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Recent Advances in Plant Genetics and Genomics
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Recent Advances in Plant Genetics and Genomics

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 16783

Special Issue Editors

Prof. Dr. Longbiao Guo

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Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, China
Interests: rice; molecular biology; gene mapping; functional genome
Special Issues, Collections and Topics in MDPI journals
Dr. Qian-Hao Zhu

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Guest Editor
Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
Interests: cotton biology; genomics; molecular breeding; plant noncoding RNAs; biostress tolerance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The publication of the genomic sequence of A. thaliana in 2000 and of a O. sativa in 2002 marked the beginning of an exciting era in which advances in technology and methodology uncovered the genetic blueprints of hundreds of plant species. This, in turn, promotes functional genome development; for example, in rice, over 4100 functionally characterized rice genes and more than 6000 gene family members have been confirmed. In recent years, a rice pangenome and genome navigation system—RiceNavi—has been developed for QTN polymerization and breeding route optimization. The Oryza super pangenome, which has the largest population size of plants and fully annotated genomes, has also been constructed. Several nitrogen-efficient genes have been identified and their molecular mechanism of nitrogen efficiency has been dissected. The expression of some genes can significantly increase rice yield under experimental conditions. Significant progress has also been made in research relating to the mechanism of rice broad-spectrum disease resistance, temperature response, and salt–alkali resistance. In gene editing, a new polynucleotide-targeted deletion system—AFIDs (APOBEC-Cas9 fusion induced deletion systems)—has been established, successfully achieving accurate and predictable polynucleotide deletion in rice and wheat genomes. Using CRISPR/Cas9 technology, gene editing has produced many practical new materials including the rice apomixis material. This Special Issue of Plants will highlight the allelic gene identification, function, evolution, and diversity of rice germplasm resources in genomic and RNA-seq levels, as well as their breeding applications.

Prof. Dr. Longbiao Guo
Dr. Qian-Hao Zhu
Guest Editors

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Keywords

  • rice
  • genomic selection
  • multi-omics
  • genetic analysis
  • gene editing
  • molecular design breeding

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Related Special Issue

Published Papers (11 papers)

