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学者姓名：吴为人
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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 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.
Keyword ：
CRISPR/Cas9 CRISPR/Cas9 inheritable mutagenicity inheritable mutagenicity off-target effects off-target effects rice (Oryza sativa L.) rice (Oryza sativa L.) RR-TZF gene subfamily RR-TZF gene subfamily
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| GB/T 7714 | Zhou, Shufen , Tian, Dagang , Liu, Huaqing et al. Editing the RR-TZF Gene Subfamily in Rice Uncovers Potential Risks of CRISPR/Cas9 for Targeted Genetic Modification [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2025 , 26 (3) . |
| MLA | Zhou, Shufen et al. "Editing the RR-TZF Gene Subfamily in Rice Uncovers Potential Risks of CRISPR/Cas9 for Targeted Genetic Modification" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 26 . 3 (2025) . |
| APA | Zhou, Shufen , Tian, Dagang , Liu, Huaqing , Lu, Xiaozhuan , Zhang, Di , Chen, Rui et al. Editing the RR-TZF Gene Subfamily in Rice Uncovers Potential Risks of CRISPR/Cas9 for Targeted Genetic Modification . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2025 , 26 (3) . |
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A spontaneous barley mutant, young leaf chlorina (ylc), was identified in this study. Young leaves of ylc exhibited a yellow base and green tip, with reduced chlorophyll content, and altered chlorophyll fluorescence pattern, and underdeveloped grana in chloroplasts. The color of mutant leaves gradually transitioned to pale green and then became green in mature leaves. The ylc phenotype was found to be controlled by a recessive locus mapped to a 2.4 Mb interval on chromosome 7HS using bulked-segregant analysis with deep sequencing and further fine mapped to a 410 kb interval using polymorphic markers. The YLC locus co-segregated with a molecular marker that led to identification of HORVU7Hr1G011570 as the most likely candidate gene. As compared to the barley reference genome, the candidate ylc allele contained nucleotide changes that would lead to functional alterations of its protein product. The candidate YLC gene encodes a DYW-type pentatricopeptide repeat (PPR) protein, implicated in RNA cleavage and RNA editing in chloroplasts. Chlorophyll fluorescence analysis suggests that the PPR protein may regulate chloroplast development through the function of NAD(P)H dehydrogenase (NDH) complex and plays a pivotal role in mediating electron flow in thylakoid membranes during leaf growth in barley.
Keyword ：
Barley Barley BSA-seq BSA-seq Fine mapping Fine mapping PPR PPR RNA-seq RNA-seq Young leaf chlorina Young leaf chlorina
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| GB/T 7714 | Huang, Biguang , Huang, Daiqing , Zhang, Jianchun et al. Barley young leaf chlorina, a putative pentatricopeptide repeat gene, is essential for chloroplast development in young leaves [J]. | PLANT MOLECULAR BIOLOGY , 2025 , 115 (2) . |
| MLA | Huang, Biguang et al. "Barley young leaf chlorina, a putative pentatricopeptide repeat gene, is essential for chloroplast development in young leaves" . | PLANT MOLECULAR BIOLOGY 115 . 2 (2025) . |
| APA | Huang, Biguang , Huang, Daiqing , Zhang, Jianchun , Xiong, Jiwei , Wu, Shiyu , Zheng, Xinrong et al. Barley young leaf chlorina, a putative pentatricopeptide repeat gene, is essential for chloroplast development in young leaves . | PLANT MOLECULAR BIOLOGY , 2025 , 115 (2) . |
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MADS6, JAGGED (JAG), and DROOPING LEAF (DL) are key regulators of floral organ patterns in rice (Oryza sativa); however, how they work together in specifying floral organs remains to be determined. Here, we extensively analyzed the coordination mechanism. Genetic interactions showed that all double/triple mutant combinations of mads6-5 with jag and/or dl-sup7 generated an inflorescence from the spikelet center and lemma-like organs (LLOs) at the periphery, indicating that these genes synergistically promote floral organ specification, inhibit inflorescence initiation, and terminate the floral meristem (FM). Particularly, a fully developed mads6-5 jag spikelet appeared as a large bouquet composed of numerous multifloral complexes (MFC), while the triple mutant was generally similar to mads6-5 jag, except for a longer pedicel and fewer MFCs. Expression analysis revealed that JAG directly inhibits the transcription of MADS6 in stamens but not in pistils, as JAG and DL co-express in pistils and form a JAG-DL complex, indicating that JAG and DL may coordinate the transcription of MADS6 in sexual organs. Protein interactions revealed that MADS6 and JAG bind to 5 spikelet-related YABBY proteins (including DL), forming 10 heterodimers, suggesting that they may promote floral differentiation through various pathways. However, MADS6 and JAG neither bound together nor formed a heterotrimer with any of the 5 YABBY proteins. These findings revealed specific synergistic patterns between MADS6, JAGGED, and YABBY proteins, which may contribute to the unique characteristics of rice spikelets and provide insights into the diversity regulation mechanisms of floral specification in plants. The transcription factors MADS6 and JAGGED synergistically determine rice spikelet characteristics by regulating MADS6 transcription and genetic and physical interaction with YABBY family proteins.
