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Genetic Research on Crop Stress Resistance and Quality Traits
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Genetic Research on Crop Stress Resistance and Quality Traits

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (25 August 2025) | Viewed by 1712

Special Issue Editors

Dr. Zenglin Zhang

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Guest Editor
Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
Interests: small peptides; leaf senescence; stress resistance
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Zhiyong Ni

E-Mail Website
Guest Editor
College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China
Interests: gene function; cotton fiber development; plant stress responses
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Lichao Zhang

E-Mail Website
Guest Editor
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: exploration of key genes underlying wheat yield traits
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Developing crop varieties with combined stress resistance and superior quality traits has become a critical challenge for ensuring food security and sustainable agricultural development. The genetic improvement of stress resistance (e.g., drought tolerance, salinity tolerance, disease resistance) and quality traits (e.g., nutritional composition, processing characteristics, postharvest stability) holds significant importance for enhancing agricultural productivity, resource-use efficiency, and food nutritional value. Recent advancements in genomics, molecular marker technologies, and gene editing have provided novel tools for deciphering the molecular mechanisms underlying stress adaptation and quality formation in crops. However, challenges persist in integrating multi-omics data, precisely identifying key regulatory genes, and translating research findings into molecular design breeding strategies.

With global climate change and population growth posing significant threats to food security, improving crop resilience and quality traits has become a critical focus in agricultural research. Balancing stress resistance (e.g., drought, salinity, disease) with desirable quality traits (e.g., nutritional value, yield, processing properties) remains a major challenge in modern breeding programs. Recent breakthroughs in genomics, molecular biology, and gene editing have provided powerful tools to unravel the genetic and molecular mechanisms underlying these traits. This Special Issue will gather cutting-edge research on the genetic basis of crop resilience and quality traits, exploring both trade-offs and synergistic solutions to advance sustainable agriculture. Contributions will cover topics such as genetic and epigenetic regulation, multi-omics approaches, molecular breeding strategies, and the development of stress-resilient, high-quality crop varieties.

Dr. Zenglin Zhang
Prof. Dr. Zhiyong Ni
Prof. Dr. Lichao Zhang
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. Genes 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

  • genetic and epigenetic regulation
  • plant stresses response
  • multi-omics data analysis
  • regulation of plant senescence
  • plant regulatory hormones
  • mechanisms of the elucidation of plant molecular and physiological traits

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Published Papers (3 papers)

