Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.1
4.9
Journals
IJMS
Special Issues
Advances in Breeding, Genetics, and Genomics of Fruit Crops
ijms-logo
Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Advances in Breeding, Genetics, and Genomics of Fruit Crops

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 June 2025 | Viewed by 4917

Special Issue Editors

Dr. Elisa Vendramin

E-Mail Website
Guest Editor
Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via di Fioranello, 52, 00134 Rome, Italy
Interests: genetics and genomics of fruit crops; new breeding techniques; biodiversity evaluation and exploitation; fruit tree crops breeding
Dr. Micali Sabrina

E-Mail Website
Guest Editor
Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via di Fioranello, 52, 00134 Rome, Italy
Interests: plant biotechnology; plant genetics; plant genomics

Special Issue Information

Dear Colleagues,

Fruit species represent a fundamental group of crops for the agri-food sector worldwide and fruit consumption contributes to a healthy and sustainable diet satisfying the requirements for vitamins, carotenoids and polyphenolic compounds, and fibers. With the ongoing climate change, increasing world population, and susceptibility to both biotic and abiotic stresses, important drawbacks on productivity and availability are expected, highlighting the need for more sustainable and resilient fruit varieties with high nutritional value. 

Genetic diversity has a key role in answering to future challenges and plant genetic resources (PGRs) are a reservoir of useful genes and alleles. The availability of genomic sequences and technical advancements enabled the massive mining of new molecular markers and the development of a number of high throughput tools to deeply characterize PGRs. 

This special issue will be focused on the evaluation of fruit crop genetic resources through genetics, genomics, and transcriptomic approaches for the exploitation of PGRs to meet the need for more sustainable and secure fruit production.

Dr. Elisa Vendramin
Dr. Micali Sabrina
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • genetics
  • genomics
  • transcriptomics
  • plant genetic resources
  • SNP
  • SSR
  • GWAS
  • QTLs
  • genomic selections
  • candidate genes

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

16 pages, 2427 KiB  
Article
Genetic Diversity Assessment and Core Germplasm Screening of Blackcurrant (Ribes nigrum) in China via Expressed Sequence Tag–Simple Sequence Repeat Markers
by Xinyu Sun, Qiang Fu, Dong Qin, Jinyu Xiong, Xin Quan, Hao Guo, Jiahan Tang, Junwei Huo and Chenqiao Zhu
Int. J. Mol. Sci. 2025, 26(5), 2346; https://doi.org/10.3390/ijms26052346 - 6 Mar 2025
Viewed by 445
Abstract
Blackcurrant (Ribes nigrum L.) has high nutritional value for human health due to its abundant vitamin C, flavonoids, and organic acids. However, its breeding and genetic research have been severely hindered by the lack of scientific tools such as molecular markers. Here, [...] Read more.
Blackcurrant (Ribes nigrum L.) has high nutritional value for human health due to its abundant vitamin C, flavonoids, and organic acids. However, its breeding and genetic research have been severely hindered by the lack of scientific tools such as molecular markers. Here, we identified 14,258 EST-SSR loci from 9531 CDS sequences with lengths greater than 1 kb, which comprised 6211 mononucleotide repeats, 4277 dinucleotide repeats, and 2469 trinucleotide repeats. We then randomly selected 228 EST-SSR loci for PCR amplification and gel electrophoresis imaging in the Ribes collection of Northeast Agricultural University (95 blackcurrant cultivars and 12 other Ribes accessions). As a result, 31 pairs of markers produced clear and reproducible bands of the expected size. Based on the 107 Ribes accessions, the allele number (Na), information index (I), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) of the 31 markers were 2–5, 0.23–1.32, 0.07–0.71, 0.11–0.68, and 0.14–0.67, respectively. For the blackcurrant gene pool, neighbor-joining and population structure analysis revealed three clusters, which did not align well with their geographical origins. Based on the results, two sets with 21 and 19 blackcurrant cultivars were identified by Power Core (PC) and Core Hunter (CH) programs. The integrated core germplasm (IC) set with 27 cultivars derived from the PC and CH sets harbored abundant genetic diversity, where the allele retention rate accounted for 98.9% of the blackcurrant gene pool. The SSR markers, data, and core germplasms presented in this study lay a solid foundation for the phylogenetic study, molecular breeding, and conservation genetics of Ribes, especially Ribes nigrum. Full article
(This article belongs to the Special Issue Advances in Breeding, Genetics, and Genomics of Fruit Crops)
►▼ Show Figures

