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Yang J, Liu Z, Liu Y, Fan X, Gao L, Li Y, Hu Y, Hu K, Huang Y. Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize ( Zea mays L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1533. [PMID: 38891341 PMCID: PMC11175157 DOI: 10.3390/plants13111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/15/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
Deep sowing is an efficient strategy for maize to ensure the seedling emergence rate under adverse conditions such as drought or low temperatures. However, the genetic basis of deep-sowing tolerance-related traits in maize remains largely unknown. In this study, we performed a genome-wide association study on traits related to deep-sowing tolerance, including mesocotyl length (ML), coleoptile length (CL), plumule length (PL), shoot length (SL), and primary root length (PRL), using 255 maize inbred lines grown in three different environments. We identified 23, 6, 4, and 4 quantitative trait loci (QTLs) associated with ML, CL, PL, and SL, respectively. By analyzing candidate genes within these QTLs, we found a γ-tubulin-containing complex protein, ZmGCP2, which was significantly associated with ML, PL, and SL. Loss of function of ZmGCP2 resulted in decreased PL, possibly by affecting the cell elongation, thus affecting SL. Additionally, we identified superior haplotypes and allelic variations of ZmGCP2 with a longer PL and SL, which may be useful for breeding varieties with deep-sowing tolerance to improve maize cultivation.
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Affiliation(s)
- Jin Yang
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Zhou Liu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Yanbo Liu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Xiujun Fan
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Lei Gao
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Yangping Li
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Yufeng Hu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Kun Hu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
- Sinograin Chengdu Storage Research Institute Co., Ltd., Chengdu 610091, China
| | - Yubi Huang
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
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2
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Yin M, Zheng Z, Zhang Y, Wang S, Zuo L, Lei Y, Zhao Y, Zhao X, Fu B, Shi Y, Xu J, Wang W. Identification of Key Genes and Pathways for Anaerobic Germination Tolerance in Rice Using Weighted Gene Co-Expression Network Analysis (WGCNA) in Association with Quantitative Trait Locus (QTL) Mapping. RICE (NEW YORK, N.Y.) 2024; 17:37. [PMID: 38819744 PMCID: PMC11143092 DOI: 10.1186/s12284-024-00714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Rice is one of the most important food crops in the world, and with the development of direct seeding methods for rice, exposure to anaerobic stress has become a major factor limiting its growth. RESULTS In this experiment, we tested the tolerance to anaerobic germination of rice varieties NIP and HD84, and they were used as parents to construct a DH (doubled-haploid) population. The transcriptomes of NIP (highly tolerant) and HD86 (intolerant), and their progeny HR (highly tolerant) and NHR (intolerant) were sequenced from normal and anaerobic environments. The differentially-expressed genes (DEGs) were subjected to GO (Gene ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), and WGCNA analyses. QTL mapping of the DH population identified tolerance to anaerobic germination-related chromosomal segments. The transcriptome results from 24 samples were combined with the anaerobic stress QTL results for 159 DH population lines to construct a metabolic network to identify key pathways and a gene interaction network to study the key genes. Essential genes were initially subjected to rigorous functional validation, followed by a comprehensive analysis aimed at elucidating their potential utility in domestication and breeding practices, particularly focusing on the exploitation of dominant haplotypes. CONCLUSION The results show that pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are the starting signals of energy metabolism for coleoptile length growth, the auxin transporter EXPA is the determining signal for coleoptile length growth. The pivotal genes Os05g0498700 and Os01g0866100 exert a negative regulatory influence on coleoptile length, ultimately enhancing tolerance to anaerobic germination in rice. Analyses of breeding potential underscore the additional value of Os05g0498700-hyp2 and Os01g0866100-hyp2, highlighting their potential utility in further improving rice through breeding programs. The results of our study will provide a theoretical basis for breeding anaerobic-tolerant rice varieties.
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Affiliation(s)
- Ming Yin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- China Agricultural University, Beijing, China
| | | | - Yue Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Hainan Yazhou Bay Seed Lab, National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
| | - Shanwen Wang
- Southwest United Graduate School, Yunnan University, Kunming, China
| | - Liying Zuo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuxin Lei
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaqiong Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuqin Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Binying Fu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Jianlong Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Wensheng Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- Anhui Agricultural University, Hefei, China.
- Hainan Yazhou Bay Seed Lab, National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China.
- Southwest United Graduate School, Yunnan University, Kunming, China.
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Hu W, Wang R, Hao X, Li S, Zhao X, Xie Z, Wu S, Huang L, Tan Y, Tian L, Li D. OsLCD3 interacts with OsSAMS1 to regulate grain size via ethylene/polyamine homeostasis control. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38703081 DOI: 10.1111/tpj.16788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 05/06/2024]
Abstract
A fundamental question in developmental biology is how to regulate grain size to improve crop yields. Despite this, little is still known about the genetics and molecular mechanisms regulating grain size in crops. Here, we provide evidence that a putative protein kinase-like (OsLCD3) interacts with the S-adenosyl-L-methionine synthetase 1 (OsSAMS1) and determines the size and weight of grains. OsLCD3 mutation (lcd3) significantly increased grain size and weight by promoting cell expansion in spikelet hull, whereas its overexpression caused negative effects, suggesting that grain size was negatively regulated by OsLCD3. Importantly, lcd3 and OsSAMS1 overexpression (SAM1OE) led to large and heavy grains, with increased ethylene and decreased polyamines production. Based on genetic analyses, it appears that OsLCD3 and OsSAMS1 control rice grain size in part by ethylene/polyamine homeostasis. The results of this study provide a genetic and molecular understanding of how the OsLCD3-OsSAMS1 regulatory module regulates grain size, suggesting that ethylene/polyamine homeostasis is an appropriate target for improving grain size and weight.
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Affiliation(s)
- Wenli Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Rong Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- College of Biology, Hunan University, Changsha, China
| | - Xiaohua Hao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- College of Life and Environmental Science, Hunan University of Arts and Science, Changde, 415000, China
| | - Shaozhuang Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xinjie Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Zijing Xie
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China
| | - Sha Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Liqun Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Ying Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lianfu Tian
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Dongping Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
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4
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Mai H, Qin T, Wei H, Yu Z, Pang G, Liang Z, Ni J, Yang H, Tang H, Xiao L, Liu H, Liu T. Overexpression of OsACL5 triggers environmentally-dependent leaf rolling and reduces grain size in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:833-847. [PMID: 37965680 PMCID: PMC10955489 DOI: 10.1111/pbi.14227] [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: 09/24/2022] [Revised: 10/21/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023]
Abstract
Major polyamines include putrescine, spermidine, spermine and thermospermine, which play vital roles in growth and adaptation against environmental changes in plants. Thermospermine (T-Spm) is synthetised by ACL5. The function of ACL5 in rice is still unknown. In this study, we used a reverse genetic strategy to investigate the biological function of OsACL5. We generated several knockout mutants by pYLCRISPR/Cas9 system and overexpressing (OE) lines of OsACL5. Interestingly, the OE plants exhibited environmentally-dependent leaf rolling, smaller grains, lighter 1000-grain weight and reduction in yield per plot. The area of metaxylem vessels of roots and leaves of OE plants were significantly smaller than those of WT, which possibly caused reduction in leaf water potential, resulting in leaf rolling with rise in the environmental temperature and light intensity and decrease in humidity. Additionally, the T-Spm contents were markedly increased by over ninefold whereas the ethylene evolution was reduced in OE plants, suggesting that T-Spm signalling pathway interacts with ethylene pathway to regulate multiple agronomic characters. Moreover, the osacl5 exhibited an increase in grain length, 1000-grain weight, and yield per plot. OsACL5 may affect grain size via mediating the expression of OsDEP1, OsGS3 and OsGW2. Furthermore, haplotypes analysis indicated that OsACL5 plays a conserved function on regulating T-Spm levels during the domestication of rice. Our data demonstrated that identification of OsACL5 provides a theoretical basis for understanding the physiological mechanism of T-Spm which may play roles in triggering environmentally dependent leaf rolling; OsACL5 will be an important gene resource for molecular breeding for higher yield.
