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Editorial

Special Issue “Molecular Genetics and Plant Breeding 3.0 and 4.0”

by
Hai Du
1,2
1
College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400715, China
2
Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Int. J. Mol. Sci. 2025, 26(5), 2030; https://doi.org/10.3390/ijms26052030
Submission received: 18 February 2025 / Accepted: 24 February 2025 / Published: 26 February 2025
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 4.0)
Versions Notes
Molecular genetics aims to understand the genetic principles and functions of genes at the molecular level, while plant breeding aims to apply this information to improve plant traits and develop new crop varieties with desired characteristics. The advent of high-throughput sequencing technologies [1,2,3], e.g., next-generation sequencing (NGS) and third-generation sequencing technologies, allows for the rapid, cost-effective, and large-scale sequencing of entire genomes [4,5,6,7,8] and transcriptomes [9,10,11,12] in plants. Accordingly, multi-omics analysis strategies and bioinformatics methods are being widely applied in molecular genetics research, providing important information for plant breeding [13,14,15,16,17]. In 2019, the first Special Issue of the International Journal of Molecular Sciences (IJMS) on “Molecular Genetics and Plant Breeding” was launched to call for original research and review articles that present innovative research in plant molecular genetics, multi-omics, and gene resources at all levels, and 36 and 32 papers were published in the first two editions [18,19]. In the present third and fourth editions of the Special Issue, nine and twelve papers were printed, respectively. A fifth edition is currently in progress with a deadline on 27 August 2025 for manuscript submission.
DNA sequencing is foundational to numerous applications, such as genetic research, evolutionary studies, and crop improvement in plant breeding [14,15,16,17]. Seven papers published in this Special Issue focus on exploring the genetic basis, genetic variation, molecular markers, and functional genes in different plant germplasms and population materials. These studies employ a series of genome-wide analyses, including genome sequencing, genome-wide association studies (GWASs), quantitative trait loci (QTL) mapping, high-resolution molecular markers, etc. (Table 1, contributions 1–7). RNA sequencing (RNA-seq) is a fundamental tool in molecular genetics, functional genomics, and systems biology studies, providing a comprehensive and quantitative view of gene expression at the genome scale in various biological processes and with applications in diverse fields such as plant breeding. Four papers published in this Special Issue report novel results exploring the expression patterns, molecular mechanisms, and gene resources associated with different plant traits. These findings provide a foundation for molecular-assisted breeding (Table 1, contributions 8–11).
In the post-genomic era, applying bioinformatics approaches to rapidly and efficiently decode evolutionary or molecular information in plant genomes and to mine critical genes [20,21,22,23,24,25,26,27] represents an important issue. This Special Issue also covers the evolution, identification, and molecular analysis of gene resources in plant genomes. Three papers published in this Special Issue provide new insights into the genome-wide identification, evolution, and characterization of different gene families in plants (Table 1, contributions 12–14). Another three papers report the functional analyses of candidate genes involved in distinct bioprocesses in Foxtail millet, Zea mays, and Sorghum bicolor, respectively, using molecular and/or RNA-seq methods (Table 1, contributions 15–17).
This Special Issue also comprises four review papers (Table 1). The review by Zhang et al. (contribution 18) focuses on the synthesis and action mechanisms of non-coding RNAs and their roles in gene expression in plants. The review by Li et al. (contribution 19) summarizes the most recent advances in understanding the roles of functional endophytes in regulating plant secondary metabolism. It also discusses the potential applications and development of endophytes in agriculture, medicine, and industry. The review by Adhikari et al. (contribution 20) presents an overview of the MADS-box gene family members in plants and discusses their roles in plant organ development and trait-linked factors across diverse plant species. It concludes that most of the studied MADS-box genes are associated with flower- and fruit-related traits, and these family members play a significant role in angiosperm evolution. Sun et al. (contribution 21) review the recent advances in the complex modulation of potato dormancy and sprouting, highlighting the influence of environmental factors, carbohydrate metabolism, and intricate hormonal regulation on these processes.
In the past two decades, with the advent of high-throughput sequencing technologies and bioinformatics skills, the field of molecular genetics and plant breeding has become highly dynamic and is rapidly evolving. A total of 22 articles were published in the third and fourth editions of this Special Issue, including 17 original research articles, 4 comprehensive reviews, and this editorial. These papers highlight the recent advances in molecular genetics and plant breeding at the genome-wide level, focusing on diverse biological processes. They represent excellent contributions to the development of knowledge in these research fields and provide important theoretical insights and genetic resources for practical applications in plant breeding.

