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Meng L, Du M, Zhu T, Li G, Ding Y, Zhang Q. PPR proteins in plants: roles, mechanisms, and prospects for rice research. FRONTIERS IN PLANT SCIENCE 2024; 15:1416742. [PMID: 38993942 PMCID: PMC11236678 DOI: 10.3389/fpls.2024.1416742] [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: 04/26/2024] [Accepted: 06/13/2024] [Indexed: 07/13/2024]
Abstract
Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants, with over 300 members in various species. Nearly all PPR proteins are nuclear-encoded and targeted to the chloroplast and mitochondria, modulating organellar gene expression by participating in RNA metabolism, including mRNA stability, RNA editing, RNA splicing, and translation initiation. Organelle RNA metabolism significantly influences chloroplast and mitochondria functions, impacting plant photosynthesis, respiration, and environmental responses. Over the past decades, PPR proteins have emerged as a research focus in molecular biology due to their diverse roles throughout plant life. This review summarizes recent progress in understanding the roles and molecular mechanisms of PPR proteins, emphasizing their functions in fertility, abiotic and biotic stress, grain quality, and chloroplast development in rice. Furthermore, we discuss prospects for PPR family research in rice, aiming to provide a theoretical foundation for future investigations and applications.
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Affiliation(s)
- Lingzhi Meng
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Mengxue Du
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Taotao Zhu
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Gang Li
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Yi Ding
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Qiang Zhang
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
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Martina M, Zayas A, Portis E, Di Nardo G, Polli MF, Comino C, Gilardi G, Martin E, Acquadro A. The Dark Side of the pollen: BSA-seq identified genomic regions linked to male sterility in globe artichoke. BMC PLANT BIOLOGY 2024; 24:415. [PMID: 38760683 PMCID: PMC11100218 DOI: 10.1186/s12870-024-05119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Globe artichoke (Cynara cardunculus var. scolymus; 2n = 2x = 34) is a food crop consumed for its immature flower heads. Traditionally, globe artichoke varietal types are vegetatively propagated. However, seed propagation makes it possible to treat the crop as annual, increasing field uniformity and reducing farmers costs, as well as pathogens diffusion. Despite globe artichoke's significant agricultural value and the critical role of heterosis in the development of superior varieties, the production of hybrids remains challenging without a reliable system for large-scale industrial seed production. Male sterility (MS) presents a promising avenue for overcoming these challenges by simplifying the hybridization process and enabling cost-effective seed production. However, within the Cynara genus, genic male sterility has been linked to three recessive loci in globe artichoke, with no definitive genetic mechanism elucidated to date. A 250 offsprings F2 population, derived from a cross between a MS globe artichoke and a male fertile (MF) cultivated cardoon (C. cardunculus var. altilis) and fitting a monogenic segregation model (3:1), was analyzed through BSA-seq, aiming at the identification of genomic regions/genes affecting male sterility. Four QTL regions were identified on chromosomes 4, 12, and 14. By analyzing the sequence around the highest pick on chromosome 14, a cytochrome P450 (CYP703A2) was identified, carrying a deleterious substitution (R/Q) fixed in the male sterile parent. A single dCAPS marker was developed around this SNP, allowing the discrimination between MS and MF genotypes within the population, suitable for applications in plant breeding programs. A 3D model of the protein was generated by homology modeling, revealing that the mutated amino acid is part of a highly conserved motif crucial for protein folding.
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Affiliation(s)
- Matteo Martina
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Aldana Zayas
- IICAR (Instituto de Investigaciones en Ciencias Agrarias de Rosario), CONICET, Campo Exp. J.F. Villarino, Zavalla, Santa Fe, Argentina
| | - Ezio Portis
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Giovanna Di Nardo
- DBIOS, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | | | - Cinzia Comino
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Gianfranco Gilardi
- DBIOS, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Eugenia Martin
- IICAR (Instituto de Investigaciones en Ciencias Agrarias de Rosario), CONICET, Campo Exp. J.F. Villarino, Zavalla, Santa Fe, Argentina.
| | - Alberto Acquadro
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy.
