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Wang W, Zhang J, Guo F, Di Y, Wang Y, Li W, Sun Y, Wang Y, Ni F, Fu D, Wang W, Hao Q. Role of reactive oxygen species in lesion mimic formation and conferred basal resistance to Fusarium graminearum in barley lesion mimic mutant 5386. FRONTIERS IN PLANT SCIENCE 2022; 13:1020551. [PMID: 36699849 PMCID: PMC9869871 DOI: 10.3389/fpls.2022.1020551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/26/2022] [Indexed: 06/17/2023]
Abstract
This study investigated the barley lesion mimic mutant (LMM) 5386, evidenced by a leaf brown spot phenotype localized on the chromosome 3H, and its conferred basal resistance to Fusarium graminearum. RNA-seq analysis identified 1453 genes that were differentially expressed in LMM 5386 compared to those in the wild type. GO and KEGG functional annotations suggested that lesion mimic formation was mediated by pathways involving oxidation reduction and glutathione metabolism. Additionally, reactive oxygen species (ROS) accumulation in brown spots was substantially higher in LMM 5386 than in the wild-type plant; therefore, antioxidant competence, which is indicated by ROS accumulation, was significantly lower in LMM 5386. Furthermore, the reduction of glycine in LMM 5386 inhibited glutathione biosynthesis. These results suggest that the decrease in antioxidant competence and glutathione biosynthesis caused considerable ROS accumulation, leading to programmed cell death, which eventually reduced the yield components in LMM 5386.
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Affiliation(s)
- Wenqiang Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
- Shandong Shofine Seed Technology Co., Ltd., Jining, China
| | - Jifa Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
- Spring Valley Agriscience Co., Ltd., Jinan, China
| | - Fenxia Guo
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Yindi Di
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Yuhui Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Wankun Li
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Yali Sun
- Qihe Bureau of Agriculture and Rural, Qihe, China
| | - Yuhai Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Fei Ni
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Daolin Fu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
- Spring Valley Agriscience Co., Ltd., Jinan, China
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Qunqun Hao
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
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Woodhouse MR, Sen S, Schott D, Portwood JL, Freeling M, Walley JW, Andorf CM, Schnable JC. qTeller: a tool for comparative multi-genomic gene expression analysis. Bioinformatics 2021; 38:236-242. [PMID: 34406385 DOI: 10.1093/bioinformatics/btab604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/23/2021] [Accepted: 08/17/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses. RESULTS To address this challenge, we revamped the comparative gene expression tool qTeller to take advantage of the growing number of public RNA-Seq datasets. qTeller allows users to evaluate gene expression data in a defined genomic interval and also perform two-gene comparisons across multiple user-chosen tissues. Though previously unpublished, qTeller has been cited extensively in the scientific literature, demonstrating its importance to researchers. Our new version of qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets. Other new features include support for additional data formats, modernized interface and back-end database and an optimized framework for adoption by other organisms' databases. AVAILABILITY AND IMPLEMENTATION The source code for qTeller is open-source and available through GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/qTeller). A maize instance of qTeller is available at the Maize Genetics and Genomics database (MaizeGDB) (https://qteller.maizegdb.org/), where we have mapped over 200 unique datasets from GenBank across 27 maize genomes. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Shatabdi Sen
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - David Schott
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Michael Freeling
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Justin W Walley
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.,Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - James C Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Zhang Z, He Y, Li L, Zhang X, Xu X, Shi Y, Wu JL. Characterization of a novel allele encoding pheophorbide a oxygenase in rice. PLANT SIGNALING & BEHAVIOR 2021; 16:1864606. [PMID: 33369525 PMCID: PMC7889113 DOI: 10.1080/15592324.2020.1864606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
We identified a rapid cell death 2 (rcd2) mutant from an indica cultivar Zhongjian100 mutant bank. The red-brown lesions appeared firstly on young seedling leaves, then gradually merged and the leaves completely withered at the late tillering stage. rcd2 displayed apparent cell death at/around the lesions, accumulation of superoxide anion (O2-) and disturbed ROS scavenging system, impaired photosynthetic capacity with significantly reduced chlorophyll content. The lesion formation was controlled by a single recessive nuclear gene and induced by natural light as well as mechanical wounding. A single base mutation (A1726T) at the 6th exon of OsMH_03G0040800 resulted in I576F substitution in the encoding protein, pheophorbide a oxygenase (PAO). Functional complementation could rescue the mutant phenotype and PAO-knockout lines exhibited the similar phenotype to rcd2. The activity of PAO decreased significantly while the content of PAO substrate, pheophorbide a, increased apparently in rcd2. The expression of chlorophyll synthesis/degradation-related genes and the contents of metabolic intermediates were largely changed. Furthermore, the level of chlorophyllide a, the product of chlorophyllase, increased significantly, indicating chlorophyllase might play a role in chlorophyll degradation in rice. Our results suggested that the I576F substitution disrupted PAO function, leading to O2- accumulation and chlorophyll degradation breakdown in rice.
