International Journal of Molecular Sciences

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17 pages, 4650 KiB

Open AccessArticle

Impact of Allele-Specific Expression on Ripening and Quality Characteristics of ABB Banana Fruit

by Fang Fang, Bin Liu, Qiuzi Chen, Lisi Xiao, Zhuozi Deng, Zhaoqi Zhang, Xuemei Huang and Xuequn Pang

Int. J. Mol. Sci. 2025, 26(9), 4090; https://doi.org/10.3390/ijms26094090 - 25 Apr 2025

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Abstract

Allele-specific expression (ASE) is a phenomenon in which the expression level of an allele from both parents is inconsistent, which is considered to play a key role in the differences between hybrids. As a typical climacteric fruit, banana undergoes a ripening process that [...] Read more.

Allele-specific expression (ASE) is a phenomenon in which the expression level of an allele from both parents is inconsistent, which is considered to play a key role in the differences between hybrids. As a typical climacteric fruit, banana undergoes a ripening process that affects the quality of the fruit. BaXi (Musa, AAA group) and Fen Jiao (Musa, ABB group) banana fruits show different traits during postharvest ripening, and their high-quality reference genomic sequences have been published. In this work, we analyzed differentially expressed genes (DEGs) in these two banana cultivars based on the transcriptomes during the postharvest stages. Additionally, the imbalance expression of alleles of DEGs in Fen Jiao banana fruit was analyzed, revealing that 27.2% (3 d) and 22.2% (6 d) of the 15,415 DEGs showed ASE. Then, the ASE profiles related to the post-ripening of banana fruit were built, focusing on ripening-related pathways, such as ethylene biosynthesis (62.5–83.3%), starch degradation (0–75%) and cell wall material degradation (34.6–90.9%). The ASE genes involved in ripening were more frequent than those associated with general gene expression. In addition, the candidate key genes of ASE alleles involved in ethylene synthesis and starch degradation were identified, including the alleles of MaACS7/MbACS7, MaACO2/MbACO6, MaACO3/MbACO7, MaACO8/MbACO13 and MaACO6/MbACO17 involved in ethylene biosynthesis, and those of MaAMY1/MbAMY3, MaBMY1/MbBMY2, MaBMY7/MbBMY8 and MaDPE2/MbDPE2 involved in starch degradation. The expression of the B genes of these key enzyme genes (ACS/ACO/AMY) is more active than that of the A genes in Fen Jiao bananas. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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18 pages, 6599 KiB

Open AccessArticle

Genome-Wide Identification of the Dof Gene Family and Functional Analysis of PeSCAP1 in Regulating Guard Cell Maturation in Populus euphratica

by Yongqiang Chen, Yang Yuan, Mingyu Jia, Huiyun Yang, Peipei Jiao and Huimin Guo

Int. J. Mol. Sci. 2025, 26(8), 3798; https://doi.org/10.3390/ijms26083798 - 17 Apr 2025

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Abstract

DNA-binding with one finger (Dof) transcription factors plays critical roles in regulating plant growth and development, as well as modulating responses to biotic and abiotic stresses. While the biological characteristics of the Dof family have been explored across various species, their functions in [...] Read more.

DNA-binding with one finger (Dof) transcription factors plays critical roles in regulating plant growth and development, as well as modulating responses to biotic and abiotic stresses. While the biological characteristics of the Dof family have been explored across various species, their functions in Populus euphratica remain largely uncharacterized. In this study, we identified 43 PeDof family genes through a genome-wide approach, revealing a total of 10 conserved motifs across all family members. Predictions of cis-acting elements indicated that Dof genes are involved in light signaling, hormone signaling, and stress responses. Phylogenetic analysis classified the 43 Dof genes of P. euphratica into six distinct groups, with genes within the same group exhibiting relatively conserved structures. Expression pattern analyses demonstrated significant regulation of PeDof genes by drought stress, with their expression also being influenced by environmental conditions during seed germination. Furthermore, we identified the Dof gene PeSCAP1, which plays a conserved role in regulating guard cell maturation, underscoring the importance of stomatal morphology and function in leaf water retention. This study enhances our understanding of the role of Dofs in abiotic stress responses and provides valuable insights into their function in Populus euphratica. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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34 pages, 5285 KiB

Open AccessArticle

GBLUP Outperforms Quantile Mapping and Outlier Detection for Enhanced Genomic Prediction

by Osval Antonio Montesinos-López, José Crossa, Paolo Vitale, Guillermo Gerard, Leonardo Crespo-Herrera, Susanne Dreisigacker, Carolina Saint Pierre, Luis G. Posadas, Afolabi Agbona, Raymundo Buenrostro-Mariscal, Abelardo Montesinos-López and Aakash Chawade

Int. J. Mol. Sci. 2025, 26(8), 3620; https://doi.org/10.3390/ijms26083620 - 11 Apr 2025

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Abstract

Genomic selection (GS) accelerates plant breeding by predicting complex traits using genomic data. This study compares genomic best linear unbiased prediction (GBLUP), quantile mapping (QM)—an adjustment to GBLUP predictions—and four outlier detection methods. Using 14 real datasets, predictive accuracy was evaluated with Pearson’s [...] Read more.

Genomic selection (GS) accelerates plant breeding by predicting complex traits using genomic data. This study compares genomic best linear unbiased prediction (GBLUP), quantile mapping (QM)—an adjustment to GBLUP predictions—and four outlier detection methods. Using 14 real datasets, predictive accuracy was evaluated with Pearson’s correlation (COR) and normalized root mean square error (NRMSE). GBLUP consistently outperformed all other methods, achieving an average COR of 0.65 and an NRMSE reduction of up to 10% compared to alternative approaches. The proportion of detected outliers was low (<7%), and their removal had minimal impact on GBLUP’s predictive performance. QM provided slight improvements in datasets with skewed distributions but showed no significant advantage in well-distributed data. These findings confirm GBLUP’s robustness and reliability, suggesting limited utility for QM when data deviations are minimal. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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18 pages, 10631 KiB

Open AccessArticle

Integrated Transcriptomic and Metabolomic Analysis Reveals Tissue-Specific Flavonoid Biosynthesis and MYB-Mediated Regulation of UGT71A1 in Panax quinquefolius

by Yumeng Wang, Jiaxin Zhang, Ping Wang, Yongkang Li, Yihan Wang, Yan Yan, Junwen Chi, Jiankang Chen, Junmei Lian, Xiangmin Piao, Xiujuan Lei, Ying Xiao, Jeremy Murray, Micheal K. Deyholos, Yingping Wang, Peng Di and Jian Zhang

Int. J. Mol. Sci. 2025, 26(6), 2669; https://doi.org/10.3390/ijms26062669 - 16 Mar 2025

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Abstract

Panax quinquefolius is a globally valued medicinal plant rich in bioactive flavonoids, yet the molecular mechanisms underlying their biosynthesis remain poorly understood. In this study, we integrated transcriptomic and metabolomic analyses to investigate tissue-specific flavonoid accumulation and regulatory networks in roots, leaves, and [...] Read more.