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| GB/T 7714 | Cai, Zhengzheng , Li, Jieqiong , Su, Yuanyuan et al. The MADS6, JAGGED, and YABBY proteins synergistically determine floral organ development in rice [J]. | PLANT PHYSIOLOGY , 2025 , 197 (3) . |
| MLA | Cai, Zhengzheng et al. "The MADS6, JAGGED, and YABBY proteins synergistically determine floral organ development in rice" . | PLANT PHYSIOLOGY 197 . 3 (2025) . |
| APA | Cai, Zhengzheng , Li, Jieqiong , Su, Yuanyuan , Zheng, Lili , Zhang, Jianwei , Zhu, Miaomiao et al. The MADS6, JAGGED, and YABBY proteins synergistically determine floral organ development in rice . | PLANT PHYSIOLOGY , 2025 , 197 (3) . |
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JAGGED (JAG) and DROOPING LEAF (DL) are two key regulators of floral organ pattern in rice, but how they work together in establishing reproductive organs and terminating FM remains to be determined. Here, we have analyzed the coordination mechanism in detail. While the floral meristem (FM) determinacy is severely compromised in null-allele jag and dl spikelets, jag dl exhibits a complete loss of FM determinacy, with a large bouquet composed of lemma-like organs sprouting from the center of spikelets replacing the stamen and pistil, indicating that they synergistically determine sexual organ identity and FM termination. Protein-protein interactions revealed that JAG binds to SUPERWOMAN1 (SPW1)/OsMADS16 and DL, forming two heterodimers, JAG-SPW1 and JAG-DL. Expression analysis revealed that JAG binds to the promoters of both DL and SPW1 and directly activates SPW1, while SPW1 and DL do not directly inhibit each other. However, JAG-SPW1 inhibits DL transcription, while JAG-DL inhibits SPW1 transcription, indicating that JAG may mediate the transcription antagonism through these two heterodimers to limit the transcription of DL in stamen and SPW1 in pistil, which is crucial for sexual organ origination in the appropriate location. Meanwhile, JAG and DL can directly inhibit OSH1 and OSH15, individually or synergistically, which is essential for timely termination of FM. These findings reveal the unique synergistic manner of JAG and DL in rice reproductive organ generation, providing insights into the regulatory mechanisms of floral morphogenesis in plants.