Funding

This work was supported by the Natural Science Foundation of Chongqing (2023NSCQ-MSX3166) and the Fundamental Research Funds for the Central Universities (SWU-KQ22037).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

For original datasets, please refer to the published articles within the Special Issue “Molecular Genetics and Plant Breeding 3.0” (https://www.mdpi.com/journal/ijms/special_issues/6W7Z125668) (accessed on 31 December 2023) and “Molecular Genetics and Plant Breeding 4.0” (https://www.mdpi.com/journal/ijms/special_issues/ZAM60GJ3Q7) (accessed on 15 February 2025).

Acknowledgments

The guest editors acknowledge the time and effort contributed by all the authors, reviewers, and editors who made possible this Special Issue on “Molecular Genetics and Plant Breeding 3.0” and “Molecular Genetics and Plant Breeding 4.0”.

Conflicts of Interest

The authors declare no conflicts of interest.

List of Contributions

1
Qin, Y.; Zhao, H.; Han, H.; Zhu, G.; Wang, Z.; Li, F. Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella. Int. J. Mol. Sci. 2023, 24, 11735. https://doi.org/10.3390/ijms241411735.
2
Qureshi, N.; Singh, R.P.; Gonzalez, B.M.; Velazquez-Miranda, H.; Bhavani, S. Genomic Regions Associated with Resistance to Three Rusts in CIMMYT Wheat Line “Mokue#1”. Int. J. Mol. Sci. 2023, 24, 12160. https://doi.org/10.3390/ijms241512160.
3
Sobiech, A.; Tomkowiak, A.; Bocianowski, J.; Szymańska, G.; Nowak, B.; Lenort, M. Identification and Analysis of Candidate Genes Associated with Maize Fusarium Cob Resistance Using Next-Generation Sequencing Technology. Int. J. Mol. Sci. 2023, 24, 16712. https://doi.org/10.3390/ijms242316712.
4
Lu, X.; Liu, P.; Tu, L.; Guo, X.; Wang, A.; Zhu, Y.; Jiang, Y.; Zhang, C.; Xu, Y.; Chen, Z.; et al. Joint-GWAS, Linkage Mapping, and Transcriptome Analysis to Reveal the Genetic Basis of Plant Architecture-Related Traits in Maize. Int. J. Mol. Sci. 2024, 25, 2694.https://doi.org/10.3390/ijms25052694.
5
Zhang, Y.; Du, A.; Tong, L.; Yan, G.; Lu, L.; Yin, Y.; Fu, X.; Yang, H.; Li, H.; Huang, W.; et al. Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding. Int. J. Mol. Sci. 2024, 25, 9012. https://doi.org/10.3390/ijms25169012.
6
He, L.; Sui, Y.; Che, Y.; Liu, L.; Liu, S.; Wang, X.; Cao, G. New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS. Int. J. Mol. Sci. 2024, 25, 4667. https://doi.org/10.3390/ijms25094667.
7
Gianinetti, A.; Ghizzoni, R.; Desiderio, F.; Morcia, C.; Terzi, V.; Baronchelli, M. QTL Analysis ofβ-Glucan Content and Other Grain Traits in a Recombinant Population of Spring Barley. Int. J. Mol. Sci. 2024, 25, 6296. https://doi.org/10.3390/ijms25126296 10.
8
Liao, J.; Zhang, Z.; Shang, Y.; Jiang, Y.; Su, Z.; Deng, X.; Pu, X.; Yang, R.; Zhang, L. Anatomy and Comparative Transcriptome Reveal the Mechanism of Male Sterility in Salvia miltiorrhiza. Int. J. Mol. Sci. 2023, 24, 10259. https://doi.org/10.3390/ijms241210259.
9