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Liu K, Xie B, Peng L, Wu Q, Hu J. Profiling of RNA editing events in plant organellar transcriptomes with high-throughput sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:345-357. [PMID: 38149801 DOI: 10.1111/tpj.16607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023]
Abstract
RNA editing is a crucial post-transcriptional modification process in plant organellar RNA metabolism. rRNA removal-based total RNA-seq is one of the most common methods to study this event. However, the lack of commercial kits to remove rRNAs limits the usage of this method, especially for non-model plant species. DSN-seq is a transcriptome sequencing method utilizing duplex-specific nuclease (DSN) to degrade highly abundant cDNA species especially those from rRNAs while keeping the robustness of transcript levels of the majority of other mRNAs, and has not been applied to study RNA editing in plants before. In this study, we evaluated the capability of DSN-seq to reduce rRNA content and profile organellar RNA editing events in plants, as well we used commercial Ribo-off-seq and standard mRNA-seq as comparisons. Our results demonstrated that DSN-seq efficiently reduced rRNA content and enriched organellar transcriptomes in rice. With high sensitivity to RNA editing events, DSN-seq and Ribo-off-seq provided a more complete and accurate RNA editing profile of rice, which was further validated by Sanger sequencing. Furthermore, DSN-seq also demonstrated efficient organellar transcriptome enrichment and high sensitivity for profiling RNA editing events in Arabidopsis thaliana. Our study highlights the capability of rRNA removal-based total RNA-seq for profiling RNA editing events in plant organellar transcriptomes and also suggests DSN-seq as a widely accessible RNA editing profiling method for various plant species.
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Affiliation(s)
- Kejia Liu
- State Key Laboratory of Hybrid Rice; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Bin Xie
- State Key Laboratory of Hybrid Rice; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Leilei Peng
- State Key Laboratory of Hybrid Rice; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Qijia Wu
- Seqhealth Technology Co., Ltd., Wuhan, Hubei, China
| | - Jun Hu
- State Key Laboratory of Hybrid Rice; Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education; College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
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Han Y, Feng YL, Wang J, Zhu SS, Jin XJ, Wu ZQ, Zhang YH. Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family. Genes (Basel) 2024; 15:98. [PMID: 38254987 PMCID: PMC10815111 DOI: 10.3390/genes15010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through a de novo assembly strategy. We carried out comparative genomic analyses and found that, in comparison with the plastid genome (plastome) showing a high degree of structural conservation, the R. chingii mitogenome structure is relatively complex, showing an intricate ring structure with 16 connections, owing to five repetitive sequences. The R. chingii mitogenome was 783,161 bp with a GC content of 44.8% and contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA genes, and 3 rRNA genes. We counted 579 RNA editing events in 47 CDS and 12,828 codons in all CDSs of the R. chingii mitogenome. Furthermore, 24 unique sequence transfer fragments were found between the mitogenome and plastome, comprising 8 mitogenome CDS genes and 16 plastome CDS genes, corresponding to 2.39% of the R. chingii mitogenome. Mitogenomes had shorter but more collinear regions, evidenced by a comparison of the organelles of non-parasitic R. chingii, hemiparasitic Pedicularis chinensis, and holoparasitic Aeginetia indica in the Orobanchaceae family. Moreover, from non-parasitic to holoparasitic species, the genome size in the mitogenomes of Orobanchaceae species did not decrease gradually. Instead, the smallest mitogenome was found in the hemiparasitic species P. chinensis, with a size of 225,612 bp. The findings fill the gap in the mitogenome research of the medicinal plant R. chingii, promote the progress of the organelle genome research of the Orobanchaceae family, and provide clues for molecular breeding.
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Affiliation(s)
- Ying Han
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Y.H.); (X.-J.J.)
| | - Yan-Lei Feng
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China;
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
| | - Shan-Shan Zhu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China;
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
| | - Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Y.H.); (X.-J.J.)
- Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Y.H.); (X.-J.J.)
- Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou 325035, China
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Devate NB, Krishna H, Mishra CN, Manjunath KK, Sunilkumar VP, Chauhan D, Singh S, Sinha N, Jain N, Singh GP, Singh PK. Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat. FRONTIERS IN PLANT SCIENCE 2023; 13:1082513. [PMID: 36726675 PMCID: PMC9885108 DOI: 10.3389/fpls.2022.1082513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Introduction Wheat is grown and consumed worldwide, making it an important staple food crop for both its calorific and nutritional content. In places where wheat is used as a staple food, suboptimal micronutrient content levels, especially of grain iron (Fe) and zinc (Zn), can lead to malnutrition. Grain nutrient content is influenced by abiotic stresses, such as drought and heat stress. The best method for addressing micronutrient deficiencies is the biofortification of food crops. The prerequisites for marker-assisted varietal development are the identification of the genomic region responsible for high grain iron and zinc contents and an understanding of their genetics. Methods A total of 193 diverse wheat genotypes were evaluated under drought and heat stress conditions across the years at the Indian Agricultural Research Institute (IARI), New Delhi, under timely sown irrigated (IR), restricted irrigated (RI) and late sown (LS) conditions. Grain iron content (GFeC) and grain zinc content (GZnC) were estimated from both the control and treatment groups. Genotyping of all the lines under study was carried out with the single nucleotide polymorphisms (SNPs) from Breeder's 35K Axiom Array. Result and Discussion Three subgroups were observed in the association panel based on both principal component analysis (PCA) and dendrogram analysis. A large whole-genome linkage disequilibrium (LD) block size of 3.49 Mb was observed. A genome-wide association study identified 16 unique stringent marker trait associations for GFeC, GZnC, and 1000-grain weight (TGW). In silico analysis demonstrated the presence of 28 potential candidate genes in the flanking region of 16 linked SNPs, such as synaptotagmin-like mitochondrial-lipid-binding domain, HAUS augmin-like complex, di-copper center-containing domain, protein kinase, chaperonin Cpn60, zinc finger, NUDIX hydrolase, etc. Expression levels of these genes in vegetative tissues and grain were also found. Utilization of identified markers in marker-assisted breeding may lead to the rapid development of biofortified wheat genotypes to combat malnutrition.
