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The Potential of Genetics and Plant Breeding in Crop Improvement
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The Potential of Genetics and Plant Breeding in Crop Improvement

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 12288

Special Issue Editors

Dr. Jianyan Zeng

E-Mail Website
Guest Editor
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Interests: crop resistance; phytohormone; cell expansion; secondary metabolism; plant signaling pathways
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yuanzhong Jiang

E-Mail Website
Guest Editor
Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
Interests: abiotic stress; molecular biology; tree breeding; gene regulation
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Chengjian Xie

E-Mail Website
Guest Editor
College of Life Science, Chongqing Normal University, Chongqing 401331, China
Interests: plant-microbe interaction; biological control; plant defense mechanisms; fungal pathogenesis

Special Issue Information

Dear Colleagues,

Genetics and plant breeding are experiencing rapid progress, notably through molecular design in crop improvement. This field incorporates essential technologies such as genomics, transcriptomics, proteomics, metabolomics, gene transformation, molecular biology, biochemistry, molecular breeding, and genomic editing. These technologies have yielded notable achievements, particularly in understanding crop origins, evolution, growth, development, quality, and stress responses. This Special Issue on “The Potential of Genetics and Plant Breeding in Crop Improvement” provides a platform for researchers, breeders, and agricultural scientists to exchange the latest advancements and explore future research directions, aiming to drive scientific progress and foster innovation in crop improvement. By gaining insights into pivotal research developments in genetics, biotechnology, and molecular breeding, it advances crop breeding and optimizes the use of germplasm resources.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  1. Growth and Development: Researching the genetic and environmental factors that regulate plant growth patterns and reproductive development.
  2. Quality Formation: Identifying the genetic and biochemical processes that determine the nutritional and organoleptic qualities of plants.
  3. Stress Response: Understanding the mechanisms by which plants respond to environmental stresses, such as drought, salinity, heavy metal, and disease.
  4. Genomics and Transcriptomics: Exploring the genetic basis of plant traits and the expression patterns that influence yield and quality.
  5. Proteomics and Metabolomics: Analyzing the protein and metabolic profiles crucial for stress tolerance and nutritional content in plants.
  6. Gene Transformation: Investigating the integration and expression of foreign genes in plants to enhance desired traits.
  7. Molecular Biology and Biochemistry: Studying the molecular mechanisms and biochemical pathways involved in plant growth and development.
  8. Molecular Breeding: Utilizing marker-assisted selection and other molecular techniques to develop new crop varieties with improved characteristics.
  9. Genome Editing: Employing CRISPR/Cas9 and other tools for precise genetic modifications to achieve crop improvement.
  10. Origin and Evolution: Examining the evolutionary history of crops to understand the basis of their adaptability and potential for future breeding.

We look forward to receiving your contributions.

Dr. Jianyan Zeng
Dr. Yuanzhong Jiang
Prof. Dr. Chengjian Xie
Guest Editors

Manuscript Submission Information

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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. Biology is an international peer-reviewed open access semimonthly 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 2700 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

  • plants
  • plant signaling pathways
  • growth and development
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • gene transformation
  • molecular biology
  • biochemistry
  • molecular breeding
  • genome editing
  • CRISPR/Cas9
  • marker-assisted selection
  • genome-wide selection
  • crop improvement
  • genetic diversity
  • quality traits
  • yield
  • disease resistance
  • environmental stress
  • plant-microbe interactions
  • drought tolerance
  • salinity resistance
  • oxidative stress
  • phytohormone

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Published Papers (12 papers)