Panax quinquefolius is a globally valued medicinal plant rich in bioactive flavonoids, yet the molecular mechanisms underlying their biosynthesis remain poorly understood. In this study, we integrated transcriptomic and metabolomic analyses to investigate tissue-specific flavonoid accumulation and regulatory networks in roots, leaves, and flowers. Metabolomic profiling identified 141 flavonoid metabolites, with flavones, flavonols, and C-glycosylflavones predominantly enriched in aerial tissues (leaves and flowers), while specific glycosides like tricin 7-O-acetylglucoside showed root-specific accumulation. Transcriptome sequencing revealed 15,551–18,946 DEGs across tissues, and the reliability of the transcriptomic data was validated by qRT-PCR. KEGG and GO annotation analyses suggested that these DEGs may play a crucial role in the biosynthesis and metabolism of secondary metabolites. From the DEGs, UGTs and MYB TFs were identified and subjected to correlation analysis. Functional validation through in vitro enzymatic assays confirmed that PqUGT71A1 catalyzes apigenin and naringenin glycosylation at the 7-OH position. Additionally, subcellular localization and yeast one-hybrid assays demonstrated that PqMYB7 and PqMYB13 interact with the PqUGT71A1 promoter and activate its expression.. This study unveils the spatial dynamics of flavonoid metabolism in P. quinquefolius and establishes a MYB-UGT regulatory axis, providing critical insights for metabolic engineering and bioactive compound optimization in medicinal plants. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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17 pages, 4798 KiB

Open AccessArticle

Identification of the MADS-Box Gene Family and the Key Role of BrAGL27 in the Regulation of Flowering in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

by Xinyu Gao, Yang Li, Yun Dai, Xiangqianchen Li, Can Huang, Shifan Zhang, Fei Li, Hui Zhang, Guoliang Li, Rifei Sun, Huanzhong Song, Li Zhang, Zhendong Chen and Shujiang Zhang

Int. J. Mol. Sci. 2025, 26(6), 2635; https://doi.org/10.3390/ijms26062635 - 14 Mar 2025

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Abstract

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a key vegetable crop in Asia, but its commercial value is often reduced by premature flowering triggered by vernalization. The molecular mechanisms behind this process are not fully understood. MADS-box genes, as crucial [...] Read more.

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a key vegetable crop in Asia, but its commercial value is often reduced by premature flowering triggered by vernalization. The molecular mechanisms behind this process are not fully understood. MADS-box genes, as crucial transcriptional regulators, play vital roles in plant development, including flowering. In this study, 102 MADS-box genes were identified in Chinese cabbage through bioinformatics analyses, covering phylogeny, chromosomal localization, and gene structure. Real-time quantitative PCR and RNA-seq data analysis revealed that the expression level of AGL27 declined as vernalization time increased. To determine BrAGL27′s functions, we obtained BrAGL27-overexpressed (OE) Arabidopsis thaliana lines that showed significantly later flowering compared with the wild type (WT). The expression levels of flowering suppressor genes AtFLC and AtTEM1 were significantly high-regulated in the BrAGL27-OE lines compared to WT plants, while the expression levels of the floral genes AtSPL15, AtSOC1, AtFT, and AtAP3 were significantly lower in the BrAGL27-overexpressed lines than in the wild type. These findings enhance understanding of MADS-box genes in vernalization and flowering regulation, offering a basis for further research on bolting resistance and flowering control in Chinese cabbage. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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20 pages, 8083 KiB

Open AccessArticle

Determining the Role of OsAGP6P in Anther Development Within the Arabinogalactan Peptide Family of Rice (Oryza sativa)

by Shuai Shao, Yuxin Wu, Lijie Zhang, Zhiyuan Zhao, Xianlong Li, Mingchong Yang, Haiyu Zhou, Songguo Wu and Lingqiang Wang

Int. J. Mol. Sci. 2025, 26(6), 2616; https://doi.org/10.3390/ijms26062616 - 14 Mar 2025

Viewed by 403

Abstract

Arabinogalactan proteins (AGPs) are complex proteoglycans present in plant cell walls across the kingdom. They play crucial roles in biological functions throughout the plant life cycle. In this study, we identified 43 gene members of the AG peptide (an AGP subfamily) within the [...] Read more.

Arabinogalactan proteins (AGPs) are complex proteoglycans present in plant cell walls across the kingdom. They play crucial roles in biological functions throughout the plant life cycle. In this study, we identified 43 gene members of the AG peptide (an AGP subfamily) within the rice genome, detailing their structure, protein-conserved domains, and motif compositions for the first time. We also examined the expression patterns of these genes across 18 tissues and organs, especially the different parts of the flower (anthers, pollen, pistil, sperm cells, and egg cells). Interestingly, the expression of some AG peptides is mainly present in the pollen grain. Transcription data and GUS staining confirmed that OsAGP6P—a member of the AG peptide gene family—is expressed in the stamen during pollen development stages 11–14, which are critical for maturation as microspores form after meiosis of pollen mother cells. It became noticeable from stage 11, when exine formation occurred—specifically at stage 12, when the intine began to develop. The overexpression of this gene in rice decreased the seed-setting rate (from 91.5% to 30.5%) and plant height (by 21.9%) but increased the tillering number (by 34.1%). These results indicate that AGP6P contributes to the development and fertility of pollen, making it a valuable gene target for future genetic manipulation of plant sterility through gene overexpression or editing. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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24 pages, 8784 KiB

Open AccessArticle

Genome-Wide Identification of GLK Family Genes in Phoebe bournei and Their Transcriptional Analysis Under Abiotic Stresses

by Yiran Lian, Liang Peng, Xinying Shi, Qiumian Zheng, Dunjin Fan, Zhiyi Feng, Xiaomin Liu, Huanhuan Ma, Shijiang Cao and Weiyin Chang

Int. J. Mol. Sci. 2025, 26(6), 2387; https://doi.org/10.3390/ijms26062387 - 7 Mar 2025

Viewed by 418

Abstract

GOLDEN2-LIKE (GLK) transcription factors are crucial regulators of chloroplast development and stress responses in plants. In this study, we investigated the GLK gene family in Phoebe bournei (Hemsl.) Yen C. Yang, a near-threatened species important for forestry and wood utilization in China. We [...] Read more.

GOLDEN2-LIKE (GLK) transcription factors are crucial regulators of chloroplast development and stress responses in plants. In this study, we investigated the GLK gene family in Phoebe bournei (Hemsl.) Yen C. Yang, a near-threatened species important for forestry and wood utilization in China. We identified 61 PbGLK genes which were classified into seven subfamilies. Our analyses of their phylogenetic relationships, gene structures, and chromosomal distribution revealed diverse characteristics. Expression profiling under different tissues and abiotic stresses showed that PbGLK25 and PbGLK30 were particularly responsive to drought, heat, light, and shade stresses, with significant upregulation. These findings highlight the potential role of PbGLK genes in stress adaptation and provide insights for the genetic improvement of P. bournei. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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21 pages, 8205 KiB

Open AccessArticle

Exploring the Roles of the Plant AT-Rich Sequence and Zinc-Binding (PLATZ) Gene Family in Tomato (Solanum lycopersicum L.) Under Abiotic Stresses

by Bei Fan, Min Ren, Guoliang Chen, Xue Zhou, Guoting Cheng, Jinyu Yang and Huiru Sun

Int. J. Mol. Sci. 2025, 26(4), 1682; https://doi.org/10.3390/ijms26041682 - 16 Feb 2025

Viewed by 469

Abstract

PLATZ transcription factors represent a novel class of zinc finger proteins unique to plants and play critical roles in plant growth and stress responses. This study performs a bioinformatic analysis on the PLATZ transcription factor family in tomato. In the tomato genome, 20 [...] Read more.