Keyword ：
DROOPING LEAF DROOPING LEAF floral meristem termination floral meristem termination floral organ specification floral organ specification JAGGED JAGGED KNOTTED-LIKE HOMEOBOX KNOTTED-LIKE HOMEOBOX rice rice SUPERWOMAN1 SUPERWOMAN1
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| GB/T 7714 | Cai, Zhengzheng , Su, Yuanyuan , Kong, Lan et al. JAGGED and DROOPING LEAF synergistically establish sexual organs and terminate floral meristem in rice [J]. | PLANT JOURNAL , 2025 , 123 (1) . |
| MLA | Cai, Zhengzheng et al. "JAGGED and DROOPING LEAF synergistically establish sexual organs and terminate floral meristem in rice" . | PLANT JOURNAL 123 . 1 (2025) . |
| APA | Cai, Zhengzheng , Su, Yuanyuan , Kong, Lan , Ren, Guangxin , Zheng, Lili , Zhu, Miaomiao et al. JAGGED and DROOPING LEAF synergistically establish sexual organs and terminate floral meristem in rice . | PLANT JOURNAL , 2025 , 123 (1) . |
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| GB/T 7714 | Guan, Huazhong , Chen, Zhiwei , Wang, Shuoxun et al. An elite RNA-DEPENDENT RNA POLYMERASE3 allele enhances preharvest sprouting resistance in rice [J]. | PLANT PHYSIOLOGY , 2025 , 198 (4) . |
| MLA | Guan, Huazhong et al. "An elite RNA-DEPENDENT RNA POLYMERASE3 allele enhances preharvest sprouting resistance in rice" . | PLANT PHYSIOLOGY 198 . 4 (2025) . |
| APA | Guan, Huazhong , Chen, Zhiwei , Wang, Shuoxun , Jiang, Bo , Zhao, Jinxiang , Gao, Yijin et al. An elite RNA-DEPENDENT RNA POLYMERASE3 allele enhances preharvest sprouting resistance in rice . | PLANT PHYSIOLOGY , 2025 , 198 (4) . |
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Linkage drag frequently impedes the utilization of beneficial genes from wild species in crop improvement. The N gene from Nicotiana glutinosa confers strong resistance to tobacco mosaic virus (TMV) but introduces linkage drag when introgressed into cultivated tobacco (Nicotiana tabacum). To address this issue, we sequenced the TMV-resistant flue-cured tobacco line 0970A and carried out comparative genomic analysis. Additionally, we used molecular markers to screen a BC4F1 population derived from the cross between 0970A and an elite flue-cured tobacco variety CB-1 (recurrent parent). As a result of sequencing 0970A, the N gene was located at the end of chromosome Nt11. The comparative genomic analysis showed that 0970A inherited approximately 3.74 Mb of N. glutinosa DNA (N-fragment) from its donor, Coker 176. From screening the BC4F1 population with molecular markers, a recombinant was identified. This recombinant had a significantly reduced N-fragment (similar to 270 kb), which minimized the linkage drag while still maintaining resistance to TMV. This research indicates that the combination of genome sequencing and marker-assisted breeding can be successfully applied to reduce linkage drag. The findings offer valuable resources for breeding tobacco with resistance to TMV.
Keyword ：
disease resistance disease resistance genomic sequencing genomic sequencing linkage drag linkage drag marker-assisted breeding marker-assisted breeding N gene N gene tobacco mosaic virus (TMV) tobacco mosaic virus (TMV)
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| GB/T 7714 | Gao, Wenxia , Yu, Wen , Lin, Jinbin et al. Genomic sequencing combined with marker-assisted breeding effectively eliminates potential linkage drag of a target gene: a case study in tobacco [J]. | FRONTIERS IN PLANT SCIENCE , 2025 , 16 . |
| MLA | Gao, Wenxia et al. "Genomic sequencing combined with marker-assisted breeding effectively eliminates potential linkage drag of a target gene: a case study in tobacco" . | FRONTIERS IN PLANT SCIENCE 16 (2025) . |
| APA | Gao, Wenxia , Yu, Wen , Lin, Jinbin , Zhao, Zhenfu , Yin, Ningning , Lai, Juxian et al. Genomic sequencing combined with marker-assisted breeding effectively eliminates potential linkage drag of a target gene: a case study in tobacco . | FRONTIERS IN PLANT SCIENCE , 2025 , 16 . |
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BackgroundDNA demethylases regulate the levels of genomic DNA methylation in plants. The demethylase REPRESSOR OF SILENCING 1 (ROS1) is a crucial factor for modulating gene expression in plant disease responses. Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. Oryzicola (Xoc), is a highly destructive disease in rice. BLS resistance in rice is known to be quantitatively inherited, but the mechanisms by which DNA methylation controls BLS resistance remain poorly understood.ResultsIn this study, we knocked down OsROS1a expression in the rice variety Nipponbare using RNA interference (RNAi). The average BLS lesion length in the transgenic (T2) OsROS1a-RNAi (RS) lines was significantly reduced compared to that in wild-type Nipponbare plants (NP). Using whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq), we analyzed the DNA methylations and transcriptomes of RS lines in comparison with NP at 0 (control), 5, 10, and 24 h post-inoculation with Xoc. A total of 1080 differentially expressed genes (DEGs) related to Xoc infection between the NP and RS lines were identified, which could be grouped into 8 clusters by K-means analysis. The DEGs in cluster 1 were enriched in the biological process related to defense response, response to stress, oxidation-reduction, etc. Integration of the methylome and transcriptome data revealed 112 overlapping differentially methylated and expressed genes (DMEGs). Gene Ontology (GO) analysis showed that the DMEGs were mainly involved in biological processes, such as metabolic process, cellular process, responses to stimulus, signaling, and immune system processes. KEGG pathway enrichment analysis revealed that these DMEGs were enriched in pathways related to glutathione metabolism, plant-pathogen interaction, cysteine and methionine, diterpenoid biosynthesis, photosynthesis, and starch and sucrose. Additionally, LOC_Os09g12660, encoding the glucose-1-phosphate adenylyl transferase large subunit, a chloroplast precursor involved in synthesizing activated glycosyl donor, showed strong potential to contribute to BLS resistance.ConclusionOsROS1a plays a crucial role in modulating rice resistance to bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc). These findings provide valuable insights into the role of OsROS1a in BLS resistance.