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Affiliation(s)
- Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | | | | | - V. P. Sunilkumar
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Divya Chauhan
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Shweta Singh
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | | | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
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Liu L, Wang Y, Tian Y, Song S, Wu Z, Ding X, Zheng H, Huang Y, Liu S, Dong X, Wan J, Liu L. Isolation and Characterization of SPOTTED LEAF42 Encoding a Porphobilinogen Deaminase in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:403. [PMID: 36679117 PMCID: PMC9866984 DOI: 10.3390/plants12020403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
The formation and development of chloroplasts play a vital role in the breeding of high-yield rice (Oryza sativa L.). Porphobilinogen deaminases (PBGDs) act in the early stage of chlorophyll and heme biosynthesis. However, the role of PBGDs in chloroplast development and chlorophyll production remains elusive in rice. Here, we identified the spotted leaf 42 (spl42) mutant, which exhibited a reddish-brown spotted leaf phenotype. The mutant showed a significantly lower chlorophyll content, abnormal thylakoid morphology, and elevated activities of reactive oxygen species (ROS)-scavenging enzymes. Consistently, multiple genes related to chloroplast development and chlorophyll biosynthesis were significantly down-regulated, whereas many genes involved in leaf senescence, ROS production, and defense responses were upregulated in the spl42 mutant. Map-based cloning revealed that SPL42 encodes a PBGD. A C-to-T base substitution occurred in spl42, resulting in an amino acid change and significantly reduced PBGD enzyme activity. SPL42 targets to the chloroplast and interacts with the multiple organelle RNA editing factors (MORFs) OsMORF8-1 and OsMORF8-2 to affect RNA editing. The identification and characterization of spl42 helps in elucidating the molecular mechanisms associated with chlorophyll synthesis and RNA editing in rice.
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Affiliation(s)
- Lin Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunpeng Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuang Song
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Zewan Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Ding
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunshuai Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoou Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Linglong Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
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Zhao X, Zhai J, Liu T, Wang G. Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins. Brief Bioinform 2022; 23:6760138. [PMID: 36239380 DOI: 10.1093/bib/bbac369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/20/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
In order to identify plant pentatricopeptide repeat (PPR) proteins, a framework of variable selection has been proposed. In fact, it is an effective feature selection strategy that focuses on the performance of classification. Random forest has been used as the classifier with certain variables automatically selected for discrimination between PPR functional and non-functional proteins. However, it is found that samples regarded as PPR functional proteins are wrongly classified in a high rate. In this paper, we plan to improve the framework in order to achieve better classification results. Modifications are made on the framework for better identifying PPR functional proteins. Instead of random forest, a hybrid ensemble classifier is built with its base classifiers derived from six different classification methods. Besides, an incremental strategy and a clustering by search in descending order are alternatively used for feature selection, which can effectively select the most representative variables for identification on PPR proteins. In addition, it can be found that different base classifiers alternately play an important role in the ensemble classifier with feature dimension increasing. The experimental results demonstrate the effectiveness of our improvements.