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20 pages, 11070 KB  
Article
A Comparative Transcriptome and WGCNA of Tomato Reveals Hub Genes and a Hormone-Mediated Defense Network Against Ralstonia solanacearum
by Chuying Yu, Xiaofang Wang, Chunchun Qin, Yi Liu, Guiyun Gan, Liangyu Cai, Rui Xiang, Yaqin Jiang, Weiliu Li, Qihong Yang and Yikui Wang
Biology 2026, 15(6), 509; https://doi.org/10.3390/biology15060509 - 22 Mar 2026
Viewed by 578
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a major constraint on tomato (Solanum lycopersicum L.) production, yet the molecular basis of quantitative resistance remains poorly understood. In this study, comparative transcriptome profiling was performed on resistant (‘ZM3’) and susceptible (‘ZM86’) tomato inbred [...] Read more.
Bacterial wilt caused by Ralstonia solanacearum is a major constraint on tomato (Solanum lycopersicum L.) production, yet the molecular basis of quantitative resistance remains poorly understood. In this study, comparative transcriptome profiling was performed on resistant (‘ZM3’) and susceptible (‘ZM86’) tomato inbred lines following pathogen inoculation in roots, stems, and leaves. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were conducted to identify resistance-associated regulatory modules and hub genes. The results revealed distinct gene expression patterns between the two genotypes after infection. Several co-expression modules were significantly associated with resistance or susceptibility traits. Functional enrichment analysis showed that differentially expressed genes were mainly involved in plant hormone signal transduction, plant–pathogen interaction, phenylpropanoid biosynthesis, and cell wall modification. Genes related to ethylene and salicylic acid signaling were strongly induced following infection, whereas brassinosteroid-associated genes showed genotype-dependent expression patterns. Network analysis further identified several hub genes within defense-related modules, including ACO (Solyc04g007980), ERF1 (Solyc09g091950), MAPK9, receptor-like kinase RLK (Solyc07g006770), and a dirigent family gene (Solyc10g008900). Taken together, our results suggest that tomato resistance to Ralstonia solanacearum involves a coordinated defense network integrating hormone-mediated transcriptional regulation and structural reinforcement, and provides candidate genes for breeding bacterial wilt-resistant cultivars. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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25 pages, 41388 KB  
Article
Isolation, Identification, and Management Strategies for the Root Rot Pathogen of Cardamine violifolia
by Shaobing Gao, Wei Yang, Wenqin Bai, Yixuan Niu, Yalan Qiao, Yuchun Dai, Yutong Si, Xin Liu, Jie Xiang, Zhiwu Pei, Aimin Liang, Yuehua Xiao, Xin Cong and Jianyan Zeng
Biology 2026, 15(4), 368; https://doi.org/10.3390/biology15040368 - 22 Feb 2026
Viewed by 546
Abstract
Root rot disease severely impacts the yield of Cardamine violifolia, a selenium-enriched cruciferous vegetable. However, the causal pathogens and effective control strategies of this disease remain poorly characterized. This study systematically isolated and identified three key pathogens from diseased tissues in the [...] Read more.
Root rot disease severely impacts the yield of Cardamine violifolia, a selenium-enriched cruciferous vegetable. However, the causal pathogens and effective control strategies of this disease remain poorly characterized. This study systematically isolated and identified three key pathogens from diseased tissues in the Enshi region: Aspergillus costaricensis, Mucor circinelloides cf. lusitanicus, and Fusarium pernambucanum. Morphological characterization, phylogenetic analysis, and pathogenicity testing were conducted. Candidate fungicides were screened using plate inhibition assays, and combinations were optimized and validated through soil drenching experiments. While propiconazole showed broad-spectrum activity, its efficacy against Aspergillus and Mucor was suboptimal. A novel ternary compound fungicide, T10, combining propiconazole, hymexazol, and difenoconazole, demonstrated significantly enhanced potency with EC50 values of 7.313, 12.2983, and 0.1781 mg/L against the three pathogens, representing reductions of 66.0%, 77.7%, and 92.1% compared to the most effective single application of propiconazole. At 10 mg/L, T10 increased inhibition rates by 62.62%, 77.53%, and 20.85% against the three pathogens, respectively, compared to propiconazole alone. Propidium iodide (PI) staining revealed increased cell membrane permeability in T10-treated pathogens, suggesting that membrane damage may contribute to its antifungal effect. This study provides a robust scientific basis for sustainable disease management of this high-value selenium-enriched vegetable crop. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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25 pages, 853 KB  
