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Special Issues
Advancing Crop Quality with Genomics, Genetics and Biotechnology
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Advancing Crop Quality with Genomics, Genetics and Biotechnology

A Special Issue of Genes (ISSN 2073-4425) belonging to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 10 November 2026 | Viewed by 2323

Editors

Prof. Dr. Xiquan Gao

E-Mail Website
Guest Editor
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
Interests: maize; genetic; breeding; disease resistance; genome; innate immunity
Special Issues, Collections and Topics in MDPI journals
Dr. José Á. Mercado Carmona

E-Mail Website
Guest Editor
1. Departamento de Botánica y Fisiología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
2. Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ (IHSM-UMA-CSIC), Universidad de Málaga, 29071 Málaga, Spain
Interests: plant physiology; fruit development and ripening; plant biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Ensuring high-quality attributes in staple and horticultural crops is paramount for global food security, nutrition, and consumer acceptance. However, traditional quality assessment and breeding methods are often slow and limited in scale. This Special Issue explores the transformative potential of integrating cutting-edge high-throughput phenotyping (HTP) technologies with advanced genomics and precision breeding for efficiently enhancing the nutritional and postharvest quality of diverse crops. This Special Issue welcomes research that employs genetic and genomic tools to dissect the genetic basis of complex quality traits. Furthermore, this Issue aims to also feature studies and reviews in the area applying genomic selection, quantitative trait loci (QTL) mapping, and genome editing to elucidate the genomic and genetic basis of crop quality, thereby accelerating the development of superior cultivars with improved quality.

Prof. Dr. Xiquan Gao
Dr. José A. Mercado
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-anonymized 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

  • crop quality
  • high throughput phenotyping
  • genome editing
  • genomic selection
  • nutritional quality
  • postharvest traits
  • precision breeding

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Published Papers (2 papers)

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Research

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15 pages, 5462 KB  
Article
Genome-Wide Association and Selective Sweep Analyses Reveal Candidate Genes Associated with Shoot Height in Maize Across Breeding Eras
by Junyue Wang and Baijuan Du
Genes 2026, 17(5), 570; https://doi.org/10.3390/genes17050570 - 18 May 2026
Cited by 1 | Viewed by 536
Abstract
Background: Maize shoot height is an important component of early vigor and plant architecture; however, its genetic basis during seedling development and its relationship with modern breeding remain insufficiently understood. This study aimed to investigate the genetic architecture of maize seedling shoot height [...] Read more.
Background: Maize shoot height is an important component of early vigor and plant architecture; however, its genetic basis during seedling development and its relationship with modern breeding remain insufficiently understood. This study aimed to investigate the genetic architecture of maize seedling shoot height across different breeding eras. Methods: Shoot height at 21 days after sowing was evaluated in 363 maize inbred lines representing three breeding eras in China. Genome-wide association analysis was performed to identify loci and candidate genes associated with shoot height variation, and selective sweep analysis was used to detect breeding-era differentiated genomic regions. Results: Modern breeding lines from the 2000–2010s exhibited significantly greater shoot height than lines from earlier breeding periods. Pearson’s correlation analysis revealed that 3-week shoot height showed highly significant positive correlations with plant height and ear height. Selective sweep analysis identified multiple differentiated genomic regions harboring previously reported height- and architecture-related genes, including ZmBR2, ZmLIL1, ZmNA1, ZmTE1, ZmSPL12, ZmBV1, ZmDIL1, ZmKN1 and ZmACS7. The GWAS identified 43 SNPs exceeding the GEC-derived suggestive threshold for shoot height, with the strongest and most continuous association signal located on chromosome 8. GWAS, together with LD analysis, haplotype analysis, and expression profiling, prioritized ZmGDCL (Zm00001d009163) as a promising candidate gene because of its strong association signal, local linkage disequilibrium support, broad expression profile, and significant haplotype effect on shoot height. Conclusions: Our results indicate that maize breeding has reshaped the genetic architecture of seedling shoot growth. ZmGDCL represents a promising candidate gene for future functional studies, while breeding-era differentiated regions provide useful genomic context for understanding maize architecture improvement. Full article
(This article belongs to the Special Issue Advancing Crop Quality with Genomics, Genetics and Biotechnology)
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Review

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31 pages, 7297 KB  
Review
Advances in Functional Genomics of Disease Resistance in Cucumber (Cucumis sativus) and Translational Prospects for the Cucurbitaceae Family
by Zhipeng Wang, Fanqi Gao and Guangchao Yu
Genes 2026, 17(5), 522; https://doi.org/10.3390/genes17050522 - 29 Apr 2026
Viewed by 1193
Abstract
Cucurbit crops—including cucumber (Cucumis sativus), watermelon (Citrullus lanatus), and melon (Cucumis melo)—are of major economic and nutritional importance worldwide. Yet their productivity and quality are severely compromised by foliar fungal diseases, particularly powdery mildew (PM), downy mildew [...] Read more.
Cucurbit crops—including cucumber (Cucumis sativus), watermelon (Citrullus lanatus), and melon (Cucumis melo)—are of major economic and nutritional importance worldwide. Yet their productivity and quality are severely compromised by foliar fungal diseases, particularly powdery mildew (PM), downy mildew (DM), and target leaf spot (TLS). While PM and DM have been extensively studied, TLS has emerged as an increasingly prevalent and damaging disease in key production regions, yet it remains comparatively understudied—especially with respect to its molecular basis and comparative pathobiology relative to PM and DM. Current reliance on chemical fungicides is hampered by escalating pathogen resistance and concerns over residual toxicity, whereas conventional breeding approaches face inherent limitations in pyramiding durable, broad-spectrum resistance against multiple pathogens. In this context, cucumber has emerged as a pivotal model species for dissecting foliar disease resistance mechanisms in cucurbits, supported by a high-quality reference genome, extensive resequencing datasets, diverse germplasm collections, and an efficient Agrobacterium-mediated transformation system. Despite these advantages, existing reviews predominantly address PM or DM resistance in isolation; comprehensive syntheses integrating TLS resistance advances—and critically, cross-disease comparisons of genetic architecture, transcriptional reprogramming, and defense signaling—are notably scarce. Furthermore, the translational pipeline—from gene discovery and functional validation to deployment in marker-assisted or genome-edited breeding—lacks systematic evaluation. Here, we provide a focused, cucumber-centered review that (i) synthesizes recent progress in mapping QTLs and GWAS loci, and characterizing key resistance-associated gene families (such as NLRs, RLKs, PR genes) conferring resistance to PM, DM, and TLS; (ii) integrates transcriptomic, epigenomic, and proteomic evidence to delineate conserved versus pathogen-specific host responses; (iii) highlights breakthroughs and unresolved questions in TLS resistance research, including the roles of novel susceptibility factors and non-canonical immune regulators; and (iv) critically assesses bottlenecks in translating resistance genes into practical breeding outcomes—such as linkage drag, functional redundancy, and genotype-by-environment interactions—and proposes empirically grounded strategies for accelerating molecular design of multi-disease-resistant cultivars. Collectively, this review aims to bridge fundamental insights with applied breeding goals, offering a conceptual and strategic framework for integrated management of foliar fungal diseases and the development of durable, broad-spectrum resistance in cucurbits. Full article
(This article belongs to the Special Issue Advancing Crop Quality with Genomics, Genetics and Biotechnology)
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