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Affiliation(s)
- Xudong Zhao
- College of Information and Computer Engineering, Northeast Forestry University, No. 26, Hexing Road, 150040, Heilongjiang Province, China
| | - Jingwen Zhai
- College of Information and Computer Engineering, Northeast Forestry University, No. 26, Hexing Road, 150040, Heilongjiang Province, China
| | - Tong Liu
- College of Information and Computer Engineering, Northeast Forestry University, No. 26, Hexing Road, 150040, Heilongjiang Province, China
| | - Guohua Wang
- College of Information and Computer Engineering, Northeast Forestry University, No. 26, Hexing Road, 150040, Heilongjiang Province, China.,State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 26, Hexing Road, 150040, Heilongjiang Province, China
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Devate NB, Krishna H, Sunilkumar VP, Manjunath KK, Mishra CN, Jain N, Singh GP, Singh PK. Identification of genomic regions of wheat associated with grain Fe and Zn content under drought and heat stress using genome-wide association study. Front Genet 2022; 13:1034947. [PMID: 36338980 PMCID: PMC9634069 DOI: 10.3389/fgene.2022.1034947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/07/2022] [Indexed: 09/10/2023] Open
Abstract
Wheat is the staple food crop of global importance for its grain nutrient quality. Grain iron and zinc content of the wheat grain is an important quantitatively inherited trait that is influenced by the environmental factors such as drought and heat stress. Phenotypic evaluation of 295 advanced breeding lines from the wheat stress breeding program of IARI was carried out under timely sown irrigated (IR), restricted irrigated, and late-sown conditions at New Delhi during the cropping season of 2020-21, and grain iron (GFeC) and zinc (GZnC) contents were estimated from both control and treatments. A statistically significant increase in GFeC and GZnC was observed under stress conditions compared to that of the control. Genotyping was carried out with the SNPs from the 35K Axiom Breeder's array, and marker-trait association was identified by GWAS analysis. Of the 23 MTAs identified, seven were linked with GFeC and sixteen were linked with GZnC. In silico analysis revealed a few important transcripts involved in various plant metabolism, growth, and development activities such as auxin response factor, root UVB sensitive proteins, potassium transporter, glycosyl transferase, COBRA, and F-box-like domain. The identified MTAs can be used for molecular breeding after validation and also for rapid development of micronutrient-rich varieties of wheat to mitigate hidden hunger.
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Affiliation(s)
- Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - V. P. Sunilkumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - C. N. Mishra
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - G. P. Singh
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | - P. K. Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Enyew M, Feyissa T, Carlsson AS, Tesfaye K, Hammenhag C, Seyoum A, Geleta M. Genome-wide analyses using multi-locus models revealed marker-trait associations for major agronomic traits in Sorghum bicolor. FRONTIERS IN PLANT SCIENCE 2022; 13:999692. [PMID: 36275578 PMCID: PMC9585286 DOI: 10.3389/fpls.2022.999692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/14/2022] [Indexed: 06/01/2023]
Abstract
Globally, sorghum is the fifth most important cereal crop, and it is a major crop in Ethiopia, where it has a high genetic diversity. The country's sorghum gene pool contributes significantly to sorghum improvement worldwide. This study aimed to identify genomic regions and candidate genes associated with major agronomic traits in sorghum by using its genetic resources in Ethiopia for a genome-wide association study (GWAS). Phenotypic data of days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT), and grain yield (GY) were collected from a GWAS panel comprising 324 sorghum accessions grown in three environments. SeqSNP, a targeted genotyping method, was used to genotype the panel using 5,000 gene-based single nucleotide polymorphism (SNP) markers. For marker-trait association (MTA) analyses, fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) models were used. In all traits, high phenotypic variation was observed, with broad-sense heritability ranging from 0.32 (for GY) to 0.90 (for PALH). A population structure, principal component analysis, and kinship analysis revealed that the accessions could be divided into two groups. In total, 54 MTAs were identified, 11 of which were detected by both BLINK and farmCPU. MTAs identified for each trait ranged from five (PAWT and GY) to fourteen (PH) representing both novel and previously identified quantitative trait loci (QTLs). Three SNPs were associated with more than one trait, including a SNP within the Sobic.004G189200 gene that was associated with PH and PAWT. Major effect SNP loci, Sbi2393610 (PVE = 23.3%), Sbi10438246 (PVE = 35.2%), Sbi17789352 (PVE = 11.9%) and Sbi30169733 (PVE = 18.9%) on chromosomes 1, 3, 5 and 9 that showed strong association signals for PAWD, DTF, GY and PALH, respectively, were major findings of this study. The SNP markers and candidate genes identified in this study provide insights into the genetic control of grain yield and related agronomic traits, and once validated, the markers could be used in genomics-led breeding.
