1
|
Fang H, Huang S, Li R, Wang P, Jiang Q, Zhong C, Yang Y, Yu W. Combined BSA-Seq and RNA-Seq to Identify Potential Genes Regulating Fruit Size in Bottle Gourd ( Lagenaria siceraria L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:2154. [PMID: 39124272 DOI: 10.3390/plants13152154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024]
Abstract
Fruit size is a crucial agronomic trait in bottle gourd, impacting both yield and utility. Despite its significance, the regulatory mechanism governing fruit size in bottle gourd remains largely unknown. In this study, we used bottle gourd (small-fruited H28 and large-fruited H17) parent plants to measure the width and length of fruits at various developmental stages, revealing a single 'S' growth curve for fruit expansion. Paraffin section observations indicated that both cell number and size significantly influence bottle gourd fruit size. Through bulked segregant analysis and combined genotype-phenotype analysis, the candidate interval regulating fruit size was pinpointed to 17,747,353 bp-18,185,825 bp on chromosome 9, encompassing 0.44 Mb and including 44 genes. Parental fruits in the rapid expansion stage were subjected to RNA-seq, highlighting that differentially expressed genes were mainly enriched in pathways related to cell wall biosynthesis, sugar metabolism, and hormone signaling. Transcriptome and resequencing analysis, combined with gene function annotation, identified six genes within the localized region as potential regulators of fruit size. This study not only maps the candidate interval of genes influencing fruit size in bottle gourd through forward genetics, but also offers new insights into the potential molecular mechanisms underlying this trait through transcriptome analysis.
Collapse
Affiliation(s)
- Huarong Fang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Shishi Huang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ruirui Li
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Peng Wang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Qingwei Jiang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Chuan Zhong
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yanjuan Yang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Wenjin Yu
- College of Agriculture, Guangxi University, Nanning 530004, China
| |
Collapse
|
2
|
Chen Y, Dan Z, Li S. GROWTH REGULATING FACTOR 7-mediated arbutin metabolism enhances rice salt tolerance. THE PLANT CELL 2024; 36:2834-2850. [PMID: 38701348 PMCID: PMC11289636 DOI: 10.1093/plcell/koae140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024]
Abstract
Salt stress is an environmental factor that limits plant growth and crop production. With the rapid expansion of salinized arable land worldwide, investigating the molecular mechanisms underlying the salt stress response in plants is urgently needed. Here, we report that GROWTH REGULATING FACTOR 7 (OsGRF7) promotes salt tolerance by regulating arbutin (hydroquinone-β-D-glucopyranoside) metabolism in rice (Oryza sativa). Overexpression of OsGRF7 increased arbutin content, and exogenous arbutin application rescued the salt-sensitive phenotype of OsGRF7 knockdown and knockout plants. OsGRF7 directly promoted the expression of the arbutin biosynthesis genes URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASE 1 (OsUGT1) and OsUGT5, and knockout of OsUGT1 or OsUGT5 reduced rice arbutin content, salt tolerance, and grain size. Furthermore, OsGRF7 degradation through its interaction with F-BOX AND OTHER DOMAINS CONTAINING PROTEIN 13 reduced rice salinity tolerance and grain size. These findings highlight an underexplored role of OsGRF7 in modulating rice arbutin metabolism, salt stress response, and grain size, as well as its broad potential use in rice breeding.
Collapse
Affiliation(s)
- Yunping Chen
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| |
Collapse
|
3
|
Shen Y, Huang D, Zhang Z, Fan Y, Sheng Z, Zhuang J, Shen B, Zhu Y. Dissection and Fine-Mapping of Two QTL Controlling Grain Size Linked in a 515.6-kb Region on Chromosome 10 of Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:2054. [PMID: 39124172 DOI: 10.3390/plants13152054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/13/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
Grain size is a primary determinant of grain weight, which is one of the three essential components of rice grain yield. Mining the genes that control grain size plays an important role in analyzing the regulation mechanism of grain size and improving grain appearance quality. In this study, two closely linked quantitative trait loci (QTL) controlling grain size, were dissected and fine-mapped in a 515.6-kb region on the long arm of chromosome 10 by using six near isogenic line populations. One of them, qGS10.2, which controlled 1000 grain weight (TGW) and grain width (GW), was delimited into a 68.1-kb region containing 14 annotated genes. The Teqing allele increased TGW and GW by 0.17 g and 0.011 mm with the R2 of 12.7% and 11.8%, respectively. The other one, qGL10.2, which controlled grain length (GL), was delimited into a 137.3-kb region containing 22 annotated genes. The IRBB52 allele increased GL by 0.018 mm with the R2 of 6.8%. Identification of these two QTL provides candidate regions for cloning of grain size genes.
Collapse
Affiliation(s)
- Yi Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310012, China
| | - Derun Huang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhenhua Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yeyang Fan
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhonghua Sheng
- Jiangxi Early-Season Rice Research Centre, China National Rice Research Institute, Hangzhou 310006, China
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Jieyun Zhuang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Bo Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310012, China
| | - Yujun Zhu
- Jiangxi Early-Season Rice Research Centre, China National Rice Research Institute, Hangzhou 310006, China
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| |
Collapse
|
4
|
Liu C, Li Q, Peng S, He L, Lin R, Zhang J, Cui P, Liu H. O-Glycosyltransferase Gene BnaC09.OGT Involved in Regulation of Unsaturated Fatty Acid Biosynthesis for Enhancing Osmotic Stress Tolerance in Brassica napus L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1964. [PMID: 39065490 PMCID: PMC11280806 DOI: 10.3390/plants13141964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
Osmotic stress is a major threaten to the growth and yield stability of Brassica napus. Post-translational modification with O-linked β-N-acetylglucosamine (O-GlcNAc) is ubiquitous in plants, and participates in a variety of signal transduction and metabolic regulation. However, studies on the role of O-GlcNAc transferase (OGT) in osmotic stress tolerance of plants are limited. In previous study, a O-glycosyltransferase, named BnaC09.OGT, was identified from the B. napus variety 'Zhongshuang 11' by yeast one hybrid with promoter of BnaA01.GPAT9. It was found that BnaC09.OGT localized in both nucleus and cytoplasm. The spatiotemporal expression pattern of BnaC09.OGT exhibited tissue specificity in developmental seed, especially in 15 days after pollination. In view of osmotic stress inducing, the BnaC09.OGT overexpression and knockout transgenic lines were constructed for biological function study. Phenotypic analysis of BnaC09.OGT overexpression seedlings demonstrated that BnaC09.OGT could enhance osmotic stress tolerance than WT and knockout lines in euphylla stage under 15% PEG6000 treatment after 7 days. In addition, compared with WT and knockout lines, overexpression of BnaC09.OGT had significantly higher activities of antioxidant enzymes (SOD and POD), higher content of soluble saccharide, and while significantly less content of malondialdehyde, proline and anthocyanidin under 15% PEG6000 treatment after 7 days. On the other hand, the unsaturated fatty acid content of BnaC09.OGT overexpression was significantly higher than that of WT and knockout lines, so it is speculated that the BnaC09.OGT could increase unsaturated fatty acid biosynthesis for osmotic stress tolerance by promoting the expression of BnaA01.GPAT9 in glycerolipid biosynthesis. In summary, the above results revealed that the function of BnaC09.OGT provides new insight for the analysis of the pathway of O-glycosylation in regulating osmotic stress tolerance in B. napus.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Peng Cui
- The College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China; (C.L.); (Q.L.); (S.P.); (L.H.); (R.L.); (J.Z.)
| | - Hongbo Liu
- The College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou 311300, China; (C.L.); (Q.L.); (S.P.); (L.H.); (R.L.); (J.Z.)
| |
Collapse
|
5
|
Jiang M, Zhang H, Song Y, Chen J, Bai J, Tang J, Wang Q, Fotopoulos V, Zhu QH, Yang R, Li R. Transcription factor OsbZIP10 modulates rice grain quality by regulating OsGIF1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38981001 DOI: 10.1111/tpj.16911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/01/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
Understanding and optimizing the process of grain filling helps the quest to maximize rice (Oryza sativa L.) seed yield and quality, yet the intricate mechanisms at play remain fragmented. Transcription factors (TFs) are major players in the gene networks underlying the grain filling process. Here, we employed grain incomplete filling (OsGIF1)/cell wall invertase 2, a key gene involved in grain filling, to explore its upstream TFs and identified a bZIP family TF, OsbZIP10, to be a transcriptional activator of OsGIF1. Rice grains of the knockouts of OsbZIP10 showed increased white-core rates but lower amylose content (AC), leading to better eating and cooking qualities in all genetic backgrounds investigated, though the impact of mutations in OsbZIP10 on grain weight depended on genetic background. Multi-omics analyses suggested that, in addition to OsGIF1, multiple genes involved in different biological processes contributing to grain filling were targeted by OsbZIP10, including OsAGPS1, a gene encoding the ADP-Glc pyrophosphorylase (AGPase) small subunit, and genes contributing to homeostasis of reactive oxygen species. Distinct genetic make-up was observed in OsbZIP10 between japonica and indica rice varieties, with the majority varieties of each subspecies belonging to two different haplotypes that were closely associated with AC. Overexpressing the haplotype linked to high-AC in the low-AC genetic background increased AC. Overall, this study sheds crucial light on the significance of the OsbZIP10-OsGIF1 module in the determination of rice grain quality, offering a potential avenue for genetic engineering of rice to produce seeds with tailored attributes.