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Research

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24 pages, 3739 KB  
Article
Screening and Evaluation of Rice to Assess Antibiosis and Antixenosis Resistance to White-Backed Planthopper (Sogatella furcifera)
by Jariya Roddee, Kamolchanok Umnajkitikorn, Napatson Chansawang, Jirapong Jairin and Jureemart Wangkeeree
Plants 2026, 15(5), 811; https://doi.org/10.3390/plants15050811 - 6 Mar 2026
Viewed by 729
Abstract
The white-backed planthopper, Sogatella furcifera, and the brown planthopper, Nilaparvata lugens, severely impact rice production, necessitating effective selection methods for resistant cultivars. S. furcifera poses a significant threat to rice cultivation, particularly in Asia. Through this study, we aimed to establish [...] Read more.
The white-backed planthopper, Sogatella furcifera, and the brown planthopper, Nilaparvata lugens, severely impact rice production, necessitating effective selection methods for resistant cultivars. S. furcifera poses a significant threat to rice cultivation, particularly in Asia. Through this study, we aimed to establish an effective approach to identifying resistant rice varieties based on feeding behavior, physiological and chemical responses, and genetic analysis. Three key activities were involved: (1) evaluation of planthopper feeding behavior utilizing the honeydew drop method, the electrical penetration graph technique, and growth rate analysis; (2) investigation into the physiological and chemical traits of rice; and (3) analysis of resistance-related gene expression. The results indicated larger honeydew drop areas, fewer and shorter probing events, and structural defenses such as increased trichome density in resistant rice genotypes, likely hindering insect attachment and feeding. We confirmed the suitability of the growth rate method for resistance screening. Gene expression analysis identified PR10a upregulation in resistant rice, suggesting a molecular basis for resistance. This study enables the selection of rice varieties resistant to planthoppers, supporting sustainable pest management and breeding programs. The findings support sustainable pest management by enabling the targeted selection of resistant varieties, ultimately aiding in the development of rice genotypes with enhanced resistance across growth stages. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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13 pages, 1718 KB  
Article
Genomic Variation and GWAS Analysis for Salt Tolerance Discovered in Egyptian Rice Germplasm
by Yueying Wang, Faming Yu, Sirinthorn Kongpraphrut, Congcong Liu, Muhammad Asad Ullah Asad, Salma Kelany, Mengrui Sun, Yuxuan Wang, Yang Lv, Galal Anis, Mohamed Hazman, Qian Qian, Yuexing Wang and Longbiao Guo
Plants 2026, 15(1), 128; https://doi.org/10.3390/plants15010128 - 1 Jan 2026
Cited by 2 | Viewed by 679
Abstract
Egyptian rice landraces represent a unique genetic reservoir shaped by arid environments, yet their genomic and transcriptional response to salt stress remains largely unexplored. Here, we integrated genomic, transcriptomic, and population genetic analyses to systematically unravel the mechanisms of salt tolerance in this [...] Read more.
Egyptian rice landraces represent a unique genetic reservoir shaped by arid environments, yet their genomic and transcriptional response to salt stress remains largely unexplored. Here, we integrated genomic, transcriptomic, and population genetic analyses to systematically unravel the mechanisms of salt tolerance in this vital germplasm. Resequencing 56 Egyptian accessions uncovered a treasure trove of genetic variation, including 18,204 novel SNPs. An expanded GWAS on 258 accessions discovered 17 novel loci for salt tolerance. Parallel RNA-Seq analysis of a salt-tolerant-susceptible pair (Giza 176 vs. 9311) under stress delineated a defense network centered on phenylpropanoid and lipid metabolic pathways in the tolerant genotype. The power of our integrated approach was exemplified by the convergent identification of ONAC063, where GWAS loci, transcriptional responsiveness, and haplotype-phenotype association collectively validated its role. Furthermore, selection sweep analysis highlighted 62 candidate genes under divergent selection. Our study not only positions Egyptian rice as a key resource for allele mining but also establishes a robust multi-omics pipeline for bridging genetic diversity with complex traits, accelerating the discovery of functional genes for breeding climate-resilient crops. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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21 pages, 9758 KB  
Article
Transcriptomic Analysis of Rice (Jijing129) Reveals Growth and Gene Expression Responses to Different Red-Blue Laser Light Treatments
by Xuemei Liang, Qi Liu, Li Qin, Peng Jia, Jianfeng Wang, Changjiang Zhang, Xintong Dai, Wenbo Yu, Xiaoyu Lei, Ningning Wang and Minglai Yang
Plants 2025, 14(24), 3712; https://doi.org/10.3390/plants14243712 - 5 Dec 2025
Viewed by 664
Abstract
Artificial supplemental lighting represents a crucial agricultural technique for enhancing plant growth and development, with researchers continuously investigating the effectiveness of various light sources in horticultural applications. Laser technology, characterized by its monochromatic nature, high coherence, and elevated energy density, presents a promising [...] Read more.