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Affiliation(s)
- Muluken Enyew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Anders S. Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Amare Seyoum
- National Sorghum Research Program, Crop Research Department, Melkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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10
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Wang Y, Yang Z, Zhang M, Ai P. A chloroplast-localized pentatricopeptide repeat protein involved in RNA editing and splicing and its effects on chloroplast development in rice. BMC PLANT BIOLOGY 2022; 22:437. [PMID: 36096762 PMCID: PMC9469629 DOI: 10.1186/s12870-022-03819-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The chloroplast is the organelle responsible for photosynthesis in higher plants. The generation of functional chloroplasts depends on the precise coordination of gene expression in the nucleus and chloroplasts and is essential for the development of plants. However, little is known about nuclear-plastid regulatory mechanisms at the early stage of chloroplast generation in rice. RESULTS In this study, we identified a rice (Oryza sativa) mutant that exhibited albino and seedling-lethal phenotypes and named it ssa1(seedling stage albino1). Transmission electron microscopy (TEM) analysis indicated that the chloroplasts of ssa1 did not have organized thylakoid lamellae and that the chloroplast structure was destroyed. Genetic analysis revealed that the albino phenotypes of ssa1 were controlled by a pair of recessive nuclear genes. Map-based cloning experiments found that SSA1 encoded a pentapeptide repeat (PPR) protein that was allelic to OSOTP51,which was previously reported to participate in Photosystem I (PSI) assembly. The albino phenotype was reversed to the wild type (WT) phenotype when the normal SSA1 sequence was expressed in ssa1 under the drive of the actin promoter. Knockout experiments further created mutants ssa1-2/1-9, which had a phenotype similar to that of ssa1. SSA1 consisted of 7 pentatricopeptide repeat domains and two C-terminal LAGLIDADG tandem sequence motifs and was located in the chloroplast. GUS staining and qRT-PCR analysis showed that SSA1 was mainly expressed in young leaves and stems. In the ssa1 mutants, plastid genes transcribed by plastid-encoded RNA polymerase decreased, while those transcribed by nuclear-encoded RNA polymerase increased at the mRNA level. Loss-of-function SSA1 destroys RNA editing of ndhB-737 and intron splicing of atpF and ycf3-2 in the plastid genome. Yeast two-hybrid and BiFC assays revealed that SSA1 physically interacted with two new RNA editing partners, OsMORF8 and OsTRXz, which have potential functions in RNA editing and chloroplast biogenesis. CONCLUSIONS Rice SSA1 encodes a pentatricopeptide repeat protein, which is targeted to the chloroplast. SSA1 regulates early chloroplast development and plays a critical role in RNA editing and intron splicing in rice. These data will facilitate efforts to further elucidate the molecular mechanism of chloroplast biogenesis.
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Affiliation(s)
- Yanwei Wang
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Zhimin Yang
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Meng Zhang
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Pengfei Ai
- Collage of Food and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China.
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11
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Luo Z, Xiong J, Xia H, Wang L, Hou G, Li Z, Li J, Zhou H, Li T, Luo L. Pentatricopeptide Repeat Gene-Mediated Mitochondrial RNA Editing Impacts on Rice Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:926285. [PMID: 35928709 PMCID: PMC9343880 DOI: 10.3389/fpls.2022.926285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/21/2022] [Indexed: 05/27/2023]
Abstract
Mitochondrial RNA editing plays crucial roles in the plant development and environmental adaptation. Pentatricopeptide repeat (PPR) genes, which are involved in the regulating mitochondrial RNA editing, are potential gene resources in the improvement of rice drought tolerance. In this study, we investigated genome-wide mitochondrial RNA editing in response to drought between upland and lowland rice. Responses of mitochondrial RNA editing to drought exhibit site-specific and genotype-specific patterns. We detected 22 and 57 ecotype-differentiated editing sites under well-watered and drought-treated conditions, respectively. Interestingly, the RNA editing efficiency was positively correlated with many agronomic traits, while it was negatively correlated with drought tolerance. We further selected two mitochondrial-localized PPR proteins, PPR035 and PPR406, to validate their functions in drought tolerance. PPR035 regulated RNA editing at rps4-926 and orfX-406, while PPR406 regulated RNA editing at orfX-355. The defectiveness in RNA editing at these sites had no apparent penalties in rice respiration and vegetative growth. Meanwhile, the knockout mutants of ppr035 and ppr406 show enhanced drought- and salt tolerance. PPR035 and PPR406 were under the balancing selection in upland rice and highly differentiated between upland and lowland rice ecotypes. The upland-dominant haplotypes of PPR035 and PPR406 shall contribute to the better drought tolerance in upland rice. They have great prospective in the improvement of rice drought tolerance.