Collapse
Affiliation(s)
- Meng Jiang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, 572000, People's Republic of China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yue Song
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, 572000, People's Republic of China
| | - Jiale Chen
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, 572000, People's Republic of China
| | - Jianjiang Bai
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Jianhao Tang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Qing Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Wuxi Hupper Bioseed Technology Institute Ltd., Wuxi, 214000, Jiangsu, People's Republic of China
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, 3603, Cyprus
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, 2601, Australian Capital Territory, Australia
| | - Ruifang Yang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Ruiqing Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, People's Republic of China
| |
Collapse
|
6
|
Han Y, Hu Q, Gong N, Yan H, Khan NU, Du Y, Sun H, Zhao Q, Peng W, Li Z, Zhang Z, Li J. Natural variation in MORE GRAINS 1 regulates grain number and grain weight in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1440-1458. [PMID: 38780111 DOI: 10.1111/jipb.13674] [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: 11/14/2023] [Accepted: 04/14/2024] [Indexed: 05/25/2024]
Abstract
Grain yield is determined mainly by grain number and grain weight. In this study, we identified and characterized MORE GRAINS1 (MOG1), a gene associated with grain number and grain weight in rice (Oryza sativa L.), through map-based cloning. Overexpression of MOG1 increased grain yield by 18.6%-22.3% under field conditions. We determined that MOG1, a bHLH transcription factor, interacts with OsbHLH107 and directly activates the expression of LONELY GUY (LOG), which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1 (EXPLA1), positively regulating grain number per panicle and grain weight. Natural variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation, leading to functional differences. Haplotype analysis revealed that Hap-HNW, which results in a greater number and heavier grains, has undergone strong selection but has been poorly utilized in modern lowland rice breeding. In summary, the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway, thereby increasing grain number and grain weight. These findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.
Collapse
Affiliation(s)
- Yingchun Han
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qianfeng Hu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Nuo Gong
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Huimin Yan
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Najeeb Ullah Khan
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
- Rice Industrial Technology Research Institute, Guizhou University, Guiyang, 550025, China
| | - Wanxi Peng
- School of Forestry, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Junzhou Li
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| |
Collapse
|
7
|
Florez-Rueda AM, Miguel CM, Figueiredo DD. Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1134-1157. [PMID: 38709819 DOI: 10.1111/tpj.16786] [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: 10/13/2023] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.
Collapse
Affiliation(s)
- Ana Marcela Florez-Rueda
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Karl-Liebknechts-Str. 24-25, Haus 26, 14476, Potsdam, Germany
| | - Célia M Miguel
- Faculty of Sciences, Biosystems and Integrative Sciences Institute (BioISI), University of Lisbon, Lisboa, Portugal
| | - Duarte D Figueiredo
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
| |
Collapse
|
8
|
Boccaccini A, Cimini S, Kazmi H, Lepri A, Longo C, Lorrai R, Vittorioso P. When Size Matters: New Insights on How Seed Size Can Contribute to the Early Stages of Plant Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1793. [PMID: 38999633 PMCID: PMC11244240 DOI: 10.3390/plants13131793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024]
Abstract
The seed habit is the most complex and successful method of sexual reproduction in vascular plants. It represents a remarkable moment in the evolution of plants that afterward spread on land. In particular, seed size had a pivotal role in evolutionary success and agronomic traits, especially in the field of crop domestication. Given that crop seeds constitute one of the primary products for consumption, it follows that seed size represents a fundamental determinant of crop yield. This adaptative feature is strictly controlled by genetic traits from both maternal and zygotic tissues, although seed development and growth are also affected by environmental cues. Despite being a highly exploited topic for both basic and applied research, there are still many issues to be elucidated for developmental biology as well as for agronomic science. This review addresses a number of open questions related to cues that influence seed growth and size and how they influence seed germination. Moreover, new insights on the genetic-molecular control of this adaptive trait are presented.
Collapse
Affiliation(s)
- Alessandra Boccaccini
- Department of Science and Technology for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, via Álvaro del Portillo, 21, 00128 Rome, Italy; (A.B.); (S.C.)
| | - Sara Cimini
- Department of Science and Technology for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, via Álvaro del Portillo, 21, 00128 Rome, Italy; (A.B.); (S.C.)
| | - Hira Kazmi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (H.K.); (A.L.); (C.L.); (R.L.)
| | - Andrea Lepri
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (H.K.); (A.L.); (C.L.); (R.L.)
| | - Chiara Longo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (H.K.); (A.L.); (C.L.); (R.L.)
| | - Riccardo Lorrai
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (H.K.); (A.L.); (C.L.); (R.L.)
| | - Paola Vittorioso
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (H.K.); (A.L.); (C.L.); (R.L.)
| |
Collapse
|
9
|
Zhang X, Han C, Wang Y, Liu T, Liang Y, Cao Y. Integrated analysis of transcriptomics and metabolomics of garden asparagus (Asparagus officinalis L.) under drought stress. BMC PLANT BIOLOGY 2024; 24:563. [PMID: 38879466 PMCID: PMC11179350 DOI: 10.1186/s12870-024-05286-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/10/2024] [Indexed: 06/19/2024]
Abstract
BACKGROUND Drought is a leading environmental factor affecting plant growth. To explore the drought tolerance mechanism of asparagus, this study analyzed the responses of two asparagus varieties, namely, 'Jilv3' (drought tolerant) and 'Pacific Early' (drought sensitive), to drought stress using metabolomics and transcriptomics. RESULTS In total, 2,567 and 7,187 differentially expressed genes (DEGs) were identified in 'Pacific Early' and 'Jilv3', respectively, by comparing the transcriptome expression patterns between the normal watering treatment and the drought stress treatment. These DEGs were significantly enriched in the amino acid biosynthesis, carbon metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. In 'Jilv3', DEGs were also enriched in the following energy metabolism-related pathways: citrate cycle (TCA cycle), glycolysis/gluconeogenesis, and pyruvate metabolism. This study also identified 112 and 254 differentially accumulated metabolites (DAMs) in 'Pacific Early' and 'Jilv3' under drought stress compared with normal watering, respectively. The amino acid, flavonoid, organic acid, and soluble sugar contents were more significantly enhanced in 'Jilv3' than in 'Pacific Early'. According to the metabolome and transcriptome analysis, in 'Jilv3', the energy supply of the TCA cycle was improved, and flavonoid biosynthesis increased. As a result, its adaptability to drought stress improved. CONCLUSIONS These findings help to better reveal the molecular mechanism underlying how asparagus responds to drought stress and improve researchers' ability to screen drought-tolerant asparagus varieties as well as breed new varieties.
Collapse
Affiliation(s)
- Xuhong Zhang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
- Shijiazhuang Landscape Management and Protection Center, Shijiazhuang, China
| | - Changzhi Han
- College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Yubo Wang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Tao Liu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Yuqin Liang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yanpo Cao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| |
Collapse
|
10
|
Cao G, Huang H, Yang Y, Xie B, Tang L. Analysis of drought and heat stress response genes in rice using co-expression network and differentially expressed gene analyses. PeerJ 2024; 12:e17255. [PMID: 38708347 PMCID: PMC11067907 DOI: 10.7717/peerj.17255] [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: 10/10/2023] [Accepted: 03/27/2024] [Indexed: 05/07/2024] Open
Abstract
Studies on Oryza sativa (rice) are crucial for improving agricultural productivity and ensuring global sustenance security, especially considering the increasing drought and heat stress caused by extreme climate change. Currently, the genes and mechanisms underlying drought and heat resistance in rice are not fully understood, and the scope for enhancing the development of new strains remains considerable. To accurately identify the key genes related to drought and heat stress responses in rice, multiple datasets from the Gene Expression Omnibus (GEO) database were integrated in this study. A co-expression network was constructed using a Weighted Correlation Network Analysis (WGCNA) algorithm. We further distinguished the core network and intersected it with differentially expressed genes and multiple expression datasets for screening. Differences in gene expression levels were verified using quantitative real-time polymerase chain reaction (PCR). OsDjC53, MBF1C, BAG6, HSP23.2, and HSP21.9 were found to be associated with the heat stress response, and it is also possible that UGT83A1 and OsCPn60a1, although not directly related, are affected by drought stress. This study offers significant insights into the molecular mechanisms underlying stress responses in rice, which could promote the development of stress-tolerant rice breeds.
Collapse
Affiliation(s)
- Gaohui Cao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Hao Huang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuejiao Yang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Bin Xie
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan City, Hubei Province, China
| | - Lulu Tang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| |
Collapse
|
11
|
Cao Y, Han Z, Zhang Z, He L, Huang C, Chen J, Dai F, Xuan L, Yan S, Si Z, Hu Y, Zhang T. UDP-glucosyltransferase 71C4 controls the flux of phenylpropanoid metabolism to shape cotton seed development. PLANT COMMUNICATIONS 2024:100938. [PMID: 38689494 DOI: 10.1016/j.xplc.2024.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
Seeds play a crucial role in plant reproduction, making it essential to identify genes that affect seed development. In this study, we focused on UDP-glucosyltransferase 71C4 (UGT71C4) in cotton, a member of the glycosyltransferase family that shapes seed width and length, thereby influencing seed index and seed cotton yield. Overexpression of UGT71C4 results in seed enlargement owing to its glycosyltransferase activity on flavonoids, which redirects metabolic flux from lignin to flavonoid metabolism. This shift promotes cell proliferation in the ovule via accumulation of flavonoid glycosides, significantly enhancing seed cotton yield and increasing the seed index from 10.66 g to 11.91 g. By contrast, knockout of UGT71C4 leads to smaller seeds through activation of the lignin metabolism pathway and redirection of metabolic flux back to lignin synthesis. This redirection leads to increased ectopic lignin deposition in the ovule, inhibiting ovule growth and development, and alters yield components, increasing the lint percentage from 41.42% to 43.40% and reducing the seed index from 10.66 g to 8.60 g. Our research sheds new light on seed size development and reveals potential pathways for enhancing seed yield.
