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Biotechnology and Genetics in Fruits
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Biotechnology and Genetics in Fruits

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 15 May 2024 | Viewed by 9701

Special Issue Editors

Prof. Dr. Enriqueta Moyano Cañete

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, University of Córdoba, Campus Rabanales, 14071 Córdoba, Spain
Interests: development and ripening; fruit biotechnology; transcription factors; functional genomics; strawberry
Prof. Dr. Juan Muñoz Blanco

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, Campus Rabanales, University of Córdoba, 14071 Córdoba, Spain
Interests: plant biotechnology; functional genomics; molecular genetics; plant genetics; strawberry

Special Issue Information

Dear Colleagues,

The rapid increase in the world population and global climate change are two factors that will affect the food supply in the very near future. Fruits are valuable components in the human diet, providing essential nutrients and healthy compounds. Their development and ripening are a genetically programmed process that involve changes in color, texture and flavor, and also affect their yield. In addition, this process is greatly affected by water shortage or high temperatures, among other abiotic stresses. Biotechnology and fruit genetics become a great challenge to cope with these situations. Transcription factors, noncoding RNAs and microRNAs play important roles in the regulation of gene expression in fruit ripening. This Special Issue will focus on advances in the identification and functional characterization of these factors, providing insight into the molecular mechanisms controlling fruit ripening, and enabling the development and efficient use of biotechnology-based systems for an improvement in fruit yield and quality, as well as resistance, under stress conditions. We welcome research based on multiomics and  functional analysis.

Prof. Dr. Enriqueta Moyano Cañete
Prof. Dr. Juan Muñoz Blanco
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. Genes 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 2600 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 ripening
  • water stress
  • abiotic stresses
  • transcription factors
  • noncoding RNAs
  • microRNAs
  • multiomics
  • functional genomics

Published Papers (6 papers)