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Affiliation(s)
- Huafu Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Tian Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Huan Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Zhen Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Gang Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Zhiman Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Jiansheng Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Haishan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Haiying Tang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Lisi Xiao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Huili Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Taibo Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
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5
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Zhao R, Wu WA, Huang YH, Li XK, Han JQ, Jiao W, Su YN, Zhao H, Zhou Y, Cao WQ, Zhang X, Wei W, Zhang WK, Song QX, He XJ, Ma B, Chen SY, Tao JJ, Yin CC, Zhang JS. An RRM domain protein SOE suppresses transgene silencing in rice. THE NEW PHYTOLOGIST 2024. [PMID: 38509454 DOI: 10.1111/nph.19686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Gene expression is regulated at multiple levels, including RNA processing and DNA methylation/demethylation. How these regulations are controlled remains unclear. Here, through analysis of a suppressor for the OsEIN2 over-expressor, we identified an RNA recognition motif protein SUPPRESSOR OF EIN2 (SOE). SOE is localized in nuclear speckles and interacts with several components of the spliceosome. We find SOE associates with hundreds of targets and directly binds to a DNA glycosylase gene DNG701 pre-mRNA for efficient splicing and stabilization, allowing for subsequent DNG701-mediated DNA demethylation of the transgene promoter for proper gene expression. The V81M substitution in the suppressor mutant protein mSOE impaired its protein stability and binding activity to DNG701 pre-mRNA, leading to transgene silencing. SOE mutation enhances grain size and yield. Haplotype analysis in c. 3000 rice accessions reveals that the haplotype 1 (Hap 1) promoter is associated with high 1000-grain weight, and most of the japonica accessions, but not indica ones, have the Hap 1 elite allele. Our study discovers a novel mechanism for the regulation of gene expression and provides an elite allele for the promotion of yield potentials in rice.
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Affiliation(s)
- Rui Zhao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Ai Wu
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi-Hua Huang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin-Kai Li
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia-Qi Han
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - He Zhao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Zhou
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wu-Qiang Cao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xun Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wei
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wan-Ke Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing-Xin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Biao Ma
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Shou-Yi Chen
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian-Jun Tao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cui-Cui Yin
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jin-Song Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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Qiao J, Quan R, Wang J, Li Y, Xiao D, Zhao Z, Huang R, Qin H. OsEIL1 and OsEIL2, two master regulators of rice ethylene signaling, promote the expression of ROS scavenging genes to facilitate coleoptile elongation and seedling emergence from soil. PLANT COMMUNICATIONS 2024; 5:100771. [PMID: 37994014 PMCID: PMC10943563 DOI: 10.1016/j.xplc.2023.100771] [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: 06/19/2023] [Revised: 10/21/2023] [Accepted: 11/20/2023] [Indexed: 11/24/2023]
Abstract
Successful emergence from the soil is a prerequisite for survival of germinating seeds in their natural environment. In rice, coleoptile elongation facilitates seedling emergence and establishment, and ethylene plays an important role in this process. However, the underlying regulatory mechanism remains largely unclear. Here, we report that ethylene promotes cell elongation and inhibits cell expansion in rice coleoptiles, resulting in longer and thinner coleoptiles that facilitate seedlings emergence from the soil. Transcriptome analysis showed that genes related to reactive oxygen species (ROS) generation are upregulated and genes involved in ROS scavenging are downregulated in the coleoptiles of ethylene-signaling mutants. Further investigations showed that soil coverage promotes accumulation of ETHYLENE INSENSITIVE 3-LIKE 1 (OsEIL1) and OsEIL2 in the upper region of the coleoptile, and both OsEIL1 and OsEIL2 can bind directly to the promoters of the GDP-mannose pyrophosphorylase (VTC1) gene OsVTC1-3 and the peroxidase (PRX) genes OsPRX37, OsPRX81, OsPRX82, and OsPRX88 to activate their expression. This leads to increased ascorbic acid content, greater peroxidase activity, and decreased ROS accumulation in the upper region of the coleoptile. Disruption of ROS accumulation promotes coleoptile growth and seedling emergence from soil. These findings deepen our understanding of the roles of ethylene and ROS in controlling coleoptile growth, and this information can be used by breeders to produce rice varieties suitable for direct seeding.
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Affiliation(s)
- Jinzhu Qiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruidang Quan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Juan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Yuxiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dinglin Xiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zihan Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China.
| | - Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China.
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7
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Luo J, Amin B, Wu B, Wu B, Huang W, Salmen SH, Fang Z. Blocking of awn development-related gene OsGAD1 coordinately boosts yield and quality of Kam Sweet Rice. PHYSIOLOGIA PLANTARUM 2024; 176:e14229. [PMID: 38413386 DOI: 10.1111/ppl.14229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/04/2024] [Accepted: 02/10/2024] [Indexed: 02/29/2024]
Abstract
Kam Sweet Rice is a high-quality local variety of Guizhou province in China, but most varieties have awns on lemma. In this study, we aimed to obtain awnless varieties of Kam Sweet Rice by blocking the awn development-related gene OsGAD1 using CRISPR/Cas9 technology. We determined that natural variations of the OsGAD1 triggered different lengths of awns of Kam Sweet Rice. We found that the awning rate of the CRISPR lines of OsGAD1 in Guxiangnuo, Goujingao and Gouhuanggang decreased by over 65%, and the number of grains per panicle and yield per plant increased by more than 17% and 20% compared to the wild-types. Furthermore, we indicated that blocking OsGAD1 resulted in an increase of over 2% in the brown rice rate and milled rice rate in these varieties. In addition, the analysis of the transcriptome revealed that the regulation of awn development and yield formation in CRISPR lines of OsGAD1 may involve genes associated with phytohormone and nitrogen pathways. These results suggest that blocking OsGAD1 in Kam Sweet Rice using CRISPR/Cas9 technology can be used for breeding programs seeking high yield and grain quality of Kam Sweet Rice.
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Affiliation(s)
- Jun Luo
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Bakht Amin
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Bilong Wu
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Bowen Wu
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
| | - Weiting Huang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Saleh H Salmen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Zhongming Fang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, Guizhou, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
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8
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Yuan H, Zheng Z, Bao Y, Zhao X, Lv J, Tang C, Wang N, Liang Z, Li H, Xiang J, Qian Y, Shi Y. Identification and Regulation of Hypoxia-Tolerant and Germination-Related Genes in Rice. Int J Mol Sci 2024; 25:2177. [PMID: 38396854 PMCID: PMC10889564 DOI: 10.3390/ijms25042177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/25/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
In direct seeding, hypoxia is a major stress faced by rice plants. Therefore, dissecting the response mechanism of rice to hypoxia stress and the molecular regulatory network is critical to the development of hypoxia-tolerant rice varieties and direct seeding of rice. This review summarizes the morphological, physiological, and ecological changes in rice under hypoxia stress, the discovery of hypoxia-tolerant and germination-related genes/QTLs, and the latest research on candidate genes, and explores the linkage of hypoxia tolerance genes and their distribution in indica and japonica rice through population variance analysis and haplotype network analysis. Among the candidate genes, OsMAP1 is a typical gene located on the MAPK cascade reaction for indica-japonica divergence; MHZ6 is involved in both the MAPK signaling and phytohormone transduction pathway. MHZ6 has three major haplotypes and one rare haplotype, with Hap3 being dominated by indica rice varieties, and promotes internode elongation in deep-water rice by activating the SD1 gene. OsAmy3D and Adh1 have similar indica-japonica varietal differentiation, and are mainly present in indica varieties. There are three high-frequency haplotypes of OsTPP7, namely Hap1 (n = 1109), Hap2 (n = 1349), and Hap3 (n = 217); Hap2 is more frequent in japonica, and the genetic background of OsTPP7 was derived from the japonica rice subpopulation. Further artificial selection, natural domestication, and other means to identify more resistance mechanisms of this gene may facilitate future research to breed superior rice cultivars. Finally, this study discusses the application of rice hypoxia-tolerant germplasm in future breeding research.
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Affiliation(s)
- Hongyan Yuan
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Zhenzhen Zheng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaling Bao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Xueyu Zhao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Jiaqi Lv
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Chenghang Tang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Nansheng Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Zhaojie Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Hua Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Jun Xiang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Yingzhi Qian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (Z.Z.); (Y.B.); (X.Z.); (J.L.); (C.T.); (N.W.); (Z.L.); (H.L.); (J.X.); (Y.Q.)
