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Agronomy
Special Issues
Crop Genomics and Omics for Future Food Security
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Crop Genomics and Omics for Future Food Security

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

Deadline for manuscript submissions: 30 December 2025 | Viewed by 1131

Special Issue Editors

Dr. Shuan Meng

E-Mail Website
Guest Editor
College of Agronomy, Hunan Agricultural University, Changsha 410128, China
Interests: crop improvement; food security; plant nutrient; abiotic stress; heavy metal; rice yield and grain quality; omics technologies; genome editing
Dr. Marco Pietrella

E-Mail Website
Guest Editor
CREA Research Centre for Olive, Fruit and Citrus Crops, Via La Canapona 1 bis, 47121 Forlì, FC, Italy
Interests: carotenoids; secondary metabolites; genomics; genetic improvement; breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Guobin Zhang

E-Mail Website
Guest Editor
College of Agriculture, Shandong Agricultural University, Taian 271018, China
Interests: plant genomics; plant molecular genetics; comparative genomics; pangenomics; plant nutrition; nitrogen nutrition
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Global food security faces significant challenges such as limited natural resources, climate change, population growth, and shifts in consumption patterns. Crop breeding and improvement are crucial means to ensure food security. Omics technologies including crop genomics, transcriptomics, metabolomics, proteomics, and epigenomics can support crop improvement at various levels, representing essential technical tools for securing future food supplies.

This Special Issue focuses on the application of omics technologies in future food security, emphasizing their roles in enhancing crop yield, improving nutritional quality, reducing the accumulation of harmful substances like heavy metals in grains, and enhancing crop environmental adaptability. It encompasses the assessment of genetic resources through genome sequencing and the exploration of underexplored yet valuable germplasm, leveraging transcriptomics, epigenomics, proteomics, and metabolomics to understand the physiological and molecular basis of crop yield, quality formation, growth, development, and environmental adaptation, and employing GWAS techniques to identify key loci and genes that regulate specific traits, thereby providing a foundation for breeding improvements.

In this Special Issue, original research articles and reviews are welcome. We look forward to receiving your contributions.

Dr. Shuan Meng
Dr. Marco Pietrella
Dr. Guobin 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. 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

  • food Security
  • crops omics
  • genomics
  • transcriptomics
  • metabolomics
  • proteomics
  • GWAS
  • crop improvement
  • crop yield
  • nutritional quality