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Affiliation(s)
- Zhi Luo
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jie Xiong
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hui Xia
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lei Wang
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Guihua Hou
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Zhaoyang Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jing Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hengling Zhou
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Tianfei Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lijun Luo
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
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12
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Baloch FS, Nadeem MA, Sönmez F, Habyarimana E, Mustafa Z, Karaköy T, Cömertpay G, Alsaleh A, Çiftçi V, Sun S, Chung G, Chung YS. Magnesium- a Forgotten Element: Phenotypic Variation and Genome Wide Association Study in Turkish Common Bean Germplasm. Front Genet 2022; 13:848663. [PMID: 35586571 PMCID: PMC9108430 DOI: 10.3389/fgene.2022.848663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022] Open
Abstract
Magnesium (Mg) is the fourth most abundant element in the human body and plays the role of cofactor for more than 300 enzymatic reactions. In plants, Mg is involved in various key physiological and biochemical processes like growth, development, photophosphorylation, chlorophyll formation, protein synthesis, and resistance to biotic and abiotic stresses. Keeping in view the importance of this element, the present investigation aimed to explore the Mg contents diversity in the seeds of Turkish common bean germplasm and to identify the genomic regions associated with this element. A total of 183 common bean accessions collected from 19 provinces of Turkey were used as plant material. Field experiments were conducted according to an augmented block design during 2018 in two provinces of Turkey, and six commercial cultivars were used as a control group. Analysis of variance depicted that Mg concentration among common bean accessions was statistically significant (p < 0.05) within each environment, however genotype × environment interaction was non-significant. A moderate level (0.60) of heritability was found in this study. Overall mean Mg contents for both environments varied from 0.33 for Nigde-Dermasyon to 1.52 mg kg−1 for Nigde-Derinkuyu landraces, while gross mean Mg contents were 0.92 mg kg−1. At the province level, landraces from Bolu were rich while the landraces from Bitlis were poor in seed Mg contents respectively. The cluster constellation plot divided the studied germplasm into two populations on the basis of their Mg contents. Marker-trait association was performed using a mixed linear model (Q + K) with a total of 7,900 DArTseq markers. A total of six markers present on various chromosomes (two at Pv01, and one marker at each chromosome i.e., Pv03, Pv07, Pv08, Pv11) showed statistically significant association for seed Mg contents. Among these identified markers, the DArT-3367607 marker present on chromosome Pv03 contributed to maximum phenotypic variation (7.5%). Additionally, this marker was found within a narrow region of previously reported markers. We are confident that the results of this study will contribute significantly to start common bean breeding activities using marker assisted selection regarding improved Mg contents.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
- *Correspondence: Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Ferit Sönmez
- Department of Seed Science and Technology, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Zemran Mustafa
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Turkey
| | - Ahmad Alsaleh
- Molecular Genetic Laboratory, Science and Technology Application and Research Center, Institute for Hemp Research, Yozgat Bozok University, Yozgat, Turkey
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Chonnam, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, South Korea
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
- *Correspondence: Faheem Shehzad Baloch, ; Yong Suk Chung,
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13
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Qin T, Zhao P, Sun J, Zhao Y, Zhang Y, Yang Q, Wang W, Chen Z, Mai T, Zou Y, Liu G, Hao W. Research Progress of PPR Proteins in RNA Editing, Stress Response, Plant Growth and Development. Front Genet 2021; 12:765580. [PMID: 34733319 PMCID: PMC8559896 DOI: 10.3389/fgene.2021.765580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
RNA editing is a posttranscriptional phenomenon that includes gene processing and modification at specific nucleotide sites. RNA editing mainly occurs in the genomes of mitochondria and chloroplasts in higher plants. In recent years, pentatricopeptide repeat (PPR) proteins, which may act as trans-acting factors of RNA editing have been identified, and the study of PPR proteins has become a research focus in molecular biology. The molecular functions of these proteins and their physiological roles throughout plant growth and development are widely studied. In this minireview, we summarize the current knowledge of the PPR family, hoping to provide some theoretical reference for future research and applications.
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Affiliation(s)
- Tengfei Qin
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Pei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jialiang Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Yuping Zhao
- Beijing River and Lake Management Office, Beijing, China
| | - Yaxin Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Qiuyue Yang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Weipeng Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Zhuanqing Chen
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Tengfei Mai
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Yingying Zou
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Guoxiang Liu
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wei Hao
- College of Medical Technology, Beihua University, Jilin City, China
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14
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Liu X, Zhang X, Cao R, Jiao G, Hu S, Shao G, Sheng Z, Xie L, Tang S, Wei X, Hu P. CDE4 encodes a pentatricopeptide repeat protein involved in chloroplast RNA splicing and affects chloroplast development under low-temperature conditions in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1724-1739. [PMID: 34219386 DOI: 10.1111/jipb.13147] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/30/2021] [Indexed: 05/24/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins play important roles in the post-transcriptional modification of organellar RNAs in plants. However, the function of most PPR proteins remains unknown. Here, we characterized the rice (Oryza sativa L.) chlorophyll deficient 4 (cde4) mutant which exhibits an albino phenotype during early leaf development, with decreased chlorophyll contents and abnormal chloroplasts at low-temperature (20°C). Positional cloning revealed that CDE4 encodes a P-type PPR protein localized in chloroplasts. In the cde4 mutant, plastid-encoded polymerase (PEP)-dependent transcript levels were significantly reduced, but transcript levels of nuclear-encoded genes were increased compared to wild-type plants at 20°C. CDE4 directly binds to the transcripts of the chloroplast genes rpl2, ndhA, and ndhB. Intron splicing of these transcripts was defective in the cde4 mutant at 20°C, but was normal at 32°C. Moreover, CDE4 interacts with the guanylate kinase VIRESCENT 2 (V2); overexpression of V2 enhanced CDE4 protein stability, thereby rescuing the cde4 phenotype at 20°C. Our results suggest that CDE4 participates in plastid RNA splicing and plays an important role in rice chloroplast development under low-temperature conditions.