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9
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Guo N, Tang S, Wang Y, Chen W, An R, Ren Z, Hu S, Tang S, Wei X, Shao G, Jiao G, Xie L, Wang L, Chen Y, Zhao F, Sheng Z, Hu P. A mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice. Nat Commun 2024; 15:1134. [PMID: 38326370 PMCID: PMC10850359 DOI: 10.1038/s41467-024-45402-z] [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: 11/27/2022] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Preharvest sprouting (PHS) is a deleterious phenotype that occurs frequently in rice-growing regions where the temperature and precipitation are high. It negatively affects yield, quality, and downstream grain processing. Seed dormancy is a trait related to PHS. Longer seed dormancy is preferred for rice production as it can prevent PHS. Here, we map QTLs associated with rice seed dormancy and clone Seed Dormancy 3.1 (SDR3.1) underlying one major QTL. SDR3.1 encodes a mediator of OsbZIP46 deactivation and degradation (MODD). We show that SDR3.1 negatively regulates seed dormancy by inhibiting the transcriptional activity of ABIs. In addition, we reveal two critical amino acids of SDR3.1 that are critical for the differences in seed dormancy between the Xian/indica and Geng/japonica cultivars. Further, SDR3.1 has been artificially selected during rice domestication. We propose a two-line model for the process of rice seed dormancy domestication from wild rice to modern cultivars. We believe the candidate gene and germplasm studied in this study would be beneficial for the genetic improvement of rice seed dormancy.
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Affiliation(s)
- Naihui Guo
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China
| | - Shengjia Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yakun Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- National Nanfan Research Academy (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, P. R. China
| | - Wei Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ruihu An
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zongliang Ren
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shikai Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Guiai Jiao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Lihong Xie
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ling Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ying Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Fengli Zhao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Jiangxi Early-season Rice Research Center, Pingxiang, Jiangxi Province, 337000, P. R. China.
| | - Peisong Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China.
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10
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Zhao X, Li J, Niu Y, Hossain Z, Gao X, Bai X, Mao T, Qi G, He F. Exogenous Serotonin (5-HT) Promotes Mesocotyl and Coleoptile Elongation in Maize Seedlings under Deep-Seeding Stress through Enhancing Auxin Accumulation and Inhibiting Lignin Formation. Int J Mol Sci 2023; 24:17061. [PMID: 38069387 PMCID: PMC10707020 DOI: 10.3390/ijms242317061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Serotonin (5-HT), an indoleamine compound, has been known to mediate many physiological responses of plants under environmental stress. The deep-seeding (≥20 cm) of maize seeds is an important cultivation strategy to ensure seedling emergence and survival under drought stress. However, the role of 5-HT in maize deep-seeding tolerance remains unexplored. Understanding the mechanisms and evaluating the optimal concentration of 5-HT in alleviating deep-seeding stress could benefit maize production. In this study, two maize inbred lines were treated with or without 5-HT at both sowing depths of 20 cm and 3 cm, respectively. The effects of different concentrations of 5-HT on the growth phenotypes, physiological metabolism, and gene expression of two maize inbred lines were examined at the sowing depths of 20 cm and 3 cm. Compared to the normal seedling depth of 3 cm, the elongation of the mesocotyl (average elongation 3.70 cm) and coleoptile (average elongation 0.58 cm), secretion of indole-3-acetic acid (IAA; average increased 3.73 and 0.63 ng g-1 FW), and hydrogen peroxide (H2O2; average increased 1.95 and 0.63 μM g-1 FW) in the mesocotyl and coleoptile were increased under 20 cm stress, with a concomitant decrease in lignin synthesis (average decreased 0.48 and 0.53 A280 g-1). Under 20 cm deep-seeding stress, the addition of 5-HT activated the expression of multiple genes of IAA biosynthesis and signal transduction, including Zm00001d049601, Zm00001d039346, Zm00001d026530, and Zm00001d049659, and it also stimulated IAA production in both the mesocotyl and coleoptile of maize seedlings. On the contrary, 5-HT suppressed the expression of genes for lignin biosynthesis (Zm00001d016471, Zm00001d005998, Zm00001d032152, and Zm00001d053554) and retarded the accumulation of H2O2 and lignin, resulting in the elongation of the mesocotyl and coleoptile of maize seedlings. A comprehensive evaluation analysis showed that the optimum concentration of 5-HT in relieving deep-seeding stress was 2.5 mg/L for both inbred lines, and 5-HT therefore could improve the seedling emergence rate and alleviate deep-seeding stress in maize seedlings. These findings could provide a novel strategy for improving maize deep-seeding tolerance, thus enhancing yield potential under drought and water stress.
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Affiliation(s)
- Xiaoqiang Zhao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiayao Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Yining Niu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Zakir Hossain
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada;
| | - Xiquan Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaodong Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Taotao Mao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Guoxiang Qi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Fuqiang He
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
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11
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Ahmar S, Hensel G, Gruszka D. CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives. Biotechnol Adv 2023; 69:108248. [PMID: 37666372 DOI: 10.1016/j.biotechadv.2023.108248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland.
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12
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Guo Y, Xu X, Lin J, Li H, Guo W, Wan S, Chen Z, Xu H, Lin F. The herbicide bensulfuron-methyl inhibits rice seedling development by blocking calcium ion flux in the OsCNGC12 channel. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1218-1233. [PMID: 37574927 DOI: 10.1111/tpj.16418] [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: 04/25/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023]
Abstract
Identification of translocator protein-related genes involved in bensulfuron-methyl (BSM) uptake and transport in rice could facilitate the development of herbicide-tolerant cultivars by inactivating them. This study found that the OsCNGC12 mutants not only reduced BSM uptake but also compromised the Ca2 ⁺ efflux caused by BSM in the roots, regulating dynamic equilibrium of Ca2 ⁺ inside the cell and conferring non-target-site tolerance to BSM.
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Affiliation(s)
- Yating Guo
- National Key Laboratory of Green Pesticide/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaohui Xu
- National Key Laboratory of Green Pesticide/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Jinbei Lin
- National Key Laboratory of Green Pesticide/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Haiqing Li
- National Key Laboratory of Green Pesticide/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Weikang Guo
- National Key Laboratory of Green Pesticide/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Shuqing Wan
- National Key Laboratory of Green Pesticide/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Zepeng Chen
- China National Tobacco Corporation Guangdong Branch, Guangzhou, 510642, China
| | - Hanhong Xu
- National Key Laboratory of Green Pesticide/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Fei Lin
- National Key Laboratory of Green Pesticide/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
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13
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Gasparis S, Miłoszewski MM. Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley. Int J Mol Sci 2023; 24:16921. [PMID: 38069243 PMCID: PMC10706642 DOI: 10.3390/ijms242316921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin-proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function.
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Affiliation(s)
- Sebastian Gasparis
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, 05-870 Błonie, Poland;
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Gao S, Hou Y, Huang Q, Wu P, Han Z, Wei D, Xie H, Gu F, Chen C, Wang J. Osa-miR11117 Targets OsPAO4 to Regulate Rice Immunity against the Blast Fungus Magnaporthe oryzae. Int J Mol Sci 2023; 24:16052. [PMID: 38003241 PMCID: PMC10670930 DOI: 10.3390/ijms242216052] [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: 10/10/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
The intricate regulatory process governing rice immunity against the blast fungus Magnaporthe oryzae remains a central focus in plant-pathogen interactions. In this study, we investigated the important role of Osa-miR11117, an intergenic microRNA, in regulating rice defense mechanisms. Stem-loop qRT-PCR analysis showed that Osa-miR11117 is responsive to M. oryzae infection, and overexpression of Osa-miR11117 compromises blast resistance. Green fluorescent protein (GFP)-based reporter assay indicated OsPAO4 is one direct target of Osa-miR11117. Furthermore, qRT-PCR analysis showed that OsPAO4 reacts to M. oryzae infection and polyamine (PA) treatment. In addition, OsPAO4 regulates rice resistance to M. oryzae through the regulation of PA accumulation and the expression of the ethylene (ETH) signaling genes. Taken together, these results suggest that Osa-miR11117 is targeting OsPAO4 to regulate blast resistance by adjusting PA metabolism and ETH signaling pathways.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jiafeng Wang
- National Plant Space Breeding Engineering Technology Research Center, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (S.G.); (Y.H.); (Q.H.); (P.W.); (Z.H.); (D.W.); (H.X.); (F.G.); (C.C.)
