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Genetic and Functional Genomics Insights into the Genetic Improvement of...
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Genetic and Functional Genomics Insights into the Genetic Improvement of Stress Resistance in Economic Crops

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

Deadline for manuscript submissions: 20 December 2025 | Viewed by 2571

Special Issue Editors

Dr. Mingku Zhu

E-Mail Website
Guest Editor
Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
Interests: sweet potato; salt tolerance; transcription factors; regulatory mechanisms
Special Issues, Collections and Topics in MDPI journals
Dr. Xiaoqing Meng

E-Mail Website
Guest Editor
Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
Interests: sweet potato; salt tolerance; transcription factors; regulatory mechanisms

Special Issue Information

Dear Colleagues,

Economic crops, such as soybean, cotton, rape, and sweet potato hold pivotal importance in global agricultural economies by driving income generation, industrial development, and sustainable livelihoods. Some economic crops, such as sweet potato, also play a key role as staple crops, especially in developing countries. Dramatic increases in population, decreases in arable land, and harsh environmental conditions have brought superimposed serious challenges to global food and energy supplies. Complicated environmental conditions such as drought, salinity, cold and biotic stress seriously affect the growth and yield of various economic crops. Genetic improvement emerges as a critical solution; leveraging genomic tools to develop stress-resilient cultivars can remarkably reduce yield losses and enhance nutritional quality. This Special Issue in Genes aims to integrate recent attempts to make progress in economic crops by expanding knowledge in various fields, such as genetics, molecular biology, functional genomics, biotic and abiotic stress responses, and omics studies, etc.

Dr. Mingku Zhu
Dr. Xiaoqing Meng
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

  • economic crops
  • functional genomics
  • molecular biology
  • genetic improvement
  • agricultural biotechnology

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Published Papers (3 papers)