Keller-Przybylkowicz, S.; Oskiera, M.; Liu, X.; Song, L.; Zhao, L.; Du, X.; Kruczynska, D.; Walencik, A.; Kowara, N.; Bartoszewski, G. Transcriptome Analysis of White- and Red-Fleshed Apple Fruits Uncovered Novel Genes Related to the Regulation of Anthocyanin Biosynthesis. Int. J. Mol. Sci. 2024, 25, 1778. https://doi.org/10.3390/ijms25031778.
10
Li, H.; Suo, Y.; Li, H.; Sun, P.; Li, S.; Yuan, D.; Han, W.; Fu, J. Cytological and Transcriptome Analyses Provide Insights into Persimmon Fruit Size Formation (Diospyros kaki Thunb.). Int. J. Mol. Sci. 2024, 25, 7238. https://doi.org/10.3390/ijms25137238.
11
Jiang, C.; Lyu, K.; Zeng, S.; Wang, X.; Chen, X. A Combined Metabolome and Transcriptome Reveals the Lignin Metabolic Pathway during the Developmental Stages of Peel Coloration in the ‘Xinyu’ Pear. Int. J. Mol. Sci. 2024, 25, 7481. https://doi.org/10.3390/ijms25137481.
12
Hu, M.; Xie, M.; Cui, X.; Huang, J.; Cheng, X.; Liu, L.; Liu, S.; Tong, C. Genome-Wide Characterization of Trehalose-6-Phosphate Synthase Gene Family of Brassica napus and Potential Links with Agronomic Traits. Int. J. Mol. Sci. 2022, 23, 15714. https://doi.org/10.3390/ijms232415714.
13
Zheng, H.; Liang, Y.; Hong, B.; Xu, Y.; Ren, M.; Wang, Y.; Huang, L.; Yang, L.; Tao, J. Genome-Scale Analysis of the Grapevine KCS Genes Reveals Its Potential Role in Male Sterility. Int. J. Mol. Sci. 2023, 24, 6510. https://doi.org/10.3390/ijms24076510.
14
Xuan, C.; Feng, M.; Li, X.; Hou, Y.; Wei, C.; Zhang, X. Genome-Wide Identification and Expression Analysis of Chitinase Genes in Watermelon under Abiotic Stimuli and Fusarium oxysporum Infection. Int. J. Mol. Sci. 2024, 25, 638. https://doi.org/10.3390/ijms25010638.
15
Li, C.; Cong, C.; Liu, F.; Yu, Q.; Zhan, Y.; Zhu, L.; Li, Y. Abundance of Transgene Transcript Variants Associated with Somatically Active Transgenic Helitrons from Multiple T-DNA Integration Sites in Maize. Int. J. Mol. Sci. 2023, 24, 6574. https://doi.org/10.3390/ijms24076574.
16
Xiong, W.; Liao, L.; Ni, Y.; Gao, H.; Yang, J.; Guo, Y. The Effects of Epicuticular Wax on Anthracnose Resistance of Sorghum bicolor. Int. J. Mol. Sci. 2023, 24, 3070. https://doi.org/10.3390/ijms24043070.
17
Meng, R.; Li, Z.; Kang, X.; Zhang, Y.; Wang, Y.; Ma, Y.; Wu, Y.; Dong, S.; Li, X.; Gao, L.; et al. High Overexpression of SiAAP9 Leads to Growth Inhibition and Protein Ectopic Localization in Transgenic Arabidopsis. Int. J. Mol. Sci. 2024, 25, 5840. https://doi.org/10.3390/ijms25115840.
18
Zhang, X.; Du, M.; Yang, Z.; Ang, Z.; Lim, K.-J. Biogenesis, Mode of Action and the Interactions of Plant Non-Coding RNAs. Int. J. Mol. Sci. 2023, 24, 10664. https://doi.org/10.3390/ijms241310664.
19
Li, Z.; Xiong, K.; Wen, W.; Li, L.; Xu, D. Functional Endophytes Regulating Plant Secondary Metabolism: Current Status, Prospects and Applications. Int. J. Mol. Sci. 2023, 24, 1153. https://doi.org/10.3390/ijms24021153.
20
Adhikari, P.B.; Kasahara, R.D. An Overview on MADS Box Members in Plants: A Meta-Review. Int. J. Mol. Sci. 2024, 25, 8233. https://doi.org/10.3390/ijms25158233.
21
Di, X.; Wang, Q.; Zhang, F.; Feng, H.; Wang, X.; Cai, C. Advances in the Modulation of Potato Tuber Dormancy and Sprouting. Int. J. Mol. Sci. 2024, 25, 5078. https://doi.org/10.3390/ijms25105078.