Keyword ：
Bacterial leaf streak Bacterial leaf streak Methylation Methylation OsROS1a OsROS1a Rice Rice Transcriptome Transcriptome
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| GB/T 7714 | Xie, Xiaofang , Yang, Xuansong , Lu, Libin et al. Exploring the molecular mechanism of OsROS1a in regulating resistance to bacterial leaf streak through transcriptome and DNA methylation profiling in rice (Oryza sativa L.) [J]. | BMC GENOMICS , 2025 , 26 (1) . |
| MLA | Xie, Xiaofang et al. "Exploring the molecular mechanism of OsROS1a in regulating resistance to bacterial leaf streak through transcriptome and DNA methylation profiling in rice (Oryza sativa L.)" . | BMC GENOMICS 26 . 1 (2025) . |
| APA | Xie, Xiaofang , Yang, Xuansong , Lu, Libin , Li, Tong , Qin, Mingyue , Guan, Huazhong et al. Exploring the molecular mechanism of OsROS1a in regulating resistance to bacterial leaf streak through transcriptome and DNA methylation profiling in rice (Oryza sativa L.) . | BMC GENOMICS , 2025 , 26 (1) . |
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Soil salinity severely inhibits rice growth. While the SBP-box gene OsSPL10 is known to negatively regulate salt tolerance, its mechanism remains unclear. Since jasmonate (JA) mediates plant stress responses, we investigated the link between OsSPL10 and JA in rice salt tolerance. Disrupting OsSPL10 reduced the shoot Na+/K+ ratio under salt stress, likely explaining the enhanced tolerance in Osspl10 mutants. As leaves are highly sensitive to Na+ toxicity, maintaining a low Na+/K+ ratio is critical for survival. Notably, ten OsJAZ genes (JA repressors) were upregulated in Osspl10 mutants. We found that OsSPL10 directly suppresses certain OsJAZ genes (including OsJAZ9, known to regulate certain ion transporters), by binding to their promoters. These findings suggest that OsSPL10 negatively modulate salt tolerance via the OsJAZ-mediated JA pathway, maintaining ion homeostasis. This study reveals new molecular mechanisms of rice salinity response, emphasizing the interplay between transcription factors and hormonal signaling.