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Affiliation(s)
- Zhihong Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yan He
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liangjian Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaobo Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xia Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yongfeng Shi
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jian-Li Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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Sathe AP, Su X, Chen Z, Chen T, Wei X, Tang S, Zhang XB, Wu JL. Identification and characterization of a spotted-leaf mutant spl40 with enhanced bacterial blight resistance in rice. RICE (NEW YORK, N.Y.) 2019; 12:68. [PMID: 31446514 PMCID: PMC6708518 DOI: 10.1186/s12284-019-0326-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/15/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Spotted leaf mutants show typical necrotic lesions that appear spontaneously in the absence of any pathogen attack. These mutants are often characterized to exhibit programmed cell death (PCD) and activation of plant defense responses resulting in enhanced disease resistance to multiple pathogens. Here, we reported a novel spotted-leaf mutant, spl40 that showed enhanced disease resistance response. RESULTS Initially lesions appeared at leaf tips during seedling stage and gradually covered the whole leaf at the tillering stage. The lesion development was light-dependent. spl40 showed obvious cell death at and around the lesion, and burst of reactive oxygen species (ROS) was accompanied by disturbed ROS scavenging system. Photosynthetic capacity was compromised as evidenced by significant reductions in chlorophyll content, important photosynthesis parameters and downregulated expression of photosynthesis-related genes which ultimately led to poor performance of major agronomic traits. spl40 exhibited enhanced resistance to 14 out of 16 races of bacterial blight pathogen of rice, caused by Xanthomonas oryzae pv. oryzae, most probably though activation of SA and JA signaling pathways, owing to upregulated expression of SA and JA signaling genes, though the exact mechanism remain to be elucidated. The spotted-leaf phenotype was controlled by a novel single recessive nuclear gene. Genetic mapping combined with high throughput sequencing analysis identified Os05G0312000 as the most probable candidate gene. Sequencing of ORF revealed a single SNP change from C to T that resulted in non-synonymous change in amino acid residue from leucine to phenylalanine. Interestingly, the complementation plants did not display lesions before heading but showed lesions at the heading stage and the transgenic T1 progenies could be classified into 3 categories based on their lesion intensity, indicating the complex genetic nature of the spl40 mutation. CONCLUSION The results obtained here clearly show that genes related to defense and PCD were upregulated in accordance with enhanced disease resistance and occurrence of PCD, whereas the photosynthetic capacity and overall ROS homeostasis was compromised in spl40. Our data suggest that a novel spotted-leaf mutant, spl40, would help to elucidate the mechanism behind lesion development involving programmed cell death and associated defense responses.
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Affiliation(s)
- Atul Prakash Sathe
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Xiaona Su
- Nanchang Business College of Jiangxi Agricultural University, Nanchang, 330044 China
| | - Zheng Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Ting Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Xiangjing Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Xiao-bo Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Jian-li Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
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Zhang Y, Liu Q, Zhang Y, Chen Y, Yu N, Cao Y, Zhan X, Cheng S, Cao L. LMM24 Encodes Receptor-Like Cytoplasmic Kinase 109, Which Regulates Cell Death and Defense Responses in Rice. Int J Mol Sci 2019; 20:ijms20133243. [PMID: 31269643 PMCID: PMC6651581 DOI: 10.3390/ijms20133243] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 11/16/2022] Open
Abstract
Lesion mimic mutants are excellent models for research on molecular mechanisms of cell death and defense responses in rice. We identified a new rice lesion mimic mutant lmm24 from a mutant pool of indica rice cultivar “ZhongHui8015”. The LMM24 gene was identified by MutMap, and LMM24 was confirmed as a receptor-like cytoplasmic kinase 109 by amino acid sequence analysis. The lmm24 mutant displayed dark brown lesions in leaves and growth retardation that were not observed in wild-type ZH8015. The results of histochemical staining and TUNEL assays showed enhanced ROS accumulation and cell death in lmm24. Chloroplast degradation was observed in lmm24 leaves, with decreased expression of photosynthesis-related genes and increased expression of the senescence-induced STAYGREEN (SGR) gene and other senescence-associated genes. Furthermore, lmm24 exhibited enhanced resistance to rice blast fungus Magnaporthe oryzae (M. oryzae) and up-regulation of defense response genes. Our data demonstrate that LMM24 regulates cell death and defense responses in rice.
