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Agronomy
Special Issues
Resistance-Related Gene Mining and Genetic Improvement in Crops
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Resistance-Related Gene Mining and Genetic Improvement in Crops

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 4287

Special Issue Editors

Dr. Panfeng Yao

E-Mail Website
Guest Editor
State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
Interests: potato; drought; ABA; cadmium stress
Dr. Chen Lin

E-Mail Website
Guest Editor
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
Interests: germplasm conservation; genetics and molecular biology; gene function; gene family; alfalfa; maize
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Research on crop stress resistance is a crucial topic in the field of agriculture. With climate change and environmental degradation, crops are facing increasingly severe non-biological stressors such as drought and salinity. Scientists explore drought-resistant genes through genetic improvement to enhance crop adaptability and yield stability. In recent years, utilizing molecular biology and genomics technologies has led to the successful discovery of multiple key drought-resistant genes, which have been introduced into crops through transgenic or hybrid breeding methods, achieving some breakthroughs. However, challenges remain, including insufficient depth in gene exploration, incomplete understanding of gene functions, and concerns about the safety of transgenic crops, thus impeding the progress of stress resistance research. Future efforts should focus on strengthening fundamental research, delving deeper into drought resistance mechanisms, exploring new genetic improvement approaches, and prioritizing ecological risk assessments to propel greater advancements in crop stress resistance research.

In this Special Issue, we are soliciting research articles on novel and underexplored crop stress resistance-related genes, as well as comprehensive reviews offering unique insights into resistance against non-biological stressors in major crops.

Dr. Panfeng Yao
Dr. Chen Lin
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. Agronomy 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 2600 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

  • agriculture
  • plant science
  • staple crops
  • abiotic stress
  • plant breeding
  • genetic improvement

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Published Papers (5 papers)