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Affiliation(s)
- Xinyong Liu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xichun Zhang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- Guizhou Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Ruijie Cao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
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15
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Wang B, Farooq Z, Chu L, Liu J, Wang H, Guo J, Tu J, Ma C, Dai C, Wen J, Shen J, Fu T, Yi B. High-generation near-isogenic lines combined with multi-omics to study the mechanism of polima cytoplasmic male sterility. BMC PLANT BIOLOGY 2021; 21:130. [PMID: 33673810 PMCID: PMC7934456 DOI: 10.1186/s12870-021-02852-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/24/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cytoplasmic male sterility (CMS), which naturally exists in higher plants, is a useful mechanism for analyzing nuclear and mitochondrial genome functions and identifying the role of mitochondrial genes in the plant growth and development. Polima (pol) CMS is the most universally valued male sterility type in oil-seed rape. Previous studies have described the pol CMS restorer gene Rfp and the sterility-inducing gene orf224 in oil-seed rape, located in mitochondria. However, the mechanism of fertility restoration and infertility remains unknown. Moreover, it is still unknown how the fecundity restorer gene interferes with the sterility gene, provokes the sterility gene to lose its function, and leads to fertility restoration. RESULT In this study, we used multi-omics joint analysis to discover candidate genes that interact with the sterility gene orf224 and the restorer gene Rfp of pol CMS to provide theoretical support for the occurrence and restoration mechanisms of sterility. Via multi-omics analysis, we screened 24 differential genes encoding proteins related to RNA editing, respiratory electron transport chain, anther development, energy transport, tapetum development, and oxidative phosphorylation. Using a yeast two-hybrid assay, we obtained a total of seven Rfp interaction proteins, with orf224 protein covering five interaction proteins. CONCLUSIONS We propose that Rfp and its interacting protein cleave the transcript of atp6/orf224, causing the infertility gene to lose its function and restore fertility. When Rfp is not cleaved, orf224 poisons the tapetum cells and anther development-related proteins, resulting in pol CMS mitochondrial dysfunction and male infertility. The data from the joint analysis of multiple omics provided information on pol CMS's potential molecular mechanism and will help breed B. napus hybrids.
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Affiliation(s)
- Benqi Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zunaira Farooq
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Chu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huadong Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Guo
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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16
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Wang X, An Y, Li Y, Xiao J. A PPR Protein ACM1 Is Involved in Chloroplast Gene Expression and Early Plastid Development in Arabidopsis. Int J Mol Sci 2021; 22:ijms22052512. [PMID: 33802303 PMCID: PMC7959153 DOI: 10.3390/ijms22052512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/24/2022] Open
Abstract
Chloroplasts cannot develop normally without the coordinated action of various proteins and signaling connections between the nucleus and the chloroplast genome. Many questions regarding these processes remain unanswered. Here, we report a novel P-type pentatricopeptide repeat (PPR) factor, named Albino Cotyledon Mutant1 (ACM1), which is encoded by a nuclear gene and involved in chloroplast development. Knock-down of ACM1 transgenic plants displayed albino cotyledons but normal true leaves, while knock-out of the ACM1 gene in seedlings was lethal. Fluorescent protein analysis showed that ACM1 was specifically localized within chloroplasts. PEP-dependent plastid transcript levels and splicing efficiency of several group II introns were seriously affected in cotyledons in the RNAi line. Furthermore, denaturing gel electrophoresis and Western blot experiments showed that the accumulation of chloroplast ribosomes was probably damaged. Collectively, our results indicate ACM1 is indispensable in early chloroplast development in Arabidopsis cotyledons.