Artificial supplemental lighting represents a crucial agricultural technique for enhancing plant growth and development, with researchers continuously investigating the effectiveness of various light sources in horticultural applications. Laser technology, characterized by its monochromatic nature, high coherence, and elevated energy density, presents a promising light source whose potential applications and underlying mechanisms in plant supplemental lighting remain to be thoroughly explored. To investigate the effects of different red-to-blue light ratios in laser supplemental lighting on rice (Oryza sativa L. cv. Jijing129) seedlings, we conducted a seedling-stage lighting experiment on the rice cultivar Jijing129 in a greenhouse using an LGI-660/450 dual-wavelength semiconductor laser system. The experimental design included a natural light control (AL) and three laser treatment groups, with red: blue (R:B) ratios and corresponding photon flux densities as follows: BL (50:50; 150:150 μmol m−2 s−1), CL (60:40; 180:120 μmol m−2 s−1), and DL (75:25; 225:75 μmol m−2 s−1). We systematically analyzed short-term morphological, physiological, and gene expression changes to elucidate the potential mechanisms underlying yield enhancement under different laser spectra. The results indicated that, compared to AL, all laser treatments (BL, CL, and DL) significantly increased root fresh weight, dry weight, and nitrogen content in seedlings. Furthermore, the final yield was significantly improved in all laser-treated groups, with the CL treatment exhibiting the highest yield. Transcriptome sequencing identified 10,497, 10,441, 10,700, and 10,757 expressed genes in the AL, BL, CL, and DL groups, respectively. Comparative analysis revealed 101, 1645, and 2247 differentially expressed genes (DEGs) in the BL/AL, CL/AL, and DL/AL comparisons, respectively. Gene Ontology (GO) enrichment analysis showed that these DEGs were significantly enriched in pathways such as metabolic processes, nitrogen metabolism, and protein amino acid phosphorylation. Notably, genes involved in the regulation of nitrogen compound metabolism were significantly upregulated in the CL and DL treatments. Further analysis of nitrogen metabolism and photosynthesis pathways revealed that laser irradiation induced the upregulation of specific genes. Interestingly, although physiological assays showed no significant changes in CAT, SOD, and POD activities, the expression of their corresponding genes was upregulated by laser treatment, suggesting these genes play a regulatory role during the supplemental lighting process. Therefore, our results indicated that laser supplemental lighting during the rice seedling stage increased the nitrogen content in plants and modulated the expression of related genes, and these changes might have been associated with the subsequent increase in rice yield. This study lays a foundation for understanding the molecular mechanisms of laser supplemental lighting and provides empirical support for the application of laser technology as an effective light source in agriculture. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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22 pages, 2955 KB  
Article
Chromatin-Associated Pea Apyrase psNTP9 Function as a DNA-Binding Regulatory Protein in Yeast and Arabidopsis
by Huan Wang, Robert D. Slocum, Xingbo Cai, Greg Clark and Stanley J. Roux
Plants 2025, 14(22), 3514; https://doi.org/10.3390/plants14223514 - 18 Nov 2025
Viewed by 567
Abstract
As reported in earlier work, when a pea apyrase, psNTP9 (PS), and a modified version of it, psNTP9-DM (DM), are expressed in Saccharomyces cerevisiae, they localize to nuclei, binding to largely non-overlapping promoter regions of chromatin. PS- and DM-expressing yeast also exhibit [...] Read more.
As reported in earlier work, when a pea apyrase, psNTP9 (PS), and a modified version of it, psNTP9-DM (DM), are expressed in Saccharomyces cerevisiae, they localize to nuclei, binding to largely non-overlapping promoter regions of chromatin. PS- and DM-expressing yeast also exhibit different expression profiles for potentially regulated target genes, consistent with observed phenotypes. In the present study, we use ChIP-seq assays to show that PS and DM also associate with largely different promoter regions of Arabidopsis genes, with similar non-overlapping expression profiles for potential target genes. Functional studies, using electrophoretic mobility shift assays (EMSA), verified PS-specific binding to yeast or plant promoter binding sites. DM binding to both heterologous dsDNA and to PS-specific binding site sequences was minimal. AlphaFold3 modeling of PS protein binding to a yeast PHM6 promoter sequence identified potential DNA-binding residues and a potential binding site motif (5′-(G/T)GG(G/T)A-3′) that is also present in two Arabidopsis promoter binding sites. These novel findings extend the previously known functions of PS and other plant apyrases in the Golgi or extracellular matrix, and support their potential function as DNA-binding proteins that can regulate gene expression in both yeast and Arabidopsis. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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16 pages, 4287 KB  