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15
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Sandhu N, Ankush AP, Singh J, Raigar OP, Bains S, Jindal T, Singh MP, Sethi M, Pruthi G, Augustine G, Verma VK, Goyal S, Kumar A, Panwar H, Sihag MK, Kaur R, Kurup S, Kumar A. Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice. RICE (NEW YORK, N.Y.) 2023; 16:46. [PMID: 37848638 PMCID: PMC10581981 DOI: 10.1186/s12284-023-00665-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Ongoing large-scale shift towards direct seeded rice (DSR) necessitates a convergence of breeding and genetic approaches for its sustenance and harnessing natural resources and environmental benefits. Improving seedling vigour remains key objective for breeders working with DSR. The present study aims to understand the genetic control of seedling vigour in deep sown DSR. Combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes were performed in the present study. RESULTS Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 881 kb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The four promising introgression lines free from linkage drag and with longer mesocotyl length, longer root length, semi-dwarf plant height have been identified. CONCLUSION The study will provide rice breeders (1) the pre breeding material in the form of anticipated DSR adapted introgression lines possessing useful traits and alleles improving germination under deep sown DSR field conditions (2) the base for the studies involving functional characterization of candidate genes. The development and utilization of improved introgression lines and molecular markers may play an important role in genomics-assisted breeding (GAB) during the pyramiding of valuable genes providing adaptation to rice under DSR. Our results offer a robust and reliable package that can contribute towards enhancing genetic gains in direct seeded rice breeding programs.
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Affiliation(s)
- Nitika Sandhu
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | | | - Jasneet Singh
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | - Sutej Bains
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Taveena Jindal
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | - Mehak Sethi
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Gomsie Pruthi
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | | | - Shivani Goyal
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Aman Kumar
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Harsh Panwar
- Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India
| | - Manvesh Kumar Sihag
- Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India
| | - Rupinder Kaur
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Smita Kurup
- Department of Plant Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Arvind Kumar
- International Rice Research Institute (IRRI) South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, 221106, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
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16
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Yamasani MR, Pandu VR, Kalluru S, Bommaka RR, Bandela R, Duddu B, Komeri S, Kumbha D, Vemireddy LR. Haplotype analysis of QTLs governing early seedling vigor-related traits under dry-direct-seeded rice (Oryza sativa L.) conditions. Mol Biol Rep 2023; 50:8177-8188. [PMID: 37555871 DOI: 10.1007/s11033-023-08714-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND The eventual shifting of cultivation method from puddle transplanted rice to direct-seeded rice (DSR) to save water prompted researchers to develop DSR-suitable varieties. To achieve this, identification of molecular markers associated with must-have traits for DSR, especially early seedling vigour related traits is crucial. METHODS AND RESULTS In the present investigation, the haplotype analysis using flanking markers of three important quantitative trait loci (QTLs) for early seedling vigour-related traits viz., qSV-6a (RM204 and RM402) for root length; qVI (RM20429 and RM3) for seedling vigour index; qGP-6 (RM528 and RM400) for germination percentage revealed that the marker alleles were found to show significant associations with qVI and qGP-6 QTLs. The majority of genotypes with high early seedling vigour are with qVIHap-1 (220 and 160 bp) and qGPHap-1 (290 and 290 bp). The rice genotypes with superior haplotypes for early seedling vigour are BMF536, BMF540, BMF525, MM129 and MDP2. CONCLUSIONS In conclusion, here we demonstrated that the markers RM20429 and RM3 are associated with seedling vigour index whereas RM528 and RM400 are associated with germination percentage. Therefore, these markers can be utilized to develop varieties suitable for DSR conditions through haplotype-based breeding. In addition, the rice genotypes with superior haplotypes can be of immense value to use as donors or can be released as varieties also under DSR conditions.
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Affiliation(s)
- Mounika Reddy Yamasani
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Vasanthi Raguru Pandu
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Sudhamani Kalluru
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Rupeshkumar Reddy Bommaka
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Ramanamurthy Bandela
- Department of Statistics and Computer Applications, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Bharathi Duddu
- Department of Genetics and Plant Breeding, Regional Agricultural Research Station, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Srikanth Komeri
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Dineshkumar Kumbha
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India.
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17
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Shi L, Su J, Cho MJ, Song H, Dong X, Liang Y, Zhang Z. Promoter editing for the genetic improvement of crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4349-4366. [PMID: 37204916 DOI: 10.1093/jxb/erad175] [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: 03/02/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023]
Abstract
Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.
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Affiliation(s)
- Lu Shi
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA
| | - Hao Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Ying Liang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhiyong Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Meng Y, Zhan J, Liu H, Liu J, Wang Y, Guo Z, He S, Nie L, Kohli A, Ye G. Natural variation of OsML1, a mitochondrial transcription termination factor, contributes to mesocotyl length variation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:910-925. [PMID: 37133286 DOI: 10.1111/tpj.16267] [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: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/27/2023] [Indexed: 05/04/2023]
Abstract
Mesocotyl length (ML) is a crucial factor in determining the establishment and yield of rice planted through dry direct seeding, a practice that is increasingly popular in rice production worldwide. ML is determined by the endogenous and external environments, and inherits as a complex trait. To date, only a few genes have been cloned, and the mechanisms underlying mesocotyl elongation remain largely unknown. Here, through a genome-wide association study using sequenced germplasm, we reveal that natural allelic variations in a mitochondrial transcription termination factor, OsML1, predominantly determined the natural variation of ML in rice. Natural variants in the coding regions of OsML1 resulted in five major haplotypes with a clear differentiation between subspecies and subpopulations in cultivated rice. The much-reduced genetic diversity of cultivated rice compared to the common wild rice suggested that OsML1 underwent selection during domestication. Transgenic experiments and molecular analysis demonstrated that OsML1 contributes to ML by influencing cell elongation primarily determined by H2 O2 homeostasis. Overexpression of OsML1 promoted mesocotyl elongation and thus improved the emergence rate under deep direct seeding. Taken together, our results suggested that OsML1 is a key positive regulator of ML, and is useful in developing varieties for deep direct seeding by conventional and transgenic approaches.
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Affiliation(s)
- Yun Meng
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Junhui Zhan
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hongyan Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Jindong Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yamei Wang
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Zhan Guo
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Sang He
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Lixiao Nie
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Ajay Kohli
- Rice Breeding Innovations Platform, International Rice Research Institute (IRRI), Metro Manila, 1301, Philippines
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Rice Breeding Innovations Platform, International Rice Research Institute (IRRI), Metro Manila, 1301, Philippines
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19
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Feng F, Ma X, Yan M, Zhang H, Mei D, Fan P, Xu X, Wei C, Lou Q, Li T, Liu H, Luo L, Mei H. Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations. PLANTS (BASEL, SWITZERLAND) 2023; 12:2743. [PMID: 37514357 PMCID: PMC10385686 DOI: 10.3390/plants12142743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by -log10(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed.
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Affiliation(s)
- Fangjun Feng
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Yan
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Hong Zhang
- Anji Administrative Station of Water and Soil Conservation, Huzhou 313300, China
| | - Daoliang Mei
- Anji Administrative Station of Water and Soil Conservation, Huzhou 313300, China
| | - Peiqing Fan
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Xiaoyan Xu
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Chunlong Wei
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Qiaojun Lou
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Hongyan Liu
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanwei Mei
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
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20
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Li X, Dong J, Zhu W, Zhao J, Zhou L. Progress in the study of functional genes related to direct seeding of rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:46. [PMID: 37309311 PMCID: PMC10248684 DOI: 10.1007/s11032-023-01388-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/20/2023] [Indexed: 06/14/2023]
Abstract
Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.
