on the set of features discussed are as follows: Feya, Soyuz, Orfej, Margo, Sirius, Noktyurn, Vasilisa Karmen, Florina, Dayton, Early Mac, Gala and Gala Schniga in the North Caucasian District; Svezhest’, Orlovskoe Poles’e, Aprel’skoe, Ven’yaminovskoe, Bolotovskoe, Vympel, Uspenskoe, Fregat, Bylina, Flagman, and Akademik Kazakov in the North Caucasian District; and varieties Imrus, Mayak Zagor’ya, and Bolotovskoe in the Central District. These cultivars are characterized by high resistance against weather anomalies, scab immunity, high yields, marketable quality, and storability. In addition, in southern regions, a prolonged bloom period acts as a protective adaptive response to low-temperature stress. Full article
(This article belongs to the Special Issue Breeding, Genetics, and Genomics of Fruit Crops)
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