Article
Molecular Marker-Based Identification of Resistance to Bipolaris sorokiniana in Kazakh and Global Wheat Germplasm
by Ardak Bolatbekova, Alma Kokhmetova, Yerlan Dutbayev, Göksel Özer, Madina Kumarbayeva, Sholpan Bastaubayeva, Aidana Kharipzhanova, Makpal Nurzhuma, Zhenis Keishilov, Assiya Kokhmetova, Kanat Bakhytuly, Kanat Mukhametzhanov and Vladimir Tsygankov
Biology 2026, 15(3), 244; https://doi.org/10.3390/biology15030244 - 28 Jan 2026
Cited by 1 | Viewed by 715
Abstract
Diseases caused by Bipolaris sorokiniana, expressed as leaf spot blotch (SB) and common root rot (CRR), continue to limit spring wheat production, particularly in dry regions where yield losses may reach 35–40%. This study evaluated resistance to SB and CRR in fifty [...] Read more.
Diseases caused by Bipolaris sorokiniana, expressed as leaf spot blotch (SB) and common root rot (CRR), continue to limit spring wheat production, particularly in dry regions where yield losses may reach 35–40%. This study evaluated resistance to SB and CRR in fifty spring wheat genotypes at both seedling and adult plant stages and identified genetic sources of resistance using molecular markers linked to the Sb1 and Sb2 genes. Field trials were conducted in 2023 and 2024 in the Aktobe region under natural infection, artificial inoculation, and a fungicide-treated background. Based on leaf spot blotch severity quantified as the area under the disease progress curve (leaf AUDPC) under natural infection, nine genotypes displayed stable resistance across both years, while fungicide-treated plots revealed twenty-three resistant genotypes in 2023 and eighteen in 2024. Artificial inoculation identified five resistant lines in 2023 and one in 2024. Resistance to common root rot (CRR) was assessed independently based on subcrown internode (SCI) browning at the adult plant stage. Seedling assays confirmed consistent resistance in six genotypes, all of which carried Sb1, Sb2, or their combination. In total, Sb genes were detected in thirty-six of the fifty accessions, including genotypes from Kazakhstan, Russia, and several other countries. The presence of Sb1 or Sb2 was associated with reduced disease severity, particularly at the seedling stage. These findings identify valuable germplasm for breeding wheat with improved resistance to B. sorokiniana in Kazakhstan. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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21 pages, 6977 KB  
Article
An Integrative Small RNA–Degradome–Transcriptome Analysis Reveals Mechanisms of Heat-Induced Anther Indehiscence in Pepper
by Gang Lei, Tao Li, Kunhua Zhou, Xinjie Yuan, Yueqin Huang, Gege Li, Yu Fang, Rong Fang and Xuejun Chen
Biology 2026, 15(2), 129; https://doi.org/10.3390/biology15020129 - 12 Jan 2026
Viewed by 570
Abstract
Heat threatens male fertility in crops, yet the regulatory basis of anther dehiscence under high temperatures remains unclear. We compared a heat-sensitive pepper cultivar (DL) with a heat-tolerant landrace (B021) across two anther stages using integrated transcriptome, small-RNA, degradome, co-expression, and enzymatic assays. [...] Read more.
Heat threatens male fertility in crops, yet the regulatory basis of anther dehiscence under high temperatures remains unclear. We compared a heat-sensitive pepper cultivar (DL) with a heat-tolerant landrace (B021) across two anther stages using integrated transcriptome, small-RNA, degradome, co-expression, and enzymatic assays. DL showed a collapse of anther dehiscence above 34–38 °C, whereas B021 retained normal dehiscence at 39 °C, and histology revealed tapetal enlargement, premature degeneration, and locule contraction only in DL. RNA-seq indicated genotype- and stage-dependent reprogramming, with DL suppressing phenylpropanoid/cell-wall, transport, and proteostasis pathways, while B021 maintained reproductive and stress-integration programs. Small-RNA profiling and degradome sequencing identified conserved miRNA families with in vivo target cleavage, and notably, miR397 targeting a laccase gene