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Affiliation(s)
- Xuezhong Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Wen Zhu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Lingyan Zhou
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
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21
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Wang Y, Liu H, Meng Y, Liu J, Ye G. Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1194119. [PMID: 37324692 PMCID: PMC10267709 DOI: 10.3389/fpls.2023.1194119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
Mesocotyl is an essential organ of rice for pushing buds out of soil and plays a crucial role in seeding emergence and development in direct-seeding. Thus, identify the loci associated with mesocotyl length (ML) could accelerate breeding progresses for direct-seeding cultivation. Mesocotyl elongation was mainly regulated by plant hormones. Although several regions and candidate genes governing ML have been reported, the effects of them in diverse breeding populations were still indistinct. In this study, 281 genes related to plant hormones at the genomic regions associated with ML were selected and evaluated by single-locus mixed linear model (SL-MLM) and multi-locus random-SNP-effect mixed linear model (mr-MLM) in two breeding panels (Trop and Indx) originated from the 3K re-sequence project. Furthermore, superior haplotypes with longer mesocotyl were also identified for marker assisted selection (MAS) breeding. Totally, LOC_Os02g17680 (explained 7.1-8.9% phenotypic variations), LOC_Os04g56950 (8.0%), LOC_Os07g24190 (9.3%) and LOC_Os12g12720 (5.6-8.0%) were identified significantly associated with ML in Trop panel, whereas LOC_Os02g17680 (6.5-7.4%), LOC_Os04g56950 (5.5%), LOC_Os06g24850 (4.8%) and LOC_Os07g40240 (4.8-7.1%) were detected in Indx panel. Among these, LOC_Os02g17680 and LOC_Os04g56950 were identified in both panels. Haplotype analysis for the six significant genes indicated that haplotype distribution of the same gene varies at Trop and Indx panels. Totally, 8 (LOC_Os02g17680-Hap1 and Hap2, LOC_Os04g56950-Hap1, Hap2 and Hap8, LOC_Os07g24190-Hap3, LOC_Os12g12720-Hap3 and Hap6) and six superior haplotypes (LOC_Os02g17680-Hap2, Hap5 and Hap7, LOC_Os04g56950-Hap4, LOC_Os06g24850-Hap2 and LOC_Os07g40240-Hap3) with higher ML were identified in Trop and Indx panels, respectively. In addition, significant additive effects for ML with more superior haplotypes were identified in both panels. Overall, the 6 significantly associated genes and their superior haplotypes could be used to enhancing ML through MAS breeding and further promote direct-seedling cultivation.
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Affiliation(s)
- Yamei Wang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Agriculture, Sun Yat-sen University, Shenzhen, China
| | - Hongyan Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
| | - Yun Meng
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
| | - Jindong Liu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
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22
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Guo N, Tang S, Wang J, Hu S, Tang S, Wei X, Shao G, Jiao G, Sheng Z, Hu P. Transcriptome and Proteome Analysis Revealed That Hormone and Reactive Oxygen Species Synergetically Regulate Dormancy of Introgression Line in Rice ( Oryza sativa L.). Int J Mol Sci 2023; 24:ijms24076088. [PMID: 37047061 PMCID: PMC10094489 DOI: 10.3390/ijms24076088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Dormancy is a complex agronomy phenotype controlled by multiple signaling and a key trait repressing pre-harvest sprouting (PHS). However, the signaling network of dormancy remains unclear. In this study, we used Zhonghua11 (ZH11) with a weak dormancy, and Introgression line (IL) with a strong dormancy to study the mechanism of hormones and reactive oxygen species (ROS) crosstalk regulating rice dormancy. The germination experiment showed that the germination rate of ZH11 was 76.86%, while that of IL was only 1.25%. Transcriptome analysis showed that there were 1658 differentially expressed genes (DEGs) between IL and ZH11, of which 577 were up-regulated and 1081 were down-regulated. Additionally, DEGs were mainly enriched in oxidoreductase activity, cell periphery, and plant hormone signal transduction pathways. Tandem mass tags (TMT) quantitative proteomics analysis showed 275 differentially expressed proteins (DEPs) between IL and ZH11, of which 176 proteins were up-regulated, 99 were down-regulated, and the DEPs were mainly enriched in the metabolic process and oxidation-reduction process. The comprehensive transcriptome and proteome analysis showed that their correlation was very low, and only 56 genes were co-expressed. Hormone content detection showed that IL had significantly lower abscisic acid (ABA) contents than the ZH11 while having significantly higher jasmonic acid (JA) contents than the ZH11. ROS content measurement showed that the hydrogen peroxide (H2O2) content of IL was significantly lower than the ZH11, while the production rate of superoxide anion (O2.-) was significantly higher than the ZH11. These results indicate that hormones and ROS crosstalk to regulate rice dormancy. In particular, this study has deepened our mechanism of ROS and JA crosstalk regulating rice dormancy and is conducive to our precise inhibition of PHS.
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Affiliation(s)
- Naihui Guo
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Shengjia Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Jiayu Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Peisong Hu
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
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23
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Yang J, Chen A, Wei J, Xu J, Chen S, Tang W, Liu J, Wang H. Identification of QTLs and candidate genes for rice seed germinability under low temperature using high‐density genetic mapping and RNA‐seq. Food Energy Secur 2023. [DOI: 10.1002/fes3.452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Affiliation(s)
- Jing Yang
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Aie Chen
- Teaching Affairs Department Yunnan Normal University Kunming China
| | - Ji Wei
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Jifen Xu
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Shengnan Chen
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Wei Tang
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Hongyang Wang
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
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24
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Edzesi WM, Dang X, Liu E, Bandoh WKN, Gakpetor PM, Ofori DA, Hong D. Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping. BMC Genom Data 2023; 24:8. [PMID: 36792993 PMCID: PMC9930352 DOI: 10.1186/s12863-023-01107-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Rice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice production unsustainable in the long term. In the present study, we mined favorable alleles for mesocotyl elongation length (MEL) by combining the phenotypic data of 543 rice accessions with genotypic data of 262 SSR markers through association mapping method. RESULTS Among the 543 rice accessions studied, we found 130 accessions could elongate mesocotyl length under dark germination condition. A marker-trait association analysis based on a mixed linear model revealed eleven SSR markers were associated with MEL trait with p-value less than 0.01. Among the 11 association loci, seven were novel. In total, 30 favorable marker alleles for MEL were mined, and RM265-140 bp showed the highest phenotypic effect value of 1.8 cm with Yuedao46 as the carrier accession. The long MEL group of rice accessions had higher seedling emergence rate than the short MEL group in the field. The correlation coefficient (r GCC-FSC = 0.485**) between growth chamber condition (GCC) and field soil condition (FSC) showed positive relationship and highly significant (P < 0.01) indicating that the result obtained in GCC could basically represent that obtained under FSC. CONCLUSION Not every genotype of the rice possesses the ability to elongate its mesocotyl length under dark or deep sowing condition. Mesocotyl elongation length is a quantitative trait controlled by many gene loci, and can be improved by pyramiding favorable alleles dispersed at different loci in different germplasm into a single genotype.
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Affiliation(s)
- Wisdom Mawuli Edzesi
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China ,grid.423756.10000 0004 1764 1672Council for Scientific and Industrial Research, Forestry Research Institute of Ghana, P. O. Box UP 63, KNUST, Fumesua, Kumasi, Ashanti Region Ghana
| | - Xiaojing Dang
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China ,grid.469521.d0000 0004 1756 0127Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Erbao Liu
- grid.27871.3b0000 0000 9750 7019State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China ,grid.411389.60000 0004 1760 4804College of Agriculture, Anhui Agricultural University, Hefei, 230036 China
| | - William Kwame Nuako Bandoh
- grid.423756.10000 0004 1764 1672Council for Scientific and Industrial Research, Forestry Research Institute of Ghana, P. O. Box UP 63, KNUST, Fumesua, Kumasi, Ashanti Region Ghana
| | - Patience Mansa Gakpetor
- grid.423756.10000 0004 1764 1672Council for Scientific and Industrial Research, Forestry Research Institute of Ghana, P. O. Box UP 63, KNUST, Fumesua, Kumasi, Ashanti Region Ghana
| | - Daniel Aninagyei Ofori
- grid.423756.10000 0004 1764 1672Council for Scientific and Industrial Research, Forestry Research Institute of Ghana, P. O. Box UP 63, KNUST, Fumesua, Kumasi, Ashanti Region Ghana
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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25
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Molecular bases of rice grain size and quality for optimized productivity. Sci Bull (Beijing) 2023; 68:314-350. [PMID: 36710151 DOI: 10.1016/j.scib.2023.01.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.