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Research

13 pages, 3572 KiB  
Article
AcMYB10 Involved in Anthocyanin Regulation of ‘Hongyang’ Kiwifruit Induced via Fruit Bagging and High-Postharvest-Temperature Treatments
by Min Yu, Jinyu Xiong, Kun Dong, Xin Quan, Hao Guo, Junwei Huo, Dong Qin, Yanchang Wang, Xuemei Lu and Chenqiao Zhu
Genes 2024, 15(1), 97; https://0-doi-org.brum.beds.ac.uk/10.3390/genes15010097 - 14 Jan 2024
Viewed by 1054
Abstract
Light and temperature are key factors influencing the accumulation of anthocyanin in fruit crops. To assess the effects of fruit bagging during development and high post-ripening temperature on ‘Hongyang’ kiwifruit, we compared the pigmentation phenotypes and expression levels of anthocyanin-related genes between bagged [...] Read more.
Light and temperature are key factors influencing the accumulation of anthocyanin in fruit crops. To assess the effects of fruit bagging during development and high post-ripening temperature on ‘Hongyang’ kiwifruit, we compared the pigmentation phenotypes and expression levels of anthocyanin-related genes between bagged and unbagged treatments, and between 25 °C and 37 °C postharvest storage temperatures. Both the bagging and 25 °C treatments showed better pigmentation phenotypes with higher anthocyanin concentrations. The results of the qRT-PCR analysis revealed that the gene expression levels of LDOX (leucoanthocyanidin dioxygenase), F3GT (UDP-flavonoid 3-O-glycosyltransferase ), AcMYB10, and AcbHLH42 were strongly correlated and upregulated by both the bagging treatment and 25 °C storage. The results of bimolecular fluorescence complementation and luciferase complementation imaging assays indicated an interaction between AcMYB10 and AcbHLH42 in plant cells, whereas the results of a yeast one-hybrid assay further demonstrated that AcMYB10 activated the promoters of AcLODX and AcF3GT. These results strongly suggest that enhanced anthocyanin synthesis is caused by the promoted expression of AcLODX and AcF3GT, regulated by the complex formed by AcMYB10–AcbHLH42. Full article
(This article belongs to the Special Issue Biotechnology and Genetics in Fruits)
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15 pages, 2540 KiB  
Article
Identification and Profiling Analysis of microRNAs in Guava Fruit (Psidium guajava L.) and Their Role during Ripening
by Mario Alejandro Mejía-Mendoza, Cristina Garcidueñas-Piña, Blanca Estela Barrera-Figueroa and José Francisco Morales-Domínguez
Genes 2023, 14(11), 2029; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14112029 - 31 Oct 2023
Viewed by 989
Abstract
The guava (Psidium guajava L.) is a climacteric fruit with an accelerated post-harvest overripening. miRNAs are small RNA sequences that function as gene regulators in eukaryotes and are essential for their survival and development. In this study, miRNA libraries were constructed, sequenced [...] Read more.
The guava (Psidium guajava L.) is a climacteric fruit with an accelerated post-harvest overripening. miRNAs are small RNA sequences that function as gene regulators in eukaryotes and are essential for their survival and development. In this study, miRNA libraries were constructed, sequenced and analyzed from the breaker and ripe stages of guava fruit cv. Siglo XXI. One hundred and seventy-four mature miRNA sequences from 28 miRNA families were identified. The taxonomic distribution of the guava miRNAs showed a high level of conservation among the dicotyledonous plants. Most of the predicted miRNA target genes were transcription factors and genes involved in the metabolism of phytohormones such as abscisic acid, auxins, and ethylene, as revealed through an ontology enrichment analysis. The miRNA families miR168, miR169, miR396, miR397, and miR482 were classified as being directly associated with maturation, whereas the miRNA families miR160, miR165, miR167, miR3930, miR395, miR398, and miR535 were classified as being indirectly associated. With this study, we intended to increase our knowledge and understanding of the regulatory process involved in the ripening process, thereby providing valuable information for future research on the ripening of guava fruit. Full article
(This article belongs to the Special Issue Biotechnology and Genetics in Fruits)
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15 pages, 6500 KiB  
Article
Genome-Wide Identification and Expression Profiling Analysis of SWEET Family Genes Involved in Fruit Development in Plum (Prunus salicina Lindl)
by Cuicui Jiang, Shaomin Zeng, Jun Yang and Xiaoan Wang
Genes 2023, 14(9), 1679; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14091679 - 25 Aug 2023
Cited by 3 | Viewed by 976
Abstract
SWEETs (sugars will eventually be exported transporters) play a vital role in longer-distance sugar transportation, and thus control carbon flow and energy metabolism in plants. SWEET genes have been identified in various plant species, but their functions in fruit development remain uncharacterized. Here, [...] Read more.
SWEETs (sugars will eventually be exported transporters) play a vital role in longer-distance sugar transportation, and thus control carbon flow and energy metabolism in plants. SWEET genes have been identified in various plant species, but their functions in fruit development remain uncharacterized. Here, we isolated 15 putative PsSWEETs from the Prunus salicina genome. For further analysis, comprehensive bioinformatics methods were applied to determine the gene structure, chromosome distribution, phylogeny, cis-acting regulatory elements, and expression profiles of PsSWEETs. qRT-PCR analysis suggested that these SWEETs might have diverse functions in the development of plum fruit. The relative expression levels of PsSWEET1 and PsSWEET9 were obviously higher in ripened fruit than the ones in other developmental stages, suggesting their possible roles in the transport and accumulation of sugars in plum fruit. Positive correlations were found between the expression level of PsSWEET3/10/13 and the content of sucrose, and the expression level of PsSWEET2 and the content of fructose, respectively, during the development of ‘Furongli’ fruit, suggesting their possible roles in the accumulation of sucrose and fructose. The current study investigated the initial genomic characterization and expression patterns of the SWEET gene family in plum, which could provide a foundation for the further understanding of the functional analysis of the SWEET gene family. Full article
(This article belongs to the Special Issue Biotechnology and Genetics in Fruits)
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15 pages, 2931 KiB  
Article
Optimised Agrobacterium-Mediated Transformation and Application of Developmental Regulators Improve Regeneration Efficiency in Melons
by Lili Wan, Zhuanrong Wang, Xuejun Zhang, Hongxia Zeng, Jian Ren, Na Zhang, Yuhong Sun and Tang Mi
