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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 4576

Special Issue Editors

Dr. Yifeng Wang

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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
Prof. Dr. Jian Zhang

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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; seed development
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jiezheng Ying

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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 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

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

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Published Papers (6 papers)

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Research

20 pages, 6244 KB  
Article
Genome-Wide Analysis of the Dof Gene Family in Soybean and Functional Identification of GmDof63 in Response to Phytophthora sojae Infection
by Sujie Fan, Haiyuan Chen, Yuhan Huo, Yang Song, Piwu Wang, Zhuo Zhang and Liangyu Jiang
Plants 2025, 14(23), 3621; https://doi.org/10.3390/plants14233621 - 27 Nov 2025
Viewed by 347
Abstract
Phytophthora root and stem infection by Phytophthora sojae is a global and devastating disease of soybeans. Selecting disease-resistant varieties is the most economical and effective measure for controlling this disease. Delving into the disease resistance and defense molecular mechanisms can lay a theoretical [...] Read more.
Phytophthora root and stem infection by Phytophthora sojae is a global and devastating disease of soybeans. Selecting disease-resistant varieties is the most economical and effective measure for controlling this disease. Delving into the disease resistance and defense molecular mechanisms can lay a theoretical foundation for solving this problem. Here, we screened the soybean genome and identified 78 GmDof genes distributed on nineteen chromosomes. Subcellular localization analysis revealed that the majority of GmDof proteins were located in the cell nucleus. Phylogenetic analysis categorized these genes into nine subfamilies. Gene structure analysis showed that all GmDofs contained 0 to 2 introns, and most of them did not have introns. Motif and conserved domain analysis showed that all GmDofs contained a common motif (motif-1) and a typical conserved C2-C2 domain. The prediction of cis-acting elements in promoter regions revealed numerous cis-regulatory elements responsible for stress responses, plant growth and development, plant hormone responses, and light responses. RNA-seq and quantitative real-time PCR results showed that GmDof63 (Glyma.16G145000) was specifically expressed at high levels after P. sojae infection. GmDof63 was strongly induced by SA and ETH treatments. The soybean seedlings overexpressing GmDof63 displayed enhanced resistance to P. sojae infection compared with the wild-type soybean seedlings. Further experiments indicated that the expression levels of pathogenesis-related protein genes PR1a, PR4, PR5a, and PR10 were significantly up-regulated in GmDof63-overexpressing transgenic soybean seedlings. Taken together, these findings reveal the mechanism by which GmDof63 directly or indirectly regulates the expression of PR genes to modulate the soybean response to P. sojae infection. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding—2nd Edition)
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19 pages, 9506 KB  
Article
The Bitter Gourd Transcription Factor McNAC087 Confers Cold Resistance in Transgenic Arabidopsis
by Xuetong Yang, Kai Wang, Feng Guan, Bo Shi, Yuanyuan Xie, Chang Du, Tong Tang, Zheng Yang, Shijie Ma and Xinjian Wan
Plants 2025, 14(22), 3440; https://doi.org/10.3390/plants14223440 - 10 Nov 2025
Viewed by 443
Abstract
Low-temperature stress severely restricts the growth, development, and yield of bitter gourd (Momordica charantia L.), a warm-loving crop with inherent low cold tolerance. NAC transcription factors (TFs) serve as crucial regulators in plant responses to abiotic stresses like cold, while their roles in [...] Read more.
Low-temperature stress severely restricts the growth, development, and yield of bitter gourd (Momordica charantia L.), a warm-loving crop with inherent low cold tolerance. NAC transcription factors (TFs) serve as crucial regulators in plant responses to abiotic stresses like cold, while their roles in coping with cold stress in bitter gourd remain unclear. This study identified cold-responsive genes in bitter gourd and characterized the candidate NAC TF McNAC087 through transcriptome analysis. Transcriptome sequencing of cold-tolerant (R) and cold-sensitive (S) bitter gourd inbred lines under 5 °C stress (0 h, 6 h, 12 h, 24 h) revealed 1157 co-expressed differentially expressed genes (DEGs), enriched via Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis in cold tolerance-related pathways (signal transduction, carbohydrate/amino acid metabolism). RT-qPCR showed higher McNAC087 expression in R than S under cold stress, and subcellular localization confirmed it as a nucleus-localized protein. McNAC087 overexpression in Arabidopsis enhanced cold tolerance after sequential stress (−14 °C for 1.5 h, 4 °C for 16 h, and 22 °C recovery for 2 days), with less damage compared to wildtype (WT). Physiologically, overexpressing lines had higher proline, elevated superoxide dismutase/peroxidase/catalase (SOD/POD/CAT) activities, lower malondialdehyde/hydrogen peroxide/superoxide anion (MDA/H2O2/O2−) accumulation under cold stress, and upregulated ICE-CBF-COR pathway marker genes (CBF1, DREB2A, RD29A, COR47). In conclusion, McNAC087 enhances Arabidopsis cold tolerance by regulating physiology and activating cold-responsive genes, providing insights for bitter gourd cold tolerance mechanisms and crop breeding. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding—2nd Edition)
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16 pages, 2906 KB  
Article
Functional Characterization of Rice Spotted-Leaf Mutant HM113 Reveals an Amino Acid Substitution in a Cysteine-Rich Receptor-like Kinase
by Ringki Kuinamei Sanglou, Marie Gorette Kampire, Xia Xu, Jian-Li Wu, Junyi Gong and Xiaobo Zhang
Plants 2025, 14(22), 3429; https://doi.org/10.3390/plants14223429 - 9 Nov 2025
Viewed by 494
Abstract
The spotted-leaf mutant, characterized by spontaneous lesion formation resembling pathogen-induced hypersensitive cell death, serves as an ideal model for studying the molecular mechanisms behind rice (Oryza sativa) disease resistance and programmed cell death, as these plants display hypersensitive responses that mimic [...] Read more.
The spotted-leaf mutant, characterized by spontaneous lesion formation resembling pathogen-induced hypersensitive cell death, serves as an ideal model for studying the molecular mechanisms behind rice (Oryza sativa) disease resistance and programmed cell death, as these plants display hypersensitive responses that mimic those triggered by pathogen infection. In this study, we generated a knockout line using CRISPR/Cas9 technology in homologous mutant HM113-induced calli. LOC_Os07g30510 encodes a cysteine-rich receptor kinase with a DUF26 domain, consisting of 688 amino acids. HM113 was localized to the cytosol and expressed in most rice tissues at various growth stages. A single nucleotide substitution from A to T was observed at the 847th base of LOC_Os07g30510, causing an amino acid change from serine to cysteine. Our results demonstrated that the A847T mutation was responsible for the spotted-leaf phenotype in the HM113 mutant through gene editing technology, as new frameshift mutations were introduced upstream of the A847T site in the HM113 gene. The mutation phenotype of HM113 was eliminated and resistance to bacterial blight was also lost, indicating that it is a gain-of-function gene. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding—2nd Edition)
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17 pages, 2876 KB  
Article
Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (Brassica napus L.)
by Mengfan Qin, Xiang Liu, Jia Song, Feixue Zhao, Yiji Shi, Yu Xu, Zhiting Guo, Tianye Zhang, Jiapeng Wu, Jinxiong Wang, Wu Li, Keqi Li, Shimeng Li, Zhen Huang and Aixia Xu
Plants 2025, 14(11), 1719; https://doi.org/10.3390/plants14111719 - 5 Jun 2025
Viewed by 967
Abstract
The leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. However, research on the leaf plastochron of crops remains limited. In this study, 2116C exhibited a rapid [...] Read more.
The leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. However, research on the leaf plastochron of crops remains limited. In this study, 2116C exhibited a rapid leaf plastochron compared to ZH18 during both rosette and bud periods. There were significant positive correlations among the leaf plastochron and primary branch number of the F2 populations (r ranging from 0.395 to 0.635, p < 0.01). Genetic analyses over two years demonstrated that two equally dominant genes might govern the leaf plastochron. Through bulk segregant analysis sequencing (BSA-seq), three novel genomic intervals were identified on chromosomes A02 (9.04–9.48 Mb and 13.52–13.66 Mb) and A04 (19.84–20.14 Mb) of ZS11 and Darmor-bzh reference genomes. By gene functional annotations, single-nucleotide variation (SNV) analyses, transcriptome data from parents, genetic progeny, and natural accessions, we identified ten candidate genes within the intervals, including FLOWERING LOCUS T, RGL1, MYB-like, CYP96A8, BLH3, NIT2, ASK6, and three CLAVATA3/ESR (CLE)-related genes. These findings lay the molecular foundation for further exploration into the leaf plastochron and the implications in plastochron-related breeding in rapeseed. Full article
(This article belongs to the Special Issue Crop Functional Genomics and Biological Breeding—2nd Edition)
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15 pages, 1672 KB  
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
Viewed by 801
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 KB  
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
Cited by 3 | Viewed by 1107
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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