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26
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Liu K, Yang J, Sun K, Li D, Luo L, Zheng T, Wang H, Chen Z, Guo T. Genome-wide association study reveals novel genetic loci involved in anaerobic germination tolerance in Indica rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:9. [PMID: 37313132 PMCID: PMC10248643 DOI: 10.1007/s11032-022-01345-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/20/2022] [Indexed: 06/15/2023]
Abstract
Increasing numbers of rice farmers are adopting methods of direct seeding in flooded paddy fields to save costs associated with labor and transplanting. Successful seedling establishment under anoxic conditions requires rapid coleoptile growth to access oxygen near the water surface. It is important to identify relevant genetic loci for coleoptile growth in rice. In this study, the coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD) of a germplasm collection consisting of 200 cultivars growing in a low-oxygen environment for 6 days varied extensively. A genome-wide association study (GWAS) was performed using 161,657 high-quality single nucleotide polymorphisms (SNPs), which were obtained via genotyping by sequencing (GBS). A total of 96 target trait-associated loci were detected, of which 14 were detected repeatedly in both the wet and dry seasons. For these 14 loci, 384 genes were located within a 200-kb genomic region (± 100 kb from the peak SNP). In addition, 12,084 differentially expressed genes (DEGs) were identified using transcriptome expression profiling. Based on the GWAS and expression profiling, we further narrowed the candidate genes down to 111. Among the 111 candidate DEGs, Os02g0285300, Os02g0639300, Os04g0671300, Os06g0702600, Os06g0707300, and Os12g0145700 were the most promising candidates associated with anaerobic germination. In addition, we performed a detailed analysis of OsTPP7 sequences from 29 samples in our panel containing 200 diverse germplasms. A total of 11 mutation sites were identified, and four haplotypes were obtained. We found that 7 varieties with the OsTPP7-1 haplotype had higher phenotypic values. This work broadens our understanding of the genetic control of germination tolerance of anaerobic conditions. This study also provides a material basis for breeding superior direct-seeded rice varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01345-1.
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Affiliation(s)
- Kai Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Jing Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, 650500 China
| | - Kai Sun
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Dongxiu Li
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Lixin Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Taotao Zheng
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
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27
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Zhong M, Yue L, Liu W, Qin H, Lei B, Huang R, Yang X, Kang Y. Genome-Wide Identification and Characterization of the Polyamine Uptake Transporter (Put) Gene Family in Tomatoes and the Role of Put2 in Response to Salt Stress. Antioxidants (Basel) 2023; 12:antiox12020228. [PMID: 36829787 PMCID: PMC9952195 DOI: 10.3390/antiox12020228] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
The polyamine uptake transporter (Put), an important polyamines-related protein, is involved in plant cell growth, developmental processes, and abiotic stimuli, but no research on the Put family has been carried out in the tomato. Herein, eight tomato Put were identified and scattered across four chromosomes, which were classified into three primary groups by phylogenetic analysis. Protein domains and gene structural organization also showed a significant degree of similarity, and the Put genes were significantly induced by various hormones and polyamines. Tissue-specific expression analysis indicated that Put genes were expressed in all tissues of the tomato. The majority of Put genes were induced by different abiotic stresses. Furthermore, Put2 transcription was found to be responsive to salt stress, and overexpression of Put2 in yeast conferred salinity tolerance and polyamine uptake. Moreover, overexpression of Put2 in tomatoes promoted salinity tolerance accompanied by a decrease in the Na+/K+ ratio, restricting the generation of reactive oxygen and increasing polyamine metabolism and catabolism, antioxidant enzyme activity (SOD, CAT, APX, and POD), and nonenzymatic antioxidant activity (GSH/GSSG and ASA/DHA ratios, GABA, and flavonoid content); loss of function of put2 produced opposite effects. These findings highlight that Put2 plays a pivotal role in mediating polyamine synthesis and catabolism, and the antioxidant capacity in tomatoes, providing a valuable gene for salinity tolerance in plants.
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Affiliation(s)
- Min Zhong
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Lingqi Yue
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Liu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hongyi Qin
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Bingfu Lei
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Riming Huang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Xian Yang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (X.Y.); (Y.K.)
| | - Yunyan Kang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (X.Y.); (Y.K.)
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28
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Chen P, Liu Q, Sun B, Lv S, Jiang L, Zhang J, Mao X, Yu H, Chen Y, Chen W, Fan Z, Pan D, Li C. Creation and gene expression analysis of a giant embryo rice mutant with high GABA content. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:3. [PMID: 37312870 PMCID: PMC10248637 DOI: 10.1007/s11032-022-01353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/27/2022] [Indexed: 06/15/2023]
Abstract
Gamma-amino butyric acid (GABA) is a natural non-protein amino acid involved in stress, signal transmission, carbon and nitrogen balance, and other physiological processes in plants. In the human body, GABA has the effects of lowering blood pressure, anti-aging, and activating the liver and kidneys. However, there are few studies on the molecular regulation mechanism of genes in the metabolic pathways of GABA during grain development of giant embryo rice with high GABA content. In this study, three glant embryo (ge) mutants of different embryo sizes were obtained by CRISPR/Cas9 knockout, and it was found that GABA, protein, crude fat, and various mineral contents of the ge mutants were significantly increased. RNA-seq and qRT-PCR analysis showed that in the GABA shunt and polyamine degradation pathways, the expression levels of most of the genes encoding enzymes promoting GABA accumulation were significantly upregulated in the ge-1 mutant, whereas, the expression levels of most of the genes encoding enzymes involved GABA degradation were significantly downregulated in the ge-1 mutant. This is most likely responsible for the significant increase in GABA content of the ge mutant. These results help reveal the molecular regulatory network of GABA metabolism in giant embryo rice and provide a theoretical basis for the study of its development mechanisms, which is conducive to the rapid cultivation of GABA-rich rice varieties, promoting human nutrition, and ensuring health. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01353-1.
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Affiliation(s)
- Pingli Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Shuwei Lv
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Yangyang Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Dajian Pan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
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Wu J, Zhu M, Liu W, Jahan MS, Gu Q, Shu S, Sun J, Guo S. CsPAO2 Improves Salt Tolerance of Cucumber through the Interaction with CsPSA3 by Affecting Photosynthesis and Polyamine Conversion. Int J Mol Sci 2022; 23:12413. [PMID: 36293280 PMCID: PMC9604536 DOI: 10.3390/ijms232012413] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 08/15/2023] Open
Abstract
Polyamine oxidases (PAOs) are key enzymes in polyamine metabolism and are related to the tolerance of plants to abiotic stresses. In this study, overexpression of cucumber (Cucumis sativus L.) PAO2 (CsPAO2) in Arabidopsis resulted in increased activity of the antioxidant enzyme and accelerated conversion from Put to Spd and Spm, while malondialdehyde content (MDA) and electrolyte leakage (EL) was decreased when compared with wild type, leading to enhanced plant growth under salt stress. Photosystem Ⅰ assembly 3 in cucumber (CsPSA3) was revealed as an interacting protein of CsPAO2 by screening yeast two-hybrid library combined with in vitro and in vivo methods. Then, CsPAO2 and CsPSA3 were silenced in cucumber via virus-mediated gene silencing (VIGS) with pV190 as the empty vector. Under salt stress, net photosynthetic rate (Pn) and transpiration rate (Tr) of CsPAO2-silencing plants were lower than pV190-silencing plants, and EL in root was higher than pV190-silencing plants, indicating that CsPAO2-silencing plants suffered more serious salt stress damage. However, photosynthetic parameters of CsPSA3-silencing plants were all higher than those of CsPAO2 and pV190-silencing plants, thereby enhancing the photosynthesis process. Moreover, CsPSA3 silencing reduced the EL in both leaves and roots when compared with CsPAO2-silencing plants, but the EL only in leaves was significantly lower than the other two gene-silencing plants, and conversion from Put to Spd and Spm in leaf was also promoted, suggesting that CsPSA3 interacts with CsPAO2 in leaves to participate in the regulation of salt tolerance through photosynthesis and polyamine conversion.
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Affiliation(s)
- Jianqiang Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengliang Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Weikang Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mohammad Shah Jahan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Horticulture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Qinsheng Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Sheng Shu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shirong Guo
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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30
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Huang L, Liu Y, Wang X, Jiang C, Zhao Y, Lu M, Zhang J. Peroxisome-Mediated Reactive Oxygen Species Signals Modulate Programmed Cell Death in Plants. Int J Mol Sci 2022; 23:ijms231710087. [PMID: 36077484 PMCID: PMC9456327 DOI: 10.3390/ijms231710087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Peroxisomes are a class of simple organelles that play an important role in plant reactive oxygen species (ROS) metabolism. Experimental evidence reveals the involvement of ROS in programmed cell death (PCD) in plants. Plant PCD is crucial for the regulation of plant growth, development and environmental stress resistance. However, it is unclear whether the ROS originated from peroxisomes participated in cellular PCD. Enzymes involved in the peroxisomal ROS metabolic pathways are key mediators to figure out the relationship between peroxisome-derived ROS and PCD. Here, we summarize the peroxisomal ROS generation and scavenging pathways and explain how peroxisome-derived ROS participate in PCD based on recent progress in the functional study of enzymes related to peroxisomal ROS generation or scavenging. We aimed to elucidate the role of the peroxisomal ROS regulatory system in cellular PCD to show its potential in terms of accurate PCD regulation, which contribute to environmental stress resistance.