Genes 2023, 14(7), 1432; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14071432 - 12 Jul 2023
Cited by 3 | Viewed by 1663
Abstract
Melon (Cucumis melo L.) is a protected crop in China with high economic value. Agrobacterium-mediated genetic transformation is a powerful tool to improve agronomic traits and obtain elite germplasm. However, current transformation protocols in melons are inefficient and highly genotype-dependent. To [...] Read more.
Melon (Cucumis melo L.) is a protected crop in China with high economic value. Agrobacterium-mediated genetic transformation is a powerful tool to improve agronomic traits and obtain elite germplasm. However, current transformation protocols in melons are inefficient and highly genotype-dependent. To improve transformation in melon, we tested different infiltration methods for Agrobacterium-mediated transformation. Among these methods, micro-brushing and sonication for 20 s, followed by vacuum infiltration at −1.0 kPa for 90 s, resulted in the strongest green fluorescent protein signal and increased the proportion of infected explants. We transformed melon with developmental regulatory genes AtGRF5, AtPLT5, AtBBM, AtWUS, AtWOX5, and AtWIND1 from Arabidopsis and estimated regeneration frequencies as the number of regenerating shoots/total number of inoculated explants in the selection medium. The overexpression of AtGRF5 and AtPLT5 in melon resulted in transformation efficiencies of 42.3% and 33% in ZHF and 45.6% and 32.9% in Z12, respectively, which were significantly higher than those of the control. AtGRF5 and AtPLT5 expression cassettes were added to CRISPR/Cas9 genome-editing vectors to obtain transgenic phytoene desaturase CmPDS knockout mutants. Using AtGRF5 or AtPLT5, multi-allelic mutations were observed at CmPDS target sites in recalcitrant melon genotypes. This strategy enables genotype-flexible transformation and promotes precise genome modification technologies in melons. Full article
(This article belongs to the Special Issue Biotechnology and Genetics in Fruits)
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17 pages, 4868 KiB  
Article
Genome-Wide Identification and Expression Analysis of m6A Writers, Erasers, and Readers in Litchi (Litchi chinensis Sonn.)
by Liwen Tang, Jiali Xue, Xingyu Ren, Yue Zhang, Liqing Du, Feng Ding, Kaibing Zhou and Wuqiang Ma
Genes 2022, 13(12), 2284; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13122284 - 04 Dec 2022
Cited by 1 | Viewed by 1911
Abstract
N6-methyladenosine (m6A) RNA modification is the most prevalent type of RNA methylation and plays a pivotal role in the development of plants. However, knowledge of the m6A modification in litchi remains limited. In this study, a complete analysis of m6A writers, erasers, and [...] Read more.
N6-methyladenosine (m6A) RNA modification is the most prevalent type of RNA methylation and plays a pivotal role in the development of plants. However, knowledge of the m6A modification in litchi remains limited. In this study, a complete analysis of m6A writers, erasers, and readers in litchi was performed and 31 litchi m6A regulatory genes were identified in total, including 7 m6A writers, 12 m6A erases, and 12 readers. Phylogeny analysis showed that all three of the kinds of litchi m6A regulatory proteins could be divided into three groups; domains and motifs exhibited similar patterns in the same group. MiRNA target site prediction showed that 77 miRNA target sites were located in 25 (80.6%) litchi m6A regulatory genes. Cis-elements analysis exhibited that litchi m6A regulatory genes were mainly responsive to light and plant hormones, followed by environmental stress and plant development. Expression analysis revealed litchi m6A regulatory genes might play an important role during the peel coloration and fruit abscission of litchi. This study provided valuable and expectable information of litchi m6A regulatory genes and their potential epigenetic regulation mechanism in litchi. Full article
(This article belongs to the Special Issue Biotechnology and Genetics in Fruits)
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28 pages, 7805 KiB  
Article
Comparative Transcriptome and sRNAome Analyses Reveal the Regulatory Mechanisms of Fruit Ripening in a Spontaneous Early-Ripening Navel Orange Mutant and Its Wild Type
by Lanfang Mi, Dong Ma, Shuping Lv, Saibing Xu, Balian Zhong, Ting Peng, Dechun Liu and Yong Liu
Genes 2022, 13(10), 1706; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13101706 - 22 Sep 2022
Cited by 4 | Viewed by 2120
Abstract
A complex molecular regulatory network plays an important role in the development and ripening of fruits and leads to significant differences in apparent characteristics. Comparative transcriptome and sRNAome analyses were performed to reveal the regulatory mechanisms of fruit ripening in a spontaneous early-ripening [...] Read more.
A complex molecular regulatory network plays an important role in the development and ripening of fruits and leads to significant differences in apparent characteristics. Comparative transcriptome and sRNAome analyses were performed to reveal the regulatory mechanisms of fruit ripening in a spontaneous early-ripening navel orange mutant (‘Ganqi 4’, Citrus sinensis L. Osbeck) and its wild type (‘Newhall’ navel orange) in this study. At the transcript level, a total of 10792 genes were found to be differentially expressed between MT and WT at the four fruit development stages by RNA-Seq. Additionally, a total of 441 differentially expressed miRNAs were found in the four periods, and some of them belong to 15 families. An integrative analysis of the transcriptome and sRNAome data revealed some factors that regulate the mechanisms of formation of early-ripening traits. First, secondary metabolic materials, especially endogenous hormones, carotenoids, cellulose and pectin, obviously changed during fruit ripening in MT and WT. Second, we found a large number of differentially expressed genes (PP2C, SnRK, JAZ, ARF, PG, and PE) involved in plant hormone signal transduction and starch and sucrose metabolism, which suggests the importance of these metabolic pathways during fruit ripening. Third, the expression patterns of several key miRNAs and their target genes during citrus fruit development and ripening stages were examined. csi-miR156, csi-miR160, csi-miR397, csi-miR3954, and miRN106 suppressed specific transcription factors (SPLs, ARFs, NACs, LACs, and TCPs) that are thought to be important regulators involved in citrus fruit development and ripening. In the present study, we analyzed ripening-related regulatory factors from multiple perspectives and provide new insights into the molecular mechanisms that operate in the early-ripening navel orange mutant ‘Ganqi 4’. Full article
(This article belongs to the Special Issue Biotechnology and Genetics in Fruits)
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