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Plants
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Functional Genomics and Molecular Breeding of Crops—3rd Edition
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Functional Genomics and Molecular Breeding of Crops—3rd Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 November 2026 | Viewed by 794

Special Issue Editors

Dr. Junjie Zou

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Guest Editor
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: plant molecular physiology; abiotic stress biology; functional genomics; molecular breeding
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Miaoyun Xu

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Guest Editor
Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
Interests: plant molecular biology; abiotic response; plant development; RNA silencing; plant genomics; nitrogen use efficiency
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yong-Gu Cho

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Guest Editor
Department of Crop Science, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju 28644, Korea
Interests: marker-assisted breeding (MAS); genome editing; functional genomics; GWAS; functional analysis of genes; plant biotechnology; molecular breeding in rice
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The functional genomics involved in model development link genotype to phenotype. The aim of functional genomics is to understand the expression pattern of genes, gene expression regulation, the interaction between genes and their products, changes in gene expression during the onset of various stress responses, and the functional roles of different genes in cellular processes, and thus to resolve how genes work together to produce a particular phenotype.

The molecular breeding of crops is a technique using DNA markers tightly linked to phenotypic traits to assist in a selection scheme for a particular crop-breeding objective. The molecular breeding of crops is involved in the identification and characterization of suitable genetic markers and is thus used to improve crops.

This Special Issue focuses on functional genomics and the molecular breeding of crops. Examples of topics of interest for this Special Issue include developmental processes, stress responses, functional genomics, comparative genomics, and the molecular breeding of crops. We welcome a variety of submissions, including original research reports, reviews, perspectives/opinions, and methodology articles.

Dr. Junjie Zou
Prof. Dr. Miaoyun Xu
Prof. Dr. Yong-Gu Cho
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. Plants is an international peer-reviewed open access semimonthly 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

  • plant development
  • function of genes
  • transcriptomics
  • transcription factors
  • plant gene regulation
  • stress biology
  • yield improvement
  • quality improvement
  • molecular breeding

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Published Papers (2 papers)

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Research

19 pages, 13315 KB  
Article
ZmPRN1 Negatively Regulates Salt Stress Tolerance by Modulating ROS Homeostasis in Maize (Zea mays L.)
by Lei Ma, Wenzong Li, Ke Zhang, Qingyun Zhang, Hua Xu, Baobao Wang, Lei Wang and Junjie Zou
Plants 2026, 15(10), 1585; https://doi.org/10.3390/plants15101585 - 21 May 2026
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Abstract
Soil salinization is a major abiotic stress limiting maize (Zea mays L.) growth and productivity worldwide. Recently, many genes involved in salt stress have been identified. However, the molecular mechanisms underlying salt tolerance in maize remain largely elusive. In this study, we [...] Read more.
Soil salinization is a major abiotic stress limiting maize (Zea mays L.) growth and productivity worldwide. Recently, many genes involved in salt stress have been identified. However, the molecular mechanisms underlying salt tolerance in maize remain largely elusive. In this study, we identified a member of the ZmPIRIN family genes, ZmPRN1, acting as a negative regulator in response to salt stress. The expression levels of ZmPRN1 were down-regulated under salt and H2O2 treatment. Subcellular localization analysis showed that ZmPRN1 is localized to the chloroplast. Under salt stress, the Zmprn1-Mu mutant exhibited higher survival rates and lower reactive oxygen species (ROS) accumulation compared to wild-type plants. Whereas, ZmPRN1 overexpression lines were more sensitive to salt stress, and had higher ROS levels and lower chlorophyll content than wild-type plants. Transcriptome analysis showed that the differentially expressed genes (DEGs) were mainly involved in the oxidation-reduction process. Furthermore, yeast-two hybrid and split-luciferase complementation assays revealed that ZmPRN1 can interact with the chloroplast NDH complex subunit NDF4, the RING-type E3 ubiquitin ligase RING371, and the auxin-responsive protein IAA27. Collectively, our findings demonstrated that ZmPRN1 negatively regulates salt tolerance in maize by modulating ROS homeostasis, providing a valuable genetic resource for breeding salt-tolerant maize varieties. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops—3rd Edition)
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18 pages, 3367 KB  
Article
A Breeding-Informed Regulatory Screen Identifies ZmSPL19 as a Negative Regulator of Nitrogen-Sufficient Growth in Maize (Zea mays L.)
by Zhijing Bai, Xinle Zhu, Changyu Li, Binbin Zhao, Lian Jin and Baobao Wang
Plants 2026, 15(9), 1387; https://doi.org/10.3390/plants15091387 - 30 Apr 2026
Viewed by 301
Abstract
Nitrogen use efficiency (NUE) is a major determinant of maize (Zea mays L.) productivity and sustainability, yet the regulatory changes associated with modern breeding remain incompletely understood. Here, we used breeding-era transcriptomic data from 137 elite Chinese maize inbred lines to identify [...] Read more.
Nitrogen use efficiency (NUE) is a major determinant of maize (Zea mays L.) productivity and sustainability, yet the regulatory changes associated with modern breeding remain incompletely understood. Here, we used breeding-era transcriptomic data from 137 elite Chinese maize inbred lines to identify transcriptional regulators associated with maize NUE. Breeding-era expression shifts in NUE effector genes were modest but tissue-specific, pointing to pathway-level transcriptional rewiring during modern breeding. Focusing on the first leaf above the uppermost ear at silking, we identified 69 breeding-era-responsive genes, including 10 transcription factors, and prioritized ZmSPL19 through Pearson correlation analysis with curated NUE-related genes. ZmSPL19 expression declined during modern breeding and showed a nitrate-repressed expression, with lower transcript abundance under nitrogen-sufficient conditions and rapid downregulation upon nitrate resupply. Loss of ZmSPL19 function promoted primary root elongation, biomass accumulation, leaf nitrogen content, soil–plant analysis development (SPAD), photosynthetic rate, kernel number, and grain yield under nitrogen-sufficient conditions. These results identify ZmSPL19 as a breeding-associated negative regulator of growth and yield formation under nitrogen-sufficient conditions and support the value of a breeding-informed strategy for discovering regulators with potential relevance to maize NUE improvement. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Crops—3rd Edition)
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