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Hu K, Ni P, Xu M, Zou Y, Chang J, Gao X, Li Y, Ruan J, Hu B, Wang J. HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation. Nat Commun 2024; 15:5573. [PMID: 38956036 PMCID: PMC11219922 DOI: 10.1038/s41467-024-49912-8] [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: 07/09/2023] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, HiTE has identified numerous novel transposons with well-defined structures containing protein-coding domains, some of which are directly inserted within crucial genes, leading to direct alterations in gene expression. A Nextflow version of HiTE is also available, with enhanced parallelism, reproducibility, and portability.
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Affiliation(s)
- Kang Hu
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Peng Ni
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Minghua Xu
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - You Zou
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Jianye Chang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center of Excellence on Smart Health, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yaohang Li
- Department of Computer Science, Old Dominion University, Norfolk, VA, 23529, USA
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Bin Hu
- Key Laboratory of Brain Health Intelligent Evaluation and Intervention, Ministry of Education (Beijing Institute of Technology), Beijing, P. R. China.
- School of Medical Technology, Beijing Institute of Technology, Beijing, P. R. China.
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
- Xiangjiang Laboratory, Changsha, 410205, China.
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China.
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2
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Liu J, Ye Q, Jiang W, Liu S, Wu Z, Hu X, Wang X, Zhang Z, Guo D, Chen X, He H, Hu L. Abnormal Degraded Tapetum 1 (ADT1) is required for tapetal cell death and pollen development in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:170. [PMID: 38913206 DOI: 10.1007/s00122-024-04677-y] [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: 03/21/2024] [Accepted: 06/14/2024] [Indexed: 06/25/2024]
Abstract
The timely degradation of tapetum, the innermost somatic anther cell layer in flowering plants, is critical for pollen development. Although several genes involved in tapetum development have been characterized, the molecular mechanisms underlying tapetum degeneration remain elusive. Here, we showed that mutation in Abnormal Degraded Tapetum 1 (ADT1) resulted in overaccumulation of Reactive Oxygen Species (ROS) and abnormal anther development, causing earlier tapetum Programmed Cell Death (PCD) and pollen abortion. ADT1 encodes a nuclear membrane localized protein, which is strongly expressed in the developing microspores and tapetal cells during early anther development. Moreover, ADT1 could interact with metallothionein MT2b, which was related to ROS scavenging and cell death regulation. These findings indicate that ADT1 is required for proper timing of tapetum PCD by regulating ROS homeostasis, expanding our understanding of the regulatory network of male reproductive development in rice.
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Affiliation(s)
- Jialin Liu
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
- School of Advanced Agricultural Sciences, Weifang University, Weifang, 261000, China
| | - Qing Ye
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wenxiang Jiang
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shiqiang Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zheng Wu
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiafei Hu
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaoqing Wang
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zelin Zhang
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dandan Guo
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaorong Chen
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haohua He
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China.
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lifang Hu
- College of Agriculture, Jiangxi Agricultural University, Nanchang, 330045, China.
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
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3
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Hu J, Liu C, Du Z, Guo F, Song D, Wang N, Wei Z, Jiang J, Cao Z, Shi C, Zhang S, Zhu C, Chen P, Larkin RM, Lin Z, Xu Q, Ye J, Deng X, Bosch M, Franklin‐Tong VE, Chai L. Transposable elements cause the loss of self-incompatibility in citrus. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1113-1131. [PMID: 38038155 PMCID: PMC11022811 DOI: 10.1111/pbi.14250] [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: 09/10/2023] [Revised: 10/25/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
Self-incompatibility (SI) is a widespread prezygotic mechanism for flowering plants to avoid inbreeding depression and promote genetic diversity. Citrus has an S-RNase-based SI system, which was frequently lost during evolution. We previously identified a single nucleotide mutation in Sm-RNase, which is responsible for the loss of SI in mandarin and its hybrids. However, little is known about other mechanisms responsible for conversion of SI to self-compatibility (SC) and we identify a completely different mechanism widely utilized by citrus. Here, we found a 786-bp miniature inverted-repeat transposable element (MITE) insertion in the promoter region of the FhiS2-RNase in Fortunella hindsii Swingle (a model plant for citrus gene function), which does not contain the Sm-RNase allele but are still SC. We demonstrate that this MITE plays a pivotal role in the loss of SI in citrus, providing evidence that this MITE insertion prevents expression of the S-RNase; moreover, transgenic experiments show that deletion of this 786-bp MITE insertion recovers the expression of FhiS2-RNase and restores SI. This study identifies the first evidence for a role for MITEs at the S-locus affecting the SI phenotype. A family-wide survey of the S-locus revealed that MITE insertions occur frequently adjacent to S-RNase alleles in different citrus genera, but only certain MITEs appear to be responsible for the loss of SI. Our study provides evidence that insertion of MITEs into a promoter region can alter a breeding strategy and suggests that this phenomenon may be broadly responsible for SC in species with the S-RNase system.
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Affiliation(s)
- Jianbing Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Chenchen Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Zezhen Du
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Furong Guo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Dan Song
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Nan Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Zhuangmin Wei
- Guangxi Subtropical Crops Research InstituteNanningP. R. China
| | - Jingdong Jiang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Zonghong Cao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Chunmei Shi
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Siqi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Chenqiao Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Peng Chen
- Horticultural Institute, Hunan Academy of Agricultural SciencesChangshaChina
| | - Robert M. Larkin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Zongcheng Lin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Junli Ye
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | | | - Lijun Chai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
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Wang H, Ye T, Guo Z, Yao Y, Tu H, Wang P, Zhang Y, Wang Y, Li X, Li B, Xiong H, Lai X, Xiong L. A double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice. Nat Commun 2024; 15:2514. [PMID: 38514621 PMCID: PMC10957929 DOI: 10.1038/s41467-024-46754-2] [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: 09/19/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Drought stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of drought resistance in rice. Here, through a genome-wide association study, we reveal that natural variations in DROUGHT RESISTANCE GENE 9 (DRG9), encoding a double-stranded RNA (dsRNA) binding protein, contribute to drought resistance. Under drought stress, DRG9 condenses into stress granules (SGs) through liquid-liquid phase separation via a crucial α-helix. DRG9 recruits the mRNAs of OsNCED4, a key gene for the biosynthesis of abscisic acid, into SGs and protects them from degradation. In drought-resistant DRG9 allele, natural variations in the coding region, causing an amino acid substitution (G267F) within the zinc finger domain, increase DRG9's binding ability to OsNCED4 mRNA and enhance drought resistance. Introgression of the drought-resistant DRG9 allele into the elite rice Huanghuazhan significantly improves its drought resistance. Thus, our study underscores the role of a dsRNA-binding protein in drought resistance and its promising value in breeding drought-resistant rice.
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Affiliation(s)
- Huaijun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Tiantian Ye
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zilong Guo
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yilong Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Bingchen Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haiyan Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuelei Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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5
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Gubaev R, Karzhaev D, Grigoreva E, Lytkin K, Safronycheva E, Volkov V, Nesterchuk V, Vetchinnikova L, Zhigunov A, Potokina E. Dissection of figured wood trait in curly birch (Betula pendula Roth var. carelica (Mercklin) Hämet-Ahti) using high-throughput genotyping. Sci Rep 2024; 14:5058. [PMID: 38424163 PMCID: PMC10904815 DOI: 10.1038/s41598-024-55404-y] [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: 09/09/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Curly (Karelian) birch is a special variety of Betula pendula Roth distributed in the northwestern part of Europe. Karelian birch is well-known for its valuable figured curly wood also known as "wooden marble". The genetic basis underlying curly wood formation has been debated since last century, however, there was no data about loci responsible for the curly wood trait. In the present study, we analyzed two full-sibs populations derived from experimental crosses of curly birches and segregating for the trait. RADseq genotyping was applied to reveal how many loci are involved in 'curliness' formation and to search for genetic variants associated with this trait. One single interval on chromosome 10 was detected containing possible candidate genes. InDel marker BpCW1 was suggested for the first time for marker-assisted selection of trees with curly wood at their earliest stages of development.
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Affiliation(s)
- Rim Gubaev
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
| | - Dmitry Karzhaev
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Research Laboratory, Saint Petersburg Forest Research Institute, St. Petersburg, Russia
| | - Elizaveta Grigoreva
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Kirill Lytkin
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
| | - Elizaveta Safronycheva
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Research Laboratory, Saint Petersburg Forest Research Institute, St. Petersburg, Russia
| | - Vladimir Volkov
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Research Laboratory, Saint Petersburg Forest Research Institute, St. Petersburg, Russia
| | - Veronika Nesterchuk
- Research Laboratory, Saint Petersburg Forest Research Institute, St. Petersburg, Russia
| | - Lidiia Vetchinnikova
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
- Forest Research Institute of Karelian Research Centre Russian Academy of Sciences, Petrozavodsk, Russia
| | - Anatoly Zhigunov
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia
| | - Elena Potokina
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg, Russia.
- Skolkovo Institute of Science and Technology, Moscow, Russia.
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Zhang H, Zhang J, Xu P, Li M, Li Y. Insertion of a miniature inverted-repeat transposable element into the promoter of OsTCP4 results in more tillers and a lower grain size in rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1421-1436. [PMID: 37988625 DOI: 10.1093/jxb/erad467] [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: 06/06/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023]
Abstract
A class I PCF type protein, TCP4, was identified as a transcription factor associated with both grain size and tillering through a DNA pull-down-MS assay combined with a genome-wide association study. This transcription factor was found to have a significant role in the variations among the 533 rice accessions, dividing them into two main subspecies. A Tourist-like miniature inverted-repeat transposable element (MITE) was discovered in the promoter of TCP4 in japonica/geng accessions (TCP4M+), which was found to suppress the expression of TCP4 at the transcriptional level. The MITE-deleted haplotype (TCP4M-) was mainly found in indica/xian accessions. ChIP-qPCR and EMSA demonstrated the binding of TCP4 to promoters of grain reservoir genes such as SSIIa and Amy3D in vivo and in vitro, respectively. The introduction of the genomic sequence of TCP4M+ into different TCP4M- cultivars was found to affect the expression of TCP4 in the transgenic rice, resulting in decreased expression of its downstream target gene SSIIa, increased tiller number, and decreased seed length. This study revealed that a Tourist-like MITE contributes to subspecies divergence by regulating the expression of TCP4 in response to environmental pressure, thus influencing source-sink balance by regulating starch biosynthesis in rice.