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

21 pages, 3470 KiB  
Article
Systematic Identification of Phosphate Transporter Family 1 (PHT1) Genes and Their Expression Profiling in Response to Low Phosphorus and Related Hormones in Fagopyrum tataricum (L.) Gaertn.
by Yanyu Zhou, Jianjiang Fan, Qingtao Wu, Haihua Wang, Xiaoyan Huang, Limei Liao, Huan Xie and Xixu Peng
Agronomy 2025, 15(3), 576; https://doi.org/10.3390/agronomy15030576 - 26 Feb 2025
Viewed by 352
Abstract
Accumulating evidence suggests that the plasma membrane-localized phosphate transporter 1 (PHT1) family plays a fundamental role in the absorption, translocation, and re-mobilization of phosphorus in plants. Buckwheat (Fagopyrum spp.) exhibits high efficiency in phosphate uptake and wide adaptability to grow in under-fertilized [...] Read more.
Accumulating evidence suggests that the plasma membrane-localized phosphate transporter 1 (PHT1) family plays a fundamental role in the absorption, translocation, and re-mobilization of phosphorus in plants. Buckwheat (Fagopyrum spp.) exhibits high efficiency in phosphate uptake and wide adaptability to grow in under-fertilized soils. Despite their physiological importance, a systematic analysis of PHT1 genes in buckwheat has not been conducted yet. In this study, we performed a genome-wide identification and expression profile of the PHT1 gene family in Tartary buckwheat (Fagopyrum tataricum Gaertn). A total of eleven putative PHT1 genes (FtPHT1;1 to 1;11) were identified with an uneven distribution on all the F. tataricum chromosomes except for chromosomes 2, 3, and 5. All the FtPHT1s share the conserved domain GGDYPLSATIxSE, a typical signature of PHT1 transporters. A phylogenetic analysis indicated that FtPHT1 proteins could be clustered into four distinct subgroups, well supported by the exon–intron structure, consensus motifs, and the domain architecture. A gene duplication analysis suggested that tandem duplication may largely contribute to the expansion of the FtPHT1 gene family members. In silico predictions of cis-acting elements revealed that low-phosphate-responsive elements, such as W-box, P1BS, and MBS, were enriched in the promoter regions of FtPHT1 genes. Quantitative real-time PCR assays showed differential but partially overlapping expression patterns of some FtPHT1 genes in various organs under limited Pi supply and hormone stimuli, implying that these FtPHT1 transporters may be essential for Pi uptake, translocation, and re-mobilization, possibly through signaling cross-talk between the low phosphate and hormones. These observations provide molecular insights into the FtPHT1 gene family, which paves the way to a functional analysis of FtPHT1 members in the future. Full article
(This article belongs to the Special Issue Crop Genomics and Omics for Future Food Security)
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19 pages, 4526 KiB  
Article
Non-Targeted Metabolomics Reveals Tobacco Metabolites Associated with Roasted Tobacco Quality Under Organic Substitution
by Feng Tian, Li Zhang, Lina Niu, Xinglong Fan, Yongliang Han, Yuanshang Liu, Jiancai Qian, Shihang Huang, Xixian Ou and Qiang Li
Agronomy 2025, 15(2), 470; https://doi.org/10.3390/agronomy15020470 - 14 Feb 2025
Viewed by 429
Abstract
The present study investigated the effect of the replacement of chemical fertilizers by organic fertilizers on agronomic traits of tobacco at maturity as well as on the conventional chemical quality of post-roasted tobacco leaves. To better understand the relationship between tobacco metabolites and [...] Read more.
The present study investigated the effect of the replacement of chemical fertilizers by organic fertilizers on agronomic traits of tobacco at maturity as well as on the conventional chemical quality of post-roasted tobacco leaves. To better understand the relationship between tobacco metabolites and roasted tobacco under organic nitrogen replacement treatments, post-roasting tobacco leaves were analyzed by an untargeted metabolomics analytical approach to identify key metabolites applicable to predicting tobacco quality. Methods: Yunyun Tobacco 87 was adopted as the test material in a field plot experiment with five fertilization treatments: T1 (100% chemical nitrogen fertilizer), T2 (25% organic nitrogen fertilizer + 75% chemical nitrogen fertilizer), T3 (50% organic nitrogen fertilizer + 50% chemical nitrogen fertilizer), T4 (75% organic nitrogen fertilizer + 25% chemical nitrogen fertilizer), and T5 (100% organic nitrogen fertilizer). Additionally, the non-targeted metabolomics approach was employed for the in-depth analysis of metabolites in roasted tobacco leaves. Results: The targeted metabolomic analysis identified 991 metabolites in the positive ion pattern and 673 in the negative ion pattern across all treatments. Among these, certain pathways such as alanine, aspartate, and glutamate metabolism, D-amino acid metabolism, purine metabolism, tryptophan metabolism, and galactose metabolism were up-regulated, whereas other pathways such as starch and sucrose metabolism, betalain biosynthesis, and biosynthesis of unsaturated fatty acids were down-regulated and significantly enriched with differential metabolites. This study revealed the significant differences in the metabolite composition under different fertilization conditions, with a strong correlation between metabolites and tobacco quality indices. Organic fertilizers were observed to enhance tobacco quality by influencing tobacco metabolism, providing a scientific basis for optimizing fertilization strategies and improving tobacco quality. Full article
(This article belongs to the Special Issue Crop Genomics and Omics for Future Food Security)
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