Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
9.0
4.9
Journals
IJMS
Special Issues
Advances in Plant Genomics and Genetics: 3rd Edition
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Advances in Plant Genomics and Genetics: 3rd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 October 2025) | Viewed by 4092

Special Issue Editor

Dr. Hengling Wei

E-Mail Website
Guest Editor
1. State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
2. Henan International Joint Laboratory of Cotton Biology, Anyang 455000, China
Interests: cotton breeding; cotton functional gene identification
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Salt stress, drought stress, high temperatures, and low temperatures are major abiotic stressors that can severely limit plant growth, distribution, and crop yield. The study of plant genetics has major economic impacts: many staple crops are genetically modified to increase yields and provide resistance to stress. Transcription factors have the ability to respond to changes in the external environment by regulating their own expression and employing the spatiotemporal specificity of gene expression to activate target genes. Next-generation sequencing (NGS) technologies accelerate crop improvement methods by enabling the rapid and cost-effective sequencing of entire genomes and transcriptomes.

This Special Issue will address a selection of recent research topics and current review articles in the field of plant genomics and genetics. Bioinformatics papers, up-to-date review articles, and commentaries are also welcome. This Special Issue is supervised by Dr. Hengling Wei and assisted by our Guest Editor's Assistant Editor, Dr. Shoujiang Sun (China Agricultural University, Beijing, China).

Dr. Hengling Wei
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • plant genomics
  • plant genetics
  • abiotic stresses
  • salt resistance
  • genome
  • next-generation sequencing

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

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

Related Special Issues

Published Papers (6 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

23 pages, 12113 KB  
Article
Genome-Wide Identification of DlGRAS Family and Functional Analysis of DlGRAS10/22 Reveal Their Potential Roles in Embryogenesis and Hormones Responses in Dimocarpus longan
by Guanghui Zhao, Mengjie Tang, Wanlong Wu, Wei Gao, Jinbing Xie, Jialing Wang, Zhongxiong Lai, Yuling Lin and Yukun Chen
Int. J. Mol. Sci. 2025, 26(21), 10323; https://doi.org/10.3390/ijms262110323 - 23 Oct 2025
Abstract
GRAS family plays a critical role in plant growth and stress responses. In this study, we identified 47 GRAS (DlGRAS) genes in the longan genome and conducted a comprehensive bioinformatics analysis of these genes. RNA-seq analysis revealed that the expression of [...] Read more.
GRAS family plays a critical role in plant growth and stress responses. In this study, we identified 47 GRAS (DlGRAS) genes in the longan genome and conducted a comprehensive bioinformatics analysis of these genes. RNA-seq analysis revealed that the expression of these DlGRAS genes differed during early SE and across various longan tissues. The quantitative real-time PCR (qRT-PCR) results indicated that the DlGRAS genes exhibited differential expression during the early SE of longan, with most of them showing high expression at the globular embryo (GE) stage. Under GA3 treatment, the transcript levels of DlGRAS12/15 decreased significantly. In contrast, exogenous ABA promoted the expression of DlGRAS6/10/23, indicating that DlGRAS genes are responsive to hormones. Compared with CaMV35S-driven GUS expression, the promoters of DlGRAS10/22 increased GUS expression, GA3 and ABA treatments enhanced promoter activity. DlGRAS10/22 were located in the nucleus. Overexpression of DlGRAS10/22 in longan SE significantly promoted the transcription levels of SE-related genes, including DlGID1, DlGA20ox2, DlLEC1, DlFUS3, DlABI3 and DlLEC2. Therefore, DlGRAS may be involved in the early morphogenesis of longan SE through the hormone signaling pathway. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 3rd Edition)
►▼ Show Figures

Figure 1

15 pages, 5630 KB  
Article
Genome-Wide Characterization of Kiwifruit Invertase Gene Family Reveals Roles of AcCWINV4 in Sugar Accumulation and Cold Tolerance
by Aoning Zhang, Xiaomeng Yang, Deshuai Liu, Zhexing Luo, Zhihao Zhang, Junwei Huo, Deguo Han, Yan Zhang and Lihua Zhang
Int. J. Mol. Sci. 2025, 26(20), 10089; https://doi.org/10.3390/ijms262010089 - 16 Oct 2025
Viewed by 195
Abstract
Invertase, a core catalyst in sugar metabolism, irreversibly hydrolyzes sucrose into hexoses, establishing the fundamental biochemical pathway for carbon allocation in plants and playing pivotal roles in plant growth development, fruit quality regulation, and stress response. In the present study, we identified a [...] Read more.
Invertase, a core catalyst in sugar metabolism, irreversibly hydrolyzes sucrose into hexoses, establishing the fundamental biochemical pathway for carbon allocation in plants and playing pivotal roles in plant growth development, fruit quality regulation, and stress response. In the present study, we identified a total of 25 invertase genes from the kiwifruit (Actinidia chinensis cv Hongyang) genome and systematically analyzed the physicochemical properties, chromosomal localization, genomic features, and gene evolution patterns of the AcINV family. The evaluation of selection pressure indices robustly demonstrated that the INV family underwent purification selection during domestication. Furthermore, based on the correlation between gene expression levels during the post-harvest ripening stage of kiwifruit and soluble sugar content, we identified the potential gene AcCWINV4 as being associated with sugar accumulation. Furthermore, virus-induced gene silencing (VIGS) of AcCWINV4 confirmed its functional role in fruit sugar accumulation and plant response to cold stress. This study provides critical theoretical support for breeding cold-tolerant and high-quality kiwifruit varieties using molecular biological methods. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 3rd Edition)
►▼ Show Figures