showed stronger evidence in B021, which is consistent with controlled lignification. Functional organization of differentially expressed miRNA targets highlighted modules in respiration/redox, hormone and terpenoid metabolism, vascular–cell-wall programs, and proteostasis/osmotic buffering. WGCNA modules correlated with heat-tolerance traits converged on the same processes. Enzyme assays corroborated multi-omics predictions, with SOD, CAT, and POD activities consistently induced in B021 and limited MDA accumulation. Together, the data supports a model in which tolerant anthers sustain dehiscence under heat by coordinating secondary-wall formation, auxin/jasmonate/gibberellin crosstalk, respiratory and reactive oxygen species buffering, and protein/membrane quality control, providing tractable targets for breeding heat-resilient peppers. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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19 pages, 90988 KB  
Article
Genome-Wide Identification and Comprehensive Analysis of the GS Gene Family in Hordeum vulgare Under Low Nitrogen Stress
by Yaping Pei, Juncheng Wang, Lirong Yao, Erjing Si, Ke Yang, Baochun Li, Yaxiong Meng, Xiaole Ma, Hong Zhang, Xunwu Shang and Huajun Wang
Biology 2025, 14(12), 1789; https://doi.org/10.3390/biology14121789 - 15 Dec 2025
Viewed by 714
Abstract
Glutamine synthetase (GS; EC 6.3.1.2) is a key enzyme for primary assimilation and re-assimilation of ammonium in higher plants. Although several GS gene families have been reported for several cereal crops, systematic studies for barley (Hordeum vulgare) under different nitrogen treatment [...] Read more.
Glutamine synthetase (GS; EC 6.3.1.2) is a key enzyme for primary assimilation and re-assimilation of ammonium in higher plants. Although several GS gene families have been reported for several cereal crops, systematic studies for barley (Hordeum vulgare) under different nitrogen treatment conditions are still lacking. In this study, we combined genome-wide bioinformatics mining with transcriptome analysis to characterize the HvGS gene family in two different genotypes of barley (nitrogen-efficient W26 and nitrogen-sensitive W20) and their responses to low nitrogen stress. Four HvGS genes were retrieved from the barley genome and named HvGS1–HvGS4. These genes were comprehensively analyzed in terms of chromosomal distribution, physicochemical properties, subcellular localization, intron-exon structure, conserved motifs, promoter cis-acting elements, evolutionary relationships, and predicted protein–protein interactions. Leaves and roots were sampled and subjected to RNA-seq analysis at 3, 18, and 21 days of low-nitrogen stress, which revealed significant expression differences among genotypes and tissues. In W26, low nitrogen (0.4 mmol·L−1) induced synergistic expression of HvGS1 and HvGS4 and suppressed expression of plastidic HvGS2, whereas W20 up-regulated the expression of HvGS1 and HvGS3 mainly in the root system. Combined GO/KEGG enrichment analysis and metabolomic characterization of the differentially expressed genes highlighted nitrogen metabolism, glutathione turnover, and amino acid biosynthesis as key hubs in the tolerant genotypes. Our results provide a genome-wide analysis of the barley GS family and highlight HvGS1 and HvGS4 as candidate genes for functional validation toward improved nitrogen use efficiency. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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21 pages, 3347 KB  
Article
Dynamic Metabolome and Transcriptome Profiling Provide Molecular Insights into Floral Bud Differentiation in Michelia ‘Xin’
by Yan Chen, Dapeng Li, Xiaoling Ji, Caixian Liu and Chenfei Huang
Biology 2025, 14(10), 1383; https://doi.org/10.3390/biology14101383 - 10 Oct 2025
Viewed by 935
Abstract
Michelia ‘Xin’ is an evergreen rare ornamental tree species that undergoes FBD only once but blooms twice a year. However, the molecular mechanisms controlling its FBD process remain largely unknown. This study characterized the FBD process and delved into the key molecular regulatory [...] Read more.
