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Crop Functional Genomics and Biological Breeding—2nd Edition
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Crop Functional Genomics and Biological Breeding—2nd 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: 28 February 2026 | Viewed by 540

Special Issue Editors

Dr. Yifeng Wang

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: seed developmental biology; seed dormancy; germination; phytohormone; molecular mechanism
Special Issues, Collections and Topics in MDPI journals
Dr. Jie Huang

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: rice (Oryza sativa L.); developmental biology; plant genetics; molecular biology
Special Issues, Collections and Topics in MDPI journals
Dr. Jian Zhang

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: plant genetics; molecular biology; biochemistry; transcriptome; proteome approaches; synthetic biology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jiezheng Ying

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
Interests: rice (Oryza sativa L.); quantitative trait locus; seed development; grain weight
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Crop breeders currently focus on improving the yield, resistance and quality of crops through biological breeding. The study of the functional genomics of crops is a crucial approach in biological breeding. Understanding the functional genomics of crops would provide insight into the genetic mechanisms that govern crucial traits such as yield, resistance to diseases and pests, tolerance to environmental stresses, and quality. This knowledge is instrumental in developing improved crop varieties with enhanced productivity and resilience, contributing to global efforts that aim to ensure an adequate and stable food supply. The aim of this Special Issue of Plants, entitled “Crop Functional Genomics and Biological Breeding”, is to provide an overview of recent research and discoveries regarding the functional genomics of crops, including the mapping and cloning of novel genes related to the yield, resistance, germination and quality of crops. This research can encompass the functional analysis of these genes and investigate their applications in biological breeding. We welcome original research articles, reviews and methodologies whose scope includes, but is not limited to, the following topics:

  • Cloning and functional studies of new crop genes;
  • Bioinformatics analysis of functional genes in crops;
  • The application of rice functional genomics in crop breeding.

Dr. Yifeng Wang
Dr. Jie Huang
Dr. Jian Zhang
Prof. Dr. Jiezheng Ying
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. 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

  • crops
  • functional genomics
  • biological breeding
  • yield
  • resistance
  • seed germination
  • quality
  • genetic improvement

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Published Papers (2 papers)

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Research

15 pages, 1672 KiB  
Article
Synergistic Response Mechanisms in Rice Seedlings Exposed to Brown Planthopper Infestation and High-Temperature Stress
by Danyun Cao, Yuchen Ping, Yiru Lin, Jinyan Hu, Zimeng Wang, Wei Yuan, Tongtong Li, Linxin Liu, Bo Zhang, Shijiao Xiong, Cong Dang and Dawei Xue
Plants 2025, 14(11), 1644; https://doi.org/10.3390/plants14111644 - 28 May 2025
Abstract
Recently, rice yield has been severely affected by both brown planthopper (BPH, Nilaparvata lugens) infestation and high-temperature stress. Numerous previous studies have identified genes conferring resistance to BPH and high-temperature tolerance in rice, respectively. However, it remains unclear how rice synergistically responds [...] Read more.
Recently, rice yield has been severely affected by both brown planthopper (BPH, Nilaparvata lugens) infestation and high-temperature stress. Numerous previous studies have identified genes conferring resistance to BPH and high-temperature tolerance in rice, respectively. However, it remains unclear how rice synergistically responds to these two stress factors. In the present study, we found that pre-treatment with high temperature can enhance rice seeding resistance to BPH, while BPH feeding did not alter the high-temperature tolerance of rice. This result can be elucidated by the subsequent transcriptome analysis. Differentially expressed genes (DEGs) following high-temperature treatment were enriched in metabolic processes and phenylpropanoid biosynthesis pathways, thereby enhancing rice resistance to BPH. Further weighted gene co-expression network analysis (WGCNA) indicated that genes in the magenta and black modules were predominantly associated with the protein folding and transmembrane transport biological processes. And several candidate genes, including Loc_Os01g02170 and Loc_Os01g59870, were identified that may play crucial roles in simultaneously regulating rice resistance to BPH and high-temperature stress. This research will provide new gene resources for cultivating rice with compound traits and provide ideas for the mechanism analysis of rice response to multiple stresses. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding—2nd Edition)
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18 pages, 2432 KiB  
Article
NAC Transcription Factor GmNAC035 Exerts a Positive Regulatory Role in Enhancing Salt Stress Tolerance in Plants
by Wanting Shi, Sixin Ye, Yiting Xin, Hongmiao Jin, Meiling Hu, Yueping Zheng, Yihua Zhan, Hongbo Liu, Yi Gan, Zhifu Zheng and Tian Pan
Plants 2025, 14(9), 1391; https://doi.org/10.3390/plants14091391 - 5 May 2025
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Abstract
Soybean, a globally significant and versatile crop, serves as a vital source of both oil and protein. However, environmental factors such as soil salinization pose substantial challenges to its cultivation, adversely affecting both yield and quality. Enhancing the salt tolerance of soybeans can [...] Read more.
Soybean, a globally significant and versatile crop, serves as a vital source of both oil and protein. However, environmental factors such as soil salinization pose substantial challenges to its cultivation, adversely affecting both yield and quality. Enhancing the salt tolerance of soybeans can mitigate yield losses and promote the development of the soybean industry. Members of the plant-specific transcription factor family NAC play crucial roles in plant adaptation to abiotic stress conditions. In this study, we screened the soybean GmNAC family genes potentially involved in the salt stress response and identified 18 GmNAC genes that may function during the early stages of salt stress. Among these, the GmNAC035 gene exhibited a rapid increase in expression within one hour of salt treatment, with its expression being induced by abscisic acid (ABA) and methyl jasmonate (MeJA), suggesting its significant role in the soybean salt stress response. We further elucidated the role of GmNAC035 in soybean salt tolerance. GmNAC035, a nuclear-localized transcriptional activator, enhances salt tolerance when overexpressed in Arabidopsis, reducing oxidative damage and boosting the expression of stress-responsive genes. It achieves this by regulating key stress response pathways, including the SOS pathway, calcium signaling, and ABA signaling. These findings highlight the potential of GmNAC035 as a genetic engineering target to improve crop salt tolerance. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding—2nd Edition)
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