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31
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Light Spectral Composition Modifies Polyamine Metabolism in Young Wheat Plants. Int J Mol Sci 2022; 23:ijms23158394. [PMID: 35955528 PMCID: PMC9369354 DOI: 10.3390/ijms23158394] [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: 06/13/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 02/04/2023] Open
Abstract
Although light-emitting diode (LED) technology has extended the research on targeted photomorphogenic, physiological, and biochemical responses in plants, there is not enough direct information about how light affects polyamine metabolism. In this study, the effect of three spectral compositions (referred to by their most typical characteristic: blue, red, and the combination of blue and red [pink] lights) on polyamine metabolism was compared to those obtained under white light conditions at the same light intensity. Although light quality induced pronounced differences in plant morphology, pigment contents, and the expression of polyamine metabolism-related genes, endogenous polyamine levels did not differ substantially. When exogenous polyamines were applied, their roborative effect were detected under all light conditions, but these beneficial changes were correlated with an increase in polyamine content and polyamine metabolism-related gene expression only under blue light. The effect of the polyamines on leaf gene expression under red light was the opposite, with a decreasing tendency. Results suggest that light quality may optimize plant growth through the adjustment of polyamine metabolism at the gene expression level. Polyamine treatments induced different strategies in fine-tuning of polyamine metabolism, which were induced for optimal plant growth and development under different spectral compositions.
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32
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Liu G, Jiang W, Tian L, Fu Y, Tan L, Zhu Z, Sun C, Liu F. Polyamine oxidase 3 is involved in salt tolerance at the germination stage in rice. J Genet Genomics 2022; 49:458-468. [PMID: 35144028 DOI: 10.1016/j.jgg.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/22/2022]
Abstract
Soil salinity inhibits seed germination and reduces seedling survival rate, resulting in significant yield reductions in crops. Here, we report the identification of a polyamine oxidase, OsPAO3, conferring salt tolerance at the germination stage in rice (Oryza sativa L.), through map-based cloning approach. OsPAO3 is up-regulated under salt stress at the germination stage and highly expressed in various organs. Overexpression of OsPAO3 increases activity of polyamine oxidases, enhancing the polyamine content in seed coleoptiles. Increased polyamine may lead to the enhance of the activity of ROS-scavenging enzymes to eliminate over-accumulated H2O2 and to reduce Na+ content in seed coleoptiles to maintain ion homeostasis and weaken Na+ damage. These changes resulted in stronger salt tolerance at the germination stage in rice. Our findings not only provide a unique gene for breeding new salt-tolerant rice cultivars but also help to elucidate the mechanism of salt tolerance in rice.
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Affiliation(s)
- Guangyu Liu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Wanxia Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Lei Tian
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yongcai Fu
- National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Lubin Tan
- National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Zuofeng Zhu
- National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
| | - Fengxia Liu
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China; National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, MOE, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
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Sukegawa S, Toki S, Saika H. Genome Editing Technology and Its Application to Metabolic Engineering in Rice. RICE (NEW YORK, N.Y.) 2022; 15:21. [PMID: 35366102 PMCID: PMC8976860 DOI: 10.1186/s12284-022-00566-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/18/2022] [Indexed: 05/18/2023]
Abstract
Genome editing technology can be used for gene engineering in many organisms. A target metabolite can be fortified by the knockout and modification of target genes encoding enzymes involved in catabolic and biosynthesis pathways, respectively, via genome editing technology. Genome editing is also applied to genes encoding proteins other than enzymes, such as chaperones and transporters. There are many reports of such metabolic engineering using genome editing technology in rice. Genome editing is used not only for site-directed mutagenesis such as the substitution of a single base in a target gene but also for random mutagenesis at a targeted region. The latter enables the creation of novel genetic alleles in a target gene. Recently, genome editing technology has been applied to random mutagenesis in a targeted gene and its promoter region in rice, enabling the screening of plants with a desirable trait from these mutants. Moreover, the expression level of a target gene can be artificially regulated by a combination of genome editing tools such as catalytically inactivated Cas protein with transcription activator or repressor. This approach could be useful for metabolic engineering, although expression cassettes for inactivated Cas fused to a transcriptional activator or repressor should be stably transformed into the rice genome. Thus, the rapid development of genome editing technology has been expanding the scope of molecular breeding including metabolic engineering. In this paper, we review the current status of genome editing technology and its application to metabolic engineering in rice.
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Affiliation(s)
- Satoru Sukegawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604 Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604 Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Shiga Japan
| | - Hiroaki Saika
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604 Japan
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Chu C, Huang R, Liu L, Tang G, Xiao J, Yoo H, Yuan M. The rice heavy-metal transporter OsNRAMP1 regulates disease resistance by modulating ROS homoeostasis. PLANT, CELL & ENVIRONMENT 2022; 45:1109-1126. [PMID: 35040151 DOI: 10.1111/pce.14263] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Crop diseases threaten food security and sustainable agriculture. Consumption of crops containing nonessential toxic metals leads to health risks for humans. Therefore, cultivation of disease-resistant and toxic metal-safe crops is a double-gain strategy that can contribute to food security. Here, we show that rice heavy-metal transporter OsNRAMP1 plays an important role in plant immunity by modulating metal ion and reactive oxygen species (ROS) homoeostasis. OsNRAMP1 expression was induced after pathogenic bacteria and fungi infections. The osnramp1 mutants had an increased content of H2 O2 and activity of superoxide dismutase, but decreased activity of catalase, showing enhanced broad-spectrum resistance against bacterial and fungal pathogens. RNA-seq analysis identified a number of differentially expressed genes that were involved in metal ion and ROS homoeostasis. Altered expression of metal ion-dependent ROS-scavenging enzymes genes and lower accumulation of cations such as Mn together induced compromised metal ion-dependent enzyme-catalysing activity and modulated ROS homoeostasis, which together contributed towards disease resistance in osnramp1 mutants. Furthermore, the osnramp1 mutants contained lower levels of toxic heavy metals Cd and Pb and micronutrients Ni and Mn in leaves and grains. Taken together, a proof of concept was achieved that broad-spectrum disease-resistant and toxic heavy-metal-safe rice was engineered by removal of the OsNRAMP1 gene.
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Affiliation(s)
- Chuanliang Chu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Renyan Huang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Liping Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guilin Tang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Heejin Yoo
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Pan Z, Tan B, Cao G, Zheng R, Liu M, Zeng R, Wang S, Zhu H, Ye H, Zhao G, Cao W, Liu G, Zhang G, Zhou Y. Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice. RICE (NEW YORK, N.Y.) 2021; 14:103. [PMID: 34910270 PMCID: PMC8674402 DOI: 10.1186/s12284-021-00544-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/03/2021] [Indexed: 05/31/2023]
Abstract
Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F2 segregating population, and five key recombinants were selected to develop F3 populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security.