Article
Rolling Leaf 2 Controls Leaf Rolling by Regulating Adaxial-Side Bulliform Cell Number and Size in Rice
by Yu-Jia Leng, Shi-Yu Qiang, Wen-Yu Zhou, Shuai Lu, Tao Tao, Hao-Cheng Zhang, Wen-Xiang Cui, Ya-Fan Zheng, Hong-Bo Liu, Qing-Qing Yang, Ming-Qiu Zhang, Zhi-Di Yang, Fu-Xiang Xu, Hai-Dong Huan, Xu Wei, Xiu-Ling Cai, Su-Kui Jin and Ji-Ping Gao
Plants 2025, 14(21), 3373; https://doi.org/10.3390/plants14213373 - 4 Nov 2025
Viewed by 1144
Abstract
Leaves represent an important organ in plant photosynthesis, and moderately rolled leaves would be beneficial in establishing an ideal plant architecture and thereby increasing rice yields. In this study, a stable inherited rolled leaf mutant was obtained via ethyl methanesulfonate (EMS) mutagenesis from [...] Read more.
Leaves represent an important organ in plant photosynthesis, and moderately rolled leaves would be beneficial in establishing an ideal plant architecture and thereby increasing rice yields. In this study, a stable inherited rolled leaf mutant was obtained via ethyl methanesulfonate (EMS) mutagenesis from japonica variety WYJ27, which was named rll2 (rolling leaf 2). rll2 showed a leaf-rolling phenotype at the seedling stage, which increased with growth. Compared with the wild type, the leaves at all levels of rll2 were significantly shorter and narrower, and the leaf-rolling index gradually decreased from the highest leaf to the third-highest leaf. Semi-thin sections showed that the bulliform cells of rll2 were significantly larger than those of the wild type, and the number of cells was significantly higher than that of the wild type. Genetic analysis showed that rll2 is controlled by a pair of recessive nuclear genes. Map-based cloning revealed that RLL2 encodes a conserved and plant-specific calpain-like cysteine proteinase. RLL2 was mainly expressed in young roots, shoots, spikelets, and panicles. Transcriptome sequencing showed that a total of 104 genes were differentially expressed in the wild type and rll2. Moreover, several transcription factor genes were significantly altered in the rll2 mutant. Taken together, our findings indicate that RLL2 plays an important role in leaf rolling by regulating bulliform cells, which may be useful in breeding rice with an ideal plant architecture. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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21 pages, 4984 KB  
Article
Genome-Wide Linkage Mapping of Root System Architecture-Related Traits Under Drought Stress in Common Wheat (Triticum aestivum L.)
by Yirong Jin, Guiju Chen, Xiaodong Qiu, Fuyan Wang, Hui Jin, Liang Zhang, Cheng Liu, Jianjun Liu, Wenjing Li and Peng Liu
Plants 2025, 14(19), 3023; https://doi.org/10.3390/plants14193023 - 30 Sep 2025
Viewed by 992
Abstract
Drought severely threatens wheat production. Under drought conditions, root system architecture (DRSA)-related traits in common wheat significantly affect wheat production. In China, Zhoumai16 is a high-yield winter wheat variety in the Huang-Huai wheat region. It is suitable for high-fertilizer and high-water cultivation and [...] Read more.
Drought severely threatens wheat production. Under drought conditions, root system architecture (DRSA)-related traits in common wheat significantly affect wheat production. In China, Zhoumai16 is a high-yield winter wheat variety in the Huang-Huai wheat region. It is suitable for high-fertilizer and high-water cultivation and has moderate drought tolerance. DK171 is a newly developed high-yield and stress-tolerant variety, with higher drought tolerance. Thus, identifying genetic loci associated with DRSA-related traits from DK171 and developing available molecular markers are of great importance for enhancing wheat stress tolerance breeding. In this study, DRSA-related traits, including the total root dry weight (DDRW), total root length (DTRL), total root area (DTRA), and the number of root tips (DNRT) under drought stress, were assessed using the hydroponic system in Zhoumai16/DK171 recombinant inbred lines (RIL) population. A total of five quantitative trait loci (QTL) for DRSA-related traits were identified, e.g., QDDRW.daas-1BL, QDTRS.daas-4AL, QDNRT.daas-4DS, QDTRL.daas-3AL, and QDDRW.daas-5D, and explained 6.1% to 18.9% of the phenotypic variances, respectively. Among these, QDTRS.daas-4AL and QDTRL.daas-3AL were consistent with previous reports, whereas the QDDRW.daas-1BL, QDNRT.daas-4DS, and QDDRW.daas-5D are novel. The favorable alleles of QDTRS.daas-4AL and QDNRT.daas-4DS were inherited from Zhoumai16, whereas the favorable alleles for QDDRW.daas-1BL, QDTRL.daas-3AL, and QDDRW.daas-5D were contributed by DK171. Furthermore, five kompetitive allele-specific PCR (KASP) markers, Kasp_1BL_DTRS (QDDRW.daas-1BL), Kasp_3AL_DTRS (QDTRL.daas-3AL), Kasp_4A_DTRS (QDTRA.daas-4A), Kasp_5D_DDRW (QDDRW.daas-5D), and Kasp_4D_DNRT (QDNRT.daas-4D), were developed and validated in a diverse panel with 108 wheat varieties mainly from China. Additionally, eight candidate genes related to plant hormone regulation, ABC transporters, and calcium-dependent lipid-binding domain proteins were identified. This study offers new loci, candidate genes, and available KASP markers for wheat drought tolerance breeding and facilitating progress in developing drought-tolerant wheat cultivars. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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17 pages, 6504 KB  
