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Biomolecules
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Molecular Genetics and Molecular Breeding in Plants: Advances, Applications, and...
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Molecular Genetics and Molecular Breeding in Plants: Advances, Applications, and Future Directions

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: 26 June 2026 | Viewed by 818

Special Issue Editors

Prof. Dr. Yurong Xie

E-Mail Website1 Website2
Guest Editor
Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100096, China
Interests: maize; plant architecture; high-temperature stress; high photosynthetic efficiency; molecular mechanism; genetic basis
Special Issues, Collections and Topics in MDPI journals
Dr. Hongbin Wei

E-Mail Website
Guest Editor
School of Life Sciences, Southwest University, Chongqing 400715, China
Interests: perennial trees; seasonal growth; shade avoidance response; cambial activity; wood formation; molecular mechanism

Special Issue Information

Dear Colleagues,

Plant molecular genetics and breeding are pivotal in addressing global challenges such as food security, sustainable agriculture and climate change. Recent advances in genome editing, high-throughput sequencing, and multi-omics technologies have revolutionized our ability to decode plant genomes, engineer desirable traits, and accelerate breeding cycles. However, translating these breakthroughs into resilient, high-yielding crops requires the mitigation of biological, technical, and ethical challenges.

This Special Issue aims to showcase cutting-edge interdisciplinary research at the intersection of molecular genetics, genomics, and breeding, emphasizing innovations that enhance crop productivity, stress tolerance, and nutritional value. We seek contributions that focus on CRISPR-based trait engineering, predictive breeding using machine learning, functional genomics, and the integration of phenomics with omics data. Studies addressing challenges such as regulatory hurdles, biodiversity conservation, and equitable technology access are also encouraged. We welcome original research articles, reviews, and perspectives that connect fundamental discoveries with practical applications. By fostering dialogue among geneticists, breeders, and policymakers, this Special Issue hopes to encourage the development of next-generation plant improvement strategies.

Prof. Dr. Yurong Xie
Dr. Hongbin Wei
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 250 words) can be sent to the Editorial Office for assessment.

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. Biomolecules 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 2700 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

  • molecular genetics
  • molecular breeding
  • genome editing (CRISPR)
  • omics technologies
  • stress resilience
  • trait discovery
  • genomic selection
  • sustainable agriculture
  • crop improvement
  • artificial intelligence in breeding

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Published Papers (2 papers)

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Research

15 pages, 5214 KB  
Article
Evaluation of the Unintended Effects of fad2-1-Gene-Edited Soybean Line AE15 Seeds
by Ruizhe Wang, Chang Guo, Jihong Zhang, Zhanchao Wang, Wujun Jin and Weixiao Liu
Biomolecules 2026, 16(1), 8; https://doi.org/10.3390/biom16010008 - 19 Dec 2025
Viewed by 125
Abstract
A data-independent acquisition (DIA)-based proteomic analysis was performed to evaluate the unintended effects of fad2-1-gene-edited soybean line AE15 seeds. A total of 561, 269, and 227 differentially expressed proteins (DEPs) were identified in seeds from three consecutive generations of AE15 soybean, respectively, [...] Read more.
A data-independent acquisition (DIA)-based proteomic analysis was performed to evaluate the unintended effects of fad2-1-gene-edited soybean line AE15 seeds. A total of 561, 269, and 227 differentially expressed proteins (DEPs) were identified in seeds from three consecutive generations of AE15 soybean, respectively, and were primarily enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to carbon metabolism, protein processing in the endoplasmic reticulum, and proteasome function. Furthermore, eight commonly differentially expressed proteins (co-DEPs) were detected across all three generations of AE15 soybean seeds, among which two—beta-amylase and endoplasmic reticulum (ER) lumen protein-retaining receptor—exhibited consistently upregulated expression. In the wild-type soybean control groups, 1063, 989, and 671 DEPs were identified across the three comparisons (ZhH302E3/ZhH10, ZhH10/ZhH42, and ZhH42/ZhH302E3), among which 71 co-DEPs were observed. These findings indicate that the protein expression profile alterations resulting from fad2-1 gene editing are considerably less pronounced compared to those caused by natural genetic variation among soybean seeds. Full article
(This article belongs to the Special Issue Molecular Genetics and Molecular Breeding in Plants: Advances, Applications, and Future Directions)
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15 pages, 4894 KB  
Article
Unveiling the Genetic Diversity and Population Structure of the Endangered Fern Angiopteris fokiensis Through Genome Survey and Genomic SSR Markers
by Yiwei Zhou, Jianjun Tan, Lishan Huang, Yanyu Luo, Shaoli Huang, Yuanjun Ye and Yechun Xu
Biomolecules 2025, 15(12), 1649; https://doi.org/10.3390/biom15121649 - 24 Nov 2025
Viewed by 415
Abstract
Angiopteris fokiensis is an endangered fern with ecological and medicinal value, yet genetic studies to support its conservation have been scarce. We performed a genome survey using high-throughput sequencing, developed genomic SSR markers from a draft assembly, and genotyped 96 individuals from 10 [...] Read more.
Angiopteris fokiensis is an endangered fern with ecological and medicinal value, yet genetic studies to support its conservation have been scarce. We performed a genome survey using high-throughput sequencing, developed genomic SSR markers from a draft assembly, and genotyped 96 individuals from 10 populations in Guangdong Province. The genome size was ~4.44 Gb (1.89% heterozygosity). From a 3.58 Gb contig assembly, 4,327,181 SSR loci were identified, with 15 highly polymorphic SSR markers being developed. Genotyping showed high within-population genetic diversity, low inter-population differentiation, and 98.55% of variation within populations. Bayesian structure, principal coordinates analysis, and neighbor-joining tree analyses consistently indicated admixed genetic clusters without clear geographical division. Additionally, the analysis revealed no significant correlation between genetic and geographic distances. Conservation should prioritize intra-population diversity via in situ/ex situ strategies. This study provides the first genomic SSR resources for A. fokiensis and underscores the importance of conserving within-population genetic diversity through integrated in situ and ex situ strategies. Full article
(This article belongs to the Special Issue Molecular Genetics and Molecular Breeding in Plants: Advances, Applications, and Future Directions)
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