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Table 1. Compilation of the 21 contributions in the Special Issue.
Table 1. Compilation of the 21 contributions in the Special Issue.
ContributionsSpeciesPurposeApproaches
1Prunus tenellaGeographic variation and population genetic structureGenetics, genomics, and transcriptomics
2Triticum aestivumGenomic regions associated with rust resistanceGenetics and genomics
3Zea maysNew markers linked to fusarium resistanceGenetics and genomics
4Zea maysGenetic basis of plant architecture traitsGenetics, genomics, and transcriptomics
5Oryza sativaGenomic variation in tetraploid rice and its potential in breedingGenetics, genomics, and bioinformatics
6Oryza sativaGenetic basis of lysine contentGenetics and metabolomics
7Hordeum vulgareQuantitative trait loci for β-Glucan content and grain traitsGenetics and physiology
8Salvia miltiorrhizaMolecular mechanism of pollen abortionTranscriptomics, genetics, and molecular biology
9Malus domesticaGenes involved in anthocyanin biosynthesisTranscriptomics and molecular biology
10Diospyros kaki Thunb.Molecular mechanism of fruit size formationTranscriptomics and molecular biology
11Pyrus pyrifoliaLignin biosynthesis and accumulationMetabolomics, transcriptomics, and molecular biology
12Brassica napusGenome-wide characteristics of trehalose-6-phosphate synthase (TPS) gene familyBioinformatics and genetics
13Vitis viniferaGenome-wide characteristics of the KCS gene family and its role in male sterilityBioinformatics and transcriptomics
14Citrullus lanatusGenome-wide characteristics of the chitinase gene family and its expression profileBioinformatics and molecular biology
15Zea maysTransposition and repair mechanism of HelitronsTranscriptomics, transformation, and molecular biology
16Sorghum bicolorEffects of epicuticular wax on anthracnose resistanceTranscriptomics, transformation, and molecular biology
17Foxtail milletFunction of amino acid permease (AAP) transporter SiAAP9 geneMolecular biology and transformation
18PlantsRoles and interactions of non-coding RNAsReview
19PlantsFunctional endophytes in regulating secondary metabolismReview
20PlantsFunctional characteristics of MADS-box genesReview
21Solanum tuberosumModulation of tuber dormancy and sproutingReview
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Du, H. Special Issue “Molecular Genetics and Plant Breeding 3.0 and 4.0”. Int. J. Mol. Sci. 2025, 26, 2030. https://doi.org/10.3390/ijms26052030

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Du, Hai. 2025. "Special Issue “Molecular Genetics and Plant Breeding 3.0 and 4.0”" International Journal of Molecular Sciences 26, no. 5: 2030. https://doi.org/10.3390/ijms26052030

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Du, H. (2025). Special Issue “Molecular Genetics and Plant Breeding 3.0 and 4.0”. International Journal of Molecular Sciences, 26(5), 2030. https://doi.org/10.3390/ijms26052030

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