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Affiliation(s)
- Xinwei Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.W.); (Y.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China;
| | - Yaqi An
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China;
| | - Ye Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.W.); (Y.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China;
| | - Jianwei Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.W.); (Y.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China;
- Correspondence: ; Tel.: +86-15010693470
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17
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Zheng P, Liu Y, Liu X, Huang Y, Sun F, Wang W, Chen H, Jan M, Zhang C, Yuan Y, Tan BC, Du H, Tu J. OsPPR939, a nad5 splicing factor, is essential for plant growth and pollen development in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:923-940. [PMID: 33386861 PMCID: PMC7925476 DOI: 10.1007/s00122-020-03742-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/25/2020] [Indexed: 05/18/2023]
Abstract
P-subfamily PPR protein OsPPR939, which can be phosphorylated by OsS6K1, regulates plant growth and pollen development by involving in the splicing of mitochondrial nad5 introns 1, 2, and 3. In land plants, pentatricopeptide repeat (PPR) proteins play key roles in mitochondrial group II intron splicing, but how these nucleus-encoded proteins are imported into mitochondria is unknown. To date, a few PPR proteins have been characterized in rice (Oryza sativa). Here, we demonstrate that the mitochondrion-localized P-subfamily PPR protein OsPPR939 is required for the splicing of nad5 introns 1, 2, and 3 in rice. Complete knockout or partial disruption of OsPPR939 function resulted in different degrees of growth retardation and pollen sterility. The dramatically reduced splicing efficiency of these introns in osppr939-4 and osppr939-5 led to reduced mitochondrial complex I abundance and activity and enhanced expression of alternative respiratory pathway genes. Complementation with OsPPR939 rescued the defective plant morphology of osppr939-4 and restored its decreased splicing efficiency of nad5 introns 1, 2, and 3. Therefore, OsPPR939 plays crucial roles in plant growth and pollen development by splicing mitochondrial nad5 introns 1, 2, and 3. More importantly, the 12th amino acid Ser in the N-terminal targeting sequence of OsPPR939 is phosphorylated by OsS6K1, and truncated OsPPR939 with a non-phosphorylatable S12A mutation in its presequence could not be imported into mitochondria, suggesting that phosphorylation of this amino acid plays an important role in the mitochondrial import of OsPPR939. To our knowledge, the 12th residue Ser on OsPPR939 is the first experimentally proven phosphorylation site in PPR proteins. Our results provide a basis for investigating the regulatory mechanism of PPR proteins at the post-translational level.
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Affiliation(s)
- Peng Zheng
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yujun Liu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
| | - Xuejiao Liu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yuqing Huang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Feng Sun
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Wenyi Wang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Hao Chen
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Mehmood Jan
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Cuicui Zhang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yue Yuan
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Hao Du
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
| | - Jumin Tu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
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18
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Jiang D, Chen J, Zhang Z, Hou X. Mitochondrial Transcription Termination Factor 27 Is Required for Salt Tolerance in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22031466. [PMID: 33540552 PMCID: PMC7867191 DOI: 10.3390/ijms22031466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 01/15/2023] Open
Abstract
In plants, mTERF proteins are primarily found in mitochondria and chloroplasts. Studies have identified several mTERF proteins that affect plant development, respond to abiotic stresses, and regulate organellar gene expression, but the functions and underlying mechanisms of plant mTERF proteins remain largely unknown. Here, we investigated the function of Arabidopsis mTERF27 using molecular genetic, cytological, and biochemical approaches. Arabidopsis mTERF27 had four mTERF motifs and was evolutionarily conserved from moss to higher plants. The phenotype of the mTERF27-knockout mutant mterf27 did not differ obviously from that of the wild-type under normal growth conditions but was hypersensitive to salt stress. mTERF27 was localized to the mitochondria, and the transcript levels of some mitochondrion-encoded genes were reduced in the mterf27 mutant. Importantly, loss of mTERF27 function led to developmental defects in the mitochondria under salt stress. Furthermore, mTERF27 formed homomers and directly interacted with multiple organellar RNA editing factor 8 (MORF8). Thus, our results indicated that mTERF27 is likely crucial for mitochondrial development under salt stress, and that this protein may be a member of the protein interaction network regulating mitochondrial gene expression.
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Wang X, An Y, Xu P, Xiao J. Functioning of PPR Proteins in Organelle RNA Metabolism and Chloroplast Biogenesis. FRONTIERS IN PLANT SCIENCE 2021; 12:627501. [PMID: 33633768 PMCID: PMC7900629 DOI: 10.3389/fpls.2021.627501] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/04/2021] [Indexed: 05/05/2023]
Abstract
The pentatricopeptide repeat (PPR) proteins constitute one of the largest nuclear-encoded protein families in higher plants, with over 400 members in most sequenced plant species. The molecular functions of these proteins and their physiological roles during plant growth and development have been widely studied. Generally, there is mounting evidence that PPR proteins are involved in the post-transcriptional regulation of chloroplast and/or mitochondrial genes, including RNA maturation, editing, intron splicing, transcripts' stabilization, and translation initiation. The cooperative action of RNA metabolism has profound effects on the biogenesis and functioning of both chloroplasts and mitochondria and, consequently, on the photosynthesis, respiration, and development of plants and their environmental responses. In this review, we summarize the latest research on PPR proteins, specifically how they might function in the chloroplast, by documenting their mechanism of molecular function, their corresponding RNA targets, and their specific effects upon chloroplast biogenesis and host organisms.
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Affiliation(s)
- Xinwei Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yaqi An
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Pan Xu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jianwei Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- *Correspondence: Jianwei Xiao,
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