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Research

16 pages, 2534 KB  
Article
Complete Chloroplast Genome Features and Phylogenetic Analysis of Linum usitatissimum L.
by Qingqing Ji, Guanghui Du, Xingcai An, Junyuan Dong, Xiahong Luo, Changli Chen, Tingting Liu, Lina Zou, Shaocui Li, Jikang Chen and Xia An
Genes 2025, 16(9), 1038; https://doi.org/10.3390/genes16091038 - 31 Aug 2025
Viewed by 665
Abstract
Background: The chloroplast genome provides rich genetic information for plant evolutionary studies. This study aimed to assemble, annotate, and analyze the complete chloroplast genome of flax cultivar ‘Longya 15’ (Linum usitatissimum L.) and clarify its phylogenetic relationships with other Linaceae species. Methods: [...] Read more.
Background: The chloroplast genome provides rich genetic information for plant evolutionary studies. This study aimed to assemble, annotate, and analyze the complete chloroplast genome of flax cultivar ‘Longya 15’ (Linum usitatissimum L.) and clarify its phylogenetic relationships with other Linaceae species. Methods: We assembled and annotated the chloroplast genome of ‘Longya 15’ and retrieved chloroplast genomes of related species (e.g., Linum grandiflorum NC_058845.1, Linum lewisii NC_058799.1) from the NCBI database for phylogenetic analysis. Results: The chloroplast genome of ‘Longya 15’ was a 157,074-bp quadripartite structure with 37.42% GC content, encoding 128 genes (83 mRNAs, 37 tRNAs, 8 rRNAs) without pseudogenes. It showed codon bias for leucine (28 codons with RSCU > 1, ending in A/U), 260 dispersed repeats, and 240 SSRs. Ka/Ks analysis revealed purifying selection for most genes, while rps18 and ycf2 had positive selection. ycf1 was identified as the hypervariable region (pi = 0.25024). Phylogenetically, it clustered closest with Linum grandiflorum, followed by L. lewisii and L. perenne, and was related to Hypericum species. Conclusions: This is the first fine assembly and annotation of ‘Longya 15’ chloroplast genome, confirming no pseudogenes in flax chloroplast. It elucidates flax chloroplast genome conservation and evolutionary dynamics, enriches the database, and provides a foundation for Linaceae phylogenetics, germplasm development, and stress-resistant breeding. Full article
(This article belongs to the Special Issue Genetic and Functional Genomics Insights into the Genetic Improvement of Stress Resistance in Economic Crops)
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19 pages, 2421 KB  
Article
Genome-Wide Identification of the Dendrocalamus latiflorus IDD Gene Family and Its Functional Role in Bamboo Shoot Development
by Yu-Han Lin, Peng-Kai Zhu, Mei-Yin Zeng, Xin-Ru Gao, Tian-You He, Jun-Dong Rong, Yu-Shan Zheng and Ling-Yan Chen
Genes 2025, 16(9), 1036; https://doi.org/10.3390/genes16091036 - 30 Aug 2025
Viewed by 659
Abstract
Background: Transcription factors (TFs) critically regulate gene expression, orchestrating plant growth, development, and stress responses. The conserved IDD (INDETERMINATE DOMAIN) TF family modulates key developmental processes, including root, stem, and seed morphogenesis. Dendrocalamus latiflorus Munro, an economically vital sympodial bamboo [...] Read more.
Background: Transcription factors (TFs) critically regulate gene expression, orchestrating plant growth, development, and stress responses. The conserved IDD (INDETERMINATE DOMAIN) TF family modulates key developmental processes, including root, stem, and seed morphogenesis. Dendrocalamus latiflorus Munro, an economically vital sympodial bamboo in southern China, suffers significant yield losses due to prevalent bamboo shoot abortion, impacting both edible shoot production and timber output. Despite the documented roles of IDD TFs in shoot apical meristem expression and lateral organ regulation, their genome-wide characterization in D. latiflorus remains unstudied. Methods: Using IDD members from Arabidopsis thaliana, Oryza sativa, and Phyllostachys edulis as references, we identified 45 DlIDD genes in D. latiflorus. Comprehensive bioinformatics analyses included gene characterization, protein physicochemical assessment, phylogenetic reconstruction, and examination of gene structures/conserved domains. Differential expression of DlIDD genes was profiled between dormant and sprouting bamboo shoots to infer putative functions. Results: The 45 DlIDD genes were phylogenetically classified into three subfamilies and unevenly distributed across 34 chromosomes. Whole-genome duplication (WGD) events drove the expansion of this gene family. Promoter analyses revealed enriched cis-regulatory elements associated with hormone response and developmental regulation. Functional analyses suggested potential roles for DlIDD genes in bamboo shoot development. Conclusions: This study provides a foundation for future research to elucidate the functions of IDD TFs and their regulatory mechanisms in bamboo shoot morphogenesis and lateral bud development within woody monocots. Full article
(This article belongs to the Special Issue Genetic and Functional Genomics Insights into the Genetic Improvement of Stress Resistance in Economic Crops)
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28 pages, 5315 KB  
Article
Integrated Transcriptome and Metabolome Analysis Provides Insights into the Low-Temperature Response in Sweet Potato (Ipomoea batatas L.)
by Zhenlei Liu, Jiaquan Pan, Sitong Liu, Zitong Yang, Huan Zhang, Tao Yu and Shaozhen He
Genes 2025, 16(8), 899; https://doi.org/10.3390/genes16080899 - 28 Jul 2025
Cited by 1 | Viewed by 911
Abstract
Background/Objectives: Sweet potato is a tropical and subtropical crop and its growth and yield are susceptible to low-temperature stress. However, the molecular mechanisms underlying the low temperature stress of sweetpotato are unknown. Methods: In this work, combined transcriptome and metabolism analysis was employed [...] Read more.
Background/Objectives: Sweet potato is a tropical and subtropical crop and its growth and yield are susceptible to low-temperature stress. However, the molecular mechanisms underlying the low temperature stress of sweetpotato are unknown. Methods: In this work, combined transcriptome and metabolism analysis was employed to investigate the low-temperature responses of two sweet potato cultivars, namely, the low-temperature-resistant cultivar “X33” and the low-temperature-sensitive cultivar “W7”. Results: The differentially expressed metabolites (DEMs) of X33 at different time stages clustered in five profiles, while they clustered in four profiles of W7 with significant differences. Differentially expressed genes (DEGs) in X33 and W7 at different time points clustered in five profiles. More DEGs exhibited continuous or persistent positive responses to low-temperature stress in X33 than in W7. There were 1918 continuously upregulated genes and 6410 persistent upregulated genes in X33, whereas 1781 and 5804 were found in W7, respectively. Core genes involved in Ca2+ signaling, MAPK cascades, the reactive oxygen species (ROS) signaling pathway, and transcription factor families (including bHLH, NAC, and WRKY) may play significant roles in response to low temperature in sweet potato. Thirty-one common differentially expressed metabolites (DEMs) were identified in the two cultivars in response to low temperature. The KEGG analysis of these common DEMs mainly belonged to isoquinoline alkaloid biosynthesis, phosphonate and phosphinate metabolism, flavonoid biosynthesis, cysteine and methionine metabolism, glycine, serine, and threonine metabolism, ABC transporters, and glycerophospholipid metabolism. Five DEMs with identified Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were selected for correlation analysis. KEGG enrichment analysis showed that the carbohydrate metabolism, phenylpropanoid metabolism, and glutathione metabolism pathways were significantly enriched and played vital roles in low-temperature resistance in sweet potato. Conclusions: These findings contribute to a deeper understanding of the molecular mechanisms underlying plant cold tolerance and offer targets for molecular breeding efforts to enhance low-temperature resistance. Full article
(This article belongs to the Special Issue Genetic and Functional Genomics Insights into the Genetic Improvement of Stress Resistance in Economic Crops)
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