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Research

14 pages, 2279 KB  
Article
Development of KASP Molecular Markers and Candidate Gene Mining for Heat Tolerance-Related Traits in Gossypium hirsutum
by Zhaolong Gong, Ni Yang, Shiwei Geng, Juyun Zheng, Zhi Liu, Fenglei Sun, Shengmei Li, Xueyuan Li, Yajun Liang and Junduo Wang
Genes 2025, 16(10), 1154; https://doi.org/10.3390/genes16101154 - 28 Sep 2025
Viewed by 412
Abstract
Background: High-temperature stress is one of the major abiotic stresses limiting cotton production. Identifying genetic loci and genes for heat tolerance is crucial for breeding heat-tolerant varieties. Methods: Given the complexity of heat tolerance phenotypes in cotton, this study, which focused [...] Read more.
Background: High-temperature stress is one of the major abiotic stresses limiting cotton production. Identifying genetic loci and genes for heat tolerance is crucial for breeding heat-tolerant varieties. Methods: Given the complexity of heat tolerance phenotypes in cotton, this study, which focused on resource materials, identified an A/C SNP mutation at position 5486185 on chromosome D06 within the heat tolerance interval through genome-wide association studies (GWAS) of natural Gossypium hirsutum populations. Results: A total of 308 resource materials were identified and evaluated for their heat tolerance phenotypes over two years of field research. Kompetitive allele-specific PCR (KASP) molecular markers were developed on the basis of the D06-5486185 SNP to characterize the heat tolerance phenotypes of these 308 resource materials. Genotyping for heat tolerance-related traits and agronomic traits was also performed. Materials with the C/C haplotype at position D06-5486185 presented increased heat tolerance (higher pollen viability (PV), leaf area (LA), chlorophyll (Chl) and number of bolls on the third fruit branch (FB3) and a lower number of dry buds (DBs) and drop rate (DR)) without negatively impacting key yield traits. This locus is located in the intergenic region of two adjacent bZIP transcription factor genes (GH_D06G0408 and GH_D06G0409). Expression analysis revealed that the expression levels of these two genes were significantly greater in heat-tolerant accessions (C/C type) than in sensitive accessions and that their expression levels were significantly correlated with multiple heat-tolerant phenotypes. Conclusions: In summary, this study developed a Kompetitive Allele Specific PCR (KASP) marker associated with heat tolerance in G. hirsutum and identified two key heat tolerance candidate genes. These results provide an efficient marker selection tool and important genetic resources for the molecular breeding of heat-tolerant G. hirsutum, laying an important foundation for further establishing a molecular marker-assisted breeding system for heat tolerance in G. hirsutum. Full article
(This article belongs to the Special Issue Genetic Research on Crop Stress Resistance and Quality Traits)
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20 pages, 13395 KB  
Article
Fine Mapping of a Major Locus for Leaf Sheath Hairiness in Wheat Identifies TaSAIN1-4D as a Candidate Gene
by Lijuan Wu, Jundong He, Shian Shen, Yulin Li, Jinbai He and Xinkun Hu
Genes 2025, 16(9), 1117; https://doi.org/10.3390/genes16091117 - 20 Sep 2025
Viewed by 347
Abstract
Background/Objectives: Leaf sheath hairiness (LSH) is an adaptive trait in wheat that improves tolerance to biotic and abiotic stresses. Although trichome development has been extensively studied in model plants, the genetic basis of LSH in Triticeae crops remains poorly defined. Methods: [...] Read more.
Background/Objectives: Leaf sheath hairiness (LSH) is an adaptive trait in wheat that improves tolerance to biotic and abiotic stresses. Although trichome development has been extensively studied in model plants, the genetic basis of LSH in Triticeae crops remains poorly defined. Methods: In this study, the inheritance and genetic architecture of LSH were investigated. Two F2 populations were used, derived from crosses between the glabrous lines ‘Shumai 830’ and ‘Shumai 2262’ and the hairy line ‘Zhongkelanmai 1’. BSA-seq was combined with KASP marker genotyping to map and refine the trait locus. Candidate genes were evaluated through comparative genomics; sequence variation; and subcellular localization prediction. Results: Phenotypic evaluation revealed that LSH is a dominant trait, segregating at a 3:1 ratio in F2 populations. BSA-seq identified a major locus, QLsh.cwnu-4D, on chromosome 4DL. Fine mapping with KASP markers refined this region to a 1.67 Mb interval overlapping a 530 kb trichome-associated linkage disequilibrium block in Aegilops tauschii. Within this interval, TaSAIN1-4D, a salt-inducible protein unique to Triticeae, was identified as the strongest candidate gene. Extensive sequence variation among alleles (TaSAIN1-4Da; TaSAIN1-4Db; TaSAIN1-4Dc), including large insertions and multiple SNPs, indicated potential functional diversification. Predicted nuclear localization of TaSAIN1-4D supports a role in trichome regulation and stress adaptation. The co-dominant KASP marker K-cwnu-4D-502238348 was tightly linked to LSH and cosegregated perfectly, making it a reliable tool for marker-assisted selection. Conclusions: This study clarifies the genetic architecture of leaf sheath hairiness in wheat and identifies TaSAIN1-4D as a likely regulator. These findings provide a practical marker-assisted selection tool that can accelerate the development of improved wheat varieties with desirable leaf surface traits. Full article
(This article belongs to the Special Issue Genetic Research on Crop Stress Resistance and Quality Traits)
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16 pages, 8038 KB  
Article
Comparative Transcriptome and Volatile Metabolome Analysis of Gossypium hirsutum Resistance to Verticillium Wilt
by Ni Yang, Chaoli Xu, Yajun Liang, Juyun Zheng, Shiwei Geng, Fenglei Sun, Shengmei Li, Chengxia Lai, Mayila Yusuyin, Zhaolong Gong and Junduo Wang
Genes 2025, 16(8), 877; https://doi.org/10.3390/genes16080877 - 25 Jul 2025
Viewed by 459
Abstract
Background: In recent years, changes in climate conditions and long-term continuous cropping have led to the increased occurrence of Verticillium wilt in various cotton-growing regions, causing significant economic losses in cotton production. Research has shown that volatile substances are closely linked to plant [...] Read more.
Background: In recent years, changes in climate conditions and long-term continuous cropping have led to the increased occurrence of Verticillium wilt in various cotton-growing regions, causing significant economic losses in cotton production. Research has shown that volatile substances are closely linked to plant disease resistance; however, studies on their roles in the response of cotton to Verticillium wilt, including their relationship with gene regulation, are limited. Methods: In this study, the transcriptomes and metabolomes of Xinluzao 57 (a highly susceptible Verticillium wilt variety) and 192,868 (a highly resistant Verticillium wilt variety) were sequenced at different time points after inoculation with Verticillium wilt. Results: A total of 21,911 commonly differentially expressed genes (DEGs) were identified within and between the materials, and they were clustered into eight groups. Significant annotations were made in pathways related to amino acids and anthocyanins. Metabolomics identified and annotated 26,200 volatile metabolites across nine categories. A total of 158 differentially accumulated metabolites (DAMs) were found within and between the materials; three clusters were identified, and the 10 metabolites with the most significant fold changes were highlighted. Weighted gene coexpression network analysis (WGCNA) revealed that 13 genes were significantly correlated with guanosine, 6 genes were correlated with 2-deoxyerythritol, and 32 genes were correlated with raffinose. Conclusions: Our results provide a foundation for understanding the role of volatile substances in the response of cotton to Verticillium wilt and offer new gene resources for future research on Verticillium wilt resistance. Full article
(This article belongs to the Special Issue Genetic Research on Crop Stress Resistance and Quality Traits)
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