Article
Identification and Expression Characteristics of the Cryptochrome Gene Family in Chimonobambusa sichuanensis
by Yining Kong, Changlai Liu, Tianshuai Li, Ji Fang and Guohua Liu
Plants 2025, 14(11), 1637; https://doi.org/10.3390/plants14111637 - 27 May 2025
Cited by 1 | Viewed by 1131
Abstract
Cryptochrome is an important class of blue-light receptors involved in various physiological activities such as photomorphogenesis and abiotic stress regulation in plants. In order to investigate the molecular mechanism of blue-light-induced color change in Chimonobambusa sichuanensis, we screened and cloned the gene [...] Read more.
Cryptochrome is an important class of blue-light receptors involved in various physiological activities such as photomorphogenesis and abiotic stress regulation in plants. In order to investigate the molecular mechanism of blue-light-induced color change in Chimonobambusa sichuanensis, we screened and cloned the gene encoding the blue-light receptor Cryptochrome. In order to investigate the molecular mechanism of blue-light-induced color change in Chimonobambusa sichuanensis, we screened and cloned the gene encoding the blue-light receptor Cryptochrome in Ch.sichuanensis, and analyzed the expression characteristics of the Cryptochrome gene in Ch.sichuanensis under different light intensities, light quality, and temperatures by qRT-PCR. Through homologous cloning, a total of four CsCRY genes were obtained in the Ch.sichuanensis genome, namely, CsCRY1a, CsCRY1b, CsCRY2, and CsCRY3. Structural domain analyses of the encoded proteins of the four genes revealed that all CsCRYs proteins had the typical photoreceptor structural domain, PRK (protein kinase C-related kinase). Phylogenetic tree analyses revealed that the four genes CsCRY1a, CsCRY1b, CsCRY2, and CsCRY3 could be categorized into three subfamilies, with CsCRY1a and CsCRY1b clustered in subfamily I, CsCRY2 classified in subfamily II, and CsCRY3 belonging to subfamily III. All CsCRYs proteins lacked signal peptides and the instability index was higher than 40, among which the isoelectric points of CsCRY1a, CsCRY1b, and CsCRY2 were around five. qRT-PCR analysis revealed that the expression of all four CsCRYs genes was up-regulated at 75 µmol·m−2·s−1 blue-light illumination for 4 h. In addition, under treatments of different light quality, the expression of CsCRY2 genes was significantly higher under blue light than under red light and a mixture of red light and blue light with a light intensity of 1:1; the expression of CsCRY1a and CsCSY1b was significantly higher in the mixed light of red and blue light than in the single light treatment, while under different temperature gradients, CsCRYs genes were highly expressed under low-temperature stress at −5 °C and 0 °C. This study provides a basis for further research on blue-light-induced color change in Ch.sichuanensis and expands the scope of Cryptochrome gene research. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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15 pages, 4324 KB  
Article
QTL-Seq and Fine-Mapping Analyses Identify QTL and Candidate Genes Controlling Snake-like Pod Surface Trait in Vegetable Cowpea Yardlong Bean
by Khwanruedee Thepphomwong, Makawan Srichan, Artitaya Deeroum, Kularb Laosatit and Prakit Somta
Plants 2025, 14(10), 1447; https://doi.org/10.3390/plants14101447 - 12 May 2025
Cited by 1 | Viewed by 1474
Abstract
Yardlong bean is a vegetable type of cowpea grown for fresh and immature pods. “Thua Ngu” is a specialty yardlong bean cultivar with its unique snake-like pod surface and highly crispy pods that may be useful for the breeding of a new cultivar(s). [...] Read more.
Yardlong bean is a vegetable type of cowpea grown for fresh and immature pods. “Thua Ngu” is a specialty yardlong bean cultivar with its unique snake-like pod surface and highly crispy pods that may be useful for the breeding of a new cultivar(s). The objectives of this study were to determine the mode of inheritance of the snake-like pod trait and locate the genome region controlling this trait in Thua Ngu. Microscopic observation revealed that the shape, size, and organization of cells of immature and mature pods of Thua Ngu were clearly different from those of “Raya” (normal yardlong bean). Fiber analysis showed that lignin content in immature and mature pods of Thua Ngu was 2.05- and 3.45-fold higher than that in Raya. Segregation analysis using F2 and F2:3 populations of the cross Thua Ngu × Raya demonstrated that a single gene controls the snake-like pod trait. QTL-seq analysis using the F2 population revealed a major locus, qSlp4.1, for the snake-like pod trait. Fine-mapping using F2 and F2:3 populations delimited qSlp4.1 to a 152.88 Kbp region containing nine genes. Genes with functions involved in cell morphology and/or lignin formation, including Vigun04g163400, Vigun04g163600, and Vigun04g163700, were identified as candidate genes for the snake-like pod trait. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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Review