PLATZ transcription factors represent a novel class of zinc finger proteins unique to plants and play critical roles in plant growth and stress responses. This study performs a bioinformatic analysis on the PLATZ transcription factor family in tomato. In the tomato genome, 20 PLATZ transcription factors were identified, distributed across nine chromosomes, including two tandem duplication clusters and two segmental duplication events. Phylogenetic analysis classified tomato PLATZ family members into five subgroups, with consistent gene structures and motif distributions within the same subfamily. The stress-responsive and hormone signaling elements were widely distributed in the promoters of SlPLATZs. The qRT-PCR results showed that most tested SlPLATZs were highly expressed in flowers and significantly expressed under different abiotic stresses (PEG, low temperature, and salt treatments) and hormone treatments (ABA and SA). In addition, we determined that SlPLATZ13/17/18/19 showed transcriptional inhibitory activities via yeast and dual-luciferase reporter assays. The interactions between SlPLATZ17, SlDREB2, and SlDREB31 were preliminarily confirmed via yeast two-hybrid assays. Overall, this study provides a valuable theoretical foundation for functional function research on PLATZ transcription factors, particularly in response to abiotic stresses. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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15 pages, 5152 KiB

Open AccessArticle

Genome-Wide Analysis of the Aspartate Aminotransferase Family in Brassica rapa and the Role of BraASP1 in Response to Nitrogen Starvation

by Yan Liu, Zihan Gao, Chuang Liang, Yuting Wei, Yuge Li, Yan Zhang and Yaowei Zhang

Int. J. Mol. Sci. 2025, 26(4), 1586; https://doi.org/10.3390/ijms26041586 - 13 Feb 2025

Viewed by 582

Abstract

Nitrogen (N) is the most important fertilizer for increasing crop production, as it is absorbed by various N transporters and metabolized by a series of enzymes. Aspartate aminotransferase (ASP) facilitates the conversion of Glu to Asp for N storage. Chinese cabbage is a [...] Read more.

Nitrogen (N) is the most important fertilizer for increasing crop production, as it is absorbed by various N transporters and metabolized by a series of enzymes. Aspartate aminotransferase (ASP) facilitates the conversion of Glu to Asp for N storage. Chinese cabbage is a typical leafy vegetable that requires a large amount of N for growth. To investigate the functions of BraASPs, 10 members of the ASP gene family in Brassica rapa (B. rapa) were identified. Phylogenetic analysis and collinearity comparisons of ASP members among B. rapa, Arabidopsis thaliana (A. thaliana), Oryza sativa (O. sativa), Brassica napus (B. napus), and Brassica oleracea (B. oleracea) were conducted to examine evolutionary associations and genome duplication events across species. Multiple cis-acting elements associated with stress responses were identified in the promoters of BraASPs, suggesting their diverse roles. Members of BraASPs were expressed in roots, stems, flowers, siliques, and leaves, with the highest expression in leaves. Their expression levels increased rapidly at 3 h under low N conditions, peaked at 6 h, and returned to low levels at 24 h. Based on transcriptomic data, BraASP1b was identified as a candidate gene in B. rapa under low N stress, localized in the nucleus and cytoplasm. Overexpression of BraASP1b in A. thaliana resulted in a higher biomass than Col-0 under low N conditions. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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16 pages, 10866 KiB

Open AccessArticle

Transcriptome and MicroRNA Analysis of Juglans regia in Response to Low-Temperature Stress

by Haochang Zhao, Xia Luo, Caihua Guo, Zhongrong Zhang, Kai Ma, Jianxin Niu and Shaowen Quan

Int. J. Mol. Sci. 2025, 26(4), 1401; https://doi.org/10.3390/ijms26041401 - 7 Feb 2025

Viewed by 836

Abstract

Walnuts are among the globally significant woody food and oil tree species. At high latitudes, they frequently experience late-frost damage, inducing low-temperature stress, which significantly affects walnut seedlings. The aim of this study was to investigate the physiological and biochemical alterations in walnut [...] Read more.

Walnuts are among the globally significant woody food and oil tree species. At high latitudes, they frequently experience late-frost damage, inducing low-temperature stress, which significantly affects walnut seedlings. The aim of this study was to investigate the physiological and biochemical alterations in walnut seedlings under low-temperature (LT) stress along with its underlying molecular mechanisms. Physiological indices were determined, and the transcriptome and miRNA were sequenced by sampling leaves (0 h, 6 h, 12 h, 24 h, and 48 h) of two-month-old live seedlings of walnuts treated with a low temperature of 4 °C. The results indicated that LT stress induced an increase in electrical conductivity and malondialdehyde content while simultaneously causing a reduction in Fv/Fm. From the transcriptome comparison between the control and treated groups, a total of 12,566 differentially expressed genes (DEGs) were identified, consisting of 6829 up-regulated and 5737 down-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs were primarily enriched in polysaccharide metabolic processes, responses to abscisic acid and phenylpropanoid biosynthesis pathways. Furthermore, the miRNA database identified 1052 miRNAs in response to low-temperature stress in walnuts; these miRNAs were found to target 7043 predicted genes. Through the integration and analysis of transcriptome and miRNA data, 244 differential DEGs were identified. Following GO and KEGG enrichment analyses of the differential target genes, we identified that these genes primarily regulate pathways involved in starch and sucrose metabolism, glyoxylate and dicarboxylate metabolism, and glycerophospholipid biosynthesis, as well as phenylalanine, tyrosine, and tryptophan biosynthesis, in walnut leaves under LT stress. Additionally, we conducted an in-depth analysis of the associations between differentially expressed genes (DEGs) and differentially expressed microRNAs (DEMs) within the starch and sucrose metabolism pathway. Real-time fluorescent quantitative PCR (qRT-PCR) validation of the expression patterns of a subset of differential genes confirmed the accuracy of the transcriptome data. This study unveils the potential molecular mechanisms underlying walnut’s response to low-temperature stress, providing valuable genetic resources for future research on the cold tolerance mechanisms of walnut in response to late-frost damage. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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16 pages, 1446 KiB

Open AccessArticle

Editing the RR-TZF Gene Subfamily in Rice Uncovers Potential Risks of CRISPR/Cas9 for Targeted Genetic Modification

by Shufen Zhou, Dagang Tian, Huaqing Liu, Xiaozhuan Lu, Di Zhang, Rui Chen, Shaohua Yang, Weiren Wu and Feng Wang

Int. J. Mol. Sci. 2025, 26(3), 1354; https://doi.org/10.3390/ijms26031354 - 5 Feb 2025

Viewed by 928

Abstract

The CRISPR/Cas9 system offers a powerful tool for gene editing to enhance rice productivity. In this study, we successfully edited eight RR-TZF genes in japonica rice Nipponbare using CRISPR-Cas9 technology, achieving a high editing efficiency of 73.8%. Sequencing revealed predominantly short insertions or [...] Read more.