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Research

20 pages, 9925 KB  
Article
Genome-Wide Identification and Characterization of Q-Type C2H2 Zinc Finger Proteins in Rapeseed (Brassica napus L.) and Their Expression Patterns Across Tissues and Under Abiotic Stress
by Yuanyuan Pu, Lijun Liu, Li Ma, Gang Yang, Wangtian Wang, Tingting Fan, Junyan Wu and Wancang Sun
Agronomy 2025, 15(9), 2085; https://doi.org/10.3390/agronomy15092085 - 29 Aug 2025
Abstract
Q-type C2H2 zinc finger protein (ZFP) transcription factors, a plant-specific subfamily of C2H2 ZFP, have been implicated in regulating abiotic stress responses, growth, and developmental processes in plants. Rapeseed (Brassica napus L.) is a crucial oil crop widely used for the production [...] Read more.
Q-type C2H2 zinc finger protein (ZFP) transcription factors, a plant-specific subfamily of C2H2 ZFP, have been implicated in regulating abiotic stress responses, growth, and developmental processes in plants. Rapeseed (Brassica napus L.) is a crucial oil crop widely used for the production of high-quality vegetable oil, animal feed, and biodiesel. Compared with studies on Q-type C2H2-ZFP genes in other plant species, systematic research has not been performed in B. napus. In this study, a comprehensive genome-wide analysis of Q-type C2H2-ZFPs in B. napus was conducted. A total of 216 Q-type C2H2-ZFP genes were identified, exhibiting extensive and uneven distribution across the 19 chromosomes. Phylogenetic analysis, based on homologs from Arabidopsis, classified these genes into eight distinct subfamilies, with each containing one to three conserved “QALGGH” motifs. Each subfamily exhibited similar motif compositions and gene structures. Evolutionary studies revealed that segmental duplication events played a crucial role in the expansion of the BnaQ-type C2H2-ZFP gene family. Expression pattern analysis in different tissues and under abiotic stress identified BnaA03g09250D, BnaC09g35160D, BnaC03g11570D, and BnaA10g25850D as candidate genes involved in the response to freezing stress. Overexpression of BnaC09g35160D provided preliminary evidence that it enhances freezing tolerance in plants. This comprehensive study of Q-type C2H2-ZFPs in B. napus will enhance our understanding of the BnaQ-type C2H2-ZFP gene family and provide valuable insights for further functional investigations of BnaC09g35160D. Full article
(This article belongs to the Special Issue Resistance-Related Gene Mining and Genetic Improvement in Crops)
16 pages, 2493 KB  
Article
Comparative Transcriptome Analysis of Susceptible and Resistant Rutaceae Plants to Huanglongbing
by Huihong Liao, Fuping Liu, Xi Wang, Hongming Huang, Qichun Huang, Nina Wang and Chizhang Wei
Agronomy 2025, 15(5), 1218; https://doi.org/10.3390/agronomy15051218 - 17 May 2025
Viewed by 547
Abstract
Huanglongbing (HLB), also known as citrus greening, is a devastating disease affecting the citrus industry worldwide. This study aimed to investigate the transcriptional responses of two Rutaceae species, Ponkan Mandarin (susceptible) and Punctate Wampee (resistant), to HLB infection. Comparative transcriptome analysis was conducted [...] Read more.
Huanglongbing (HLB), also known as citrus greening, is a devastating disease affecting the citrus industry worldwide. This study aimed to investigate the transcriptional responses of two Rutaceae species, Ponkan Mandarin (susceptible) and Punctate Wampee (resistant), to HLB infection. Comparative transcriptome analysis was conducted to identify differentially expressed genes (DEGs) and pathways involved in defense mechanisms. The transcriptome data showed that in the susceptible Ponkan Mandarin, there were 1519 upregulated genes and 700 downregulated genes, while in the resistant Punctate Wampee variety, there were 1611 upregulated genes and 1727 downregulated genes. Upon infection, 297 genes were upregulated in both varieties, while 211 genes were downregulated in both. These genes included transcription factors from different families such as WRKY, ERF, and MYB. Ponkan Mandarin primarily relies on pathways like lignin synthesis and cell wall modification to defend against HLB, whereas Punctate Wampee mainly resists HLB by regulating cellular homeostasis and metabolism. Weighted Gene Co-expression Network Analysis (WGCNA) identified ten potential key resistance genes in the resistant Punctate Wampee variety, including genes involved in lignin biosynthesis and genes related to cellular signaling pathways. These findings not only enhance our understanding of the distinct defense mechanisms employed by citrus species against HLB infection but also offer novel perspectives for developing effective prevention and management strategies against this disease. Full article
(This article belongs to the Special Issue Resistance-Related Gene Mining and Genetic Improvement in Crops)
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17 pages, 6375 KB  
Article
Identification and Expression of Laccase Gene Family in Potato (Solanum tuberosum)
by Hongyu Luo, Zhen Liu, Jinyong Zhu, Zhitao Li, Xiaoqiang Qiu, Weilu Wang, Chengwei Gao, Jiangpeng Qi, Minmin Bao and Yuhui Liu
Agronomy 2025, 15(3), 585; https://doi.org/10.3390/agronomy15030585 - 27 Feb 2025
Viewed by 685
Abstract
Through the identification and expression pattern analysis of potato Laccase (LAC) gene family members, the characteristics of the StLAC gene family were elucidated, and the biological function of potato StLACs was further analyzed. In this study, bioinformatics approaches were employed to identify the [...] Read more.