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31 pages, 4168 KB  
Review
Protein Post-Translational Modifications in Plant Abiotic Stress Responses
by Gengmi Li, Baohua Feng, Qian-Hao Zhu, Kaifeng Jiang and Tao Zhang
Plants 2026, 15(1), 52; https://doi.org/10.3390/plants15010052 - 23 Dec 2025
Cited by 1 | Viewed by 2245
Abstract
Protein post-translational modifications (PTMs), as an important biological process of plants responding to environmental stimuli, can regulate the chemical decoration and properties of translated proteins by altering amino acid side chains or protein terminal structures, thereby affecting the synthesis, assembly, localization, function, and [...] Read more.
Protein post-translational modifications (PTMs), as an important biological process of plants responding to environmental stimuli, can regulate the chemical decoration and properties of translated proteins by altering amino acid side chains or protein terminal structures, thereby affecting the synthesis, assembly, localization, function, and degradation of proteins. Notably, PTMs regulate protein function without changing protein expression levels. Two dozen types of PTMs have been identified. This review summarizes the molecular mechanisms of major types of PTMs, including phosphorylation, ubiquitination, SUMOylation, glycosylation, methylation, and acetylation, with a focus on their regulatory roles in plant responses to abiotic stresses. Under heat stress, phosphorylation activates transcription factors such as HSFA1 (heat shock transcription factor 1), while SUMOylation regulates the activity of HSFA1/HSFA2 in the heat stress signaling pathway. Upon cold stress, phosphorylation, ubiquitination, and S-acylation collectively regulate the expression of cold tolerance-related genes. The drought stress response relies on SnRK2s (Sucrose 321 non-Fermenting 1-related protein kinase 2s) -mediated phosphorylation, regulation of ARF7 (auxin response factor 7) by SUMOylation, and ubiquitination. In salt stress, the coupling of phosphorylation of SOS (salt overly sensitive) pathway-related proteins, ubiquitination, and phospholipid metabolism maintains ion homeostasis. Additionally, PTMs play a key role in ABA-mediated abiotic stress responses by regulating core components of signal transduction, such as PYR (pyrabactin resistance)/PYL (PYR1-LIKE)/RCAR (regulatory components of ABA receptor) receptors, PP2Cs (protein phosphatases type 2C), and SnRK2s. On the basis of the synthesis of the regulatory mechanisms of PTMs, we discuss how PTMs can be manipulated to breed abiotic stress resilient crops and the issues to be addressed to achieve the goal, such as crosstalk between PTMs, technical challenges in investigating PTMs and identifying PTM substrates. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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28 pages, 2235 KB  
Review
Research Progress on Rice-Blast-Resistance-Related Genes
by Biaobiao Cheng, Beibei Lv, Qiangbing Xuan, Yunfang Li, Jing Li, Weihong Liang and Junjie Wang
Plants 2025, 14(17), 2698; https://doi.org/10.3390/plants14172698 - 29 Aug 2025
Cited by 4 | Viewed by 5000
Abstract
As a staple food crop, Oryza sativa L. is not only the basis of global food and nutrition security but also an important cornerstone of national economic development and social stability. However, the growth of rice is often accompanied by the threat of [...] Read more.
As a staple food crop, Oryza sativa L. is not only the basis of global food and nutrition security but also an important cornerstone of national economic development and social stability. However, the growth of rice is often accompanied by the threat of rice blast, which can lead to the death of seedlings or plants before heading. In the later stages of growth, a severe leaf blast infection will reduce the leaf area at the filling stage, thereby reducing the grain yield. The study of rice blast resistance genes and susceptibility genes is a key strategy for controlling the occurrence of rice blast and ensuring sustainable rice production. This paper reviews the impact of rice blast on the global economy and food security in recent years, describes the immune mechanism of rice blast resistance, and introduces the latest progress in related research. At the same time, the main genes of rice blast resistance and the resistance-related genes, as well as the susceptibility genes identified or cloned in recent years, are summarized. This paper also discusses the application of conventional breeding, molecular-marker-assisted breeding, gene editing, and other technologies in rice blast resistance breeding. The problem of accurately finding avirulence genes for R genes in current disease-resistant breeding is discussed and explored, aiming to improve rice blast resistance, agronomic traits, and yield in a sustainable way. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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Other