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| GB/T 7714 | Chen, Jilin , Lan, Tong , Dong, Tongtong et al. OsSPL10 negatively regulates seedling salt tolerance through OsJAZ-mediated jasmonate pathway in rice (Oryza sativa L.) [J]. | THEORETICAL AND APPLIED GENETICS , 2025 , 138 (11) . |
| MLA | Chen, Jilin et al. "OsSPL10 negatively regulates seedling salt tolerance through OsJAZ-mediated jasmonate pathway in rice (Oryza sativa L.)" . | THEORETICAL AND APPLIED GENETICS 138 . 11 (2025) . |
| APA | Chen, Jilin , Lan, Tong , Dong, Tongtong , Liao, Qiaoling , An, Xiaoxiao , Fang, Chao et al. OsSPL10 negatively regulates seedling salt tolerance through OsJAZ-mediated jasmonate pathway in rice (Oryza sativa L.) . | THEORETICAL AND APPLIED GENETICS , 2025 , 138 (11) . |
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BackgroundResponse regulator proteins (RRs) are integral components of two-component regulatory systems and play critical roles in cytokinin signaling, regulation of plant growth and development, and responses to biotic and abiotic stresses. While numerous RR families have been identified, comprehensive characterization and functional studies of RR genes in eggplant have not been reported.ResultsIn this study, we conducted a genome-wide identification and analysis of RR genes in eggplant. Through Blastp and HMM methods, a total of 32 RRs were identified. Phylogenetic analysis classified all RRs into three categories: type-A, type-B RRs, and PRRs (Pseudo-RRs), while no type-C genes were detected. Gene structure and motif analysis demonstrated similarities within each type. Gene duplication and tandem repeats suggested these mechanisms might have facilitated the expansion of the RR gene family in the eggplant genome. Synteny analysis uncovered 18 syntenic blocks between eggplant and Arabidopsis and 33 between eggplant and tomato. Promoter analysis indicated their potential roles in hormone signaling and stress responses. Tissue expression data showed that 12 genes had no or undetectable expression across 17 tested tissues, while others exhibited significant tissue specificity, with most genes showing higher expression in roots. Dynamic expression of 11 selected RR genes in response to salt, drought stress, and IAA hormone treatment in eggplant seedlings revealed that most genes responded to all three treatments. Notably, SmRR9 exhibited the most profound response to salt stress, SmRR1 and SmRR9 to drought stress, and SmRR5 and SmRR6 to IAA treatment. These four genes were proposed as key candidates for future studies on RR gene functions in abiotic stress responses and hormone signaling pathways.ConclusionThe findings of this study provide a foundation for future research on the functional roles of SmRRs in abiotic stress responses and hormone signaling pathways in eggplant, serving as a guide for improving stress tolerance in eggplant.
Keyword ：
Abiotic stress Abiotic stress Eggplant Eggplant Genome-wide identification Genome-wide identification IAA treatment IAA treatment RR gene family RR gene family
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| GB/T 7714 | Li, Wenjing , Li, Hui , Lin, Yanyu et al. Genome-wide identification and analysis of SmRR gene family in eggplant (Solanum melongena L.) and their response to abiotic stress and auxin [J]. | BMC GENOMICS , 2025 , 26 (1) . |
| MLA | Li, Wenjing et al. "Genome-wide identification and analysis of SmRR gene family in eggplant (Solanum melongena L.) and their response to abiotic stress and auxin" . | BMC GENOMICS 26 . 1 (2025) . |
| APA | Li, Wenjing , Li, Hui , Lin, Yanyu , Li, Yutong , Xie, Xiaofang , Zheng, Xuefang et al. Genome-wide identification and analysis of SmRR gene family in eggplant (Solanum melongena L.) and their response to abiotic stress and auxin . | BMC GENOMICS , 2025 , 26 (1) . |
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Bulked-segregant analysis by deep sequencing (BSA-seq) is a widely used method for mapping QTL (quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F-2 populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F-3 populations offering notable advantages over F-2 populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading (DTH) in a 7200-plant rice F-3 population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near 41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F-3 populations and multi-environment experiments can achieve high power, resolution, and reliability. (c) 2024 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.
Keyword ：
BSA-seq BSA-seq Cross-validation Cross-validation Large F-3 population Large F-3 population Multi-environment experiment Multi-environment experiment QTL mapping QTL mapping
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| GB/T 7714 | Zheng, Yan , Khine, Ei Ei , Thi, Khin Mar et al. Multi-environment BSA-seq using large F3 populations is able to achieve reliable QTL mapping with high power and resolution: An experimental demonstration in rice [J]. | CROP JOURNAL , 2024 , 12 (2) : 549-557 . |
| MLA | Zheng, Yan et al. "Multi-environment BSA-seq using large F3 populations is able to achieve reliable QTL mapping with high power and resolution: An experimental demonstration in rice" . | CROP JOURNAL 12 . 2 (2024) : 549-557 . |
| APA | Zheng, Yan , Khine, Ei Ei , Thi, Khin Mar , Nyein, Ei Ei , Huang, Likun , Lin, Lihui et al. Multi-environment BSA-seq using large F3 populations is able to achieve reliable QTL mapping with high power and resolution: An experimental demonstration in rice . | CROP JOURNAL , 2024 , 12 (2) , 549-557 . |
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