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Affiliation(s)
- Hui Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Juncheng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Pengkun Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
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7
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Chen Z, Zhou W, Guo X, Ling S, Li W, Wang X, Yao J. Heat Stress Responsive Aux/IAA Protein, OsIAA29 Regulates Grain Filling Through OsARF17 Mediated Auxin Signaling Pathway. RICE (NEW YORK, N.Y.) 2024; 17:16. [PMID: 38374238 PMCID: PMC10876508 DOI: 10.1186/s12284-024-00694-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/13/2024] [Indexed: 02/21/2024]
Abstract
High temperature during grain filling considerably reduces yield and quality in rice, but its molecular mechanisms are not fully understood. We investigated the functions of a seed preferentially expressed Aux/IAA gene, OsIAA29, under high temperature-stress in grain filling using CRISPR/Cas9, RNAi, and overexpression. We observed that the osiaa29 had a higher percentage of shrunken and chalkiness seed, as well as lower 1000-grain weight than ZH11 under high temperature. Meanwhile, the expression of OsIAA29 was induced and the IAA content was remarkably reduced in the ZH11 seeds under high temperature. In addition, OsIAA29 may enhance the transcriptional activation activity of OsARF17 through competition with OsIAA21 binding to OsARF17. Finally, chromatin immunoprecipitation quantitative real-time PCR (ChIP-qPCR) results proved that OsARF17 regulated expression of several starch and protein synthesis related genes (like OsPDIL1-1, OsSS1, OsNAC20, OsSBE1, and OsC2H2). Therefore, OsIAA29 regulates seed development in high temperature through competition with OsIAA21 in the binding to OsARF17, mediating auxin signaling pathway in rice. This study provides a theoretical basis and gene resources for auxin signaling and effective molecular design breeding.
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Affiliation(s)
- Zhanghao Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Zhou
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Xianyu Guo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Ling
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wang Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China.
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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8
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Yao Y, Xiang D, Wu N, Wang Y, Chen Y, Yuan Y, Ye Y, Hu D, Zheng C, Yan Y, Lv Q, Li X, Chen G, Hu H, Xiong H, Peng S, Xiong L. Control of rice ratooning ability by a nucleoredoxin that inhibits histidine kinase dimerization to attenuate cytokinin signaling in axillary buds. MOLECULAR PLANT 2023; 16:1911-1926. [PMID: 37853691 DOI: 10.1016/j.molp.2023.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/24/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023]
Abstract
Rice ratooning, the fast outgrowth of dormant buds on stubble, is an important cropping practice in rice production. However, the low ratooning ability (RA) of most rice varieties restricts the application of this cost-efficient system, and the genetic basis of RA remains unknown. In this study, we dissected the genetic architecture of RA by a genome-wide association study in a natural rice population. Rice ratooning ability 3 (RRA3), encoding a hitherto not characterized nucleoredoxin involved in reduction of disulfide bonds, was identified as the causal gene of a major locus controlling RA. Overexpression of RRA3 in rice significantly accelerated leaf senescence and reduced RA, whereas knockout of RRA3 significantly delayed leaf senescence and increased RA and ratoon yield. We demonstrated that RRA3 interacts with Oryza sativa histidine kinase 4 (OHK4), a cytokinin receptor, and inhibits the dimerization of OHK4 through disulfide bond reduction. This inhibition ultimately led to decreased cytokinin signaling and reduced RA. In addition, variations in the RRA3 promoter were identified to be associated with RA. Introgression of a superior haplotype with weak expression of RRA3 into the elite rice variety Guichao 2 significantly increased RA and ratoon yield by 23.8%. Collectively, this study not only uncovers an undocumented regulatory mechanism of cytokinin signaling through de-dimerization of a histidine kinase receptor-but also provides an eximious gene with promising value for ratoon rice breeding.
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Affiliation(s)
- Yilong Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Denghao Xiang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Nai Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Yuan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Ye
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Chang Zheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qingya Lv
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Guoxing Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Haiyan Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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9
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Kan Q, Li Q. Post-transcriptional and translational regulation of plant gene expression by transposons. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102438. [PMID: 37619514 DOI: 10.1016/j.pbi.2023.102438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 08/26/2023]
Abstract
Transposons are mobile DNA sequences that can move within the genome and integrate in new genomic locations. They are widespread in eukaryotes and prokaryotes and can influence gene expression when landing within or nearby a gene. Although transposon-induced regulation of gene expression at the transcriptional level has been extensively studied, there has been less focus on regulation at the post-transcriptional and translational levels. Recent studies in maize (Zea mays) and other plant species suggest that transposon insertions can affect RNA processing, RNA stability, protein translation and protein stability. We will describe the diverse mechanisms by which transposons can influence gene expression at the post-transcriptional and translational levels, and discuss the interactions between these mechanisms.
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Affiliation(s)
- Qiuxin Kan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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10
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Fan X, Wang P, Qi F, Hu Y, Li S, Zhang J, Liang L, Zhang Z, Liu J, Xiong L, Xing Y. The CCT transcriptional activator Ghd2 constantly delays the heading date by upregulating CO3 in rice. J Genet Genomics 2023; 50:755-764. [PMID: 36906137 DOI: 10.1016/j.jgg.2023.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
CONSTANS, CO-like, and TOC1 (CCT) family genes play important roles in regulating heading date, which exerts a large impact on the regional and seasonal adaptation of rice. Previous studies have shown that Grain number, plant height, and heading date2 (Ghd2) exhibits a negative response to drought stress by directly upregulating Rubisco activase and exerting a negative effect on heading date. However, the target gene of Ghd2 regulating heading date is still unknown. In this study, CO3 is identified by analyzing Ghd2 ChIP-seq data. Ghd2 activates CO3 expression by binding to the CO3 promoter through its CCT domain. EMSA experiments show that the motif CCACTA in the CO3 promoter was recognized by Ghd2. A comparison of the heading dates among plants with CO3 knocked out or overexpressed and double-mutants with Ghd2 overexpressed and CO3 knocked out shows that CO3 negatively and constantly regulates flowering by repressing the transcription of Ehd1, Hd3a, and RFT1. In addition, the target genes of CO3 are explored via a comprehensive analysis of DAP-seq and RNA-seq data. Taken together, these results suggest that Ghd2 directly binds to the downstream gene CO3, and the Ghd2-CO3 module constantly delays heading date via the Ehd1-mediated pathway.
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Affiliation(s)
- Xiaowei Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Feixiang Qi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shuangle Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jia Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Liwen Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Juhong Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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11
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Xia A, Zheng L, Wang Z, Wang Q, Lu M, Cui Z, He Y. The RHW1-ZCN4 regulatory pathway confers natural variation of husk leaf width in maize. THE NEW PHYTOLOGIST 2023; 239:2367-2381. [PMID: 37403373 DOI: 10.1111/nph.19116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/06/2023] [Indexed: 07/06/2023]
Abstract
Maize husk leaf - the outer leafy layers covering the ear - modulates kernel yield and quality. Despite its importance, however, the genetic controls underlying husk leaf development remain elusive. Our previous genome-wide association study identified a single nucleotide polymorphism located in the gene RHW1 (Regulator of Husk leaf Width) that is significantly associated with husk leaf-width diversity in maize. Here, we further demonstrate that a polymorphic 18-bp InDel (insertion/deletion) variant in the 3' untranslated region of RHW1 alters its protein abundance and accounts for husk leaf width variation. RHW1 encodes a putative MYB-like transcriptional repressor. Disruption of RHW1 altered cell proliferation and resulted in a narrower husk leaf, whereas RHW1 overexpression yielded a wider husk leaf. RHW1 positively regulated the expression of ZCN4, a well-known TFL1-like protein involved in maize ear development. Dysfunction of ZCN4 reduced husk leaf width even in the context of RHW1 overexpression. The InDel variant in RHW1 is subject to selection and is associated with maize husk leaf adaption from tropical to temperate regions. Overall, our results identify that RHW1-ZCN4 regulates a pathway conferring husk leaf width variation at a very early stage of husk leaf development in maize.
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Affiliation(s)
- Aiai Xia
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Leiming Zheng
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Zi Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Qi Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Ming Lu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Zhenhai Cui
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
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12
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Gebrie A. Transposable elements as essential elements in the control of gene expression. Mob DNA 2023; 14:9. [PMID: 37596675 PMCID: PMC10439571 DOI: 10.1186/s13100-023-00297-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Interspersed repetitions called transposable elements (TEs), commonly referred to as mobile elements, make up a significant portion of the genomes of higher animals. TEs contribute in controlling the expression of genes locally and even far away at the transcriptional and post-transcriptional levels, which is one of their significant functional effects on gene function and genome evolution. There are different mechanisms through which TEs control the expression of genes. First, TEs offer cis-regulatory regions in the genome with their inherent regulatory features for their own expression, making them potential factors for controlling the expression of the host genes. Promoter and enhancer elements contain cis-regulatory sites generated from TE, which function as binding sites for a variety of trans-acting factors. Second, a significant portion of miRNAs and long non-coding RNAs (lncRNAs) have been shown to have TEs that encode for regulatory RNAs, revealing the TE origin of these RNAs. Furthermore, it was shown that TE sequences are essential for these RNAs' regulatory actions, which include binding to the target mRNA. By being a member of cis-regulatory and regulatory RNA sequences, TEs therefore play essential regulatory roles. Additionally, it has been suggested that TE-derived regulatory RNAs and cis-regulatory regions both contribute to the evolutionary novelty of gene regulation. Additionally, these regulatory systems arising from TE frequently have tissue-specific functions. The objective of this review is to discuss TE-mediated gene regulation, with a particular emphasis on the processes, contributions of various TE types, differential roles of various tissue types, based mostly on recent studies on humans.
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Affiliation(s)
- Alemu Gebrie
- Department of Biomedical Sciences, School of Medicine, Debre Markos University, Debre Markos, Ethiopia.
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13
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Berthelier J, Furci L, Asai S, Sadykova M, Shimazaki T, Shirasu K, Saze H. Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana. Nat Commun 2023; 14:3248. [PMID: 37277361 DOI: 10.1038/s41467-023-38954-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, ParasiTE, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.
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Grants
- JP20H02995 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP22H00364 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05909 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05913 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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Affiliation(s)
- Jérémy Berthelier
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
| | - Leonardo Furci
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Shuta Asai
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Munissa Sadykova
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Tomoe Shimazaki
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
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14
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Zheng W, Zhang W, Liu D, Yin M, Wang X, Wang S, Shen S, Liu S, Huang Y, Li X, Zhao Q, Yan L, Xu Y, Yu S, Hu B, Yuan T, Mei Z, Guo L, Luo J, Deng X, Xu Q, Huang L, Ma Z. Evolution-guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37115171 PMCID: PMC10363765 DOI: 10.1111/pbi.14058] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
Pummelo (Citrus maxima or Citrus grandis) is a basic species and an important type for breeding in Citrus. Pummelo is used not only for fresh consumption but also for medicinal purposes. However, the molecular basis of medicinal traits is unclear. Here, compared with wild citrus species/Citrus-related genera, the content of 43 bioactive metabolites and their derivatives increased in the pummelo. Furthermore, we assembled the genome sequence of a variety for medicinal purposes with a long history, Citrus maxima 'Huazhouyou-tomentosa' (HZY-T), at the chromosome level with a genome size of 349.07 Mb. Comparative genomics showed that the expanded gene family in the pummelo genome was enriched in flavonoids-, terpenoid-, and phenylpropanoid biosynthesis. Using the metabolome and transcriptome of six developmental stages of HZY-T and Citrus maxima 'Huazhouyou-smooth' (HZY-S) fruit peel, we generated the regulatory networks of bioactive metabolites and their derivatives. We identified a novel MYB transcription factor, CmtMYB108, as an important regulator of flavone pathways. Both mutations and expression of CmtMYB108, which targets the genes PAL (phenylalanine ammonia-lyase) and FNS (flavone synthase), displayed differential expression between Citrus-related genera, wild citrus species and pummelo species. This study provides insights into the evolution-associated changes in bioactive metabolism during the origin process of pummelo.
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Affiliation(s)
- Weikang Zheng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Wang Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Dahui Liu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Minqiang Yin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Xia Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | | | | | - Shengjun Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Yue Huang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Xinxin Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Qian Zhao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Lu Yan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Yuantao Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Shiqi Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Bin Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Tao Yuan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Zhinan Mei
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhaocheng Ma
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
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15
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Chen G, Wang R, Jiang Y, Dong X, Xu J, Xu Q, Kan Q, Luo Z, Springer N, Li Q. A novel active transposon creates allelic variation through altered translation rate to influence protein abundance. Nucleic Acids Res 2023; 51:595-609. [PMID: 36629271 PMCID: PMC9881132 DOI: 10.1093/nar/gkac1195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 01/12/2023] Open
Abstract
Protein translation is tightly and precisely controlled by multiple mechanisms including upstream open reading frames (uORFs), but the origins of uORFs and their role in maize are largely unexplored. In this study, an active transposition event was identified during the propagation of maize inbred line B73. The transposon, which was named BTA for 'B73 active transposable element hAT', creates a novel dosage-dependent hypomorphic allele of the hexose transporter gene ZmSWEET4c through insertion within the coding sequence in the first exon, and results in reduced kernel size. The BTA insertion does not affect transcript abundance but reduces protein abundance of ZmSWEET4c, probably through the introduction of a uORF. Furthermore, the introduction of BTA sequence in the exon of other genes can regulate translation efficiency without affecting their mRNA levels. A transposon capture assay revealed 79 novel insertions for BTA and BTA-like elements. These insertion sites have typical euchromatin features, including low levels of DNA methylation and high levels of H3K27ac. A putative autonomous element that mobilizes BTA and BTA-like elements was identified. Together, our results suggest a transposon-based origin of uORFs and document a new role for transposable elements to influence protein abundance and phenotypic diversity by affecting the translation rate.
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Affiliation(s)
| | | | | | - Xiaoxiao Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiuxin Kan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhixiang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Qing Li
- To whom correspondence should be addressed.
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16
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Zhang T, Xiang Y, Geng L, Jiang W, Cheng S, Zhao Y. A Non-Canonical MITE in the WOX11 Promoter Is Associated with Robust Crown Root development in Rice. PLANT & CELL PHYSIOLOGY 2022; 63:1052-1062. [PMID: 35727725 DOI: 10.1093/pcp/pcac075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
The formation of tissues and organs in multicellular organisms is tightly controlled by transcriptional programs determined by temporal and spatial patterns of gene expression. As an important regulator of rice crown root development, WOX11 is essential for crown root formation and its transcript level is positively correlated with crown root biomass. However, how WOX11 is regulated during crown root primordium emergence and outgrowth still remains unknown. In this study, variations of the WOX11 genomic sequence were analyzed, and the highest genetic diversity was found within its promoter, which contained a non-canonical miniature inverted-repeat transposable element (ncMITE) sequence. Analysis of the WOX11 promoter-driven reporter gene GUS (β-glucuronidase) transgenic plants pWOX11(ncMITE+):GUS and pWOX11(ncMITE-):GUS uncovered higher GUS expression levels in crown roots of pWOX11(ncMITE+):GUS plants. Furthermore, pWOX11(ncMITE+):WOX11-FLAG in wox11 background could complement the crown root number and length compared to those of the wild type, while pWOX11(ncMITE-):WOX11-FLAG could not. These results suggested that the ncMITE was positively associated with WOX11 transcripts in rice crown roots. In addition, DNA methylation nearby the ncMITE region attenuated the activation effect of the ncMITE on WOX11 expression, which might also be the cause conferred to the root-specific expression of WOX11. This work provides novel insight into WOX11 expression regulation and reveals a promising target for genetic improvement of root architecture in rice.
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Affiliation(s)
- Ting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
- College of Bioengineering, Jingchu University of Technology, Jingmen, No. 33 Xiangshan Avenue, Jingmen, Hubei 448000, China
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, No. 33 Xiangshan Avenue, Jingmen, Hubei 448000, China
| | - Yimeng Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Leping Geng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Wei Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Saifeng Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
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17
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Bandara WW, Wijesundera WSS, Hettiarachchi C. Rice and Arabidopsis BBX proteins: toward genetic engineering of abiotic stress resistant crops. 3 Biotech 2022; 12:164. [PMID: 36092969 PMCID: PMC9452616 DOI: 10.1007/s13205-022-03228-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 06/17/2022] [Indexed: 11/01/2022] Open
Abstract
Productivity of crop plants are enormously affected by biotic and abiotic stresses. The co-occurrence of several abiotic stresses may lead to death of crop plants. Hence, it is the responsibility of plant scientists to develop crop plants equipped with multistress tolerance pathways. A subgroup of zinc finger transcription factor family, known as B-box (BBX) proteins, play a key role in light and hormonal regulation pathways. In addition, BBX proteins act as key regulatory proteins in many abiotic stress regulatory pathways, including Ultraviolet-B (UV-B), salinity, drought, heat and cold, and heavy metal stresses. Most of the BBX proteins identified in Arabidopsis and rice respond to more than one abiotic stress. Considering the requirement of improving rice for multistress tolerance, this review discusses functionally characterized Arabidopsis and rice BBX proteins in the development of abiotic stress responses. Furthermore, it highlights the participation of BBX proteins in multistress regulation and crop improvement through genetic engineering.
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18
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Tang Y, Li X, Hu C, Qiu X, Li J, Li X, Zhu H, Wang J, Sui J, Qiao L. Identification and characterization of transposable element AhMITE1 in the genomes of cultivated and two wild peanuts. BMC Genomics 2022; 23:500. [PMID: 35820800 PMCID: PMC9277781 DOI: 10.1186/s12864-022-08732-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/30/2022] [Indexed: 12/04/2022] Open
Abstract
Background The cultivated peanut (Arachis hypogaea L., AABB) is an allotetraploid hybrid between two diploid peanuts, A. duranensis (AA genome) and A. ipaensis (BB genome). Miniature inverted-repeat transposable elements (MITEs), some of which are known as active nonautonomous DNA transposons with high copy numbers, play important roles in genome evolution and diversification. AhMITE1, a member of the MITE family of transposons, but information on the peanut genomes is still limited. Here, we analyzed AhMITE1, AuMITE1 and ApMITE1 in the cultivated (A. hypogaea) and two wild peanut (A. duranensis and A. ipaensis) genomes. Results The cultivated and the two wild peanut genomes harbored 142, 14 and 21 AhMITE1, AuMITE1 and ApMITE1 family members, respectively. These three family members exhibited highly conserved TIR sequences, and insertions preferentially occurred within 2 kb upstream and downstream of gene-coding and AT-rich regions. Phylogenetic and pairwise nucleotide diversity analysis showed that AhMITE1 and ApMITE1 family members have undergone one round of amplification bursts during the evolution of the peanut genome. PCR analyses were performed in 23 peanut varieties and demonstrated that AhMITE1 is an active transposon and that hybridization or chemical mutagenesis can promote the mobilization of AhMITE1. Conclusions AhMITE1, AuMITE1 and ApMITE1 family members were identified based on local BLAST search with MAK between the cultivated and the two wild peanut genomes. The phylogenetic, nucleotide diversity and variation copy numbers of AhMITE1, AuMITE1 and ApMITE1 members provides opportunities for investigating their roles during peanut evolution. These findings will contribute to knowledge on diversity of AhMITE1, provide information about the potential impact on the gene expression and promote the development of DNA markers in peanut. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08732-0.
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Affiliation(s)
- Yanyan Tang
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaoting Li
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China
| | - Changli Hu
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaochen Qiu
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jingjing Li
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Li
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hong Zhu
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jingshan Wang
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiongming Sui
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Lixian Qiao
- College of Agronomy, Dry-Land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao Agricultural University, Qingdao, 266109, China.
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Li C, Wang J, Li L, Li J, Zhuang M, Li B, Li Q, Huang J, Du Y, Wang J, Fan Z, Mao X, Jing R. TaMOR is essential for root initiation and improvement of root system architecture in wheat. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:862-875. [PMID: 34890129 PMCID: PMC9055823 DOI: 10.1111/pbi.13765] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/25/2021] [Accepted: 12/07/2021] [Indexed: 05/13/2023]
Abstract
Optimal root system architecture is beneficial for water-fertilizer use efficiency, stress tolerance and yield improvement of crops. However, because of the complexity of root traits and difficulty in phenotyping deep roots, the study on mechanisms of root development is rarely reported in wheat (Triticum aestivum L.). In this study, we identified that the LBD (LATERAL ORGAN BOUNDARIES DOMAIN) gene TaMOR (MORE ROOT in wheat) determines wheat crown root initiation. The mor mutants exhibited less or even no crown root, dwarfism, less grain number and lodging caused by few roots. The observation of cross sections showed that crown root initiation is inhibited in the mor mutants. Molecular assays revealed that TaMOR interacts with the auxin response factor ARF5 to directly induce the expression of the auxin transporter gene PIN2 (PIN-FORMED 2) in the root base to regulate crown root initiation. In addition, a 159-bp MITE (miniature inverted-repeat transposable element) insertion causing DNA methylation and lower expression of TaMOR-B was identified in TaMOR-B promoter, which is associated with lower root dry weight and shorter plant height. The results bring new light into regulation mechanisms of crown root initiation and offer a new target for the improvement of root system architecture in wheat.
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Affiliation(s)
- Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jialu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Mengjia Zhuang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Bo Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Qiaoru Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Junfang Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yan Du
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jinping Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zipei Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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20
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Fan X, Liu J, Zhang Z, Xi Y, Li S, Xiong L, Xing Y. A long transcript mutant of the rubisco activase gene RCA upregulated by the transcription factor Ghd2 enhances drought tolerance in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:673-687. [PMID: 35106849 DOI: 10.1111/tpj.15694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The transcription factor Ghd2 increases rice yield potential under normal conditions and accelerates leaf senescence under drought stress. However, its mechanism on the regulation of leaf senescence under drought stress remains unclear. In the present study, to unveil the mechanism, one target of Ghd2, the Rubisco activase gene RCA, was identified through the combined analysis of Ghd2-CRISPR transcriptome data and Ghd2-overexpression microarray data. Ghd2 binds to the 'CACA' motif in the RCA promoter by its CCT domain and upregulates RCA expression. RCA has alternative transcripts, RCAS and RCAL, which are predominantly expressed under normal conditions and drought stress, respectively. Similar to Ghd2-overexpressing plants, RCAL-overexpressing plants were more sensitive to drought stress than the wild-type. However, the plants overexpressing RCAS showed a weak drought-sensitive phenotype. Moreover, RCAL knockdown and knockout plants did not show yield loss under normal conditions, but exhibited enhanced drought tolerance and delayed leaf senescence. The chlorophyll content, the free amino acid content and the expression of senescence-related genes in the RCAL mutant were lower than those in the wild-type plants under drought stress. In summary, Ghd2 induces leaf senescence by upregulating RCAL expression under drought stress, and the RCAL mutant has important values in breeding drought-tolerant varieties.
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Affiliation(s)
- Xiaowei Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Juhong Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanli Xi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangle Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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21
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Wu N, Yao Y, Xiang D, Du H, Geng Z, Yang W, Li X, Xie T, Dong F, Xiong L. A MITE variation-associated heat-inducible isoform of a heat-shock factor confers heat tolerance through regulation of JASMONATE ZIM-DOMAIN genes in rice. THE NEW PHYTOLOGIST 2022; 234:1315-1331. [PMID: 35244216 DOI: 10.1111/nph.18068] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
High temperatures cause huge yield losses in rice. Heat-shock factors (Hsfs) are key transcription factors which regulate the expression of heat stress-responsive genes, but natural variation in and functional characterization of Hsfs have seldom been reported. A significant heat response locus was detected via a genome-wide association study (GWAS) using green leaf area as an indicative trait. A miniature inverted-repeat transposable element (MITE) in the promoter of a candidate gene, HTG3 (heat-tolerance gene on chromosome 3), was found to be significantly associated with heat-induced expression of HTG3 and heat tolerance (HT). The MITE-absent variant has been selected in heat-prone rice-growing regions. HTG3a is an alternatively spliced isoform encoding a functional Hsf, and experiments using overexpression and knockout rice lines showed that HTG3a positively regulates HT at both vegetative and reproductive stages. The HTG3-regulated genes were enriched for heat shock proteins and jasmonic acid signaling. Two heat-responsive JASMONATE ZIM-DOMAIN (JAZ) genes were confirmed to be directly upregulated by HTG3a, and one of them, OsJAZ9, positively regulates HT. We conclude that HTG3 plays an important role in HT through the regulation of JAZs and other heat-responsive genes. The MITE-absent allele may be valuable for HT breeding in rice.
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Affiliation(s)
- Nai Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Yilong Yao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Denghao Xiang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Hao Du
- Institute of Crop science, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zedong Geng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Tingting Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Faming Dong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
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22
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Li M, Zhang H, He D, Damaris RN, Yang P. A stress-associated protein OsSAP8 modulates gibberellic acid biosynthesis by reducing the promotive effect of transcription factor OsbZIP58 on OsKO2. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2420-2433. [PMID: 35084453 DOI: 10.1093/jxb/erac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Gibberellic acid (GA) is a vital phytohormone for plant growth and development. GA biosynthesis is a complex pathway regulated by various transcription factors. Here we report a stress-associated protein 8 (OsSAP8), negatively involved in GA biosynthesis. Overexpression of OsSAP8 in rice resulted in a semi-dwarfism phenotype and reduced endogenous GA3 content. In contrast, an OsSAP8 knockout mutant exhibited higher endogenous GA3 content and slightly increased plant height. Sub-cellular localization analysis of OsSAP8 showed that it could enter the nucleus. Based on electrophoretic mobility shift assay and yeast one hybrid experiments, OsSAP8 was found to bind to the cis-acting regulatory element GADOWNAT of ent-kaurene oxidases (KO2, KO3, KO5). The results from dual-luciferase reporter assays showed that OsSAP8 does not activate LUC reporter gene expression. However, it could interact with basic leucine zipper 58 (OsbZIP58), which has strong transcriptional activation potential on OsKO2. Moreover, the interaction between OsSAP8, rice lesion simulating disease 1-like 1 (OsLOL1), and OsbZIP58 could reduce the promotive effect of transcription factor OsbZIP58 on OsKO2. These results provide some new insights on the regulation of GA biosynthesis in rice.
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Affiliation(s)
- Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Hui Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
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23
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Li A, Hao C, Wang Z, Geng S, Jia M, Wang F, Han X, Kong X, Yin L, Tao S, Deng Z, Liao R, Sun G, Wang K, Ye X, Jiao C, Lu H, Zhou Y, Liu D, Fu X, Zhang X, Mao L. Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield. MOLECULAR PLANT 2022; 15:504-519. [PMID: 35026438 DOI: 10.1016/j.molp.2022.01.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/24/2021] [Accepted: 01/07/2022] [Indexed: 05/10/2023]
Abstract
Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement, which is still poorly understood in wheat. In this study, we exome sequenced 287 wheat accessions that were collected in the past 100 years. Population genetics analysis identified that 6.7% of the wheat genome falls within the selective sweeps between landraces and cultivars, which harbors the genes known for yield improvement. These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected. Genome-wide association study (GWAS) identified genomic loci associated with traits for yield potential, and two underlying genes, TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-protein γ-subunit, were located and characterized to pleiotropically regulate both plant height and grain weight. Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding. Interestingly, we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus, leading to propose a "Green Revolution"-based working model for historical wheat breeding. Collectively, our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community.
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Affiliation(s)
- Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Chenyang Hao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Meiling Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiang Han
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingchen Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lingjie Yin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shu Tao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhongyin Deng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruyi Liao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoliang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ke Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingguo Ye
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengzhi Jiao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Yun Zhou
- Collaborative Innovation Center of Crop Stress Biology & Institute of Plant Stress Biology, School of Life Science, Henan University, Kaifeng 475004, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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24
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Zhao Y, Li X, Xie J, Xu W, Chen S, Zhang X, Liu S, Wu J, El-Kassaby YA, Zhang D. Transposable Elements: Distribution, Polymorphism, and Climate Adaptation in Populus. FRONTIERS IN PLANT SCIENCE 2022; 13:814718. [PMID: 35178060 PMCID: PMC8843856 DOI: 10.3389/fpls.2022.814718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs) are a class of mobile genetic elements that make effects on shaping rapid phenotypic traits of adaptive significance. TE insertions are usually related to transcription changes of nearby genes, and thus may be subjected to purifying selection. Based on the available genome resources of Populus, we found that the composition of Helitron DNA family were highly variable and could directly influence the transcription of nearby gene expression, which are involving in stress-responsive, programmed cell death, and apoptosis pathway. Next, we indicated TEs are highly enriched in Populus trichocarpa compared with three other congeneric poplar species, especially located at untranslated regions (3'UTRs and 5'UTRs) and Helitron transposons, particularly 24-nt siRNA-targeted, are significantly associated with reduced gene expression. Additionally, we scanned a representative resequenced Populus tomentosa population, and identified 9,680 polymorphic TEs loci. More importantly, we identified a Helitron transposon located at the 3'UTR, which could reduce WRKY18 expression level. Our results highlight the importance of TE insertion events, which could regulate gene expression and drive adaptive phenotypic variation in Populus.
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Affiliation(s)
- Yiyang Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xian Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Weijie Xu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Sisi Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Sijia Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jiadong Wu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Forest Sciences Centre, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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25
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Nicolau M, Picault N, Moissiard G. The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation. Cells 2021; 10:cells10112952. [PMID: 34831175 PMCID: PMC8616336 DOI: 10.3390/cells10112952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.
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Affiliation(s)
- Melody Nicolau
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Nathalie Picault
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Guillaume Moissiard
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Correspondence:
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Castanera R, Vendrell-Mir P, Bardil A, Carpentier MC, Panaud O, Casacuberta JM. Amplification dynamics of miniature inverted-repeat transposable elements and their impact on rice trait variability. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:118-135. [PMID: 33866641 DOI: 10.1111/tpj.15277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted-repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut-and-paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103 109 transposon insertion polymorphisms (TIPs) in 738 Oryza sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-genome-wide association studies (TIP-GWAS) to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than single nucleotide polymorphisms (SNPs) on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidence of the replicative amplification of MITEs.
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Affiliation(s)
- Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Pol Vendrell-Mir
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex, 66860, France
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex, 66860, France
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
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A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome. Genes (Basel) 2021; 12:genes12060859. [PMID: 34205210 PMCID: PMC8227079 DOI: 10.3390/genes12060859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/26/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack of coding capacity, the identification of MITEs has been demanding. However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes. We mined MITEs in the carrot reference genome DH1 using MITE-hunter and developed a curated carrot MITE repository comprising 428 families. Of the 31,025 MITE copies spanning 10.34 Mbp of the carrot genome, 54% were positioned in genic regions. Stowaways and Tourists were frequently present in the vicinity of genes, while Mutator-like MITEs were relatively more enriched in introns. hAT-like MITEs were relatively more frequently associated with transcribed regions, including untranslated regions (UTRs). Some carrot MITE families were shared with other Apiaceae species. We showed that hAT-like MITEs were involved in the formation of new splice variants of insertion-harboring genes. Thus, carrot MITEs contributed to the accretion of new diversity by altering transcripts and possibly affecting the regulation of many genes.
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Xia T, Yang Y, Zheng H, Han X, Jin H, Xiong Z, Qian W, Xia L, Ji X, Li G, Wang D, Zhang K. Efficient expression and function of a receptor-like kinase in wheat powdery mildew defence require an intron-located MYB binding site. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:897-909. [PMID: 33225586 PMCID: PMC8131041 DOI: 10.1111/pbi.13512] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 05/10/2023]
Abstract
The LRK10-like receptor kinases (LRK10L-RLKs) are ubiquitously present in higher plants, but knowledge of their expression and function is still limited. Here, we report expression and functional analysis of TtdLRK10L-1, a typical LRK10L-RLK in durum wheat (Triticum turgidum L. ssp. durum). The introns of TtdLRK10L-1 contained multiple kinds of predicted cis-elements. To investigate the potential effect of these cis-elements on TtdLRK10L-1 expression and function, two types of transgenic wheat lines were prepared, which expressed a GFP-tagged TtdLRK10L-1 protein (TtdLRK10L-1:GFP) from the cDNA or genomic DNA (gDNA) sequence of TtdLRK10L-1 under the native promoter. TtdLRK10L-1:GFP expression was up-regulated by the powdery mildew pathogen Blumeria graminis f. sp. tritici (Bgt) in both types of transgenic plants, with the scale of the elevation being much stronger in the gDNA lines. Both types of transgenic plants exhibited enhanced resistance to Bgt infection relative to wild type control. Notably, the Bgt defence activated in the gDNA lines was significantly stronger than that in the cDNA lines. Further analysis revealed that a putative MYB transcription factor binding site (MYB-BS, CAGTTA) located in TtdLRK10L-1 intron I was critical for the efficient expression and function of TtdLRK10L-1 in Bgt defence. This MYB-BS could also increase the activity of a superpromoter widely used in ectopic gene expression studies in plants. Together, our results deepen the understanding of the expression and functional characteristics of LRK10L-RLKs. TtdLRK10L-1 is likely useful for further dissecting the molecular processes underlying wheat defence against Bgt and for developing Bgt resistant wheat crops.
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Affiliation(s)
- Tengfei Xia
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yanping Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hongyuan Zheng
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Xinyun Han
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Huaibing Jin
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Zijun Xiong
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
| | - Lanqi Xia
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xiang Ji
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Guangwei Li
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Daowen Wang
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kunpu Zhang
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
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Ren Y, Huang Z, Jiang H, Wang Z, Wu F, Xiong Y, Yao J. A heat stress responsive NAC transcription factor heterodimer plays key roles in rice grain filling. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2947-2964. [PMID: 33476364 DOI: 10.1093/jxb/erab027] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 01/19/2021] [Indexed: 05/10/2023]
Abstract
High temperature often leads to failure of grain filling in rice (Oryza sativa) causing yield loss, but the underlying mechanisms are still not elucidated. Here, we report that two genes encoding seed-specific NAM/ATAF/CUC (NAC) domain transcription factors, ONAC127 and ONAC129, are responsive to heat stress and involved in the grain filling process of rice. ONAC127 and ONAC129 are dominantly expressed in the pericarp and can form a heterodimer during rice grain filling. CRISPR/Cas9 induced mutants and overexpression lines were then generated to investigate the function of these two transcription factors. Interestingly, both knock-out and overexpression plants showed incomplete grain filling and shrunken grains, which became more severe under heat stress. Transcriptome analysis revealed that ONAC127 and ONAC129 mainly regulate stimulus response and nutrient transport. ChIP-seq analysis identified that the direct target genes of ONAC127 and ONAC129 in developing rice seeds include monosaccharide transporter gene OsMST6, sugar transporter gene OsSWEET4, calmodulin-like protein gene OsMSR2 and AP2/ERF factor gene OsEATB. These results suggest that ONAC127 and ONAC129 regulate grain filling by affecting sugar transportation and abiotic stress responses. Overall, this study demonstrates a transcriptional regulatory network with ONAC127 and ONAC129 coordinating multiple pathways to modulate seed development and heat stress responses at rice reproductive stages.
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Affiliation(s)
- Ye Ren
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhouquan Huang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Jiang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhuo Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengsheng Wu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yufei Xiong
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Li W, Wang L, Zhou F, Li C, Ma W, Chen H, Wang G, Pickett JA, Zhou JJ, Lin Y. Overexpression of the homoterpene synthase gene, OsCYP92C21, increases emissions of volatiles mediating tritrophic interactions in rice. PLANT, CELL & ENVIRONMENT 2021; 44:948-963. [PMID: 33099790 DOI: 10.1111/pce.13924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/12/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Plant defence homoterpenes can be used to attract pest natural enemies. However, the biosynthetic pathway of homoterpenes is still unknown in rice, and the practical application of such indirect defence systems suffers from inherent limitations due to their low emissions from plants. Here, we demonstrated that the protein OsCYP92C21 is responsible for homoterpene biosynthesis in rice. We also revealed that the ability of rice to produce homoterpenes is dependent on the subcellular precursor pools. By increasing the precursor pools through specifically subcellular targeting expression, genetic transformation and genetic introgression, we significantly enhanced homoterpene biosynthesis in rice. The final introgressed GM rice plants exhibited higher homoterpene emissions than the wild type rice and the highest homoterpene emission reported so far for such GM plants even without the induction of herbivore attack. As a result, these GM rice plants demonstrated strong attractiveness to the parasitic wasp Cotesia chilonis. This study discovered the homoterpene biosynthesis pathway in rice, and lays the foundation for the utilisation of plant indirect defence mechanism in the "push-pull" strategy of integrated pest management through increasing precursor pools in the subcellular compartments and overexpressing homoterpene synthase by genetic transformation.
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Affiliation(s)
- Wei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Lingnan Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Changyan Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Jing-Jiang Zhou
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, China
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
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Sun J, Cui X, Teng S, Kunnong Z, Wang Y, Chen Z, Sun X, Wu J, Ai P, Quick WP, Lu T, Zhang Z. HD-ZIP IV gene Roc8 regulates the size of bulliform cells and lignin content in rice. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2559-2572. [PMID: 32559019 PMCID: PMC7680540 DOI: 10.1111/pbi.13435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 05/31/2020] [Indexed: 05/27/2023]
Abstract
The morphology of bulliform cells located on the upper epidermis of leaves is one of the most important cell structures affecting leaf shape. Although many mechanisms regulating the development of bulliform cells have been reported, the fine regulatory mechanisms governing this process have rarely been described. To identify novel components regulating rice leaf morphology, a mutant showing a constitutively rolling phenotype from the seedling stage to flowering, known as crm1-D, was selected for further analysis. Anatomical analyses in crm1-D were attributable to the size reduction of bulliform cells. The crm1-D was controlled by a single dominant nuclear gene. Map-based cloning revealed that Roc8, an HD zipper class IV family member, was responsible for the crm1-D phenotype. Notably, the 50-bp sequence in the 3'-untranslated region (3'-UTR) of the Roc8 gene represses Roc8 at the translational level. Moreover, the roc8 knockdown lines notably increased the size of bulliform cells. A series of assays revealed that Roc8 negatively regulates the size of bulliform cells. Unexpectedly, Roc8 was also observed to positively mediate lignin biosynthesis without incurring a production penalty. The above results show that Roc8 may have a practical application in cultivating materials with high photosynthetic efficiency and low lignin content.
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Affiliation(s)
- Jing Sun
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
| | - Xuean Cui
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
| | - Shouzhen Teng
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
| | - Zhao Kunnong
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
| | - Yanwei Wang
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
| | - Zhenhua Chen
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
| | - Xuehui Sun
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
| | - Jinxia Wu
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
| | - Pengfei Ai
- College of Bioscience and BioengineeringHebei University of Science and TechnologyHebeiChina
| | - William Paul Quick
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
- C4 Rice CenterInternational Rice Research Institute (IRRI)UPLBLos BañosLagunaPhilippines
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Tiegang Lu
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
| | - Zhiguo Zhang
- Joint CAAS/IRRI Laboratory for Photosynthetic EnhancementBiotechnology Research Institute/National Key Facility for Genetic Resources and Gene ImprovementThe Chinese Academy of Agricultural SciencesBeijingChina
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Zhang B, Zhang H, Li F, Ouyang Y, Yuan M, Li X, Xiao J, Wang S. Multiple Alleles Encoding Atypical NLRs with Unique Central Tandem Repeats in Rice Confer Resistance to Xanthomonas oryzae pv. oryzae. PLANT COMMUNICATIONS 2020; 1:100088. [PMID: 33367251 PMCID: PMC7748011 DOI: 10.1016/j.xplc.2020.100088] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/17/2020] [Accepted: 06/16/2020] [Indexed: 05/03/2023]
Abstract
Plants have developed various mechanisms for avoiding pathogen invasion, including resistance (R) genes. Most R genes encode nucleotide-binding domain and leucine-rich repeat containing proteins (NLRs). Here, we report the isolation of three new bacterial blight R genes in rice, Xa1-2, Xa14, and Xa31(t), which were allelic to Xa1 and encoded atypical NLRs with unique central tandem repeats (CTRs). We also found that Xa31(t) was the same gene as Xa1-2. Although Xa1-2 and Xa14 conferred different resistance spectra, their performance could be attenuated by iTALEs, as has previously been reported for Xa1. XA1, XA1-2, XA14, and non-resistant RGAF differed mainly in the substructure of the leucine-rich repeat domain. They all contained unique CTRs and belonged to the CTR-NLRs, which existed only in Gramineae. We also found that interactions among these genes led to differing resistance performance. In conclusion, our results uncover a unique locus in rice consisting of at least three multiple alleles (Xa1, Xa1-2, and Xa14) that encode CTR-NLRs and confer resistance to Xanthomonas oryzae pv. oryzae (Xoo).
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Affiliation(s)
- Biaoming Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Haitao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Fang Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Yang J, Chang Y, Qin Y, Chen D, Zhu T, Peng K, Wang H, Tang N, Li X, Wang Y, Liu Y, Li X, Xie W, Xiong L. A lamin-like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice. THE NEW PHYTOLOGIST 2020; 227:65-83. [PMID: 32129897 DOI: 10.1111/nph.16518] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/18/2020] [Indexed: 05/28/2023]
Abstract
Lamin proteins in animals are implicated in important nuclear functions, including chromatin organization, signalling transduction, gene regulation and cell differentiation. Nuclear Matrix Constituent Proteins (NMCPs) are lamin analogues in plants, but their regulatory functions remain largely unknown. We report that OsNMCP1 is localized at the nuclear periphery in rice (Oryza sativa) and induced by drought stress. OsNMCP1 overexpression resulted in a deeper and thicker root system, and enhanced drought resistance compared to the wild-type control. An assay for transposase accessible chromatin with sequencing (ATAC-seq) analysis revealed that OsNMCP1-overexpression altered chromatin accessibility in hundreds of genes related to drought resistance and root growth, including OsNAC10, OsERF48, OsSGL, SNAC1 and OsbZIP23. OsNMCP1 can interact with SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodelling complex subunit OsSWI3C. The reported drought resistance or root growth-related genes that were positively regulated by OsNMCP1 were negatively regulated by OsSWI3C under drought stress conditions, and OsSWI3C overexpression led to decreased drought resistance. We propose that the interaction between OsNMCP1 and OsSWI3C under drought stress conditions may lead to the release of OsSWI3C from the SWI/SNF gene silencing complex, thus changing chromatin accessibility in the genes related to root growth and drought resistance.
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Affiliation(s)
- Jun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu Chang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yonghua Qin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- South-Central University for Nationalities, Wuhan, 430074, China
| | - Dijun Chen
- Department for Plant Cell and Molecular Biology (AG Kaufmann) Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Tao Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Kaiqing Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Huaijun Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Ning Tang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yusen Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yinmeng Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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Xu Y, Hu D, Hou X, Shen J, Liu J, Cen X, Fu J, Li X, Hu H, Xiong L. OsTMF attenuates cold tolerance by affecting cell wall properties in rice. THE NEW PHYTOLOGIST 2020; 227:498-512. [PMID: 32176820 DOI: 10.1111/nph.16549] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/04/2020] [Indexed: 05/15/2023]
Abstract
Plant cell wall composition and structure can be modified as plants adapt to environmental stresses; however, the underlying regulatory mechanisms remain elusive. Here, we report that OsTMF, a homologue of the human TATA modulatory factor (TMF) in rice (Oryza sativa) and highly conserved in plants, negatively regulates cold tolerance through modification of cell wall properties. Cold stress increased the expression of OsTMF and accumulation of OsTMF in the nucleus, where OsTMF acts as a transcription activator and modulates the expression of genes involved in pectin degradation (OsBURP16), cellulose biosynthesis (OsCesA4 and OsCesA9), and cell wall structural maintenance (genes encoding proline-rich proteins and peroxidases). OsTMF directly activated the expression of OsBURP16, OsCesA4, and OsCesA9 through binding to the TATA cis-elements in their promoters. Under cold stress conditions, OsTMF negatively regulated pectin content and peroxidase activity and positively regulated cellulose content, causing corresponding alterations to cell wall properties, all of which collectively contribute to the negative effect of OsTMF on cold tolerance. Our findings unravel a previously unreported molecular mechanism of a conserved plant TMF protein in the regulation of cell wall changes under cold stress.
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Affiliation(s)
- Yan Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Dan Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Hou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianqiang Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Juhong Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiang Cen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Fu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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Integrative analysis of reference epigenomes in 20 rice varieties. Nat Commun 2020; 11:2658. [PMID: 32461553 PMCID: PMC7253419 DOI: 10.1038/s41467-020-16457-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/05/2020] [Indexed: 11/08/2022] Open
Abstract
Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin immunoprecipitation (eChIP) approach for plants, and generate genome-wide profiling of five histone modifications and RNA polymerase II occupancy with it. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we construct comprehensive epigenome landscapes across various tissues in 20 representative rice varieties. Approximately 81.8% of rice genomes are annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provides insight into transcriptional regulation. We identify extensive enhancer-like promoters with potential enhancer function on transcriptional regulation through chromatin interactions. Active and repressive histone modifications and the predicted enhancers vary largely across tissues, whereas inactive chromatin states are relatively stable. Together, these datasets constitute a valuable resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.
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Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding. Mol Biol Rep 2020; 47:3155-3167. [PMID: 32162128 DOI: 10.1007/s11033-020-05365-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/29/2020] [Indexed: 12/20/2022]
Abstract
Plant molecular breeding is expected to give significant gains in cultivar development through development and utilization of suitable molecular marker systems for genetic diversity analysis, rapid DNA fingerprinting, identification of true hybrids, trait mapping and marker-assisted selection. Transposable elements (TEs) are the most abundant component in a genome and being used as genetic markers in the plant molecular breeding. Here, we review on the high copious transposable element belonging to class-II DNA TEs called "miniature inverted-repeat transposable elements" (MITEs). MITEs are ubiquitous, short and non-autonomous DNA transposable elements which have a tendency to insert into genes and genic regions have paved a way for the development of functional DNA marker systems in plant genomes. This review summarises the characteristics of MITEs, principles and methodologies for development of MITEs based DNA markers, bioinformatics tools and resources for plant MITE discovery and their utilization in crop improvement.
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Drongitis D, Aniello F, Fucci L, Donizetti A. Roles of Transposable Elements in the Different Layers of Gene Expression Regulation. Int J Mol Sci 2019; 20:ijms20225755. [PMID: 31731828 PMCID: PMC6888579 DOI: 10.3390/ijms20225755] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 02/03/2023] Open
Abstract
The biology of transposable elements (TEs) is a fascinating and complex field of investigation. TEs represent a substantial fraction of many eukaryotic genomes and can influence many aspects of DNA function that range from the evolution of genetic information to duplication, stability, and gene expression. Their ability to move inside the genome has been largely recognized as a double-edged sword, as both useful and deleterious effects can result. A fundamental role has been played by the evolution of the molecular processes needed to properly control the expression of TEs. Today, we are far removed from the original reductive vision of TEs as “junk DNA”, and are more convinced that TEs represent an essential element in the regulation of gene expression. In this review, we summarize some of the more recent findings, mainly in the animal kingdom, concerning the active roles that TEs play at every level of gene expression regulation, including chromatin modification, splicing, and protein translation.
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Affiliation(s)
- Denise Drongitis
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy;
| | - Francesco Aniello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
| | - Laura Fucci
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
| | - Aldo Donizetti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
- Correspondence:
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38
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Darier disease: first molecular study of a Portuguese family. Heliyon 2019; 5:e02520. [PMID: 31687605 PMCID: PMC6819764 DOI: 10.1016/j.heliyon.2019.e02520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/26/2019] [Accepted: 09/23/2019] [Indexed: 11/22/2022] Open
Abstract
Background Darier disease (DD) is a rare autosomal dominant condition characterized by skin lesions. Additionally, a wide range of neuropsychiatric symptoms is frequently reported in DD patients. This genodermatosis relies on mutations in the ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 (ATP2A2) gene, which encodes an ATPase responsible for pumping Ca2+ from the cytosol to the lumen of the ER. Objective Herein we studied the molecular aspect of a two-generation Portuguese family with DD history with clinical variability. Methods All exons and intron-exon borders of genomic ATP2A2, as well as coding ATP2A2, were sequenced. Relative levels of SERCA2 mRNA and protein were quantified by qPCR and western blotting, respectively. Results The c.1287+1G > T variant was identified in all affected individuals, whereas the unaffected individual was shown to carry the wild-type ATP2A2 sequence in both alleles. This variant leads to the skipping of full exon 10, which consequently generates a frameshift originating a premature STOP codon in exon 11 (p.V395 = fs*19). Although the mutant mRNA seems to partially escape degradation, results suggest synthesis inhibition or immediate degradation of the mutant protein. Neuropsychiatric and other occurrences affecting certain patients are also reported. Conclusion This is the first study of DD in Portugal, the variant identified, previously described in a single Japanese patient, may be considered a pathogenic mutation, and haploinsufficiency the mechanism underlying DD pathology in these patients. This study also highlights the co-occurrence of neuropsychiatric features in DD.
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Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower. Proc Natl Acad Sci U S A 2019; 116:17578-17583. [PMID: 31409706 DOI: 10.1073/pnas.1903131116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Transposable elements (TEs) are extremely abundant in complex plant genomes. siRNAs of 24 nucleotides in length control transposon activity in a process that involves de novo methylation of targeted loci. Usually, these epigenetic modifications trigger nucleosome condensation and a permanent silencing of the affected loci. Here, we show that a TE-derived inverted repeat (IR) element, inserted near the sunflower HaWRKY6 locus, dynamically regulates the expression of the gene by altering chromatin topology. The transcripts of this IR element are processed into 24-nt siRNAs, triggering DNA methylation on its locus. These epigenetic marks stabilize the formation of tissue-specific loops in the chromatin. In leaves, an intragenic loop is formed, blocking HaWRKY6 transcription. While in cotyledons (Cots), formation of an alternative loop, encompassing the whole HaWRKY6 gene, enhances transcription of the gene. The formation of this loop changes the promoter directionality, reducing IR transcription, and ultimately releasing the loop. Our results provide evidence that TEs can act as active and dynamic regulatory elements within coding loci in a mechanism that combines RNA silencing, epigenetic modification, and chromatin remodeling machineries.
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40
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Hou J, Lu D, Mason AS, Li B, Xiao M, An S, Fu D. Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses. PLANTA 2019; 250:23-40. [PMID: 30993403 DOI: 10.1007/s00425-019-03166-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.
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Affiliation(s)
- Jinna Hou
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Dandan Lu
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Annaliese S Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Baoquan Li
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sufang An
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
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41
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Xin Y, Ma B, Xiang Z, He N. Amplification of miniature inverted-repeat transposable elements and the associated impact on gene regulation and alternative splicing in mulberry ( Morus notabilis). Mob DNA 2019; 10:27. [PMID: 31289464 PMCID: PMC6593561 DOI: 10.1186/s13100-019-0169-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
Background Miniature inverted-repeat transposable elements (MITEs) are common in eukaryotic genomes, and are important for genomic evolution. Results In the present study, the identification of MITEs in the mulberry genome revealed 286,122 MITE-related sequences, including 90,789 full-length elements. The amplification of mulberry MITEs and the influence of MITEs on the evolution of the mulberry genome were analyzed. The timing of MITE amplifications varied considerably among the various MITE families. Fifty-one MITE families have undergone a single round of amplification, while the other families developed from multiple amplifications. Most mulberry MITEs were inserted near genes and some could regulate gene expression through small RNAs. An analysis of transgenic plants indicated that MITE insertions can upregulate the expression of a target gene. Moreover, MITEs are frequently associated with alternative splicing events (exonizations). Conclusion The data presented herein provide insights into the generation of MITEs as well as their impact on gene regulation and evolution in mulberry. Electronic supplementary material The online version of this article (10.1186/s13100-019-0169-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youchao Xin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
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42
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Tang Y, Ma X, Zhao S, Xue W, Zheng X, Sun H, Gu P, Zhu Z, Sun C, Liu F, Tan L. Identification of an active miniature inverted-repeat transposable element mJing in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:639-653. [PMID: 30689248 PMCID: PMC6850418 DOI: 10.1111/tpj.14260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/01/2019] [Accepted: 01/18/2019] [Indexed: 05/27/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are structurally homogeneous non-autonomous DNA transposons with high copy numbers that play important roles in genome evolution and diversification. Here, we analyzed the rice high-tillering dwarf (htd) mutant in an advanced backcross population between cultivated and wild rice, and identified an active MITE named miniature Jing (mJing). The mJing element belongs to the PIF/Harbinger superfamily. japonica rice var. Nipponbare and indica var. 93-11 harbor 72 and 79 mJing family members, respectively, have undergone multiple rounds of amplification bursts during the evolution of Asian cultivated rice (Oryza sativa L.). A heterologous transposition experiment in Arabidopsis thaliana indicated that the autonomous element Jing is likely to have provides the transposase needed for mJing mobilization. We identified 297 mJing insertion sites and their presence/absence polymorphism among 71 rice samples through targeted high-throughput sequencing. The results showed that the copy number of mJing varies dramatically among Asian cultivated rice (O. sativa), its wild ancestor (O. rufipogon), and African cultivated rice (O. glaberrima) and that some mJing insertions are subject to directional selection. These findings suggest that the amplification and removal of mJing elements have played an important role in rice genome evolution and species diversification.
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Affiliation(s)
- Yanyan Tang
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xin Ma
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Shuangshuang Zhao
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Wei Xue
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xu Zheng
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Hongying Sun
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Ping Gu
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Zuofeng Zhu
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Fengxia Liu
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Lubin Tan
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
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Fuentes RR, Chebotarov D, Duitama J, Smith S, De la Hoz JF, Mohiyuddin M, Wing RA, McNally KL, Tatarinova T, Grigoriev A, Mauleon R, Alexandrov N. Structural variants in 3000 rice genomes. Genome Res 2019; 29:870-880. [PMID: 30992303 PMCID: PMC6499320 DOI: 10.1101/gr.241240.118] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 03/11/2019] [Indexed: 12/24/2022]
Abstract
Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5′ UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights into rice genome biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.
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Affiliation(s)
- Roven Rommel Fuentes
- International Rice Research Institute, Laguna 4031, Philippines.,Bioinformatics Group, Wageningen University and Research, 6708 PB Wageningen, the Netherlands
| | | | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá 111711, Colombia.,Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | - Sean Smith
- Biology Department, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Juan Fernando De la Hoz
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | | | - Rod A Wing
- International Rice Research Institute, Laguna 4031, Philippines.,Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA.,King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | | | - Tatiana Tatarinova
- Department of Biology, University of La Verne, La Verne, California 91750, USA.,Vavilov Institute of General Genetics, Moscow 119333, Russia.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia.,Laboratory of Forest Genomics, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Andrey Grigoriev
- Biology Department, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Ramil Mauleon
- International Rice Research Institute, Laguna 4031, Philippines
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44
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Abstract
The mechanisms underlying rapid adaptation to changing environments in species with reduced genetic variation, referred to as the “genetic paradox of invasion,” are unknown. We report that transposable elements (TEs) are highly enriched in the gene promoter regions of Capsella rubella compared with its outcrossing sister species Capsella grandiflora. We also show that a number of polymorphic TEs in C. rubella are associated with changes in gene expression. Frequent TE insertions at FLOWERING LOCUS C of C. rubella affect flowering-time variation, an important life history trait correlated with fitness. These results indicate that TE insertions drive rapid phenotypic variation, which could potentially help adapting to novel environments in species with limited genetic variation. Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched in C. rubella compared with its outcrossing sister species Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at FLOWERING LOCUS C (FLC) in natural populations of C. rubella could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3′ UTR of FLC affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.
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45
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Ma S, Tang N, Li X, Xie Y, Xiang D, Fu J, Shen J, Yang J, Tu H, Li X, Hu H, Xiong L. Reversible Histone H2B Monoubiquitination Fine-Tunes Abscisic Acid Signaling and Drought Response in Rice. MOLECULAR PLANT 2019; 12:263-277. [PMID: 30578854 DOI: 10.1016/j.molp.2018.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/09/2018] [Accepted: 12/09/2018] [Indexed: 05/23/2023]
Abstract
Histone H2B monoubiquitination (H2Bub1) plays important roles in several physiological and developmental processes, but its roles in the regulation of plant stress responses remain elusive. Here, we report that H2Bub1 is crucially involved in abscisic acid (ABA) signaling and drought response in rice. We found that rice HISTONE MONOUBIQUITINATION2 (OsHUB2), an E3 ligase for H2Bub1, interacted with OsbZIP46, a key transcription factor regulating ABA signaling and drought response in rice. Genetic analyses suggest that OsHUB2, upregulated by drought and ABA, positively modulates ABA sensitivity and drought resistance. The H2Bub1 levels were increased in the target genes of OsbZIP46 under the drought stress and ABA treatments, which were positively correlated with their increased expression levels. Interestingly, MODD, a reported suppressor of ABA signaling and drought resistance by mediating OsbZIP46 deactivation and degradation, could reduce the H2Bub1 levels in the target genes of OsbZIP46 by recruiting a putative deubiquitinase OsOTLD1. Suppression of OsOTLD1 in vivo resulted in increased H2Bub1 levels and expression of OsbZIP46 target genes. Collectively, these findings established an elaborate mechanism of histone monoubiquitination in the fine-turning of ABA signaling and drought response by balancing H2Bub1 deposition and removal.
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Affiliation(s)
- Siqi Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Ning Tang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, 34060 Montpellier, France.
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yongjun Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Denghao Xiang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Fu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jianqiang Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Grativol C, Thiebaut F, Sangi S, Montessoro P, Santos WDS, Hemerly AS, Ferreira PC. A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses. PeerJ 2019; 7:e6080. [PMID: 30648010 PMCID: PMC6331000 DOI: 10.7717/peerj.6080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 11/07/2018] [Indexed: 11/25/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.
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Affiliation(s)
- Clicia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Flavia Thiebaut
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sara Sangi
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Patricia Montessoro
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Walaci da Silva Santos
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Adriana S. Hemerly
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo C.G. Ferreira
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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Lu H, Cui X, Liu Z, Liu Y, Wang X, Zhou Z, Cai X, Zhang Z, Guo X, Hua J, Ma Z, Wang X, Zhang J, Zhang H, Liu F, Wang K. Discovery and annotation of a novel transposable element family in Gossypium. BMC PLANT BIOLOGY 2018; 18:307. [PMID: 30486783 PMCID: PMC6264596 DOI: 10.1186/s12870-018-1519-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 11/13/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Fluorescence in situ hybridization (FISH) is an efficient cytogenetic technology to study chromosome structure. Transposable element (TE) is an important component in eukaryotic genomes and can provide insights in the structure and evolution of eukaryotic genomes. RESULTS A FISH probe derived from bacterial artificial chromosome (BAC) clone 299N22 generated striking signals on all 26 chromosomes of the cotton diploid A genome (AA, 2x=26) but very few on the diploid D genome (DD, 2x=26). All 26 chromosomes of the A sub genome (At) of tetraploid cotton (AADD, 2n=4x=52) also gave positive signals with this FISH probe, whereas very few signals were observed on the D sub genome (Dt). Sequencing and annotation of BAC clone 299N22, revealed a novel Ty3/gypsy transposon family, which was named as 'CICR'. This family is a significant contributor to size expansion in the A (sub) genome but not in the D (sub) genome. Further FISH analysis with the LTR of CICR as a probe revealed that CICR is lineage-specific, since massive repeats were found in A and B genomic groups, but not in C-G genomic groups within the Gossypium genus. Molecular evolutionary analysis of CICR suggested that tetraploid cottons evolved after silence of the transposon family 1-1.5 million years ago (Mya). Furthermore, A genomes are more homologous with B genomes, and the C, E, F, and G genomes likely diverged from a common ancestor prior to 3.5-4 Mya, the time when CICR appeared. The genomic variation caused by the insertion of CICR in the A (sub) genome may have played an important role in the speciation of organisms with A genomes. CONCLUSIONS The CICR family is highly repetitive in A and B genomes of Gossypium, but not amplified in the C-G genomes. The differential amount of CICR family in At and Dt will aid in partitioning sub genome sequences for chromosome assemblies during tetraploid genome sequencing and will act as a method for assessing the accuracy of tetraploid genomes by looking at the proportion of CICR elements in resulting pseudochromosome sequences. The timeline of the expansion of CICR family provides a new reference for cotton evolutionary analysis, while the impact on gene function caused by the insertion of CICR elements will be a target for further analysis of investigating phenotypic differences between A genome and D genome species.
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Affiliation(s)
- Hejun Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
- Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Xinglei Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Zhen Liu
- Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Zhenmei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Xinlei Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Jinping Hua
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhiying Ma
- Key Laboratory for Crop Germplasm Resources of Hebei province, Hebei Agricultural University, Baoding, 071000 Hebei China
| | - Xiyin Wang
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000 Hebei China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 88003 USA
| | - Hong Zhang
- Department of Biological Sciences, Texas Tech University, Lubbock, 79409 USA
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
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48
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Keidar-Friedman D, Bariah I, Kashkush K. Genome-wide analyses of miniature inverted-repeat transposable elements reveals new insights into the evolution of the Triticum-Aegilops group. PLoS One 2018; 13:e0204972. [PMID: 30356268 PMCID: PMC6200218 DOI: 10.1371/journal.pone.0204972] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 09/08/2018] [Indexed: 11/19/2022] Open
Abstract
The sequence drafts of wild emmer and bread wheat facilitated high resolution, genome-wide analysis of transposable elements (TEs), which account for up to 90% of the wheat genome. Despite extensive studies, the role of TEs in reshaping nascent polyploid genomes remains to be fully understood. In this study, we retrieved miniature inverted-repeat transposable elements (MITEs) from the recently published genome drafts of Triticum aestivum, Triticum turgidum ssp. dicoccoides, Aegilops tauschii and the available genome draft of Triticum urartu. Overall, 239,126 MITE insertions were retrieved, including 3,874 insertions of a newly identified, wheat-unique MITE family that we named "Inbar". The Stowaway superfamily accounts for ~80% of the retrieved MITE insertions, while Thalos is the most abundant family. MITE insertions are distributed in the seven homologous chromosomes of the wild emmer and bread wheat genomes. The remarkably high level of insertions in the B sub-genome (~59% of total retrieved MITE insertions in the wild emmer genome draft, and ~41% in the bread wheat genome draft), emphasize its highly repetitive nature. Nearly 52% of all MITE insertions were found within or close (less than 100bp) to coding genes, and ~400 MITE sequences were found in the bread wheat transcriptome, indicating that MITEs might have a strong impact on wheat genome expression. In addition, ~40% of MITE insertions were found within TE sequences, and remarkably, ~90% of Inbar insertions were located in retrotransposon sequences. Our data thus shed new light on the role of MITEs in the diversification of allopolyploid wheat species.
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Affiliation(s)
| | - Inbar Bariah
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
- * E-mail:
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49
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Besnard J, Zhao C, Avice JC, Vitha S, Hyodo A, Pilot G, Okumoto S. Arabidopsis UMAMIT24 and 25 are amino acid exporters involved in seed loading. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5221-5232. [PMID: 30312461 PMCID: PMC6184519 DOI: 10.1093/jxb/ery302] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 08/14/2018] [Indexed: 05/17/2023]
Abstract
Phloem-derived amino acids are the major source of nitrogen supplied to developing seeds. Amino acid transfer from the maternal to the filial tissue requires at least one cellular export step from the maternal tissue prior to the import into the symplasmically isolated embryo. Some members of UMAMIT (usually multiple acids move in an out transporter) family (UMAMIT11, 14, 18, 28, and 29) have previously been implicated in this process. Here we show that additional members of the UMAMIT family, UMAMIT24 and UMAMIT25, also function in amino acid transfer in developing seeds. Using a recently published yeast-based assay allowing detection of amino acid secretion, we showed that UMAMIT24 and UMAMIT25 promote export of a broad range of amino acids in yeast. In plants, UMAMIT24 and UMAMIT25 are expressed in distinct tissues within developing seeds; UMAMIT24 is mainly expressed in the chalazal seed coat and localized on the tonoplast, whereas the plasma membrane-localized UMAMIT25 is expressed in endosperm cells. Seed amino acid contents of umamit24 and umamit25 knockout lines were both decreased during embryogenesis compared with the wild type, but recovered in the mature seeds without any deleterious effect on yield. The results suggest that UMAMIT24 and 25 play different roles in amino acid translocation from the maternal to filial tissue; UMAMIT24 could have a role in temporary storage of amino acids in the chalaza, while UMAMIT25 would mediate amino acid export from the endosperm, the last step before amino acids are taken up by the developing embryo.
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Affiliation(s)
- Julien Besnard
- Department of Soil and Crop, Texas A&M, College Station, TX, USA
| | - Chengsong Zhao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Jean-Christophe Avice
- UMR INRA - UCBN 950 EVA, UFR des Sciences, Département de Biologie, Université de Caen Normandie, Esplanade de la Paix, Caen cedex, France
| | - Stanislav Vitha
- Microscopy and Imaging Center, Texas A&M, College Station, TX, USA
| | - Ayumi Hyodo
- Stable Isotopes for Biosphere Science Laboratory, Texas A&M, College Station, TX, USA
| | - Guillaume Pilot
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Sakiko Okumoto
- Department of Soil and Crop, Texas A&M, College Station, TX, USA
- Correspondence: or
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50
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Yi F, Jia Z, Xiao Y, Ma W, Wang J. SPTEdb: a database for transposable elements in salicaceous plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4925802. [PMID: 29688371 PMCID: PMC5846285 DOI: 10.1093/database/bay024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 02/12/2018] [Indexed: 01/10/2023]
Abstract
Although transposable elements (TEs) play significant roles in structural, functional and evolutionary dynamics of the salicaceous plants genome and the accurate identification, definition and classification of TEs are still inadequate. In this study, we identified 18 393 TEs from Populus trichocarpa, Populus euphratica and Salix suchowensis using a combination of signature-based, similarity-based and De novo method, and annotated them into 1621 families. A comprehensive and user-friendly web-based database, SPTEdb, was constructed and served for researchers. SPTEdb enables users to browse, retrieve and download the TEs sequences from the database. Meanwhile, several analysis tools, including BLAST, HMMER, GetORF and Cut sequence, were also integrated into SPTEdb to help users to mine the TEs data easily and effectively. In summary, SPTEdb will facilitate the study of TEs biology and functional genomics in salicaceous plants. Database URL: http://genedenovoweb.ticp.net:81/SPTEdb/index.php
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Affiliation(s)
- Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China and.,College of Biological and Pharmaceutical Sciences, Three Gorges University, Yichang 443002, China
| | - Zirui Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China and
| | - Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China and
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China and
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China and
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