Through the identification and expression pattern analysis of potato Laccase (LAC) gene family members, the characteristics of the StLAC gene family were elucidated, and the biological function of potato StLACs was further analyzed. In this study, bioinformatics approaches were employed to identify the members of the potato LAC family at the whole-genome level. Subsequently, their physicochemical properties, chromosomal localizations, gene structures, gene duplication events, and expression patterns were thoroughly analyzed. By leveraging the RNA-seq data retrieved from the PGSC database, the expression patterns of StLACs in diploid monoploid (DM) potatoes under various tissue, stress, and hormone treatments were investigated. Moreover, real-time fluorescence quantitative polymerase chain reaction (qPCR) was utilized to analyze the relative expression levels of StLACs in the “Atlantic” potato cultivar under salt stress treatments at different time points (zero hours, one hour, three hours, twelve hours, and twenty-four hours), aiming to screen for the StLAC genes potentially involved in the potato’s response to salt stress. Forty-five members of the potato StLAC gene family were identified, unevenly distributed across 12 chromosomes. Through the analysis of their gene structures and phylogenetic characteristics, the 45 StLACs members were classified into five subgroups. Collinearity analysis indicated that segmental duplication and tandem repeats played major roles in the expansion of the StLAC genes. Using RNA-seq and qPCR analyses, two candidate StLAC genes (Soltu09G001990 and Soltu04G028320) involved in the potato’s response to salt stress were screened out. This study provides a theoretical basis for further understanding StLAC gene family characteristics and an in-depth analysis of StLAC gene function in potato. Full article
(This article belongs to the Special Issue Resistance-Related Gene Mining and Genetic Improvement in Crops)
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16 pages, 10863 KB  
Article
Genome-Wide Identification of Epidermal Pattern Factor (EPF) Gene Family in Potato and Functional Characterization of StEPF4 in Regulating Drought Stress
by Run Qiao, Jiangwei Yang, Yurong Deng, Xiaoqin Duan, Xinxia Li, Fengjiao Zhu, Mei Liu, Jiani Mou, Ning Zhang and Huaijun Si
Agronomy 2024, 14(12), 2948; https://doi.org/10.3390/agronomy14122948 - 11 Dec 2024
Cited by 2 | Viewed by 1158
Abstract
Plants require adequate water for growth, development, and reproduction. Peptides play a key role in plant growth and development and act in a similar manner to plant hormones. However, only a few peptides have been identified to play a role in abiotic stress [...] Read more.
Plants require adequate water for growth, development, and reproduction. Peptides play a key role in plant growth and development and act in a similar manner to plant hormones. However, only a few peptides have been identified to play a role in abiotic stress tolerance in potato. In this study, we identified fourteen members of the epidermal patterning factor (EPF) family in potato, which were designated as StEPF1-14 according to their chromosomal locations. We also conducted a comprehensive analysis of their chromosomal distribution, gene structures, physicochemical properties, phylogenetic relationships, and tissue-specific expression patterns. RT-qPCR analysis revealed that the StEPF4 gene is significantly induced by drought stress, suggesting its potential role as a negative regulator in the plant’s response to drought. Furthermore, multiple cis-regulatory elements associated with drought-responsive regulation were identified within the promoter region of the StEPF genes. Here, we isolated an EPF secreted Cys-rich small peptide StEPF4 from ‘Atlantic’ and explored its mechanism in plant response to drought stress. We found that StEPF4 was greatly induced by dehydration treatment in potato. To investigate its potential biological functions, StEPF4 was knocked down in potato. The StEPF4 knocked down lines (KdStEPF4) significantly decreased stomatal density, resulting in a decrease in the transpiration rate. KdStEPF4 lines maintained a higher photosynthetic rate and lowered the water loss rate of leaves compared with the control, resulting in increased drought resistance. Taken together, this study provides detailed information about StEPFs, and our findings also show that StEPF4 plays an essential role in regulating drought resistance by reducing stomatal density in potato. Full article
(This article belongs to the Special Issue Resistance-Related Gene Mining and Genetic Improvement in Crops)
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20 pages, 6323 KB  
Article
Identification of Shade Avoidance Response MicroRNAs and Their Targets in Solanum tuberosum L. via High-Throughput Sequencing
by Mei Liu, Jiangwei Yang, Ning Zhang, Run Qiao, Xinxia Li, Fengjiao Zhu and Huaijun Si
Agronomy 2024, 14(12), 2833; https://doi.org/10.3390/agronomy14122833 - 28 Nov 2024
Viewed by 858
Abstract
MicroRNAs (miRNAs) are non-coding, single-stranded RNA molecules that regulate gene expression post-transcriptionally. Potato, an essential crop for food and fodder, experiences reduced quality and yield under shading. Although miRNAs have known roles in various plants, their regulatory mechanisms in potato shade avoidance remain [...] Read more.
MicroRNAs (miRNAs) are non-coding, single-stranded RNA molecules that regulate gene expression post-transcriptionally. Potato, an essential crop for food and fodder, experiences reduced quality and yield under shading. Although miRNAs have known roles in various plants, their regulatory mechanisms in potato shade avoidance remain unexplored. To investigate this, we constructed nine small RNA libraries from potato samples at 0, 5, and 10 days post-shade treatment. High-throughput sequencing identified 525 miRNAs (307 known and 218 novel) from 99 families, and 166 differentially expressed miRNAs (DEMs) were detected. qRT-PCR verified 10 DEMs, confirming sequencing reliability. Using TargetFinder, we predicted 4320 target genes of DEMs, which were enriched in plant–pathogen interaction and hormone signal transduction pathways, among others. These findings indicate that miRNAs may play key regulatory roles in potato shade avoidance by targeting specific genes, providing valuable insights for future functional studies and potential yield enhancement. Full article
(This article belongs to the Special Issue Resistance-Related Gene Mining and Genetic Improvement in Crops)
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