The CRISPR/Cas9 system offers a powerful tool for gene editing to enhance rice productivity. In this study, we successfully edited eight RR-TZF genes in japonica rice Nipponbare using CRISPR-Cas9 technology, achieving a high editing efficiency of 73.8%. Sequencing revealed predominantly short insertions or deletions near the PAM sequence, along with multi-base deletions often flanked by identical bases. Off-target analysis identified 5 out of 31 predicted sites, suggesting the potential for off-target effects, which can be mitigated by designing gRNAs with more than three base mismatches. Notably, new mutations emerged in the progeny of several gene-edited mutants, indicating inheritable genetic mutagenicity. Phenotypic analysis of homozygous mutants revealed varied agronomic traits, even within the same gene, highlighting the complexity of gene-editing outcomes. These findings underscore the importance of backcrossing to minimize off-target and inheritable mutagenicity effects, ensuring more accurate trait evaluation. This study offers insights into CRISPR/Cas9 mechanisms and uncertain factors and may inform future strategies for rice improvement, prompting further research into CRISPR/Cas9’s precision and long-term impacts. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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19 pages, 4240 KiB

Open AccessArticle

Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes in Cannabis sativa Using Seven De Novo Genome Assemblies

by George M. Stack, Michael A. Quade, Dustin G. Wilkerson, Luis A. Monserrate, Philip C. Bentz, Sarah B. Carey, Jane Grimwood, Jacob A. Toth, Seth Crawford, Alex Harkess and Lawrence B. Smart

Int. J. Mol. Sci. 2025, 26(3), 1165; https://doi.org/10.3390/ijms26031165 - 29 Jan 2025

Viewed by 1616

Abstract

Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes [...] Read more.

Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We performed a k-mer-based pangenome analysis to contextualize these assemblies within over 200 existing assemblies. This allowed us to identify unique haplotypes and genomic diversity among Cannabis sativa genotypes. We leveraged linkage maps constructed from F₂ progeny of two of the assembled genotypes to characterize the recombination rate across the genome showing strong periphery-biased recombination. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus Early1 to several of the new assemblies to evaluate the impact of reference bias on the mapping results and narrow the locus to a smaller region of the chromosome. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for C. sativa to accelerate future research efforts. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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20 pages, 4091 KiB

Open AccessArticle

Multi-Omics Analysis Decodes Biosynthesis of Specialized Metabolites Constituting the Therapeutic Terrains of Magnolia obovata

by Megha Rai, Amit Rai, Towa Yokosaka, Tetsuya Mori, Ryo Nakabayashi, Michimi Nakamura, Hideyuki Suzuki, Kazuki Saito and Mami Yamazaki

Int. J. Mol. Sci. 2025, 26(3), 1068; https://doi.org/10.3390/ijms26031068 - 26 Jan 2025

Viewed by 821

Abstract

Magnolia obovata is renowned for its unique bioactive constituents with medicinal properties traditionally used to treat digestive disorders, anxiety, and respiratory conditions. This study aimed to establish a comprehensive omics resource through untargeted metabolome and transcriptome profiling to explore biosynthesis of pharmacologically active [...] Read more.

Magnolia obovata is renowned for its unique bioactive constituents with medicinal properties traditionally used to treat digestive disorders, anxiety, and respiratory conditions. This study aimed to establish a comprehensive omics resource through untargeted metabolome and transcriptome profiling to explore biosynthesis of pharmacologically active compounds of M. obovata using seven tissues: young leaf, mature leaf, stem, bark, central cylinder, floral bud, and pistil. Untargeted metabolomic analysis identified 6733 mass features across seven tissues and captured chemo-diversity and its tissue-specificity in M. obovata. Through a combination of cheminformatics and manual screening approach, we confirmed the identities of 105 metabolites, including neolignans, such as honokiol and magnolol, which were found to be spatially accumulated in the bark tissue. RNA sequencing generated a comprehensive transcriptome resource, and expression analysis revealed significant tissue-specific expression patterns. Omics dataset integration identified T12 transcript module from WGCNA being correlated with the biosynthesis of magnolol and honokiol in M. obovata. Notably, phylogenetic analysis using transcripts from T12 module identified two laccase (Mo_LAC1 and Mo_LAC2) and three dirigent proteins from the DIR-b/d subfamily as potential candidate genes involved in neolignan biosynthesis. This research established omics resources of M. obovata and laid the groundwork for future studies aimed at optimizing and further understanding the biosynthesis of metabolites of therapeutic potential. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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15 pages, 5245 KiB

Open AccessArticle

Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14

by Dingkun Jiang, Xinfeng Zhang, Lin Luo, Tian Li, Hao Chen, Nana Ma, Lufeng Fu, Peng Tian, Fei Mao, Peitao Lü, Honghong Guo and Fangjie Zhu

Int. J. Mol. Sci. 2025, 26(2), 763; https://doi.org/10.3390/ijms26020763 - 17 Jan 2025

Cited by 1 | Viewed by 684

Abstract

The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, its genome-wide regulatory targets, and how these are affected by DNA methylation remain uncharacterized. To clarify the biochemistry underlying the [...] Read more.

The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, its genome-wide regulatory targets, and how these are affected by DNA methylation remain uncharacterized. To clarify the biochemistry underlying the regulatory function of AtWOX14, using the recently developed 5mC-incorporation strategy, this study performed SELEX and DAP-seq for AtWOX14 both in the presence and absence of cytosine methylation, systematically curated 65 motif models and identified 51,039 genomic binding sites for AtWOX14, and examined how 5mC affects DNA binding of AtWOX14 through bioinformatic analyses. Overall, 5mC represses the DNA binding of AtWOX14 monomers but facilitates the binding of its dimers, and the methylation effect on a cytosine’s affinity to AtWOX14 is position-dependent. Notably, we found that the most preferred homodimeric configuration of AtWOX14 has changed from ER1 to ER0 upon methylation. This change has the potential to rewire the regulatory network downstream of AtWOX14, as suggested by the GO analyses and the strength changes in the DAP-seq peaks upon methylation. Therefore, this work comprehensively illustrates the specificity and targets of AtWOX14 and reports a previously unrecognized effect of DNA methylation on transcription factor binding. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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15 pages, 10249 KiB

Open AccessArticle

Deciphering the Proteome and Phosphoproteome of Peanut (Arachis hypogaea L.) Pegs Penetrating into the Soil

by Sha Yang, Mei He, Zhaohui Tang, Keke Liu, Jianguo Wang, Li Cui, Feng Guo, Ping Liu, Jialei Zhang and Shubo Wan

Int. J. Mol. Sci. 2025, 26(2), 634; https://doi.org/10.3390/ijms26020634 - 14 Jan 2025

Viewed by 807

Abstract

Peanut (Arachis hypogaea L.) is one of the most important crops for oil and protein production. The unique characteristic of peanut is geocarpy, which means that it blooms aerially and the peanut gynophores (pegs) penetrate into the soil, driving the fruit underground. [...] Read more.

Peanut (Arachis hypogaea L.) is one of the most important crops for oil and protein production. The unique characteristic of peanut is geocarpy, which means that it blooms aerially and the peanut gynophores (pegs) penetrate into the soil, driving the fruit underground. In order to fully understand this phenomenon, we investigated the dynamic proteomic and phosphoproteomic profiling of the pegs aerially and underground in this study. A total of 6859 proteins and 4142 unique phosphoproteins with 10,070 phosphosites were identified. The data were validated and quantified using samples randomly selected from arial pegs (APs) and underground pegs (UPs) by parallel reaction monitoring (PRM). Function analyses of differentially abundant proteins (DAPs) and differentially regulated phosphoproteins (DRPPs) exhibited that they were mainly related to stress response, photosynthesis, and substance metabolism. Once the pegs successfully entered the soil, disease-resistant and stress response proteins, such as glutathione S-transferase, peroxidase, and cytochrome P450, significantly increased in the UP samples in order to adapt to the new soil environment. The increased abundance of photosynthesis-associated proteins in the UP samples provided more abundant photosynthetic products, which provided the preparation for subsequent pod development. Phosphoproteomics reveals the regulatory network of the synthesis of nutrients such as starch, protein, and fatty acid (FA). These results provide new insights into the mechanism, indicating that after the pegs are inserted into the soil, phosphorylation is involved in the rapid elongation of the pegs, accompanied by supplying energy for pod development and preparing for the synthesis of metabolites during pod development following mechanical stimulation and darkness. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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16 pages, 5330 KiB

Open AccessArticle

Mitochondrial Genome Characteristics Reveal Evolution of Danxiaorchis yangii and Phylogenetic Relationships

by Xuedie Liu, Huolin Luo, Zhong-Jian Liu and Bo-Yun Yang

Int. J. Mol. Sci. 2025, 26(2), 562; https://doi.org/10.3390/ijms26020562 - 10 Jan 2025

Cited by 1 | Viewed by 801

Abstract

Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding [...] Read more.

Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS). Additionally, we sequenced and assembled its plastome, which has a reduced size of 110,364 bp (GC content: 36.60%), comprising 48 PCGs, 26 tRNAs, and 4 rRNAs. We identified 64 potential chloroplast DNA fragments transferred to the mitogenome. Phylogenomic analysis focusing on 33 mitogenomes, with Vitis vinifera as the outgroup, indicated that D. yangii is grouped as follows: D. yangii + ((Dendrobium wilsonii + Dendrobium wilsonii henanense) + Phalaenopsis aphrodite). Phylogenetic analysis based on 83 plastid PCGs from these species showed that D. yangii is grouped as follows: (D. yangii + Pha. aphrodite) + (Den. wilsonii + Den. henanense). Gene selective pressure analysis revealed that most mitochondrial and plastid genes in D. yangii are under purifying selection, ensuring functional stability, and certain genes may have undergone positive selection or adaptive evolution, reflecting the species’ adaptation to specific ecological environments. Our study provides valuable data on the plastomes and mitogenomes of D. yangii and lays the groundwork for future research on genetic variation, evolutionary relationships, and the breeding of orchids. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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21 pages, 9363 KiB

Open AccessArticle

Complete Chloroplast Genomes of 9 Impatiens Species: Genome Structure, Comparative Analysis, and Phylogenetic Relationships

by Hui Ma, Zhiqiang Liu, Wenxiang Lan, Mengqing Yang, Qing Mo, Xi Huang, Peiqing Wu, Haiquan Huang and Meijuan Huang

Int. J. Mol. Sci. 2025, 26(2), 536; https://doi.org/10.3390/ijms26020536 - 10 Jan 2025

Cited by 1 | Viewed by 1062 | Correction

Abstract

Impatiens is a genus of functional herbaceous plants in the Balsaminaceae, which are not only of great ornamental value and one of the world’s top three flower bedding plants but also have a wide range of medicinal and edible uses. Currently, the taxonomy [...] Read more.

Impatiens is a genus of functional herbaceous plants in the Balsaminaceae, which are not only of great ornamental value and one of the world’s top three flower bedding plants but also have a wide range of medicinal and edible uses. Currently, the taxonomy and phylogenetic relationships of Impatiens species are still controversial. In order to better understand their chloroplast properties and phylogenetic evolution, nine Impatiens plants (Impatiens repens, Impatiens rectirostrata, Impatiens baishaensis, Impatiens rostellata, Impatiens faberi, Impatiens oxyanthera, Impatiens tienchuanensis, Impatiens blepharosepala, Impatiens distracta) were sequenced, and their complete chloroplast genomes were analysed. Nine species of Impatiens chloroplast genomes ranged in length from 150,810 bp (I. rectirostrata) to 152,345 bp (I. blepharosepala). The chloroplast genomes were all typical circular DNA molecules, and the GC content in each region was consistent with the published chloroplast genomes of Impatiens plants. The results showed that the seven mutational hotspots (trnL-UAG, ndhG, ycf1, ccsA, rrn23, trnA-UGC, and ycf2) could be used as supporting data for further analyses of the phylogenetic tree and species identification. In addition, the results of the phylogenetic tree support that Balsaminaceae is a monophyletic taxon, and that Hydrocera triflora is at the base of the branch, is the original species of Balsaminaceae, and is in a sister group relationship with Impatiens species. The results of this paper enrich the data of Impatiens chloroplast genomes, and the availability of these chloroplast genomes will provide rich genetic information for species identification, thus enhancing the taxonomic accuracy and phylogenetic resolution of Impatiens, and further promoting the investigation and rational use of Impatiens plant resources. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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19 pages, 3347 KiB

Open AccessArticle

Comparative Analysis of Active LTR Retrotransposons in Sunflower (Helianthus annuus L.): From Extrachromosomal Circular DNA Detection to Protein Structure Prediction

by Mikhail Kazancev, Pavel Merkulov, Kirill Tiurin, Yakov Demurin, Alexander Soloviev and Ilya Kirov

Int. J. Mol. Sci. 2024, 25(24), 13615; https://doi.org/10.3390/ijms252413615 - 19 Dec 2024

Viewed by 1071

Abstract

Plant genomes possess numerous transposable element (TE) insertions that have occurred during evolution. Most TEs are silenced or diverged; therefore, they lose their ability to encode proteins and are transposed in the genome. Knowledge of active plant TEs and TE-encoded proteins essential for [...] Read more.

Plant genomes possess numerous transposable element (TE) insertions that have occurred during evolution. Most TEs are silenced or diverged; therefore, they lose their ability to encode proteins and are transposed in the genome. Knowledge of active plant TEs and TE-encoded proteins essential for transposition and evasion of plant cell transposon silencing mechanisms remains limited. This study investigated active long terminal repeat (LTR) retrotransposons (RTEs) in sunflowers (Helianthus annuus), revealing heterogeneous and phylogenetically distinct RTEs triggered by epigenetic changes and heat stress. Many of these RTEs belong to three distinct groups within the Tekay clade, showing significant variations in chromosomal insertion distribution. Through protein analysis of these active RTEs, it was found that Athila RTEs and Tekay group 2 elements possess additional open reading frames (aORFs). The aORF-encoded proteins feature a transposase domain, a transmembrane domain, and nuclear localization signals. The aORF proteins of the Tekay subgroup exhibited remarkable conservation among over 500 Tekay members, suggesting their functional importance in RTE mobility. The predicted 3D structure of the sunflower Tekay aORF protein showed significant homology with Tekay proteins in rice, maize, and sorghum. Additionally, the structural features of aORF proteins resemble those of plant DRBM-containing proteins, suggesting their potential role in RNA-silencing modulation. These findings offer insights into the diversity and activity of sunflower RTEs, emphasizing the conservation and structural characteristics of aORF-encoded proteins. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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21 pages, 3237 KiB

Open AccessArticle

Analysis of Plant Physiological Parameters and Gene Transcriptional Changes Under the Influence of Humic Acid and Humic Acid-Amino Acid Combinations in Maize

by Kincső Decsi, Mostafa Ahmed, Roquia Rizk, Donia Abdul-Hamid and Zoltán Tóth

Int. J. Mol. Sci. 2024, 25(24), 13280; https://doi.org/10.3390/ijms252413280 - 11 Dec 2024

Viewed by 872

Abstract

The study investigated the application of humic acids (HAs) and a combination of humic acids and amino acids (HA+AA) in maize under field conditions. Based on preliminary data in the literature, the aim was to investigate the effects of the two plant conditioning [...] Read more.

The study investigated the application of humic acids (HAs) and a combination of humic acids and amino acids (HA+AA) in maize under field conditions. Based on preliminary data in the literature, the aim was to investigate the effects of the two plant conditioning compounds on plant physiological parameters. In addition to measuring plant physiological parameters in the field, a complete transcriptome analysis was performed to determine exactly which genes were expressed after the treatments and in which physiological processes they play a role. Maize plants showed significant positive yield changes after two priming treatments. Genome-wide transcriptomic analysis revealed the activation of photosynthetic and cellular respiration processes, as well as protein synthesis pathways, which explains the increased yield even under extreme precipitation conditions. The results show that the HA treatment helped in water management and increased the chlorophyll content, while the HA+AA treatment led to higher protein and dry matter contents. The post-harvest tests also show that the HA+AA treatment resulted in the highest yield parameters. Functional annotation of the maize super transcriptome revealed genes related to translation processes, photosynthesis, and cellular respiration. The combined pathway analysis showed that the HA and combined treatments activated genes related to photosynthesis, carbon fixation, and cellular respiration, providing valuable in-depth insight into the usefulness of the HA and HA+AA treatments in priming. Based on the studies, we believe that the use of natural-based humic acid plant conditioners may provide a beneficial opportunity to promote renewable, regenerative agriculture. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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11 pages, 3100 KiB

Open AccessArticle

A 2.9 Mb Chromosomal Segment Deletion Is Responsible for Early Ripening and Deep Red Fruit in Citrus sinensis

by Jianmei Chen, Zhenmin Chen, Quming Xie, Xiaotong Wu, Qingyu Pei, Yi Lin, Qiong Chen and Shubei Wan

Int. J. Mol. Sci. 2024, 25(23), 12931; https://doi.org/10.3390/ijms252312931 - 2 Dec 2024

Viewed by 847

Abstract

Sweet orange (Citrus sinensis) is an economically important fruit crop worldwide. Mining for genes associated with ripening periods and fruit color traits is crucial for plant genetics and for the improvement of external fruit quality traits. The present study identified a [...] Read more.

Sweet orange (Citrus sinensis) is an economically important fruit crop worldwide. Mining for genes associated with ripening periods and fruit color traits is crucial for plant genetics and for the improvement of external fruit quality traits. The present study identified a novel navel orange accession, designated as Ganhong, with early ripening and deep red fruit traits. DNA sequence analysis showed a 2.9 Mb deletion in one copy of chromosome 7 in Ganhong navel orange. Flesh samples from Ganhong and its parental variety, Newhall navel orange, were sampled for RNA sequence analysis 200 days after flowering; 958 differentially expressed genes (DEGs) were identified between the two varieties. Functional enrichment analysis indicated that these DEGs were mainly enriched in phytohormones, particularly abscisic acid (ABA), related to fruit ripening. The deletion interval has 343 annotated genes, among which 4 genes (Cs_ont_7g018990, Cs_ont_7g019400, Cs_ont_7g019650, and Cs_ont_7g019820) were inferred to be candidate causal genes for early ripening and deep red fruit traits based on gene functionality and gene expression analysis. The present study laid a foundation for further elucidation of the mechanisms underlying the early ripening and deep red fruit trait in Ganhong navel orange. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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15 pages, 10071 KiB

Open AccessArticle

Genome-Wide Analysis of BURP Domain-Containing Gene Family in Solanum lycopersicum and Functional Analysis of SlRD1 Under Drought and Salt Stresses

by Huiru Sun, Jinyu Yang, Bei Fan, Min Ren, Yanfeng Wang, Guoliang Chen and Guoting Cheng

Int. J. Mol. Sci. 2024, 25(23), 12539; https://doi.org/10.3390/ijms252312539 - 22 Nov 2024

Cited by 2 | Viewed by 727

Abstract

The BURP domain-containing (BURP) genes belong to plant-specific families and are known as essential for various biological processes in plants. However, knowledge of the functions of BURP genes in tomato (Solanum lycopersicum) is lacking. In our study, bioinformatics analysis [...] Read more.

The BURP domain-containing (BURP) genes belong to plant-specific families and are known as essential for various biological processes in plants. However, knowledge of the functions of BURP genes in tomato (Solanum lycopersicum) is lacking. In our study, bioinformatics analysis was performed for the SlBURP gene family, including phylogeny, chromosomal localization, gene structure, cis-acting elements and expression. In addition, the function of SlRD1 in drought and salt stresses was explored. In tomato, fourteen BURP family members were identified, located on five chromosomes, including two tandem duplication clusters. These BURP members were classified into four subfamilies. The promoter regions of SlBURPs harbored numerous hormone- and stress-response elements. Tissue expression analysis showed that several SlBURPs were highly expressed in roots, flowers or fruits. Meanwhile, the expressions of most SlBURPs could be regulated by drought, salt and cold treatments, and some of them also responded to ABA treatment. Moreover, the ectopic expression of SlRD1 in Arabidopsis enhanced tolerances to drought and salt stresses and increased the sensitivity of seed germination to ABA. In conclusion, the comprehensive analysis of the SlBURP family in tomato and the functional exploration of SlRD1 in drought and salt stresses provide a basis for further dissecting the roles of tomato BURP genes. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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21 pages, 4811 KiB

Open AccessArticle

Genome-Wide Identification of GATA Family Genes in Potato and Characterization of StGATA12 in Response to Salinity and Osmotic Stress

by Xi Zhu, Huimin Duan, Ning Zhang, Yasir Majeed, Hui Jin, Wei Li, Zhuo Chen, Shu Chen, Jinghua Tang, Yu Zhang and Huaijun Si

Int. J. Mol. Sci. 2024, 25(22), 12423; https://doi.org/10.3390/ijms252212423 - 19 Nov 2024

Cited by 1 | Viewed by 1246

Abstract

GATA factors are evolutionarily conserved transcription regulators that are implicated in the regulation of physiological changes under abiotic stress. Unfortunately, there are few studies investigating the potential role of GATA genes in potato plants responding to salt and osmotic stresses. The physicochemical properties, [...] Read more.

GATA factors are evolutionarily conserved transcription regulators that are implicated in the regulation of physiological changes under abiotic stress. Unfortunately, there are few studies investigating the potential role of GATA genes in potato plants responding to salt and osmotic stresses. The physicochemical properties, chromosomal distribution, gene duplication, evolutionary relationships and classification, conserved motifs, gene structure, interspecific collinearity relationship, and cis-regulatory elements were analyzed. Potato plants were treated with NaCl and PEG to induce salinity and osmotic stress responses. qRT-PCR was carried out to characterize the expression pattern of StGATA family genes in potato plants subjected to salinity and osmotic stress. StGATA12 loss-of-function and gain-of-function plants were established. Morphological phenotypes and growth were indicated. Photosynthetic gas exchange was suggested by the net photosynthetic rate, transpiration rate, and stomatal conductance. Physiological indicators and the corresponding genes were indicated by enzyme activity and mRNA expression of genes encoding CAT, SOD, POD, and P5CS, and contents of H₂O₂, MDA, and proline. The expression patterns of StGATA family genes were altered in response to salinity and osmotic stress. StGATA12 protein is located in the nucleus. StGATA12 is involved in the regulation of potato plant growth in response to salinity and osmotic stress. Overexpression of StGATA12 promoted photosynthesis, transpiration, and stomatal conductance under salinity and osmotic stress. StGATA12 overexpression induced biochemical responses of potato plants to salinity and osmotic stress by regulating the levels of H₂O₂, MDA, and proline and the activity of CAT, SOD, and POD. StGATA12 overexpression induced the up-regulation of StCAT, StSOD, StPOD, and StP5CS against salinity and osmotic stress. StGATA12 could reinforce the ability of potato plants to resist salinity and osmosis-induced damages, which may provide an effective strategy to engineer potato plants for better adaptability to adverse salinity and osmotic conditions. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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18 pages, 4385 KiB

Open AccessArticle

Comparative Analyses of the Complete Mitogenomes of Two Oxyria Species (Polygonaceae) Provide Insights into Understanding the Mitogenome Evolution Within the Family

by Lijuan Li, Zhuo Jiang, Ye Xiong, Caleb Onoja Akogwu, Olutayo Mary Tolulope, Hao Zhou, Yanxia Sun, Hengchang Wang and Huajie Zhang

Int. J. Mol. Sci. 2024, 25(22), 11930; https://doi.org/10.3390/ijms252211930 - 6 Nov 2024

Viewed by 904

Abstract

Oxyria (Polygonaceae) is a small genus only comprising two species, Oxyria digyna and O. sinensis. Both species have well-documented usage in Chinese herbal medicine. We sequenced and assembled the complete mitogenomes of these two species and conducted a comparative analysis of the [...] Read more.

Oxyria (Polygonaceae) is a small genus only comprising two species, Oxyria digyna and O. sinensis. Both species have well-documented usage in Chinese herbal medicine. We sequenced and assembled the complete mitogenomes of these two species and conducted a comparative analysis of the mitogenomes within Polygonaceae. Both O. digyna and O. sinensis displayed distinctive multi-branched conformations, consisting of one linear and one circular molecule. These two species shared similar gene compositions and exhibited distinct codon preferences, with mononucleotides as the most abundant type of simple sequence repeats. In the mitogenome of O. sinensis, a pair of long forward repeat sequences can mediate the division of molecule 1 into two sub-genomic circular molecules. Homologous sequence analysis revealed the occurrence of gene transfer between the chloroplast and mitochondrial genomes within Oxyria species. Additionally, a substantial number of homologous collinear blocks with varied arrangements were observed across different Polygonaceae species. Phylogenetic analysis suggested that mitogenome genes can serve as reliable markers for constructing phylogenetic relationships within Polygonaceae. Comparative analysis of eight species revealed Polygonaceae mitogenomes exhibited variability in gene presence, and most protein-coding genes (PCGs) have undergone negative selection. Overall, our study provided a comprehensive overview of the structural, functional, and evolutionary characteristics of the Polygonaceae mitogenomes. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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12 pages, 2301 KiB

Open AccessArticle

Developing Adventitious Root Meristems Induced by Layering for Plant Chromosome Preparation

by Xu Yan, Zizhou Wu, Honglin Wang, Yanchun Zuo and Zhouhe Du

Int. J. Mol. Sci. 2024, 25(21), 11723; https://doi.org/10.3390/ijms252111723 - 31 Oct 2024

Viewed by 1011

Abstract

Chromosome numbers and morphology are important characteristics of a species and its evolution. Root tips are the most commonly used tissue as a source of actively dividing cells for chromosome visualization in plants. Previously, rapidly growing root tips were collected from germinating kernels [...] Read more.

Chromosome numbers and morphology are important characteristics of a species and its evolution. Root tips are the most commonly used tissue as a source of actively dividing cells for chromosome visualization in plants. Previously, rapidly growing root tips were collected from germinating kernels or from seedlings growing in pots or fields. However, the use of adventitious roots (ARs) derived from aerial tissue as meristems for chromosome visualization has always been overlooked. Here, we successfully induced ARs in 12 materials that were investigated, with the exception of Sorghum nitidum. Using ARs meristem we obtained high-quality chromosome spreads for Morus alba, Broussonetia papyrifera, Lolium multiflorum, Sorghum sudanense, S. propinquum, S. bicolor × S. sudanense, Zea mays, Z. mexicana, Glycine max, Medicago sativa, and Brassica napus. The results reported here demonstrate that layering is an alternative and effective method for producing meristematic cells for high-quality chromosome preparation in plant species producing ARs. For species that produce ARs by layering, this protocol is particularly valuable for the development of cost-effective and high-throughput non-invasive cytogenetic studies. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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15 pages, 5348 KiB

Open AccessArticle

Identification of Potato StPIN Gene Family and Regulation of Root Development by StPIN4

by Qian Zhang, Qing Liu, Jiangwei Yang, Ning Zhang and Huaijun Si

Int. J. Mol. Sci. 2024, 25(21), 11517; https://doi.org/10.3390/ijms252111517 - 26 Oct 2024

Viewed by 1023

Abstract

The growth hormone export PIN-FORMED (PIN) is an important carrier for regulating the polar transport of plant growth hormones and plays an important role in plant growth and development. However, little is known about the characteristics and functions of PINs in potatoes. In [...] Read more.

The growth hormone export PIN-FORMED (PIN) is an important carrier for regulating the polar transport of plant growth hormones and plays an important role in plant growth and development. However, little is known about the characteristics and functions of PINs in potatoes. In this study, 10 PIN members were identified from potatoes and named StPIN1, StPIN2, StPIN3, StPIN4, StPIN5, StPIN6, StPIN7, StPIN8, StPIN9, and StPIN10 according to their positions in the potato chromosome In addition, the expression of 10 StPINs was analyzed by qRT-PCR during potato root development. The results showed that the StPIN4 gene plays an important regulatory role in potato root development, and its tissue expression varied greatly. Several cis-regulatory elements related to growth factors were also detected in the promoter region of the StPIN gene. The transgenic overexpressing StPIN4 in potato showed suppressed growth in root length and lateral root number, and StPIN4-interfering plants showed the opposite. These results suggested that StPIN4 plays a key role in the regulation of the potato root architecture. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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19 pages, 3437 KiB

Open AccessArticle

Genome Analysis of BnCNGC Gene Family and Function Exploration of BnCNGC57 in Brassica napus L.

by Yue Wang, Qing Chi, Wenjing Jia, Tiantian Zheng, Binghua Li, Lin Li, Ting Li, Rui Gao, Wenzhe Liu, Shenglin Ye, Ruqiang Xu and Hanfeng Zhang

Int. J. Mol. Sci. 2024, 25(21), 11359; https://doi.org/10.3390/ijms252111359 - 22 Oct 2024

Viewed by 1260

Abstract

The cyclic nucleotide-gated ion channel (CNGC), as a non-selective cation channel, plays a pivotal role in plant growth and stress response. A systematic analysis and identification of the BnCNGC gene family in Brassica napus is crucial for uncovering its biological functions and potential [...] Read more.