Collapse
Affiliation(s)
- Yiwen Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Lu He
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chujun Huang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fan Dai
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lisha Xuan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sunyi Yan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China.
| |
Collapse
|
12
|
Zuo H, Chen J, Lv Z, Shao C, Chen Z, Zhou Y, Shen C. Tea-Derived Polyphenols Enhance Drought Resistance of Tea Plants ( Camellia sinensis) by Alleviating Jasmonate-Isoleucine Pathway and Flavonoid Metabolism Flow. Int J Mol Sci 2024; 25:3817. [PMID: 38612625 PMCID: PMC11011871 DOI: 10.3390/ijms25073817] [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: 01/28/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Extreme drought weather has occurred frequently in recent years, resulting in serious yield loss in tea plantations. The study of drought in tea plantations is becoming more and more intensive, but there are fewer studies on drought-resistant measures applied in actual production. Therefore, in this study, we investigated the effect of exogenous tea polyphenols on the drought resistance of tea plant by pouring 100 mg·L-1 of exogenous tea polyphenols into the root under drought. The exogenous tea polyphenols were able to promote the closure of stomata and reduce water loss from leaves under drought stress. Drought-induced malondialdehyde (MDA) accumulation in tea leaves and roots was also significantly reduced by exogenous tea polyphenols. Combined transcriptomic and metabolomic analyses showed that exogenous tea polyphenols regulated the abnormal responses of photosynthetic and energy metabolism in leaves under drought conditions and alleviated sphingolipid metabolism, arginine metabolism, and glutathione metabolism in the root system, which enhanced the drought resistance of tea seedlings. Exogenous tea polyphenols induced jasmonic acid-isoleucine (JA-ILE) accumulation in the root system, and the jasmonic acid-isoleucine synthetase gene (TEA028623), jasmonic acid ZIM structural domain proteins (JAMs) synthesis genes (novel.22237, TEA001821), and the transcription factor MYC2 (TEA014288, TEA005840) were significantly up-regulated. Meanwhile, the flavonoid metabolic flow was significantly altered in the root; for example, the content of EGCG, ECG, and EGC was significantly increased. Thus, exogenous tea polyphenols enhance the drought resistance of tea plants through multiple pathways.
Collapse
Affiliation(s)
- Haoming Zuo
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Jiahao Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Zhidong Lv
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Chenyu Shao
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Ziqi Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Yuebin Zhou
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| | - Chengwen Shen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (H.Z.); (C.S.)
- National Research Center of Engineering & Technology for Utilization of Functional Ingredients from Botanicals, Collaborative Innovation Center of Utilization of Functional Ingredients from Botanicals and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|
13
|
Wei S, Yu Z, Du F, Cao F, Yang M, Liu C, Qi Z, Chen Q, Zou J, Wang J. Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:908. [PMID: 38592937 PMCID: PMC10975824 DOI: 10.3390/plants13060908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent 'Suinong14' (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.
Collapse
Affiliation(s)
- Siming Wei
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Zhenhai Yu
- Heilongjiang Province Green Food Science Institute, Harbin 150028, China;
| | - Fangfang Du
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Fubin Cao
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Mingliang Yang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Chunyan Liu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Zhaoming Qi
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Qingshan Chen
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Jianan Zou
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Jinhui Wang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| |
Collapse
|
14
|
Yan Y, Zhu X, Qi H, Zhang H, He J. Regulatory mechanism and molecular genetic dissection of rice ( Oryza sativa L.) grain size. Heliyon 2024; 10:e27139. [PMID: 38486732 PMCID: PMC10938125 DOI: 10.1016/j.heliyon.2024.e27139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/18/2024] [Accepted: 02/25/2024] [Indexed: 03/17/2024] Open
Abstract
With the sharp increase of the global population, adequate food supply is a great challenge. Grain size is an essential determinant of rice yield and quality. It is a typical quantitative trait controlled by multiple genes. In this paper, we summarized the quantitative trait loci (QTL) that have been molecularly characterized and provided a comprehensive summary of the regulation mechanism and genetic pathways of rice grain size. These pathways include the ubiquitin-proteasome system, G-protein, mitogen-activated protein kinase, phytohormone, transcriptional factors, abiotic stress. In addition, we discuss the possible application of advanced molecular biology methods and reasonable breeding strategies, and prospective on the development of high-yielding and high-quality rice varieties using molecular biology techniques.
Collapse
Affiliation(s)
- Yuntao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Xiaoya Zhu
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Hui Qi
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
- Hunan Institute of Nuclear Agricultural Science and Space Breeding, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haiqing Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Jiwai He
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| |
Collapse
|
15
|
Yin M, Tong X, Yang J, Cheng Y, Zhou P, Li G, Wang Y, Ying J. Dissecting the Genetic Basis of Yield Traits and Validation of a Novel Quantitative Trait Locus for Grain Width and Weight in Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:770. [PMID: 38592774 PMCID: PMC10975080 DOI: 10.3390/plants13060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Grain yield in rice is a complex trait and it is controlled by a number of quantitative trait loci (QTL). To dissect the genetic basis of rice yield, QTL analysis for nine yield traits was performed using an F2 population containing 190 plants, which was developed from a cross between Youyidao (YYD) and Sanfenhe (SFH), and each plant in the population evaluated with respect to nine yield traits. In this study, the correlations among the nine yield traits were analyzed. The grain yield per plant positively correlated with six yield traits, except for grain length and grain width, and showed the highest correlation coefficient of 0.98 with the number of filled grains per plant. A genetic map containing 133 DNA markers was constructed and it spanned 1831.7 cM throughout 12 chromosomes. A total of 36 QTLs for the yield traits were detected on nine chromosomes, except for the remaining chromosomes 5, 8, and 9. The phenotypic variation was explained by a single QTL that ranged from 6.19% to 36.01%. Furthermore, a major QTL for grain width and weight, qGW2-1, was confirmed to be newly identified and was narrowed down to a relatively smaller interval of about ~2.94-Mb. Collectively, we detected a total of 36 QTLs for yield traits and a major QTL, qGW2-1, was confirmed to control grain weight and width, which laid the foundation for further map-based cloning and molecular design breeding in rice.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Jiezheng Ying
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China; (M.Y.); (J.Y.); (Y.C.); (P.Z.); (G.L.); (Y.W.)
| |
Collapse
|
16
|
Xu M, Hu J, Li H, Li K, Xu D. Research overview on the genetic mechanism underlying the biosynthesis of polysaccharide in tuber plants. PeerJ 2024; 12:e17052. [PMID: 38464751 PMCID: PMC10924778 DOI: 10.7717/peerj.17052] [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: 10/10/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
Tuber plants are of great significance in the world as human food crops. Polysaccharides, important metabolites in tuber plants, also serve as a source of innovative drugs with significant pharmacological effects. These drugs are particularly known for their immunomodulation and antitumor properties. To fully exploit the potential value of tuber plant polysaccharides and establish a synthetic system for their targeted synthesis, it is crucial to dissect their metabolic processes and genetic regulatory mechanisms. In this article, we provide a comprehensive summary of the basic pathways involved in the synthesis of various types of tuber plant polysaccharides. We also outline the key research progress that has been made in this area in recent years. We classify the main types and functions of tuber plant polysaccharides and analyze the biosynthetic processes and genetic regulation mechanisms of key enzymes involved in the metabolic pathways of starch, cellulose, pectin, and fructan in tuber plants. We have identified hexokinase and glycosyltransferase as the key enzymes involved in the polysaccharide synthesis process. By elucidating the synthesis pathway of polysaccharides in tuber plants and understanding the underlying mechanism of action of key enzymes in the metabolic pathway, we can provide a theoretical framework for enhancing the yield of polysaccharides and other metabolites in plant culture cells. This will ultimately lead to increased production efficiency.
Collapse
Affiliation(s)
- Mengwei Xu
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jiao Hu
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongwei Li
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
| | - Kunqian Li
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
| | - Delin Xu
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou, China
- Guizhou Provincial Demonstration Center of Basic Medical Experimental Teaching, Zunyi Medical University, Zunyi, Guizhou, China
| |
Collapse
|
17
|
Li Y, Zhao W, Tang J, Yue X, Gu J, Zhao B, Li C, Chen Y, Yuan J, Lin Y, Li Y, Kong F, He J, Wang D, Zhao TJ, Wang ZY. Identification of the domestication gene GmCYP82C4 underlying the major quantitative trait locus for the seed weight in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:62. [PMID: 38418640 DOI: 10.1007/s00122-024-04571-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
KEY MESSAGE A major quantitative trait locus (QTL) for the hundred-seed weight (HSW) was identified and confirmed in the two distinct soybean populations, and the target gene GmCYP82C4 underlying this locus was identified that significantly associated with soybean seed weight, and it was selected during the soybean domestication and improvement process. Soybean is a major oil crop for human beings and the seed weight is a crucial goal of soybean breeding. However, only a limited number of target genes underlying the quantitative trait loci (QTLs) controlling seed weight in soybean are known so far. In the present study, six loci associated with hundred-seed weight (HSW) were detected in the first population of 573 soybean breeding lines by genome-wide association study (GWAS), and 64 gene models were predicted in these candidate QTL regions. The QTL qHSW_1 exhibits continuous association signals on chromosome four and was also validated by region association study (RAS) in the second soybean population (409 accessions) with wild, landrace, and cultivar soybean accessions. There were seven genes in qHSW_1 candidate region by linkage disequilibrium (LD) block analysis, and only Glyma.04G035500 (GmCYP82C4) showed specifically higher expression in flowers, pods, and seeds, indicating its crucial role in the soybean seed development. Significant differences in HSW trait were detected when the association panels are genotyped by single-nucleotide polymorphisms (SNPs) in putative GmCYP82C4 promoter region. Eight haplotypes were generated by six SNPs in GmCYP82C4 in the second soybean population, and two superior haplotypes (Hap2 and Hap4) of GmCYP82C4 were detected with average HSW of 18.27 g and 18.38 g, respectively. The genetic diversity of GmCYP82C4 was analyzed in the second soybean population, and GmCYP82C4 was most likely selected during the soybean domestication and improvement process, leading to the highest proportion of Hap2 of GmCYP82C4 both in landrace and cultivar subpopulations. The QTLs and GmCYP82C4 identified in this study provide novel genetic resources for soybean seed weight trait, and the GmCYP82C4 could be used for soybean molecular breeding to develop desirable seed weight in the future.
Collapse
Affiliation(s)
- Yang Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Wenqian Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jiajun Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xiuli Yue
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Biyao Zhao
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Cong Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yanhang Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Jianbo Yuan
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yan Lin
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jin He
- College of Agriculture, Guizhou University, Guiyang, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, China
| | - Tuan-Jie Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China.
| |
Collapse
|
18
|
Lethe MCL, Paris V, Wang X, Chan CTY. Similarities in Structure and Function of UDP-Glycosyltransferase Homologs from Human and Plants. Int J Mol Sci 2024; 25:2782. [PMID: 38474028 PMCID: PMC10932239 DOI: 10.3390/ijms25052782] [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: 01/25/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
The uridine diphosphate glycosyltransferase (UGT) superfamily plays a key role in the metabolism of xenobiotics and metabolic wastes, which is essential for detoxifying those species. Over the last several decades, a huge effort has been put into studying human and mammalian UGT homologs, but family members in other organisms have been explored much less. Potentially, other UGT homologs can have desirable substrate specificity and biological activities that can be harnessed for detoxification in various medical settings. In this review article, we take a plant UGT homology, UGT71G1, and compare its structural and biochemical properties with the human homologs. These comparisons suggest that even though mammalian and plant UGTs are functional in different environments, they may support similar biochemical activities based on their protein structure and function. The known biological functions of these homologs are discussed so as to provide insights into the use of UGT homologs from other organisms for addressing human diseases related to UGTs.
Collapse
Affiliation(s)
- Mary Caroline L. Lethe
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA (V.P.)
| | - Vincent Paris
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA (V.P.)
| | - Xiaoqiang Wang
- Department of Biological Sciences, College of Science, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA;
- BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| | - Clement T. Y. Chan
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA (V.P.)
- BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| |
Collapse
|
19
|
Simoni S, Vangelisti A, Clemente C, Usai G, Santin M, Ventimiglia M, Mascagni F, Natali L, Angelini LG, Cavallini A, Tavarini S, Giordani T. Transcriptomic Analyses Reveal Insights into the Shared Regulatory Network of Phenolic Compounds and Steviol Glycosides in Stevia rebaudiana. Int J Mol Sci 2024; 25:2136. [PMID: 38396813 PMCID: PMC10889303 DOI: 10.3390/ijms25042136] [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: 01/10/2024] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Stevia rebaudiana (Bertoni) is a highly valuable crop for the steviol glycoside content in its leaves, which are no-calorie sweeteners hundreds of times more potent than sucrose. The presence of health-promoting phenolic compounds, particularly flavonoids, in the leaf of S. rebaudiana adds further nutritional value to this crop. Although all these secondary metabolites are highly desirable in S. rebaudiana leaves, the genes regulating the biosynthesis of phenolic compounds and the shared gene network between the regulation of biosynthesis of steviol glycosides and phenolic compounds still need to be investigated in this species. To identify putative candidate genes involved in the synergistic regulation of steviol glycosides and phenolic compounds, four genotypes with different contents of these compounds were selected for a pairwise comparison RNA-seq analysis, yielding 1136 differentially expressed genes. Genes that highly correlate with both steviol glycosides and phenolic compound accumulation in the four genotypes of S. rebaudiana were identified using the weighted gene co-expression network analysis. The presence of UDP-glycosyltransferases 76G1, 76H1, 85C1, and 91A1, and several genes associated with the phenylpropanoid pathway, including peroxidase, caffeoyl-CoA O-methyltransferase, and malonyl-coenzyme A:anthocyanin 3-O-glucoside-6″-O-malonyltransferase, along with 21 transcription factors like SCL3, WRK11, and MYB111, implied an extensive and synergistic regulatory network involved in enhancing the production of such compounds in S. rebaudiana leaves. In conclusion, this work identified a variety of putative candidate genes involved in the biosynthesis and regulation of particular steviol glycosides and phenolic compounds that will be useful in gene editing strategies for increasing and steering the production of such compounds in S. rebaudiana as well as in other species.
Collapse
Affiliation(s)
- Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Clarissa Clemente
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Marco Santin
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Maria Ventimiglia
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Lucia Natali
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Luciana G. Angelini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
- Interdepartmental Research Centre “Nutraceuticals and Food for Health—NUTRAFOOD”, University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Silvia Tavarini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
- Interdepartmental Research Centre “Nutraceuticals and Food for Health—NUTRAFOOD”, University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| |
Collapse
|
20
|
Xing J, Zhang J, Wang Y, Wei X, Yin Z, Zhang Y, Pu A, Dong Z, Long Y, Wan X. Mining genic resources regulating nitrogen-use efficiency based on integrative biological analyses and their breeding applications in maize and other crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1148-1164. [PMID: 37967146 DOI: 10.1111/tpj.16550] [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: 08/18/2023] [Revised: 10/08/2023] [Accepted: 11/05/2023] [Indexed: 11/17/2023]
Abstract
Nitrogen (N) is an essential factor for limiting crop yields, and cultivation of crops with low nitrogen-use efficiency (NUE) exhibits increasing environmental and ecological risks. Hence, it is crucial to mine valuable NUE improvement genes, which is very important to develop and breed new crop varieties with high NUE in sustainable agriculture system. Quantitative trait locus (QTL) and genome-wide association study (GWAS) analysis are the most common methods for dissecting genetic variations underlying complex traits. In addition, with the advancement of biotechnology, multi-omics technologies can be used to accelerate the process of exploring genetic variations. In this study, we integrate the substantial data of QTLs, quantitative trait nucleotides (QTNs) from GWAS, and multi-omics data including transcriptome, proteome, and metabolome and further analyze their interactions to predict some NUE-related candidate genes. We also provide the genic resources for NUE improvement among maize, rice, wheat, and sorghum by homologous alignment and collinearity analysis. Furthermore, we propose to utilize the knowledge gained from classical cases to provide the frameworks for improving NUE and breeding N-efficient varieties through integrated genomics, systems biology, and modern breeding technologies.
Collapse
Affiliation(s)
- Jiapeng Xing
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Juan Zhang
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Yanbo Wang
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Zechao Yin
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yuqian Zhang
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yan Long
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, Shunde Innovation School, Zhongzhi International Institute of Agricultural Biosciences, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| |
Collapse
|
21
|
Kumar S, Chakraborty S, Chakraborty N. Dehydration-responsive cytoskeleton proteome of rice reveals reprograming of key molecular pathways to mediate metabolic adaptation and cell survival. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108359. [PMID: 38237420 DOI: 10.1016/j.plaphy.2024.108359] [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: 09/29/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/16/2024]
Abstract
The plant cytoskeletal proteins play a key role that control cytoskeleton dynamics, contributing to crucial biological processes such as cell wall morphogenesis, stomatal conductance and abscisic acid accumulation in repercussion to water-deficit stress or dehydration. Yet, it is still completely unknown which specific biochemical processes and regulatory mechanisms the cytoskeleton uses to drive dehydration tolerance. To better understand the role of cytoskeleton, we developed the dehydration-responsive cytoskeletal proteome map of a resilient rice cultivar. Initially, four-week-old rice plants were exposed to progressive dehydration, and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical indices. The organelle fractionation in conjunction with label-free quantitative proteome analysis led to the identification of 955 dehydration-responsive cytoskeletal proteins (DRCPs). To our knowledge, this is the first report of a stress-responsive plant cytoskeletal proteome, representing the largest inventory of cytoskeleton and cytoskeleton-associated proteins. The DRCPs were apparently involved in a wide array of intra-cellular molecules transportation, organelles positioning, cytoskeleton organization followed by different metabolic processes including amino acid metabolism. These findings presented open a unique view on global regulation of plant cytoskeletal proteome is intimately linked to cellular metabolic rewiring of adaptive responses, and potentially confer dehydration tolerance, especially in rice, and other crop species, in general.
Collapse
Affiliation(s)
- Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
22
|
Ouyang L, Liu Y, Yao R, He D, Yan L, Chen Y, Huai D, Wang Z, Yu B, Kang Y, Jiang H, Lei Y, Liao B, Wang X. Genome-wide analysis of UDP-glycosyltransferase gene family and identification of a flavonoid 7-O-UGT (AhUGT75A) enhancing abiotic stress in peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2023; 23:626. [PMID: 38062387 PMCID: PMC10702079 DOI: 10.1186/s12870-023-04656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Glycosylation, catalyzed by UDP-glycosyltransferase (UGT), was important for enhancing solubility, bioactivity, and diversity of flavonoids. Peanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. In addition to provide high quality of edible oils and proteins, peanut seeds contain a rich source of flavonoid glycosides that benefit human health. However, information of UGT gene family was quite limited in peanut. RESULTS In present study, a total of 267 AhUGTs clustered into 15 phylogenetic groups were identified in peanut genome. Group I has greatly expanded to contain the largest number of AhUGT genes. Segmental duplication was the major driving force for AhUGT gene family expansion. Transcriptomic analysis of gene expression profiles in various tissues and under different abiotic stress treatments indicated AhUGTs were involved in peanut growth and abiotic stress response. AhUGT75A (UGT73CG33), located in mitochondria, was characterized as a flavonoid 7-O-UGT by in vitro enzyme assays. The transcript level of AhUGT75A was strongly induced by abiotic stress. Overexpression of AhUGT75A resulted in accumulating less amount of malondialdehyde (MDA) and superoxide, and enhancing tolerance against drought and/or salt stress in transgenic Arabidopsis. These results indicated AhUGT75A played important roles in conferring abiotic stress tolerance through reactive oxygen species scavenging. CONCLUSIONS Our research only not provides valuable information for functional characterization of UGTs in peanut, but also gives new insights into potential applications in breeding new cultivars with both desirable stress tolerance and health benefits.
Collapse
Affiliation(s)
- Lei Ouyang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, P.R. China
| | - Yue Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
| | - Ruonan Yao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, P.R. China
| | - Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, P.R. China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
| | - Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
| | - Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China.
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China.
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P.R. China.
| |
Collapse
|
23
|
Rates ADB, Cesarino I. Pour some sugar on me: The diverse functions of phenylpropanoid glycosylation. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154138. [PMID: 38006622 DOI: 10.1016/j.jplph.2023.154138] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The phenylpropanoid metabolism is the source of a vast array of specialized metabolites that play diverse functions in plant growth and development and contribute to all aspects of plant interactions with their surrounding environment. These compounds protect plants from damaging ultraviolet radiation and reactive oxygen species, provide mechanical support for the plants to stand upright, and mediate plant-plant and plant-microorganism communications. The enormous metabolic diversity of phenylpropanoids is further expanded by chemical modifications known as "decorative reactions", including hydroxylation, methylation, glycosylation, and acylation. Among these modifications, glycosylation is the major driving force of phenylpropanoid structural diversification, also contributing to the expansion of their properties. Phenylpropanoid glycosylation is catalyzed by regioselective uridine diphosphate (UDP)-dependent glycosyltransferases (UGTs), whereas glycosyl hydrolases known as β-glucosidases are the major players in deglycosylation. In this article, we review how the glycosylation process affects key physicochemical properties of phenylpropanoids, such as molecular stability and solubility, as well as metabolite compartmentalization/storage and biological activity/toxicity. We also summarize the recent knowledge on the functional implications of glycosylation of different classes of phenylpropanoid compounds. A balance of glycosylation/deglycosylation might represent an essential molecular mechanism to regulate phenylpropanoid homeostasis, allowing plants to dynamically respond to diverse environmental signals.
Collapse
Affiliation(s)
- Arthur de Barros Rates
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil; Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues 370, 05508-020, São Paulo, Brazil.
| |
Collapse
|
24
|
Yang J, Miao J, Li N, Zhou Z, Dai K, Ji F, Yang M, Tan C, Liu J, Wang H, Tang W. Genetic dissection of cold tolerance at the budding stage of rice in an indica-japonica recombination inbred line population. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108086. [PMID: 37890228 DOI: 10.1016/j.plaphy.2023.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Rice is highly cold-sensitive, and thus, the promotion of cold resistance in buds is essential. In this study, we conducted a mapping analysis to identify quantitative trait loci (QTLs) associated with cold tolerance in buds. The analysis was performed using a recombinant inbred line (RIL) population consisting of 192 lines derived from the cold-tolerant strain 02428 and the cold-sensitive strain YZX. Seven additive loci on chromosomes 1, 4, 5, and 6 were identified, of which loci 3 and 7 were found in two crop seasons, indicating stability. Three epistatic interactions, one present over two seasons, were found. Loci 3 and 7 pyramided with two main-effect QTLs observed to control the rate of low-temperature germination in our previous study. Two materials with good cold resistance at the germination and bud stages were obtained, namely, G93 and G146. Transcriptome sequencing analysis of the two parent buds after cold treatment found that genes expressed differentially between the two parents were related to photosynthesis, energy metabolism, and reactive oxygen scavenging. Five candidate genes, namely, Os01g0385400, Os01g0388000, Os06g0287700, Os06g0289200, and Os06g0291100, were selected in the two stable intervals based on gene expression profiles and annotations. These genetic loci exhibit strong potential as targets for breeding cold tolerance in buds and require additional investigation. In conclusion, this work provides valuable genetic resources that can be utilized to improve the cold tolerance of rice.
Collapse
Affiliation(s)
- Jing Yang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Jiahao Miao
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Nan Li
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Zixian Zhou
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Kunyan Dai
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Faru Ji
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Min Yang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Chen Tan
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
| | - Hongyang Wang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
| | - Wei Tang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
| |
Collapse
|
25
|
Kan Y, Mu XR, Gao J, Lin HX, Lin Y. The molecular basis of heat stress responses in plants. MOLECULAR PLANT 2023; 16:1612-1634. [PMID: 37740489 DOI: 10.1016/j.molp.2023.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Global warming impacts crop production and threatens food security. Elevated temperatures are sensed by different cell components. Temperature increases are classified as either mild warm temperatures or excessively hot temperatures, which are perceived by distinct signaling pathways in plants. Warm temperatures induce thermomorphogenesis, while high-temperature stress triggers heat acclimation and has destructive effects on plant growth and development. In this review, we systematically summarize the heat-responsive genetic networks in Arabidopsis and crop plants based on recent studies. In addition, we highlight the strategies used to improve grain yield under heat stress from a source-sink perspective. We also discuss the remaining issues regarding the characteristics of thermosensors and the urgency required to explore the basis of acclimation under multifactorial stress combination.
Collapse
Affiliation(s)
- Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiao-Rui Mu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Youshun Lin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
26
|
Gharabli H, Della Gala V, Welner DH. The function of UDP-glycosyltransferases in plants and their possible use in crop protection. Biotechnol Adv 2023; 67:108182. [PMID: 37268151 DOI: 10.1016/j.biotechadv.2023.108182] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 06/04/2023]
Abstract
Glycosyltransferases catalyse the transfer of a glycosyl moiety from a donor to an acceptor. Members of this enzyme class are ubiquitous throughout all kingdoms of life and are involved in the biosynthesis of countless types of glycosides. Family 1 glycosyltransferases, also referred to as uridine diphosphate-dependent glycosyltransferases (UGTs), glycosylate small molecules such as secondary metabolites and xenobiotics. In plants, UGTs are recognised for their multiple functionalities ranging from roles in growth regulation and development, in protection against pathogens and abiotic stresses and in adaptation to changing environments. In this study, we review UGT-mediated glycosylation of phytohormones, endogenous secondary metabolites, and xenobiotics and contextualise the role this chemical modification plays in the response to biotic and abiotic stresses and plant fitness. Here, the potential advantages and drawbacks of altering the expression patterns of specific UGTs along with the heterologous expression of UGTs across plant species to improve stress tolerance in plants are discussed. We conclude that UGT-based genetic modification of plants could potentially enhance agricultural efficiency and take part in controlling the biological activity of xenobiotics in bioremediation strategies. However, more knowledge of the intricate interplay between UGTs in plants is needed to unlock the full potential of UGTs in crop resistance.
Collapse
Affiliation(s)
- Hani Gharabli
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kgs. Lyngby DK-2800, Denmark
| | - Valeria Della Gala
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kgs. Lyngby DK-2800, Denmark
| | - Ditte Hededam Welner
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kgs. Lyngby DK-2800, Denmark.
| |
Collapse
|
27
|
Cai Q, Jiao F, Wang Q, Zhang E, Song X, Pei Y, Li J, Zhao M, Guo X. Multiomics comparative analysis of the maize large grain mutant tc19 identified pathways related to kernel development. BMC Genomics 2023; 24:537. [PMID: 37697229 PMCID: PMC10496403 DOI: 10.1186/s12864-023-09567-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: 03/29/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND The mechanism of grain development in elite maize breeding lines has not been fully elucidated. Grain length, grain width and grain weight are key components of maize grain yield. Previously, using the Chinese elite maize breeding line Chang7-2 and its large grain mutant tc19, we characterized the grain size developmental difference between Chang7-2 and tc19 and performed transcriptomic analysis. RESULTS In this paper, using Chang7-2 and tc19, we performed comparative transcriptomic, proteomic and metabolomic analyses at different grain development stages. Through proteomics analyses, we found 2884, 505 and 126 differentially expressed proteins (DEPs) at 14, 21 and 28 days after pollination, respectively. Through metabolomics analysis, we identified 51, 32 and 36 differentially accumulated metabolites (DAMs) at 14, 21 and 28 days after pollination, respectively. Through multiomics comparative analysis, we showed that the phenylpropanoid pathways are influenced at transcriptomic, proteomic and metabolomic levels in all the three grain developmental stages. CONCLUSION We identified several genes in phenylpropanoid biosynthesis, which may be related to the large grain phenotype of tc19. In summary, our results provided new insights into maize grain development.
Collapse
Affiliation(s)
- Qing Cai
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qianqian Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Enying Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiyun Song
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuhe Pei
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jun Li
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Meiai Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xinmei Guo
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
28
|
He JZ, Dorion S, Carmona-Rojas LM, Rivoal J. Carbon Fluxes in Potato ( Solanum tuberosum) Remain Stable in Cell Cultures Exposed to Nutritional Phosphate Deficiency. BIOLOGY 2023; 12:1190. [PMID: 37759596 PMCID: PMC10525292 DOI: 10.3390/biology12091190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
Nutritional phosphate deficiency is a major limitation to plant growth. Here, we monitored fluxes in pathways supporting respiratory metabolism in potato (Solanum tuberosum) cell cultures growing in control or limiting phosphate conditions. Sugar uptake was quantified using [U-14C]sucrose as precursor. Carbohydrate degradation through glycolysis and respiratory pathways was estimated using the catabolism of [U-14C]sucrose to 14CO2. Anaplerotic carbon flux was assessed by labeling with NaH14CO3. The data showed that these metabolic fluxes displayed distinct patterns over culture time. However, phosphate depletion had relatively little impact on the various fluxes. Sucrose uptake was higher during the first six days of culture, followed by a decline, which was steeper in Pi-sufficient cells. Anaplerotic pathway flux was more important at day three and decreased thereafter. In contrast, the flux between sucrose and CO2 was at a maximum in the mid-log phase of the culture, with a peak at Day 6. Metabolization of [U-14C]sucrose into neutral, basic and acidic fractions was also unaffected by phosphate nutrition. Hence, the well-documented changes in central metabolism enzymes activities in response to Pi deficiency do not drastically modify metabolic fluxes, but rather result in the maintenance of the carbon fluxes that support respiration.
Collapse
Affiliation(s)
- Jiang Zhou He
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada; (J.Z.H.); (S.D.); (L.M.C.-R.)
| | - Sonia Dorion
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada; (J.Z.H.); (S.D.); (L.M.C.-R.)
| | - Laura Michell Carmona-Rojas
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada; (J.Z.H.); (S.D.); (L.M.C.-R.)
- Grupo de Biotecnologiía, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medelliín 050010, Colombia
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada; (J.Z.H.); (S.D.); (L.M.C.-R.)
| |
Collapse
|
29
|
Zhao H, Ding X, Chu X, Zhang H, Wang X, Zhang X, Liu H, Zhang X, Yin Z, Li Y, Ding X. Plant immune inducer ZNC promotes rutin accumulation and enhances resistance to Botrytis cinerea in tomato. STRESS BIOLOGY 2023; 3:36. [PMID: 37676331 PMCID: PMC10444710 DOI: 10.1007/s44154-023-00106-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 07/09/2023] [Indexed: 09/08/2023]
Abstract
Gray mold is a destructive disease caused by Botrytis cinerea, a pervasive plant pathogen, which poses a threat to both tomato growth and postharvest storage. The utilization of induced resistance presents a potential strategy for combating plant pathogenic attacks. ZNC (zhinengcong), an extract derived from the endophytic fungus Paecilomyces variotii, has been discovered to play a vital role in preventing diverse forms of bacterial infections. Nevertheless, the precise mechanism behind its ability to enhance tomato resistance to fungi remains unclear. In this study, we found that the exogenous spraying of ZNC could significantly improve the resistance of tomato plants to B. cinerea. The results of both the metabolomic analysis and high-performance liquid chromatography (HPLC) demonstrated that tomato plants responded to ZNC treatment by accumulating high levels of rutin. Additional transcriptome analysis uncovered that rutin enhances tomato resistance possible by initiating the generation of reactive oxygen species (ROS) and phosphorylation of mitogen-activated protein kinases (MPKs) related genes expression during the initial phase of invasion by B. cinerea. In addition, we also found that rutin might activate plant immunity by eliciting ethylene (ET) and jasmonic acid (JA)-mediated pathways. Therefore, plant immune inducer ZNC and rutin has bright application prospects and high utilization value to control gray mold.
Collapse
Affiliation(s)
- Haipeng Zhao
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China
| | - Xiangyu Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China
| | - Xiaomeng Chu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China
| | - Haimiao Zhang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China
| | - Xinyu Wang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China
| | - Xinwen Zhang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China
| | - Haoqi Liu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China
| | - Xiaoying Zhang
- Shandong Pengbo Biotechnology Co., Ltd., Taian, 271000, China
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China.
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China.
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China.
| |
Collapse
|
30
|
Long L, Zhao XT, Feng YM, Fan ZH, Zhao JR, Wu JF, Xu FC, Yuan M, Gao W. Profile of cotton flavonoids: Their composition and important roles in development and adaptation to adverse environments. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107866. [PMID: 37392667 DOI: 10.1016/j.plaphy.2023.107866] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023]
Abstract
Cotton is a commercial crop that is cultivated in more than 50 countries. The production of cotton has severely diminished in recent years owing to adverse environments. Thus, it is a high priority of the cotton industry to produce resistant cultivars to prevent diminished cotton yields and quality. Flavonoids comprise one of the most important groups of phenolic metabolites in plants. However, the advantage and biological roles of flavonoids in cotton have yet not been studied in depth. In this study, we performed a widely targeted metabolic study and identified 190 flavonoids in cotton leaves that span seven different classes with flavones and flavonols as the dominant groups. Furthermore, flavanone-3-hydroxylase was cloned and silenced to knock down flavonoid production. The results show that the inhibition of flavonoid biosynthesis affects the growth and development of cotton and causes semi-dwarfing in cotton seedlings. We also revealed that the flavonoids contribute to cotton defense against ultraviolet radiation and Verticillium dahliae. Moreover, we discuss the promising role of flavonoids in cotton development and defense against biotic and abiotic stresses. This study provides valuable information to study the variety and biological functions of flavonoids in cotton and will help to profile the advantages of flavonoids in cotton breeding.
Collapse
Affiliation(s)
- Lu Long
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Henan, 475004, PR China; School of Life Science, Henan University, Henan, 4750004, PR China; State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Henan, 475004, PR China
| | - Xiao-Tong Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Henan, 475004, PR China
| | - Ya-Mei Feng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Henan, 475004, PR China
| | - Zhi-Hao Fan
- School of Life Science, Henan University, Henan, 4750004, PR China
| | - Jing-Ruo Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Henan, 475004, PR China
| | - Jian-Feng Wu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Henan, 475004, PR China; School of Life Science, Henan University, Henan, 4750004, PR China
| | - Fu-Chun Xu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Henan, 475004, PR China; Changzhi Medical College, Shanxi, 046000, PR China
| | - Man Yuan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Henan, 475004, PR China
| | - Wei Gao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Henan, 475004, PR China; School of Life Science, Henan University, Henan, 4750004, PR China; State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Henan, 475004, PR China.
| |
Collapse
|
31
|
Li Z, Liu Q, Zhao K, Cao D, Cao Z, Zhao K, Ma Q, Zhai G, Hu S, Li Z, Wang K, Gong F, Ma X, Zhang X, Ren R, Qiu D, Zhao Y, Yin D. Dynamic DNA methylation modification in peanut seed development. iScience 2023; 26:107062. [PMID: 37534185 PMCID: PMC10391728 DOI: 10.1016/j.isci.2023.107062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/21/2023] [Accepted: 06/02/2023] [Indexed: 08/04/2023] Open
Abstract
Cytosine methylation is an important epigenetic modification involved in regulation of plant development. However, the epigenetic mechanisms governing peanut seed development remain unclear. Herein, we generated DNA methylation profiles of developmental seeds of peanut H2014 and its smaller seed mutant H1314 at 15 and 60 days after pegging (DAP, S1, S4). Accompanying seed development, globally elevated methylation was observed in both lines. The mutant had a higher methylation level of 31.1% than wild type at S4, and 27.1-35.9% of the differentially methylated regions (DMRs) between the two lines were distributed in promoter or genic regions at both stages. Integrated methylome and transcriptome analysis revealed important methylation variations closely associated with seed development. Furthermore, some genes showed significantly negative correlation of expression with the methylation level within promoter or gene body. The results provide insights into the roles of DNA methylation in peanut seed development.
Collapse
Affiliation(s)
- Zhongfeng Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Qian Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Kai Zhao
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Di Cao
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Zenghui Cao
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Kunkun Zhao
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Qian Ma
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Gaidan Zhai
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Sasa Hu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Zhan Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Kuopeng Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Fangping Gong
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Xingli Ma
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Xingguo Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Rui Ren
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Ding Qiu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Dongmei Yin
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| |
Collapse
|
32
|
Lu R, Song M, Wang Z, Zhai Y, Hu C, Perl A, Ma H. Independent flavonoid and anthocyanin biosynthesis in the flesh of a red-fleshed table grape revealed by metabolome and transcriptome co-analysis. BMC PLANT BIOLOGY 2023; 23:361. [PMID: 37454071 DOI: 10.1186/s12870-023-04368-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Red flesh is a desired fruit trait, but the regulation of red flesh formation in grape is not well understood. 'Mio Red' is a seedless table grape variety with light-red flesh and blue-purple skin. The skin color develops at veraison whereas the flesh color develops at a later stage of berry development. The flesh and skin flavonoid metabolomes and transcriptomes were analyzed. RESULTS A total of 161 flavonoids were identified, including 16 anthocyanins. A total of 66 flavonoids were found at significantly different levels in the flesh and skin (fold change ≥ 2 or ≤ 0.5, variable importance in projection (VIP) ≥ 1). The main anthocyanins in the flesh were pelargonidin and peonidin, and in the skin were peonidin, delphinidin, and petunidin. Transcriptome comparison revealed 57 differentially expressed structural genes of the flavonoid-metabolism pathway (log2fold change ≥ 1, FDR < 0.05, FPKM ≥ 1). Two differentially expressed anthocyanin synthase (ANS) genes were annotated, ANS2 (Vitvi02g00435) with high expression in flesh and ANS1 (Vitvi11g00565) in skin, respectively. One dihydro flavonol 4-reductase (DFR, Vitvi18g00988) gene was differentially expressed although high in both skin and flesh. Screened and correlation analysis of 12 ERF, 9 MYB and 3 bHLH genes. The Y1H and dual luciferase assays showed that MYBA1 highly activates the ANS2 promoter in flesh and that ERFCBF6 was an inhibitory, EFR23 and bHLH93 may activate the DFR gene. These genes may be involved in the regulation of berry flesh color. CONCLUSIONS Our study revealed that anthocyanin biosynthesis in grape flesh is independent of that in the skin. Differentially expressed ANS, MYB and ERF transcription factors provide new clues for the future breeding of table grapes that will provide the health benefits as red wine.
Collapse
Affiliation(s)
- Renxiang Lu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Miaoyu Song
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhe Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yanlei Zhai
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Chaoyang Hu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Avihai Perl
- Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Huiqin Ma
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
33
|
Cerqueira JVA, de Andrade MT, Rafael DD, Zhu F, Martins SVC, Nunes-Nesi A, Benedito V, Fernie AR, Zsögön A. Anthocyanins and reactive oxygen species: a team of rivals regulating plant development? PLANT MOLECULAR BIOLOGY 2023; 112:213-223. [PMID: 37351824 PMCID: PMC10352431 DOI: 10.1007/s11103-023-01362-4] [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: 09/30/2022] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Anthocyanins are a family of water-soluble vacuolar pigments present in almost all flowering plants. The chemistry, biosynthesis and functions of these flavonoids have been intensively studied, in part due to their benefit for human health. Given that they are efficient antioxidants, intense research has been devoted to studying their possible roles against damage caused by reactive oxygen species (ROS). However, the redox homeostasis established between antioxidants and ROS is important for plant growth and development. On the one hand, high levels of ROS can damage DNA, proteins, and lipids, on the other, they are also required for cell signaling, plant development and stress responses. Thus, a balance is needed in which antioxidants can remove excessive ROS, while not precluding ROS from triggering important cellular signaling cascades. In this article, we discuss how anthocyanins and ROS interact and how a deeper understanding of the balance between them could help improve plant productivity, nutritional value, and resistance to stress, while simultaneously maintaining proper cellular function and plant growth.
Collapse
Affiliation(s)
- João Victor A Cerqueira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Moab T de Andrade
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Diego D Rafael
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Feng Zhu
- Max-Planck-Institute for Molecular Plant Physiology, 14476, Potsdam, Germany
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National R&D Center for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Samuel V C Martins
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Vagner Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Alisdair R Fernie
- Max-Planck-Institute for Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Max-Planck-Institute for Molecular Plant Physiology, 14476, Potsdam, Germany
| |
Collapse
|
34
|
Xie D, Hao M, Zhao L, Chen X, Chen X, Jiang B, Ning S, Yuan Z, Zhang L, Shu K, Zhang Y, Liu D, Wu P. Transcriptomic analysis provides insight into the genetic regulation of shade avoidance in Aegilops tauschii. BMC PLANT BIOLOGY 2023; 23:336. [PMID: 37353759 DOI: 10.1186/s12870-023-04348-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: 12/11/2022] [Accepted: 06/14/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND Weeds are not only economically important but also fascinating models for studying the adaptation of species in human-mediated environments. Aegilops tauschii is the D-genome donor species of common wheat but is also a weed that influences wheat production. How shading stress caused by adjacent wheat plants affects Ae. tauschii growth is a fundamental scientific question but is also important in agriculture, such as for weed control and wheat breeding. RESULT The present study indicated that shade avoidance is a strategy of Ae. tauschii in response to shading stress. Ae. tauschii plants exhibited growth increases in specific organs, such as stem and leaf elongation, to avoid shading. However, these changes were accompanied by sacrificing the growth of other parts of the plants, such as a reduction in tiller number. The two reverse phenotype responses seem to be formed by systemically regulating the expression of different genes. Fifty-six genes involved in the regulation of cell division and cell expansion were found to be downregulated, and one key upstream negative regulator (RPK2) of cell division was upregulated under shading stress. On the other hand, the upregulated genes under shading stress were mainly enriched in protein serine/threonine kinase activity and carbon metabolism, which are associated with cell enlargement, signal transduction and energy supply. The transcription factor WRKY72 may be important in regulating genes in response to shading stress, which can be used as a prior candidate gene for further study on the genetic regulation of shade avoidance. CONCLUSIONS This study sheds new light on the gene expression changes and molecular processes involved in the response and avoidance of Ae. tauschii to shading stress, which may aid more effective development of shading stress avoidance or cultivars in wheat and other crops in the future.
Collapse
Affiliation(s)
- Die Xie
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Laibin Zhao
- Henan Provincial Key Laboratory of Hybrid Wheat, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Kai Shu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China.
| | - Peipei Wu
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China.
| |
Collapse
|
35
|
Ding K, Jia Z, Rui P, Fang X, Zheng H, Chen J, Yan F, Wu G. Proteomics Identified UDP-Glycosyltransferase Family Members as Pro-Viral Factors for Turnip Mosaic Virus Infection in Nicotiana benthamiana. Viruses 2023; 15:1401. [PMID: 37376700 DOI: 10.3390/v15061401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
Viruses encounter numerous host factors that facilitate or suppress viral infection. Although some host factors manipulated by viruses were uncovered, we have limited knowledge of the pathways hijacked to promote viral replication and activate host defense responses. Turnip mosaic virus (TuMV) is one of the most prevalent viral pathogens in many regions of the world. Here, we employed an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics approach to characterize cellular protein changes in the early stages of infection of Nicotiana benthamiana by wild type and replication-defective TuMV. A total of 225 differentially accumulated proteins (DAPs) were identified (182 increased and 43 decreased). Bioinformatics analysis showed that a few biological pathways were associated with TuMV infection. Four upregulated DAPs belonging to uridine diphosphate-glycosyltransferase (UGT) family members were validated by their mRNA expression profiles and their effects on TuMV infection. NbUGT91C1 or NbUGT74F1 knockdown impaired TuMV replication and increased reactive oxygen species production, whereas overexpression of either promoted TuMV replication. Overall, this comparative proteomics analysis delineates the cellular protein changes during early TuMV infection and provides new insights into the role of UGTs in the context of plant viral infection.
Collapse
Affiliation(s)
- Kaida Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhaoxing Jia
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Penghuan Rui
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xinxin Fang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| |
Collapse
|
36
|
Wu ZZ, Gan ZW, Zhang YX, Chen SB, Gan CD, Yang K, Yang JY. Transcriptomic and metabolomic perspectives for the growth of alfalfa (Medicago sativa L.) seedlings with the effect of vanadium exposure. CHEMOSPHERE 2023:139222. [PMID: 37343642 DOI: 10.1016/j.chemosphere.2023.139222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
Hitherto, the effect of vanadium on higher plant growth remains an open topic. Therefore, nontargeted metabolomic and RNA-Seq profiling were implemented to unravel the possible alteration in alfalfa seedlings subjected to 0.1 mg L-1 (B group) and 0.5 mg L-1 (C group) pentavalent vanadium [(V(V)] versus control (A group) in this study. Results revealed that vanadium exposure significantly altered some pivotal transcripts and metabolites. The number of differentially expressed genes (DEGs) markedly up- and down-regulated was 21 and 23 in B_vs_A, 27 and 33 in C_vs_A, and 24 and 43 in C_vs_B, respectively. The number for significantly up- and down-regulated differential metabolites was 17 and 15 in B_vs_A, 43 and 20 in C_vs_A, and 24 and 16 in C_vs_B, respectively. Metabolomics and transcriptomics co-analysis characterized three significantly enriched metabolic pathways in C_vs_A comparing group, viz., α-linolenic acid metabolism, flavonoid biosynthesis, and phenylpropanoid biosynthesis, from which some differentially expressed genes and differential metabolites participated. The metabolite of traumatic acid in α-linolenic acid metabolism and apigenin in flavonoid biosynthesis were markedly upregulated, while phenylalanine in phenylpropanoid biosynthesis was remarkably downregulated. The genes of allene oxide cyclase (AOC) and acetyl-CoA acyltransferase (fadA) in α-linolenic acid metabolism, and chalcone synthase (CHS), flavonoid 3'-monooxygenase (CYP75B1), and flavonol synthase (FLS) in flavonoid biosynthesis, and caffeoyl-CoA O-methyltransferase (CCoAOMT) in phenylpropanoid biosynthesis were significantly downregulated. While shikimate O-hydroxycinnamoyltransferase (HCT) in flavanoid and phenylpropanoid biosynthesis were conspicuously upregulated. Briefly, vanadium exposure induces a readjustment yielding in metabolite and the correlative synthetic precursors (transcripts/unigenes) in some branched metabolic pathways. This study provides a practical and in-depth perspective from transcriptomics and metabolomics in investigating the effects conferred by vanadium on plant growth and development.