Figure 1

18 pages, 15081 KB  
Article
Leveraging GWAS-Identified Markers in Combination with Bayesian and Machine Learning Models to Improve Genomic Selection in Soybean
by Yongguo Xue, Xiaofei Tang, Xiaoyue Zhu, Ruixin Zhang, Yubo Yao, Dan Cao, Wenjin He, Qi Liu, Xiaoyan Luan, Yongjun Shu and Xinlei Liu
Int. J. Mol. Sci. 2025, 26(19), 9586; https://doi.org/10.3390/ijms26199586 - 1 Oct 2025
Viewed by 448
Abstract
Soybean (Glycine max (L.) Merr.) is one of the most important global economic crops, extensively utilized in the production of food, animal feed, and industrial raw materials. As the demand for soybeans continues to rise, improving both the yield and quality of [...] Read more.
Soybean (Glycine max (L.) Merr.) is one of the most important global economic crops, extensively utilized in the production of food, animal feed, and industrial raw materials. As the demand for soybeans continues to rise, improving both the yield and quality of soybeans has become a central focus of agricultural research. To accelerate the genetic improvement of soybean, genome selection (GS) and genome-wide association studies (GWAS) have emerged as effective tools and have been widely applied in various crops. In this study, we conducted GWAS and GS model evaluations across five soybean phenotypes (Glycitin content, Oil, Pod, Total isoflavone content, and Total tocopherol content) to explore the effectiveness of different GWAS methods and GS models in soybean genetic improvement. We applied several GWAS methods, including fastGWA, BOLT-LMM, FarmCPU, GLM, and MLM, and compared the predictive performance of various GS models, such as BayesA, BayesB, BayesC, BL, BRR, SVR_poly, SVR_linear, Ridge, PLS_Regression, and Linear_Regression. Our results indicate that markers selected through GWAS, when used in GS, achieved a prediction accuracy of 0.94 at a 5 K density. Furthermore, Bayesian models proved to be more stable than machine learning models. Overall, this study offers new insights into soybean genome selection and provides a scientific foundation for future soybean breeding strategies. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 3rd Edition)
►▼ Show Figures

Figure 1

19 pages, 13575 KB  
Article
Genetic Diversity Evaluation and Population Structure Analysis of the Genus Paphiopedilum in Guangxi: Promoting the Selection and Breeding of New Species
by Jianmin Tang, Kanghua Xian, Jiang Su, Li Lu, Xinru Cai, Yishan Yang, Bo Pan, Tao Ding, Xianliang Zhu, Shengfeng Chai, Rong Zou and Xiao Wei
Int. J. Mol. Sci. 2025, 26(17), 8543; https://doi.org/10.3390/ijms26178543 - 2 Sep 2025
Viewed by 547
Abstract
The genus Paphiopedilum (Orchidaceae) has high ornamental value due to its long flowering period, brilliant flower color, and peculiar floral morphology. Guangxi is the center of ecological diversity of Paphiopedilum, and therefore it is urgent to conduct rescue studies on the genetic [...] Read more.
The genus Paphiopedilum (Orchidaceae) has high ornamental value due to its long flowering period, brilliant flower color, and peculiar floral morphology. Guangxi is the center of ecological diversity of Paphiopedilum, and therefore it is urgent to conduct rescue studies on the genetic resources and genetic structure of this genus in Guangxi. In this study, the genetic diversity of 39 populations from eight Paphiopedilum species in Guangxi was analyzed using ten selected EST-SSR primer pairs and fluorescent PCR amplification. The results show that genetic diversity varied among species, with large differences in expected heterozygosity (He). The highest genetic diversity was observed in P. barbigerum (I = 0.923; He = 0.480), while P. dianthum (I = 0.179; He = 0.098) showed the lowest diversity. From the genus perspective, molecular variance analysis (AMOVA) revealed that 57% of the genetic variation occurred among populations and 43% within populations, with inter-population variation being the main source of genetic variation. From a species perspective, genetic differentiation varied, with inter-individual differentiation ranging from 79% to 95%. The percentage of molecular variance indicated that genetic variation mainly occurred among individuals, which was the main source of total variation. According to the principle of maximum likelihood, the optimal K value was determined to be 6, and 760 Paphiopedilum samples were divided into six subgroups. The results of this study not only identify priority populations for conservation and establish a germplasm repository to preserve existing resources, but also provide references for research on asexual reproduction, seed propagation, and hybrid breeding of Paphiopedilum, thereby promoting the conservation and sustainable utilization of Paphiopedilum germplasm resources. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 3rd Edition)
►▼ Show Figures