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Affiliation(s)
- Yue Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qunen Liu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yingxin Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yuyu Chen
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Ning Yu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yongrun Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiaodeng Zhan
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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A Very Oil Yellow1 Modifier of the Oil Yellow1-N1989 Allele Uncovers a Cryptic Phenotypic Impact of Cis-regulatory Variation in Maize. G3-GENES GENOMES GENETICS 2019; 9:375-390. [PMID: 30518539 PMCID: PMC6385977 DOI: 10.1534/g3.118.200798] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Forward genetics determines the function of genes underlying trait variation by identifying the change in DNA responsible for changes in phenotype. Detecting phenotypically-relevant variation outside protein coding sequences and distinguishing this from neutral variants is not trivial; partly because the mechanisms by which DNA polymorphisms in the intergenic regions affect gene regulation are poorly understood. Here we utilized a dominant genetic reporter to investigate the effect of cis and trans-acting regulatory variation. We performed a forward genetic screen for natural variation that suppressed or enhanced the semi-dominant mutant allele Oy1-N1989, encoding the magnesium chelatase subunit I of maize. This mutant permits rapid phenotyping of leaf color as a reporter for chlorophyll accumulation, and mapping of natural variation in maize affecting chlorophyll metabolism. We identified a single modifier locus segregating between B73 and Mo17 that was linked to the reporter gene itself, which we call very oil yellow1 (vey1). Based on the variation in OY1 transcript abundance and genome-wide association data, vey1 is predicted to consist of multiple cis-acting regulatory sequence polymorphisms encoded at the wild-type oy1 alleles. The vey1 locus appears to be a common polymorphism in the maize germplasm that alters the expression level of a key gene in chlorophyll biosynthesis. These vey1 alleles have no discernable impact on leaf chlorophyll in the absence of the Oy1-N1989 reporter. Thus, the use of a mutant as a reporter for magnesium chelatase activity resulted in the detection of expression-level polymorphisms not readily visible in the laboratory.
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Chen Z, Chen T, Sathe AP, He Y, Zhang XB, Wu JL. Identification of a Novel Semi-Dominant Spotted-Leaf Mutant with Enhanced Resistance to Xanthomonas oryzae pv. oryzae in Rice. Int J Mol Sci 2018; 19:E3766. [PMID: 30486418 PMCID: PMC6321207 DOI: 10.3390/ijms19123766] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/15/2018] [Accepted: 11/22/2018] [Indexed: 12/26/2022] Open
Abstract
Many spotted-leaf mutants show enhanced disease resistance to multiple pathogen attacks; however, the mechanisms are largely unknown. Here, we reported a novel semi-dominant spotted-leaf mutant 24 (spl24) obtained from an ethyl methane sulfonate (EMS)-induced IR64 mutant bank. spl24 developed tiny brown lesions on the leaf tip and spread down gradually to the leaf base as well as the sheath at the early heading stage. The performances of major agronomic traits such as the plant height, panicle length, number of panicles/plant, and 1000-grain weight were significantly altered in spl24 when compared to the wild-type IR64. Furthermore, spl24 exhibited a premature senescing phenotype with degeneration of nuclear acids, significantly reduced soluble protein content, increased level of malonaldehyde (MDA), and lowered activities of reactive oxygen species (ROS) scavenging enzymes. Disease evaluation indicated that spl24 showed enhanced resistance to multiple races of Xanthomonas oryzae pv. oryzae, the causal pathogen of bacterial leaf blight in rice, with elevated expression of pathogenesis-related genes, salicylic acid (SA) signaling pathway-associated genes revealed by real-time quantitative PCR and high-throughput RNA sequencing analysis. Genetic analysis and gene mapping indicated that the lesion mimic phenotype was controlled by a novel semi-dominant nuclear gene. The mutation, tentatively termed as OsSPL24, was in a 110 kb region flanked by markers Indel-33 and Indel-12 in chromosome 11. Together, our data suggest that spl24 is a novel lesion mimic mutant with enhanced innate immunity and would facilitate the isolation and functional characterization of the target gene.
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Affiliation(s)
- Zheng Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ting Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Atul Prakash Sathe
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Yuqing He
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiao-Bo Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jian-Li Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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