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12 pages, 2521 KB  
Brief Report
Expression of the Nicotiana benthamiana Retrozyme 1 (NbRZ1) Genomic Locus
by Alexander A. Lezzhov, Anastasia K. Atabekova, Denis A. Chergintsev, Andrey G. Solovyev and Sergey Y. Morozov
Plants 2025, 14(8), 1205; https://doi.org/10.3390/plants14081205 - 14 Apr 2025
Viewed by 1077
Abstract
Retrozymes are a class of non-autonomous plant retrotransposons that have long terminal repeats (LTRs) containing hammerhead ribozymes (HHRs) that facilitate the circularization of the retrozyme RNA. The LTR of Nicotiana benthamiana retrozyme 1 (NbRZ1) has been shown to contain a promoter that directs [...] Read more.
Retrozymes are a class of non-autonomous plant retrotransposons that have long terminal repeats (LTRs) containing hammerhead ribozymes (HHRs) that facilitate the circularization of the retrozyme RNA. The LTR of Nicotiana benthamiana retrozyme 1 (NbRZ1) has been shown to contain a promoter that directs transcription of this retroelement. In this study, we identified the transcription start site of the promoter contained in the LTR of NbRZ1 and mapped the promoter region essential for its transcriptional activity. Using transgenic Arabidopsis thaliana plants carrying the GUS gene under the control of the NbRZ1 LTR, the NbRZ1 transcript was demonstrated to potentially encode a protein targeted for proteasomal degradation in the plant cell. Overexpression of this protein in plants using a viral expression vector was found to cause severe necrosis. The data presented suggest a tight regulation of the expression of the NbRZ1-encoded polypeptide in plants and its potential functional importance, although further research is needed to determine whether circular and/or linear retrozyme RNA forms can be translated in plants. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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