Figure 1

23 pages, 1565 KB  
Article
Proteomic Analysis and Expression of Selected Genes During the Early Somatic Embryogenesis of Jatropha curcas L.
by Anamarel Edzná Medina-Hernández, Ileana Vera-Reyes, Emmanuel Ríos-Castro, Juan José Torres-Ruiz, Teresa Ponce-Noyola, Gabriela Trejo-Tapia, Adriana Garay-Arroyo, Josefina Barrera-Cortés and Ana C. Ramos-Valdivia
Int. J. Mol. Sci. 2025, 26(13), 6384; https://doi.org/10.3390/ijms26136384 - 2 Jul 2025
Viewed by 1644
Abstract
Jatropha curcas L. is a shrub of the Euphorbiaceae family with non-toxic varieties found in Mexico that holds significant potential for biofuel production and other industrial applications. However, its limited in vitro regenerative capacity is a barrier to the development of productive species. [...] Read more.
Jatropha curcas L. is a shrub of the Euphorbiaceae family with non-toxic varieties found in Mexico that holds significant potential for biofuel production and other industrial applications. However, its limited in vitro regenerative capacity is a barrier to the development of productive species. Somatic embryogenesis (SE) offers a strategy to establish a regeneration system to overcome these challenges and enable genetic improvement. In this work, proteomic and gene expression analyses were utilized to identify key factors involved in SE induction in a non-toxic variety of J. curcas. Two-dimensional electrophoresis (2-DE) in combination with mass spectrometry was used to compare the proteomes of pre-globular and globular somatic embryos. RT-qPCR was used for gene expression analysis of the BBM, AGL15, SERK, IAA26 and eIF3f genes. The globular stage showed enrichment in the pathways related to carbohydrate and energy metabolism, protein folding, and stress response. In addition, the gene expression analysis of selected genes revealed a significantly elevated expression of BBM, AGL15, and IAA26 in globular embryos compared to pre-globular embryos. In contrast, SERK expression was low, and eIF3f expression remained unchanged between stages. These expression patterns may contribute to developmental arrest at the globular stage. These findings provide new insights into the molecular mechanisms regulating early SE in J. curcas and offer potential strategies for improving its propagation and industrial applications. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 3rd Edition)
►▼ Show Figures

Figure 1

16 pages, 2634 KB  
Article
QTL Mapping and Developing KASP Markers for High-Temperature Adult-Plant Resistance to Stripe Rust in Argentinian Spring Wheat William Som (PI 184597)
by Arjun Upadhaya, Meinan Wang, Chao Xiang, Nosheen Fatima, Sheri Rynearson, Travis Ruff, Deven R. See, Michael Pumphrey and Xianming Chen
Int. J. Mol. Sci. 2025, 26(11), 5072; https://doi.org/10.3390/ijms26115072 - 24 May 2025
Viewed by 900
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive disease of wheat worldwide. William Som (WS), an Argentinian spring wheat landrace, has consistently exhibited high-level resistance to stripe rust for over 20 years in our field evaluations [...] Read more.
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive disease of wheat worldwide. William Som (WS), an Argentinian spring wheat landrace, has consistently exhibited high-level resistance to stripe rust for over 20 years in our field evaluations in Washington state, USA. A previous study showed high-temperature adult-plant (HTAP) resistance in WS. To map the HTAP resistance quantitative trait loci (QTL) in WS, 114 F5-8 recombinant inbred lines (RILs) from the cross AvS/WS were evaluated for their stripe rust response in seven field environments in Washington. The RILs and parents were genotyped with the Infinium 90K SNP chip. Four stable QTL, QYrWS.wgp-1BL on chromosome 1B (669–682 Mb), QyrWS.wgp-2AL on 2A (611–684 Mb), QyrWS.wgp-3AS on 3A (9–13 Mb), and QyrWS.wgp-3BL on 3B (476–535 Mb), were identified, and they explained 10.0–19.0%, 10.2–16.7%, 7.0–15.9%, and 12.0–27.8% of the phenotypic variation, respectively. The resistance in WS was found to be due to additive interactions of the four QTL. For each QTL, two Kompetitive allele-specific PCR (KASP) markers were developed, and these markers should facilitate the introgression of the HTAP resistance QTL into new wheat cultivars. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 3rd Edition)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-6
Back to TopTop