Michelia ‘Xin’ is an evergreen rare ornamental tree species that undergoes FBD only once but blooms twice a year. However, the molecular mechanisms controlling its FBD process remain largely unknown. This study characterized the FBD process and delved into the key molecular regulatory mechanisms through transcriptomic and metabolomic analyses of developing flower buds. FBD in Michelia ‘Xin’ was characterized into five stages, including vegetative (T1), floral meristem transition (T2), tepal primordia differentiation (T3), stamen primordia differentiation (T4), and pistil primordia differentiation (T5). Analyses revealed a stage-specific metabolic and transcriptional regulation of FBD, with increasing numbers of differential metabolites and a decreasing number of DEGs from T1 to T5. Most phytohormone and transcription factor-related DEGs were highly induced from T2. The down-regulation of dormancy-associated protein homologs and CONSTANS-LIKE proteins associated with significant induction of flowering-promoting factor, CLAVATA3, trichome birefringence-like, and GRAVITROPIC IN THE LIGHT proteins was essential for the induction and reproductive organs’ development. Porphyrin biosynthesis, chlorophyll a-b binding proteins, DNA replication, flavonoid biosynthesis, and starch and sucrose metabolism were also significantly induced from T2. Key pivotal candidate genes were screened out. Our results provide fundamental resources for dissecting the molecular network regulating FBD and molecular-assisted flowering control in Michelia ‘Xin’. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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14 pages, 3451 KB  
Article
An Assessment of the Effective Pollination Period and Its Main Limiting Factor in Wurfbainia villosa var. villosa (Lour.) Škorničk. & A. D. Poulsen (Zingiberaceae)
by Qianxia Li, Yanqian Wang, Ge Li, Shuang Li, Hongyou Zhao, Chunyong Yang, Zhibing Guan, Yating Zhu, Lin Xiao, Yanfang Wang and Lixia Zhang
Biology 2025, 14(9), 1134; https://doi.org/10.3390/biology14091134 - 27 Aug 2025
Viewed by 955
Abstract
Low fruit set in Wurfbainia villosa var. villosa has been a major constraint in its cultivation, with the effective pollination period (EPP) identified as a key factor. In this study, the EPP was assessed for the first time by examining stigma receptivity, style [...] Read more.
Low fruit set in Wurfbainia villosa var. villosa has been a major constraint in its cultivation, with the effective pollination period (EPP) identified as a key factor. In this study, the EPP was assessed for the first time by examining stigma receptivity, style suitability, pollen tube growth rate, and ovule longevity, determined by fluorescence emission microscopy, along with initial fruit set (IFS) determined by sequential hand-pollination of flowers of two cultivars of W. villosa var. villosa under field conditions in Xishuangbanna, South China, in 2022 and 2023. The results showed that the inner surface of the stigma is the receptive region, with receptivity lasting more than three days, as confirmed by pollen adhesion and pollen germination. Style suitability, determined by successful pollen tube entry into the ovule, was maintained for two days; most pollen tubes reached the ovules within one day when stigma receptivity was highest. Ovule longevity persisted for at least three days. The IFS was highest when pollinated at 0–1 days after anthesis (DAA) but dropped sharply to near 0% by 2 DAA. Both EPP estimates, based on its components and IFS, indicated that the EPP is two days, with style suitability being the primary limiting factor. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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20 pages, 6424 KB  
Article
Combined Multi-Omics and Co-Expression Network Analyses Uncover the Pigment Accumulation Mechanism of Orange-Red Petals in Brassica napus L.
by Ledong Jia, Shengting Li, Chao Zhang, Lijun Zeng, Shulin Shen, Nengwen Yin, Huiyan Zhao, Zhanglin Tang, Cunmin Qu, Jiana Li and Zhiyou Chen
Biology 2025, 14(6), 693; https://doi.org/10.3390/biology14060693 - 13 Jun 2025
Cited by 1 | Viewed by 1315
Abstract
Rapeseed (Brassica napus L.) has been cultivated as an ornamental plant in recent years. However, the metabolic and regulatory processes involved in pigment accumulation in. B. napus flowers are poorly understood. To address this knowledge gap, we conducted a multi-omics analysis of [...] Read more.