Figure 1

15 pages, 3714 KiB  
Article
Genetic Diversity and Fingerprinting of 231 Mango Germplasm Using Genome SSR Markers
by Jinyuan Yan, Bin Zheng, Songbiao Wang, Wentian Xu, Minjie Qian, Xiaowei Ma and Hongxia Wu
Int. J. Mol. Sci. 2024, 25(24), 13625; https://doi.org/10.3390/ijms252413625 - 19 Dec 2024
Viewed by 1061
Abstract
Mango (Mangifera indica L.) (2n = 40) is an important perennial fruit tree in tropical and subtropical regions. The lack of information on genetic diversity at the molecular level hinders efforts in mango genetic improvement and molecular marker-assisted breeding. In this study, [...] Read more.
Mango (Mangifera indica L.) (2n = 40) is an important perennial fruit tree in tropical and subtropical regions. The lack of information on genetic diversity at the molecular level hinders efforts in mango genetic improvement and molecular marker-assisted breeding. In this study, a genome-wide screening was conducted to develop simple sequence repeat (SSR) markers using the Alphonso reference genome. A total of 187 SSR primer pairs were designed based on SSR loci with consisting of tri- to hexa-nucleotide motifs, and 34 highly polymorphic primer pairs were selected to analyze the diversity of 231 germplasm resources. These primers amplified 219 alleles (Na) across 231 accessions, averaging of 6.441 alleles for per marker. The polymorphic information content (PIC) values ranged from 0.509 to 0.757 with a mean of 0.620. Genetic diversity varied among populations, with Southeast Asia showing the highest diversity, and Australia the lowest. Population structure analysis, divided the accessions into two groups, Group I (India) and Group II (Southeast Asia), containing 104 and 127 accessions, respectively, consistent with results from phylogenetic analysis and principal component analysis (PCA). Sixteen SSR primer pairs capable of distinguishing all tested accessions, were selected as core primers for constructing fingerprints of 229 mango accessions. These findings offer valuable resources for enhancing the utilization of mango germplasm in breeding programs. Full article
(This article belongs to the Special Issue Advances in Breeding, Genetics, and Genomics of Fruit Crops)
►▼ Show Figures

Figure 1

18 pages, 3981 KiB  
Article
Genome-Wide Association Study of Grape Texture Based on Puncture
by Meiling Lin, Lei Sun, Xuewei Liu, Xiucai Fan, Ying Zhang, Jianfu Jiang and Chonghuai Liu
Int. J. Mol. Sci. 2024, 25(23), 13065; https://doi.org/10.3390/ijms252313065 - 5 Dec 2024
Viewed by 801
Abstract
Grapes are grown extensively around the world and play a crucial role in overall fruit production globally. The quality of the grape is largely determined by the texture of the flesh, making it a key focus for grape breeders. Our study was conducted [...] Read more.
Grapes are grown extensively around the world and play a crucial role in overall fruit production globally. The quality of the grape is largely determined by the texture of the flesh, making it a key focus for grape breeders. Our study was conducted on 437 grape accessions using a puncture method to analyze berry texture characteristics. The results reveal strong correlations among the five texture parameters of grape accessions. Following the GWAS analysis using 2,124,668 population SNPs, 369 significant SNP locations linked to the grape berry texture were discovered. Through the process of gene annotation and expression analysis in the localization regions, several genes potentially linked to berry texture were identified, including E13A, FIS1A, CML35, AGL2, and AGL62. E13A, FIS1A, and CML35 were identified as potentially more relevant to grape berry texture based on gene expression analysis. Further investigation through transient transformation demonstrated that overexpressing E13A and CML35 resulted in notable changes in grape pulp texture. During this study, the berry textures of 437 grape accessions were comprehensively evaluated, and several important candidate genes were screened based on GWAS and analysis of gene function. This discovery paves the way for future research and breeding initiatives related to grape berry texture. Full article
(This article belongs to the Special Issue Advances in Breeding, Genetics, and Genomics of Fruit Crops)
►▼ Show Figures

Figure 1

19 pages, 5542 KiB  
Article
Dissection of Metabolome and Transcriptome—Insights into Capsaicin and Flavonoid Accumulation in Two Typical Yunnan Xiaomila Fruits
by Huaran Hu, Lei Du, Ruihao Zhang, Qiuyue Zhong, Fawan Liu, Weifen Li and Min Gui
Int. J. Mol. Sci. 2024, 25(14), 7761; https://doi.org/10.3390/ijms25147761 - 16 Jul 2024
Cited by 2 | Viewed by 1411
Abstract
Pepper is an economically important vegetable worldwide, containing various specialized metabolites crucial for its development and flavor. Capsaicinoids, especially, are genus-specialized metabolites that confer a spicy flavor to Capsicum fruits. In this work, two pepper cultivars, YB (Capsicum frutescens L.) and JC [...] Read more.
Pepper is an economically important vegetable worldwide, containing various specialized metabolites crucial for its development and flavor. Capsaicinoids, especially, are genus-specialized metabolites that confer a spicy flavor to Capsicum fruits. In this work, two pepper cultivars, YB (Capsicum frutescens L.) and JC (Capsicum baccatum L.) pepper, showed distinct differences in the accumulation of capsaicin and flavonoid. However, the molecular mechanism underlying them was still unclear. Metabolome analysis showed that the JC pepper induced a more abundant accumulation of metabolites associated with alkaloids, flavonoids, and capsaicinoids in the red ripening stages, leading to a spicier flavor in the JC pepper. Transcriptome analysis confirmed that the increased expression of transcripts associated with phenylpropanoid and flavonoid metabolic pathways occurred in the JC pepper. Integrative analysis of metabolome and transcriptome suggested that four structural genes, 4CL7, 4CL6, CHS, and COMT, were responsible for the higher accumulation of metabolites relevant to capsaicin and flavonoids. Through weighted gene co-expression network analyses, modules related to flavonoid biosynthesis and potential regulators for candidate genes were identified. The promoter analysis of four candidate genes showed they contained several cis-elements that were bonded to MYB, bZIP, and WRKY transcription factors. Further RT-qPCR examination verified three transcription factors, MYB, bZIP53, and WRKY25, that exhibited increased expression in the red ripening stage of the JC pepper compared to YB, which potentially regulated their expression. Altogether, our findings provide comprehensive understanding and valuable information for pepper breeding programs in the future. Full article
(This article belongs to the Special Issue Advances in Breeding, Genetics, and Genomics of Fruit Crops)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop