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Bai R, Zhou M, Zheng Y, Shi H. Transcription factor AHL17 fine-tunes reactive oxygen species accumulation and cassava disease resistance. PLANT PHYSIOLOGY 2024; 195:1148-1151. [PMID: 38417067 DOI: 10.1093/plphys/kiae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/22/2024] [Accepted: 01/28/2024] [Indexed: 03/01/2024]
Abstract
Zinc finger protein 67 interacts with a transcription factor to fine-tune reactive oxygen species accumulation and immune responses during pathogen infection in cassava.
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Affiliation(s)
- Ruoyu Bai
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, 572025 Sanya, Hainan, China
| | - Mengmeng Zhou
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, 572025 Sanya, Hainan, China
| | - Yu Zheng
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, 572025 Sanya, Hainan, China
| | - Haitao Shi
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, 572025 Sanya, Hainan, China
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2
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Yan Y, Wang P, He J, Shi H. KIN10-mediated HB16 protein phosphorylation and self-association improve cassava disease resistance by transcriptional activation of lignin biosynthesis genes. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38768314 DOI: 10.1111/pbi.14386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/07/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Cassava bacterial blight significantly affects cassava yield worldwide, while major cassava cultivars are susceptible to this disease. Therefore, it is crucial to identify cassava disease resistance gene networks and defence molecules for the genetic improvement of cassava cultivars. In this study, we found that MeHB16 transcription factor as a differentially expressed gene in cassava cultivars with contrasting disease resistance, positively modulated disease resistance by modulating defence molecule lignin accumulation. Further investigation showed that MeHB16 physically interacted with itself via the leucine-Zippe domain (L-Zip), which was necessary for the transcriptional activation of downstream lignin biosynthesis genes. In addition, protein kinase MeKIN10 directly interacted with MeHB16 to promote its phosphorylation at Ser6, which in turn enhanced MeHB16 self-association and downstream lignin biosynthesis. In summary, this study revealed the molecular network of MeKIN10-mediated MeHB16 protein phosphorylation improved cassava bacterial blight resistance by fine-tuning lignin biosynthesis and provides candidate genes and the defence molecule for improving cassava disease resistance.
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Affiliation(s)
- Yu Yan
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan province, China
| | - Peng Wang
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan province, China
| | - Jiaoyan He
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan province, China
| | - Haitao Shi
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan province, China
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3
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Kang H, Huang T, Duan G, Meng Y, Chen X, He S, Xia Z, Zhou X, Chao J, Tang B, Wang Z, Zhu J, Du Z, Sun Y, Zhang S, Xiao J, Tian W, Wang W, Zhao W. TCOD: an integrated resource for tropical crops. Nucleic Acids Res 2024; 52:D1651-D1660. [PMID: 37843152 PMCID: PMC10767838 DOI: 10.1093/nar/gkad870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023] Open
Abstract
Tropical crops are vital for tropical agriculture, with resource scarcity, functional diversity and extensive market demand, providing considerable economic benefits for the world's tropical agriculture-producing countries. The rapid development of sequencing technology has promoted a milestone in tropical crop research, resulting in the generation of massive amount of data, which urgently needs an effective platform for data integration and sharing. However, the existing databases cannot fully satisfy researchers' requirements due to the relatively limited integration level and untimely update. Here, we present the Tropical Crop Omics Database (TCOD, https://ngdc.cncb.ac.cn/tcod), a comprehensive multi-omics data platform for tropical crops. TCOD integrates diverse omics data from 15 species, encompassing 34 chromosome-level de novo assemblies, 1 255 004 genes with functional annotations, 282 436 992 unique variants from 2048 WGS samples, 88 transcriptomic profiles from 1997 RNA-Seq samples and 13 381 germplasm items. Additionally, TCOD not only employs genes as a bridge to interconnect multi-omics data, enabling cross-species comparisons based on homology relationships, but also offers user-friendly online tools for efficient data mining and visualization. In short, TCOD integrates multi-species, multi-omics data and online tools, which will facilitate the research on genomic selective breeding and trait biology of tropical crops.
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Affiliation(s)
- Hailong Kang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianhao Huang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangya Duan
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuyan Meng
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoning Chen
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuang He
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Zhiqiang Xia
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Xincheng Zhou
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jinquan Chao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bixia Tang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhonghuang Wang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junwei Zhu
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhenglin Du
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yanlin Sun
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Sisi Zhang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Jingfa Xiao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weimin Tian
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wenquan Wang
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Wenming Zhao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Zeng J, Wu C, Ye X, Zhou J, Chen Y, Li L, Lin M, Wang S, Liu S, Yan Y, Tie W, Yang J, Yan F, Zeng L, Liu Y, Hu W. MePP2C24, a cassava (Manihot esculenta) gene encoding protein phosphatase 2C, negatively regulates drought stress and abscisic acid responses in transgenic Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108291. [PMID: 38141400 DOI: 10.1016/j.plaphy.2023.108291] [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: 06/13/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Abscisic acid (ABA) signaling plays a crucial role in plant development and response to abiotic/biotic stress. However, the function and regulation of protein phosphatase 2C (PP2C), a key component of abscisic acid signaling, under abiotic stress are still unknown in cassava, a drought-tolerant crop. In this study, a cassava PP2C gene (MePP2C24) was cloned and characterized. The MePP2C24 transcripts increased in response to mannitol, NaCl, and ABA. Overexpression of MePP2C24 in Arabidopsis resulted in increased sensitivity to drought stress and decreased sensitivity to exogenous ABA. This was demonstrated by transgenic lines having higher levels of malondialdehyde (MDA), ion leakage (IL), and reactive oxygen species (ROS), lower activities of catalase (CAT) and peroxidase (POD), and lower proline content than wild type (WT) under drought stress. Moreover, MePP2C24 overexpression caused decrease in expression of drought-responsive genes related to ABA signaling pathway. In addition, MePP2C24 was localized in the cell nucleus and showed self-activation. Furthermore, many MePYLs (MePYL1, MePYL4, MePYL7-9, and MePYL11-13) could interact with MePP2C24 in the presence of ABA, and MePYL1 interacted with MePP2C24 in both the presence and absence of ABA. Additionally, MebZIP11 interacted with the promoter of MePP2C24 and exerted a suppressive effect. Taken together, our results suggest that MePP2C24 acts as a negative regulator of drought tolerance and ABA response.
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Affiliation(s)
- Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China.
| | - Chunlai Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China; The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, 430074, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Xiaoxue Ye
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Jiewei Zhou
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Yingtong Chen
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Lizhen Li
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Man Lin
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Shuting Wang
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Siwen Liu
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yan Yan
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Weiwei Tie
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Jinghao Yang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Fei Yan
- Shaanxi Provincial Bioresource Key Laboratory, College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Liwang Zeng
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China.
| | - Yujia Liu
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China.
| | - Wei Hu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China.
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5
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Ding Z, Fu L, Wang B, Ye J, Ou W, Yan Y, Li M, Zeng L, Dong X, Tie W, Ye X, Yang J, Xie Z, Wang Y, Guo J, Chen S, Xiao X, Wan Z, An F, Zhang J, Peng M, Luo J, Li K, Hu W. Metabolic GWAS-based dissection of genetic basis underlying nutrient quality variation and domestication of cassava storage root. Genome Biol 2023; 24:289. [PMID: 38098107 PMCID: PMC10722858 DOI: 10.1186/s13059-023-03137-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/04/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Metabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient quality and domestication of root and tuber crops remain largely unknown. RESULTS We report a comprehensive study combining metabolic and phenotypic genome-wide association studies to dissect the genetic basis of metabolites in the storage root (SR) of cassava. We quantify 2,980 metabolic features in 299 cultivated cassava accessions. We detect 18,218 significant marker-metabolite associations via metabolic genome-wide association mapping and identify 12 candidate genes responsible for the levels of metabolites that are of potential nutritional importance. Me3GT, MeMYB4, and UGT85K4/UGT85K5, which are involved in flavone, anthocyanin, and cyanogenic glucoside metabolism, respectively, are functionally validated through in vitro enzyme assays and in vivo gene silencing analyses. We identify a cluster of cyanogenic glucoside biosynthesis genes, among which CYP79D1, CYP71E7b, and UGT85K5 are highly co-expressed and their allelic combination contributes to low linamarin content. We find MeMYB4 is responsible for variations in cyanidin 3-O-glucoside and delphinidin 3-O-rutinoside contents, thus controlling SR endothelium color. We find human selection affects quercetin 3-O-glucoside content and SR weight per plant. The candidate gene MeFLS1 is subject to selection during cassava domestication, leading to decreased quercetin 3-O-glucoside content and thus increased SR weight per plant. CONCLUSIONS These findings reveal the genetic basis of cassava SR metabolome variation, establish a linkage between metabolites and agronomic traits, and offer useful resources for genetically improving the nutrition of cassava and other root crops.
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Affiliation(s)
- Zehong Ding
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lili Fu
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Jianqiu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenjun Ou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Yan
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Meiying Li
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Liwang Zeng
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- Institute of Scientific and Technical Information, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xuekui Dong
- Wuhan Healthcare Metabolic Biotechnology Co., Ltd, Wuhan, China
| | - Weiwei Tie
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xiaoxue Ye
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jinghao Yang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhengnan Xie
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yu Wang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jianchun Guo
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xinhui Xiao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhongqing Wan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Feifei An
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiaming Zhang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ming Peng
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jie Luo
- Hainan Yazhou Bay Seed Laboratory, Sanya, China.
- Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.
| | - Kaimian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Wei Hu
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
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6
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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of 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 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of 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 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of 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 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of 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 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of 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 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of 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 518120, China.
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Klimova A, Ruiz Mondragón KY, Aguirre-Planter E, Valiente A, Lira R, Eguiarte LE. Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia. AMERICAN JOURNAL OF BOTANY 2023; 110:e16216. [PMID: 37478873 DOI: 10.1002/ajb2.16216] [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: 05/04/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/23/2023]
Abstract
PREMISE The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics. METHODS Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations. RESULTS Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation. CONCLUSIONS The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.
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Affiliation(s)
- Anastasia Klimova
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Karen Y Ruiz Mondragón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alfonso Valiente
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rafael Lira
- Laboratorio de Recursos Naturales, Unidad de Biotecnología y Prototipos (UBIPRO), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis E Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Gao Y, Huang S, Wang Y, Lin H, Pan Z, Zhang S, Zhang J, Wang W, Cheng S, Chen Y. Analysis of the molecular and biochemical mechanisms involved in the symbiotic relationship between Arbuscular mycorrhiza fungi and Manihot esculenta Crantz. FRONTIERS IN PLANT SCIENCE 2023; 14:1130924. [PMID: 36959933 PMCID: PMC10028151 DOI: 10.3389/fpls.2023.1130924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/22/2023] [Indexed: 05/27/2023]
Abstract
INTRODUCTION Plants and arbuscular mycorrhizal fungi (AMF) mutualistic interactions are essential for sustainable agriculture production. Although it is shown that AMF inoculation improves cassava physiological performances and yield traits, the molecular mechanisms involved in AM symbiosis remain largely unknown. Herein, we integrated metabolomics and transcriptomics analyses of symbiotic (Ri) and asymbiotic (CK) cassava roots and explored AM-induced biochemical and transcriptional changes. RESULTS Three weeks (3w) after AMF inoculations, proliferating fungal hyphae were observable, and plant height and root length were significantly increased. In total, we identified 1,016 metabolites, of which 25 were differentially accumulated (DAMs) at 3w. The most highly induced metabolites were 5-aminolevulinic acid, L-glutamic acid, and lysoPC 18:2. Transcriptome analysis identified 693 and 6,481 differentially expressed genes (DEGs) in the comparison between CK (3w) against Ri at 3w and 6w, respectively. Functional enrichment analyses of DAMs and DEGs unveiled transport, amino acids and sugar metabolisms, biosynthesis of secondary metabolites, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interactions as the most differentially regulated pathways. Potential candidate genes, including nitrogen and phosphate transporters, transcription factors, phytohormone, sugar metabolism-related, and SYM (symbiosis) signaling pathway-related, were identified for future functional studies. DISCUSSION Our results provide molecular insights into AM symbiosis and valuable resources for improving cassava production.
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Affiliation(s)
- Yu Gao
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
| | - Siyuan Huang
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Yujie Wang
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
| | - Hongxin Lin
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Zhiyong Pan
- College of Horticulture and Forestry of Huazhong Agricultural University, Wuhan, China
| | - Shubao Zhang
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
| | - Jie Zhang
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Wenquan Wang
- College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Shanhan Cheng
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute of Hainan University, School of Life Science, Hainan University, Haikou, Hainan, China
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In Silico Identification of Cassava Genome-Encoded MicroRNAs with Predicted Potential for Targeting the ICMV-Kerala Begomoviral Pathogen of Cassava. Viruses 2023; 15:v15020486. [PMID: 36851701 PMCID: PMC9963618 DOI: 10.3390/v15020486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Cassava mosaic disease (CMD) is caused by several divergent species belonging to the genus Begomovirus (Geminiviridae) transmitted by the whitefly Bemisia tabaci cryptic species group. In India and other parts of Asia, the Indian cassava mosaic virus-Kerala (ICMV-Ker) is an emergent begomovirus of cassava causing damage that results in reduced yield loss and tuber quality. Double-stranded RNA-mediated interference (RNAi) is an evolutionary conserved mechanism in eukaryotes and highly effective, innate defense system to inhibit plant viral replication and/or translation. The objective of this study was to identify and characterize cassava genome-encoded microRNAs (mes-miRNA) that are predicted to target ICMV-Ker ssDNA-encoded mRNAs, based on four in silico algorithms: miRanda, RNA22, Tapirhybrid, and psRNA. The goal is to deploy the predicted miRNAs to trigger RNAi and develop cassava plants with resistance to ICMV-Ker. Experimentally validated mature cassava miRNA sequences (n = 175) were downloaded from the miRBase biological database and aligned with the ICMV-Ker genome. The miRNAs were evaluated for base-pairing with the cassava miRNA seed regions and to complementary binding sites within target viral mRNAs. Among the 175 locus-derived mes-miRNAs evaluated, one cassava miRNA homolog, mes-miR1446a, was identified to have a predicted miRNA target binding site, at position 2053 of the ICMV-Ker genome. To predict whether the cassava miRNA might bind predicted ICMV-Ker mRNA target(s) that could disrupt viral infection of cassava plants, a cassava locus-derived miRNA-mRNA regulatory network was constructed using Circos software. The in silico-predicted cassava locus-derived mes-miRNA-mRNA network corroborated interactions between cassava mature miRNAs and the ICMV-Ker genome that warrant in vivo analysis, which could lead to the development of ICMV-Ker resistant cassava plants.
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Yin H, Yan Y, Hu W, Liu G, Zeng H, Wei Y, Shi H. Genome-wide association studies reveal genetic basis of ionomic variation in cassava. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1212-1223. [PMID: 36239073 DOI: 10.1111/tpj.16006] [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: 07/27/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
As one of the most important food crops, cassava (Manihot esculenta) is the main dietary source of micronutrients for about 1 billion people. However, the ionomic variation in cassava and the underlying genetic mechanisms remain unclear so far. Herein, genome-wide association studies were performed to reveal the specific single nucleotide polymorphisms (SNPs) that affect the ionomic variation in cassava. We identified 164 SNPs with P-values lower than the threshold located in 88 loci associated with divergent ionomic variations. Among them, 13 SNPs are related to both calcium (Ca) and magnesium (Mg), and many loci for different ionomic traits seem to be clustered on specific chromosome regions. Moreover, we identified the peak SNPs in the promoter regions of Sc10g003170 (encoding methionyl-tRNA synthetase [MetRS]) and Sc18g015190 (encoding the transcriptional regulatory protein AlgP) for nitrogen (N) and phosphorus (P) accumulation, respectively. Notably, these two SNPs (chr10_32807962 and chr18_31343738) were directly correlated with the transcript levels of Sc10g003170 (MetRS) and Sc18g015190 (AlgP), which positively modulated N accumulation and P concentration in cassava, respectively. Taken together, this study provides important insight into the genetic basis of cassava natural ionomic variation, which will promote genetic breeding to improve nutrient use and accumulation of elements in cassava.
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Affiliation(s)
- Hongyan Yin
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
| | - Yu Yan
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Hainan Province, Haikou, Xueyuan Road 4, China
| | - Guoyin Liu
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Hongqiu Zeng
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Yunxie Wei
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
| | - Haitao Shi
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Hainan Province, Sanya and Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Province, Sanya, China
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Bai Y, Wei Y, Yin H, Hu W, Cheng X, Guo J, Dong Y, Zheng L, Xie H, Zeng H, Reiter RJ, Shi H. PP2C1 fine-tunes melatonin biosynthesis and phytomelatonin receptor PMTR1 binding to melatonin in cassava. J Pineal Res 2022; 73:e12804. [PMID: 35488179 DOI: 10.1111/jpi.12804] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022]
Abstract
Melatonin is an important molecule in both animals and plants, regulating circadian rhythms and stress responses. Therefore, the improvement of melatonin accumulation not only strengthens the function of melatonin but also improves stress resistance in crops. Although melatonin biosynthetic enzymes have been identified through reverse genetics previously, an investigation of melatonin level-related genes through forward genetics in plants has yet to be performed. In this study, a genome-wide association study using cassava natural population of 298 genetic resources identified melatonin accumulation 1 (MA1), which regulates the natural variation of melatonin levels in cassava. We found that MA1 encodes type 2C protein phosphatase 1 (PP2C1), which serves as a negative regulator of melatonin levels in cassava. MePP2C1 physically interacts with MeRAV1/2 and MeWRKY20 and dephosphorylates them at serine (S) 35 residue, S34 residue, and S176 residue, respectively, thereby hindering their transcriptional activation on downstream melatonin biosynthetic genes. Notably, MePP2C1 interacts with phytomelatonin receptor MePMTR1 and dephosphorylates it at S11 residue, repressing its binding to melatonin. In summary, this study demonstrates that MePP2C1 as MA1 plays dual roles in negatively regulating both melatonin accumulation and signaling, extending the understanding of the molecular mechanism underlying melatonin accumulation and signaling through forward genetics in plants.
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Affiliation(s)
- Yujing Bai
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
| | - Yunxie Wei
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan province, China
| | - Hongyan Yin
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan province, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan province, China
| | - Xiao Cheng
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
| | - Jingru Guo
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
| | - Yabin Dong
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
| | - Liyan Zheng
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
| | - Haoqi Xie
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
| | - Hongqiu Zeng
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan province, China
| | - Russel J Reiter
- Department of Cellular and Structural Biology, UT Health San Antonio, Long School of Medicine, San Antonio, Texas, USA
| | - Haitao Shi
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building National Key Laboratory Breeding Base), College of Tropical Crops, Hainan University, Haikou, Hainan province, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan province, China
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