Rapeseed (Brassica napus L.) has been cultivated as an ornamental plant in recent years. However, the metabolic and regulatory processes involved in pigment accumulation in. B. napus flowers are poorly understood. To address this knowledge gap, we conducted a multi-omics analysis of the orange-red-flowered ‘OrP’ and the yellow-flowered ‘ZS11’ rapeseed cultivars. The total anthocyanin content of ‘OrP’ petals was 5.420-fold and 3.345-fold higher than ‘ZS11’ petals at the S2 and S4 developmental stages, respectively. The red coloration of ‘OrP’ flowers resulted primarily from the presence of anthocyanin pigment derivatives. The up-regulated differentially expressed genes (DEGs) of four stages in ‘OrP’ were found to be significantly enriched in phenylpropanoid, flavonoid, and anthocyanin metabolism-associated GO and KEGG terms. Weighted Gene Co-expression Network Analysis (WGCNA) revealed that 51 DEGs were linked to anthocyanin metabolism, including several structural genes such as BnaCHS, BnaF3H, BnaF3′H, BnaCHS, BnaDFR, BnaANS, BnaUGTs, and the transcription factor (TF) genes BnaHY5, BnaBBX22, BnaPIL1, BnaPAP2, BnaTT8, BnaTTG2, and BnaMYBL2. Furthermore, we found that three main factors affecting the relative content of anthocyanins in petals were likely responsible for the fading of ‘OrP’ petals, namely the significantly down-regulated expression of genes (BnaDFR, BnaANS, BnaPAP2, BnaTT8, and BnaTTG2) related to anthocyanin biosynthesis, the significantly up-regulated expression of genes (Bna.BGLUs, Bna.PRXs, and BnaMYBL2) related to anthocyanin degradation or the negative regulation of anthocyanin biosynthesis, and the rapidly increasing petals area. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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15 pages, 10694 KB  
Article
RNA Interference-Mediated Suppression of GhSP (SELF-PRUNING) Modulates the Plant Architecture of Transgenic Cotton in a Dose-Dependent Manner
by Yi Wang, Qinzhao Liu, Wanting Yu, Junmin Chen, Qingwei Suo, Zhong Chen, Jianyan Zeng, Aimin Liang, Jie Kong and Yuehua Xiao
Biology 2025, 14(6), 601; https://doi.org/10.3390/biology14060601 - 25 May 2025
Viewed by 1167
Abstract
Cotton exhibits indeterminate growth potential at its apical meristem. In field cultivation, it is often necessary to restrict plant height by the foliar application of plant growth regulators or artificial topping. The genetic engineering of cotton architecture offers an efficient, environmentally friendly, and [...] Read more.
Cotton exhibits indeterminate growth potential at its apical meristem. In field cultivation, it is often necessary to restrict plant height by the foliar application of plant growth regulators or artificial topping. The genetic engineering of cotton architecture offers an efficient, environmentally friendly, and low-cost alternative to current field management. Our study aimed to improve the plant architecture of transgenic cotton by the suppression of GhSP, a key flowering repressor, via the RNA interference method. Sixteen independent transgenic lines were generated and classified as mildly, moderately, and severely suppressed, according to GhSP expression levels. Field evaluation revealed the dose-dependent effects of GhSP silencing on plant height. The mildly suppressed line GhSPi-#5 exhibited a semi-dwarf phenotype of approximately 70~100 cm in height. Negative phenotypes, including excessive dwarf plant architecture and inferior fiber quality and yield traits, were observed in severely GhSP-suppressed transgenic lines. Notably, the mild silencing of GhSP in GhSPi-#5 did not negatively affect leaf and flower organ growth, pollen fertility, major agronomic traits, or fiber quality compared with the wild type. These observations demonstrate the feasibility of manipulating the architecture of transgenic cotton via GhSP silencing. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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17 pages, 3117 KB  
Article
Arabidopsis P4-ATPases ALA1 and ALA7 Enhance Resistance to Verticillium dahliae via Detoxifying Vd-Toxins
by Fanlong Wang, Mingliang Qiu, Xiaoxia Yao, Jiancong Li, Hui Ren, Mei Su, Jiaohuan Shen, Caiwang Li, Qian Jiang, Zixuan Zhang, Yundi Li, Jiyu Tang, Xianbi Li, Yanhua Fan and Yan Pei
Biology 2025, 14(6), 595; https://doi.org/10.3390/biology14060595 - 23 May 2025
Viewed by 1169
Abstract
Background: Verticillium wilt, which is a soil-borne vascular disease, causes serious economic losses worldwide. Various toxins secreted by V. dahliae are key factors that lead to wilt symptoms. Methods: The Vd-toxins CIA, indazole, and 3ICD were labeled with fluorescence groups, respectively, to observe [...] Read more.
Background: Verticillium wilt, which is a soil-borne vascular disease, causes serious economic losses worldwide. Various toxins secreted by V. dahliae are key factors that lead to wilt symptoms. Methods: The Vd-toxins CIA, indazole, and 3ICD were labeled with fluorescence groups, respectively, to observe the transport pathway. Transcriptome sequencing and qRT-PCR were employed to assess the expression patterns under Vd-toxin treatment. Results: AtALA1 and AtALA7 were up-regulated by V. dahliae and LC-toxins, and overexpression of either AtALA1 or AtALA7 increased Arabidopsis resistance against LC-toxins. Overexpression of AtALA1 improved the resistance of Arabidopsis to 4MBA, 3ICD, and indazole, while AtALA7 enhanced resistance to 4MBA, 3ICD, and CIA. AtALA7-overexpressing plants showed a stronger capability to transport CIAFITC and 3ICD5-FAM into vacuoles, while AtALA1-overexpressing plants accumulated indazole5-FAM and 3ICD5-FAM. Aggregation of AtALA1 and AtALA7 enhances the resistance of plants to V. dahliae. Conclusions: Arabidopsis P4-ATPase genes AtALA1 and AtALA7 mediated cell detoxification by transporting different Vd-toxins to vacuoles for degradation, thereby increasing resistance to Verticillium wilt. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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17 pages, 11525 KB  
Article
Alpine Adaptive Mechanism on Rhizosphere Microbes Recruitment of Crepis napifera (Franch.) Babc. by Multi-Omics Analysis
by Genlin Yang, Weiwei Liu, Xinchun Mo and Zhinan Mei
Biology 2025, 14(4), 345; https://doi.org/10.3390/biology14040345 - 27 Mar 2025
Viewed by 1363
Abstract
Background: The accumulation of secondary metabolites in medicinal plants is often influenced by a variety of factors, and rhizosphere microorganisms typically engage in complex interactions with their host plants. Crepis napifera (Franch.) Babc., a regionally significant medicinal plant, contains a diverse array of [...] Read more.
Background: The accumulation of secondary metabolites in medicinal plants is often influenced by a variety of factors, and rhizosphere microorganisms typically engage in complex interactions with their host plants. Crepis napifera (Franch.) Babc., a regionally significant medicinal plant, contains a diverse array of terpenoids and demonstrates substantial potential for resource development and utilization. Methods: Transcriptome sequencing, metabolomic profiling, and 16S rRNA gene amplicon sequencing were employed to assess the transcriptional expression patterns, metabolic variations, and rhizosphere microbial community composition of C. napifera (Franch.) Babc. roots distributed across various regions. Results: A total of 3679, 8615, and 11,333 differentially expressed genes (DEGs) were identified in the pairwise comparisons between H1 vs. H2, H2 vs. H3, and H1 vs. H3, respectively. Notably, 497 DEGs were consistently detected across all three comparisons. Additionally, Weighted Gene Co-expression Network Analysis (WGCNA) revealed that the expression levels of genes within the turquoise and yellow modules exhibited a significant positive correlation with elevation. In total, 462 differentially expressed metabolites (DEMs) were identified across the same comparisons. Among these compounds, terpenoids, phenolic acids, amino acids and their derivatives, lipids, and alkaloids accounted for 62.98% of the total differential metabolite content. The accumulation patterns of DEMs varied significantly across different regions in the roots of C. napifera (Franch.) Babc. under the three altitude conditions. In response to environmental conditions and the survival strategy of C. napifera (Franch.) Babc. in alpine areas, an investigation into the rhizosphere microbial community was conducted. Four key microbial genera were identified as being correlated with terpenoid biosynthesis and plant nutritional metabolism. Specifically, Pedosphaera, Acidothermus, and Nevskia exhibited terpene biosynthesis capabilities. Additionally, Herbaspirillum, a common microorganism involved in plant nitrogen fixation, respiration, carbon metabolism, and cell wall metabolism, was also enriched in the rhizosphere of C. napifera (Franch.) Babc. These findings suggested that C. napifera (Franch.) Babc. might recruit these microorganisms to enhance its resistance to environmental stress in alpine areas. Conclusions: The accumulation of terpene in C. napifera (Franch.) Babc. across different regions was influenced by transcriptional changes. The rhizosphere microbial communities also changed during this process, showing a recruitment effect that enhances plant growth and offers potential value. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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Review

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Review
The Multifunctional Role of Patatin in Potato Tuber Sink Strength, Starch Biosynthesis, and Stress Adaptation: A Systematic Review
by Yicong Wu, Yunxia Zeng, Wenying Zhang and Yonghong Zhou
Biology 2026, 15(1), 29; https://doi.org/10.3390/biology15010029 - 24 Dec 2025
Cited by 1 | Viewed by 1146
Abstract
Potato (Solanum tuberosum) is one of the world’s most important food crops, with tuber sink strength and starch deposition determining yield, quality, and processing performance. While starch is the dominant carbohydrate reserve, its accumulation is tightly linked with protein metabolism. Patatin, [...] Read more.
Potato (Solanum tuberosum) is one of the world’s most important food crops, with tuber sink strength and starch deposition determining yield, quality, and processing performance. While starch is the dominant carbohydrate reserve, its accumulation is tightly linked with protein metabolism. Patatin, the major soluble storage protein, constitutes up to 40% of total tuber protein. In addition to serving as a nitrogen and carbon reserve, patatin exhibits lipid acyl hydrolase (phospholipase A2-like) activity, suggesting roles in membrane remodeling and stress signaling. This dual identity places patatin at the intersection of storage, metabolic regulation, and defense. A structured review of studies published between 1980 and 2025 was developed using PubMed, Web of Science, Frontiers, and MDPI databases. Prioritized research included molecular, physiological, and multi-omics analyses of patatin expression, regulation, and function under optimal and stress conditions. Evidence indicates that patatin contributes to carbon–nitrogen balance and sink strength by affecting sucrose import, vacuolar osmotic capacity, and starch biosynthesis. Under drought, salinity, and pathogen stress, patatin transcript levels, protein stability, and enzymatic activity shift, leading to reduced starch deposition, altered sugar accumulation, osmoprotection, and reallocation toward defense responses. Despite these insights, major knowledge gaps remain. These include isoform-specific roles, integration into sugar–hormone regulatory networks, and field-scale responses under fluctuating environments. Future progress will require integrated multi-omics, fluxomics, and proximity-labeling approaches, combined with CRISPR-based isoform editing and promoter engineering. Targeting patatin as both a biomarker and an engineering node offers opportunities to develop climate-ready potato cultivars with improved starch yield, tuber quality, and stress resilience. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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