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Affiliation(s)
- Zhaoyuan Pan
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Bin Tan
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guiyuan Cao
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Rongqi Zheng
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Meng Liu
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Ruizhen Zeng
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Heng Ye
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Guangmiao Zhao
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Cao
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guifu Liu
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guiquan Zhang
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Yuliang Zhou
- Guangdong Key Laboratory of Plant Molecular Breeding and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
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Wang Y, Wang Y, Yang R, Wang F, Fu J, Yang W, Bai T, Wang S, Yin H. Effects of gibberellin priming on seedling emergence and transcripts involved in mesocotyl elongation in rice under deep direct-seeding conditions. J Zhejiang Univ Sci B 2021; 22:1002-1021. [PMID: 34904413 DOI: 10.1631/jzus.b2100174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mesocotyl elongation is a key trait influencing seedling emergence and establishment in direct-seeding rice cultivation. The phytohormone gibberellin (GA) has positive effects on mesocotyl elongation in rice. However, the physiological and molecular basis underlying the regulation of mesocotyl elongation mediated by GA priming under deep-sowing conditions remains largely unclear. In the present study, we performed a physiological and comprehensive transcriptomic analysis of the function of GA priming in mesocotyl elongation and seedling emergence using a direct-seeding japonica rice cultivar ZH10 at a 5-cm sowing depth. Physiological experiments indicated that GA priming significantly improved rice seedling emergence by increasing the activity of starch-metabolizing enzymes and compatible solute content to supply the energy essential for subsequent development. Transcriptomic analysis revealed 7074 differentially expressed genes (false discovery rate of <0.05, |log2(fold change)| of ≥1) after GA priming. Furthermore, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses revealed that genes associated with transcriptional regulation, plant hormone biosynthesis or signaling, and starch and sucrose metabolism were critical for GA-mediated promotion of rice mesocotyl elongation. Further analyses showed that the expression of the transcription factor (TF) genes (v-myb avian myeloblastosis viral oncogene homolog (MYB) alternative splicing 1 (MYBAS1), phytochrome-interacting factors 1 (PIF1), Oryza sativa teosinte branched 1/cycloidea/proliferating cell factor 5 (OsTCP5), slender 1 (SLN1), and mini zinc finger 1 (MIF1)), plant hormone biosynthesis or signaling genes (brassinazole-resistant 1 (BZR1), ent-kaurenoic acid oxidase-like (KAO), GRETCHEN HAGEN 3.2 (GH3.2), and small auxin up RNA 36 (SAUR36)), and starch and sucrose metabolism genes (α-amylases (AMY2A and AMY1.4)) was highly correlated with the mesocotyl elongation and deep-sowing tolerance response. These results enhance our understanding of how nutrient metabolism-related substances and genes regulate rice mesocotyl elongation. This may facilitate future studies on related genes and the development of novel rice varieties tolerant to deep sowing.
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Affiliation(s)
- Ya Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yuetao Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ruifang Yang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Fuhua Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Jing Fu
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wenbo Yang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Tao Bai
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Shengxuan Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Haiqing Yin
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
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Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice. Genomics 2021; 113:4227-4236. [PMID: 34774680 DOI: 10.1016/j.ygeno.2021.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/22/2021] [Accepted: 11/07/2021] [Indexed: 11/22/2022]
Abstract
Seedling vigour is an important agronomic trait and is gaining attention in Asian rice (Oryza sativa) as cultivation practices shift from transplanting to forms of direct seeding. To understand the genetic control of rice seedling vigour in dry direct seeded (aerobic) conditions we measured multiple seedling traits in 684 accessions from the 3000 Rice Genomes (3K-RG) population in both the laboratory and field at three planting depths. Our data show that phenotyping of mesocotyl length in laboratory conditions is a good predictor of field performance. By performing a genome wide association study, we found that the main QTL for mesocotyl length, percentage seedling emergence and shoot biomass are co-located on the short arm of chromosome 7. We show that haplotypes in the indica subgroup from this region can be used to predict the seedling vigour of 3K-RG accessions. The selected accessions may serve as potential donors in genomics-assisted breeding programs.
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38
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Polyamine Metabolism under Different Light Regimes in Wheat. Int J Mol Sci 2021; 22:ijms222111717. [PMID: 34769148 PMCID: PMC8583935 DOI: 10.3390/ijms222111717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 01/12/2023] Open
Abstract
Although the relationship between polyamines and photosynthesis has been investigated at several levels, the main aim of this experiment was to test light-intensity-dependent influence of polyamine metabolism with or without exogenous polyamines. First, the effect of the duration of the daily illumination, then the effects of different light intensities (50, 250, and 500 μmol m–2 s–1) on the polyamine metabolism at metabolite and gene expression levels were investigated. In the second experiment, polyamine treatments, namely putrescine, spermidine and spermine, were also applied. The different light quantities induced different changes in the polyamine metabolism. In the leaves, light distinctly induced the putrescine level and reduced the 1,3-diaminopropane content. Leaves and roots responded differently to the polyamine treatments. Polyamines improved photosynthesis under lower light conditions. Exogenous polyamine treatments influenced the polyamine metabolism differently under individual light regimes. The fine-tuning of the synthesis, back-conversion and terminal catabolism could be responsible for the observed different polyamine metabolism-modulating strategies, leading to successful adaptation to different light conditions.
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39
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Wang Y, Liu J, Meng Y, Liu H, Liu C, Ye G. Rapid Identification of QTL for Mesocotyl Length in Rice Through Combining QTL-seq and Genome-Wide Association Analysis. Front Genet 2021; 12:713446. [PMID: 34349792 PMCID: PMC8326918 DOI: 10.3389/fgene.2021.713446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/15/2021] [Indexed: 02/01/2023] Open
Abstract
Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F2 populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or G-value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3–14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, Indel-Chr1:18932318 and Indel-Chr7:15404166 for loci qML1.3 and qML7.2 respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding.
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Affiliation(s)
- Yamei Wang
- 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, China.,CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jindong Liu
- 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, China.,CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yun Meng
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,College of Tropical Crops, Hainan University, Haikou, China
| | - Hongyan Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,College of Tropical Crops, Hainan University, Haikou, China
| | - Chang Liu
- 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, China.,CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoyou Ye
- 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, China.,CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Rice Breeding Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
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40
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Pál M, Szalai G, Gondor OK, Janda T. Unfinished story of polyamines: Role of conjugation, transport and light-related regulation in the polyamine metabolism in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 308:110923. [PMID: 34034871 DOI: 10.1016/j.plantsci.2021.110923] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 05/27/2023]
Abstract
Polyamines play a fundamental role in the functioning of all cells. Their regulatory role in plant development, their function under stress conditions, and their metabolism have been well documented as regards both synthesis and catabolism in an increasing number of plant species. However, the majority of these studies concentrate on the levels of the most abundant polyamines, sometimes providing data on the enzyme activity or gene expression levels during polyamine synthesis, but generally making no mention of the fact that changes in the polyamine pool are very dynamic, and that other processes are also involved in the regulation of actual polyamine levels. Differences in the distribution of individual polyamines and their conjugation with other compounds were described some time ago, but these have been given little attention. In addition, the role of polyamine transporters in plants is only now being recognised. The present review highlights the importance of conjugated polyamines and also points out that investigations should not only deal with the polyamine metabolism itself, but should also cover other important questions, such as the relationship between light perception and the polyamine metabolism, or the involvement of polyamines in the circadian rhythm.
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Affiliation(s)
- Magda Pál
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, H-2462, Hungary.
| | - Gabriella Szalai
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, H-2462, Hungary
| | - Orsolya Kinga Gondor
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, H-2462, Hungary
| | - Tibor Janda
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, H-2462, Hungary
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41
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Li C, Brant E, Budak H, Zhang B. CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement. J Zhejiang Univ Sci B 2021; 22:253-284. [PMID: 33835761 PMCID: PMC8042526 DOI: 10.1631/jzus.b2100009] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since it was first recognized in bacteria and archaea as a mechanism for innate viral immunity in the early 2010s, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) has rapidly been developed into a robust, multifunctional genome editing tool with many uses. Following the discovery of the initial CRISPR/Cas-based system, the technology has been advanced to facilitate a multitude of different functions. These include development as a base editor, prime editor, epigenetic editor, and CRISPR interference (CRISPRi) and CRISPR activator (CRISPRa) gene regulators. It can also be used for chromatin and RNA targeting and imaging. Its applications have proved revolutionary across numerous biological fields, especially in biomedical and agricultural improvement. As a diagnostic tool, CRISPR has been developed to aid the detection and screening of both human and plant diseases, and has even been applied during the current coronavirus disease 2019 (COVID-19) pandemic. CRISPR/Cas is also being trialed as a new form of gene therapy for treating various human diseases, including cancers, and has aided drug development. In terms of agricultural breeding, precise targeting of biological pathways via CRISPR/Cas has been key to regulating molecular biosynthesis and allowing modification of proteins, starch, oil, and other functional components for crop improvement. Adding to this, CRISPR/Cas has been shown capable of significantly enhancing both plant tolerance to environmental stresses and overall crop yield via the targeting of various agronomically important gene regulators. Looking to the future, increasing the efficiency and precision of CRISPR/Cas delivery systems and limiting off-target activity are two major challenges for wider application of the technology. This review provides an in-depth overview of current CRISPR development, including the advantages and disadvantages of the technology, recent applications, and future considerations.
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Affiliation(s)
- Chao Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Eleanor Brant
- Agronomy Department, University of Florida, Gainesville, FL 32611, USA
| | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT 59802, USA.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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