The cyclic nucleotide-gated ion channel (CNGC), as a non-selective cation channel, plays a pivotal role in plant growth and stress response. A systematic analysis and identification of the BnCNGC gene family in Brassica napus is crucial for uncovering its biological functions and potential applications in plant science. In this study, we identified 61 BnCNGC members in the B. napus genome, which are phylogenetically similar to Arabidopsis and can be classified into Groups I-IV (with Group IV further subdivided into IV-a and IV-b). Collinearity analysis with other species provided insights into the evolution of BnCNGC. By homology modeling, we predicted the three-dimensional structure of BnCNGC proteins and analyzed cis-acting elements in their promoters, revealing diverse roles in hormone regulation, growth, and stress response. Notably, overexpression of BnCNGC57 (BnaC09g42460D) significantly increased seed size, possibly through regulating cell proliferation via the MAPK signaling pathway. Our findings contribute to a better understanding of the BnCNGC gene family and highlight the potential regulatory role of BnCNGC57 in the seed development of B. napus. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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14 pages, 4449 KiB

Open AccessArticle

Downregulation of the GhROD1 Gene Improves Cotton Fiber Fineness by Decreasing Acyl Pool Saturation, Stimulating Small Heat Shock Proteins (sHSPs), and Reducing H₂O₂ Production

by Bo Ding, Bi Liu, Xi Zhu, Huiming Zhang, Rongyu Hu, Silu Li, Liuqin Zhang, Linzhu Jiang, Yang Yang, Mi Zhang, Juan Zhao, Yan Pei and Lei Hou

Int. J. Mol. Sci. 2024, 25(20), 11242; https://doi.org/10.3390/ijms252011242 - 19 Oct 2024

Cited by 1 | Viewed by 1003

Abstract

Cotton fiber is one of the most important natural fiber sources in the world, and lipid metabolism plays a critical role in its development. However, the specific role of lipid molecules in fiber development and the impact of fatty acid alterations on fiber [...] Read more.

Cotton fiber is one of the most important natural fiber sources in the world, and lipid metabolism plays a critical role in its development. However, the specific role of lipid molecules in fiber development and the impact of fatty acid alterations on fiber quality remain largely unknown. In this study, we demonstrate that the downregulation of GhROD1, a gene encoding phosphatidylcholine diacylglycerol cholinephosphotransferase (PDCT), results in an improvement of fiber fineness. We found that GhROD1 downregulation significantly increases the proportion of linoleic acid (18:2) in cotton fibers, which subsequently upregulates genes encoding small heat shock proteins (sHSPs). This, in turn, reduces H₂O₂ production, thus delaying secondary wall deposition and leading to finer fibers. Our findings reveal how alterations in linoleic acid influence cellulose synthesis and suggest a potential strategy to improve cotton fiber quality by regulating lipid metabolism pathways. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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Review

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25 pages, 82520 KiB

Open AccessReview

Research Progress of Genomics Applications in Secondary Metabolites of Medicinal Plants: A Case Study in Safflower

by Zhihua Wu, Yan Hu, Ruru Hao, Ruting Li, Xiaona Lu, Mdachi Winfrida Itale, Yang Yuan, Xiaoxian Zhu, Jiaqiang Zhang, Longxiang Wang, Meihao Sun and Xianfei Hou

Int. J. Mol. Sci. 2025, 26(8), 3867; https://doi.org/10.3390/ijms26083867 - 19 Apr 2025

Viewed by 260

Abstract

Medicinal plants, recognized as significant natural resources, have gained prominence in response to the increasing global demand for herbal medicines, necessitating the large-scale production of these plants and their derivatives. Medicinal plants are exposed to a variety of internal and external factors that [...] Read more.

Medicinal plants, recognized as significant natural resources, have gained prominence in response to the increasing global demand for herbal medicines, necessitating the large-scale production of these plants and their derivatives. Medicinal plants are exposed to a variety of internal and external factors that interact to influence the biosynthesis and accumulation of secondary metabolites. With the rapid development of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics, multi-omics technologies have become important tools for revealing the complexity and functionality of organisms. They are conducive to further uncovering the biological activities of secondary metabolites in medicinal plants and clarifying the molecular mechanisms underlying the production of secondary metabolites. Also, artificial intelligence (AI) technology accelerates the comprehensive utilization of high-dimensional datasets and offers transformative potential for multi-omics analysis. However, there is currently no systematic review summarizing the genomic mechanisms of secondary metabolite biosynthesis in medicinal plants. Safflower (Carthamus tinctorius L.) has rich and diverse bioactive flavonoids, among of which Hydroxysafflor yellow A (HSYA) is specific to safflower and emerging as a potential medication for treating a wide range of diseases. Hence, significant progress has been made in the study of safflower as an excellent example for the regulation of secondary metabolites in medicinal plants in recent years. Here, we review the progress on the understanding of the regulation of main secondary metabolites at the multi-omics level, and summarize the influence of various factors on their types and contents, with a particular focus on safflower flavonoids. This review aims to provide a comprehensive insight into the regulatory mechanisms of secondary metabolite biosynthesis from the perspective of genomics. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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22 pages, 2008 KiB

Open AccessReview

Enhancing Crop Resilience: The Role of Plant Genetics, Transcription Factors, and Next-Generation Sequencing in Addressing Salt Stress

by Akhilesh Kumar Singh, Priti Pal, Uttam Kumar Sahoo, Laxuman Sharma, Brijesh Pandey, Anand Prakash, Prakash Kumar Sarangi, Piotr Prus, Raul Pașcalău and Florin Imbrea

Int. J. Mol. Sci. 2024, 25(23), 12537; https://doi.org/10.3390/ijms252312537 - 22 Nov 2024

Cited by 2 | Viewed by 1859

Abstract

Salt stress is a major abiotic stressor that limits plant growth, development, and agricultural productivity, especially in regions with high soil salinity. With the increasing salinization of soils due to climate change, developing salt-tolerant crops has become essential for ensuring food security. This [...] Read more.

Salt stress is a major abiotic stressor that limits plant growth, development, and agricultural productivity, especially in regions with high soil salinity. With the increasing salinization of soils due to climate change, developing salt-tolerant crops has become essential for ensuring food security. This review consolidates recent advances in plant genetics, transcription factors (TFs), and next-generation sequencing (NGS) technologies that are pivotal for enhancing salt stress tolerance in crops. It highlights critical genes involved in ion homeostasis, osmotic adjustment, and stress signaling pathways, which contribute to plant resilience under saline conditions. Additionally, specific TF families, such as DREB, NAC (NAM, ATAF, and CUC), and WRKY, are explored for their roles in activating salt-responsive gene networks. By leveraging NGS technologies—including genome-wide association studies (GWASs) and RNA sequencing (RNA-seq)—this review provides insights into the complex genetic basis of salt tolerance, identifying novel genes and regulatory networks that underpin adaptive responses. Emphasizing the integration of genetic tools, TF research, and NGS, this review presents a comprehensive framework for accelerating the development of salt-tolerant crops, contributing to sustainable agriculture in saline-prone areas. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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Jump to: Research, Review

2 pages, 433 KiB

Open AccessCorrection

Correction: Ma et al. Complete Chloroplast Genomes of 9 Impatiens Species: Genome Structure, Comparative Analysis, and Phylogenetic Relationships. Int. J. Mol. Sci. 2025, 26, 536

by Hui Ma, Zhiqiang Liu, Wenxiang Lan, Mengqing Yang, Qing Mo, Xi Huang, Peiqing Wu, Haiquan Huang and Meijuan Huang

Int. J. Mol. Sci. 2025, 26(7), 3240; https://doi.org/10.3390/ijms26073240 - 31 Mar 2025

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(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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