Collapse
Affiliation(s)
- Zhen-Zhong Wu
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China; College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Zhi-Wei Gan
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - You-Xian Zhang
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Si-Bei Chen
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Chun-Dan Gan
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Kai Yang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Jin-Yan Yang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China.
| |
Collapse
|
37
|
Galić V, Anđelković V, Kravić N, Grčić N, Ledenčan T, Jambrović A, Zdunić Z, Nicolas S, Charcosset A, Šatović Z, Šimić D. Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels. BMC PLANT BIOLOGY 2023; 23:315. [PMID: 37316827 PMCID: PMC10265872 DOI: 10.1186/s12870-023-04336-2] [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: 01/25/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023]
Abstract
Southeast Europe (SEE) is a very important maize-growing region, comparable to the Corn belt region of the United States, with similar dent germplasm (dent by dent hybrids). Historically, this region has undergone several genetic material swaps, following the trends in the US, with one of the most significant swaps related to US aid programs after WWII. The imported accessions used to make double-cross hybrids were also mixed with previously adapted germplasm originating from several more distant OPVs, supporting the transition to single cross-breeding. Many of these materials were deposited at the Maize Gene Bank of the Maize Research Institute Zemun Polje (MRIZP) between the 1960s and 1980s. A part of this Gene Bank (572 inbreds) was genotyped with Affymetrix Axiom Maize Genotyping Array with 616,201 polymorphic variants. Data were merged with two other genotyping datasets with mostly European flint (TUM dataset) and dent (DROPS dataset) germplasm. The final pan-European dataset consisted of 974 inbreds and 460,243 markers. Admixture analysis showed seven ancestral populations representing European flint, B73/B14, Lancaster, B37, Wf9/Oh07, A374, and Iodent pools. Subpanel of inbreds with SEE origin showed a lack of Iodent germplasm, marking its historical context. Several signatures of selection were identified at chromosomes 1, 3, 6, 7, 8, 9, and 10. The regions under selection were mined for protein-coding genes and were used for gene ontology (GO) analysis, showing a highly significant overrepresentation of genes involved in response to stress. Our results suggest the accumulation of favorable allelic diversity, especially in the context of changing climate in the genetic resources of SEE.
Collapse
Affiliation(s)
- Vlatko Galić
- Agricultural Institute Osijek, Južno predgrađe 17, Osijek, HR31000, Croatia.
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Svetošimunska cesta 25, Zagreb, HR10000, Croatia.
| | - Violeta Anđelković
- Maize Research Institute Zemun Polje, Slobodana Bajića 1, Belgrade, 11185, Serbia
| | - Natalija Kravić
- Maize Research Institute Zemun Polje, Slobodana Bajića 1, Belgrade, 11185, Serbia
| | - Nikola Grčić
- Maize Research Institute Zemun Polje, Slobodana Bajića 1, Belgrade, 11185, Serbia
| | - Tatjana Ledenčan
- Agricultural Institute Osijek, Južno predgrađe 17, Osijek, HR31000, Croatia
| | - Antun Jambrović
- Agricultural Institute Osijek, Južno predgrađe 17, Osijek, HR31000, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Svetošimunska cesta 25, Zagreb, HR10000, Croatia
| | - Zvonimir Zdunić
- Agricultural Institute Osijek, Južno predgrađe 17, Osijek, HR31000, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Svetošimunska cesta 25, Zagreb, HR10000, Croatia
| | - Stéphane Nicolas
- GQE ‑ Le Moulon, INRAE, Univ. Paris‑Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif‑sur‑Yvette, 91190, France
| | - Alain Charcosset
- GQE ‑ Le Moulon, INRAE, Univ. Paris‑Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif‑sur‑Yvette, 91190, France
| | - Zlatko Šatović
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Svetošimunska cesta 25, Zagreb, HR10000, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, HR10000, Croatia
| | - Domagoj Šimić
- Agricultural Institute Osijek, Južno predgrađe 17, Osijek, HR31000, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Svetošimunska cesta 25, Zagreb, HR10000, Croatia
| |
Collapse
|
38
|
Usman B, Derakhshani B, Jung KH. Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2019. [PMID: 37653936 PMCID: PMC10221523 DOI: 10.3390/plants12102019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.
Collapse
Affiliation(s)
- Babar Usman
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Behnam Derakhshani
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Ki-Hong Jung
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
- Research Center for Plant Plasticity, Kyung Hee University, Yongin 17104, Republic of Korea
| |
Collapse
|
39
|
Takai T, Taniguchi Y, Takahashi M, Nagasaki H, Yamamoto E, Hirose S, Hara N, Akashi H, Ito J, Arai-Sanoh Y, Hori K, Fukuoka S, Sakai H, Tokida T, Usui Y, Nakamura H, Kawamura K, Asai H, Ishizaki T, Maruyama K, Mochida K, Kobayashi N, Kondo M, Tsuji H, Tsujimoto Y, Hasegawa T, Uga Y. MORE PANICLES 3, a natural allele of OsTB1/FC1, impacts rice yield in paddy fields at elevated CO 2 levels. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:729-742. [PMID: 36974032 DOI: 10.1111/tpj.16143] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/06/2023] [Indexed: 05/27/2023]
Abstract
Improving crop yield potential through an enhanced response to rising atmospheric CO2 levels is an effective strategy for sustainable crop production in the face of climate change. Large-sized panicles (containing many spikelets per panicle) have been a recent ideal plant architecture (IPA) for high-yield rice breeding. However, few breeding programs have proposed an IPA under the projected climate change. Here, we demonstrate through the cloning of the rice (Oryza sativa) quantitative trait locus for MORE PANICLES 3 (MP3) that the improvement in panicle number increases grain yield at elevated atmospheric CO2 levels. MP3 is a natural allele of OsTB1/FC1, previously reported as a negative regulator of tiller bud outgrowth. The temperate japonica allele advanced the developmental process in axillary buds, moderately promoted tillering, and increased the panicle number without negative effects on the panicle size or culm thickness in a high-yielding indica cultivar with large-sized panicles. The MP3 allele, containing three exonic polymorphisms, was observed in most accessions in the temperate japonica subgroups but was rarely observed in the indica subgroup. No selective sweep at MP3 in either the temperate japonica or indica subgroups suggested that MP3 has not been involved and utilized in artificial selection during domestication or breeding. A free-air CO2 enrichment experiment revealed a clear increase of grain yield associated with the temperate japonica allele at elevated atmospheric CO2 levels. Our findings show that the moderately increased panicle number combined with large-sized panicles using MP3 could be a novel IPA and contribute to an increase in rice production under climate change with rising atmospheric CO2 levels.
Collapse
Affiliation(s)
- Toshiyuki Takai
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Yojiro Taniguchi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, 305-8634, Japan
| | - Megumu Takahashi
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki, 305-8519, Japan
| | - Hideki Nagasaki
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Eiji Yamamoto
- Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Sakiko Hirose
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, 305-8634, Japan
| | - Naho Hara
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, 305-8634, Japan
| | - Hiroko Akashi
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - Jun Ito
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - Yumiko Arai-Sanoh
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Kiyosumi Hori
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Hidemitsu Sakai
- Institute for Agro-Environmental Sciences, NARO, Tsukuba, Ibaraki, 305-8604, Japan
| | - Takeshi Tokida
- Institute for Agro-Environmental Sciences, NARO, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yasuhiro Usui
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, 305-8666, Japan
| | | | - Kensuke Kawamura
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Hidetoshi Asai
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Takuma Ishizaki
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Kyonoshin Maruyama
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Keiichi Mochida
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Nagasaki, 852-8521, Japan
| | - Nobuya Kobayashi
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Motohiko Kondo
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yasuhiro Tsujimoto
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Toshihiro Hasegawa
- Institute for Agro-Environmental Sciences, NARO, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| |
Collapse
|
40
|
Zhao L, Liu H, Peng K, Huang X. Cold-upregulated glycosyltransferase gene 1 (OsCUGT1) plays important roles in rice height and spikelet fertility. JOURNAL OF PLANT RESEARCH 2023; 136:383-396. [PMID: 36952116 DOI: 10.1007/s10265-023-01455-7] [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: 01/24/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Glycosyltransferases (GTs) regulate many physiological processes and stress responses in plants. However, little is known about the function of GT in rice development. In this study, molecular analyses revealed that the expression of a rice GT gene (Cold-Upregulated Glycosyltransferase Gene 1, CUGT1) is developmentally controlled and stress-induced. OsCUGT1 was knocked out by using the clustered regularly interspaced short palindromic repeats (CRISPR) system to obtain the mutant oscugt1, which showed a severe dwarf and sterility phenotype. Further cytological analyses indicated that the dwarfism seen in the oscugt1 mutant might be caused by fewer and smaller cells. Histological pollen analysis suggests that the spikelet sterility in oscugt1 mutants may be caused by abnormal microsporogenesis. Moreover, multiple transgenic plants with knockdown of OsCUGT1 expression through RNA interference were obtained, which also showed obvious defects in plant height and fertility. RNA sequencing revealed that multiple biological processes associated with phenylpropanoid biosynthesis, cytokinin metabolism and pollen development are affected in the oscugt1 mutant. Overall, these results suggest that rice OsCUGT1 plays an essential role in rice development.
Collapse
Affiliation(s)
- Lanxin Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China
| | - Hui Liu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China
| | - Kangli Peng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China
| | - Xiaozhen Huang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China.
- College of Tea Sciences, Guizhou University, Guiyang, 550025, China.
| |
Collapse
|
41
|
Ramazan S, Jan N, John R. Comparative protein analysis of two maize genotypes with contrasting tolerance to low temperature. BMC PLANT BIOLOGY 2023; 23:183. [PMID: 37020183 PMCID: PMC10074880 DOI: 10.1186/s12870-023-04198-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Low temperature (LT) stress is one of the major environmental stress factors affecting the growth and yield of maize (Zea mays L.). Hence, it is important to unravel the molecular mechanisms behind LT stress tolerance to improve molecular breeding in LT tolerant genotypes. In the present study, two maize genotypes viz. Gurez local from Kashmir Himalaya and tropical grown GM6, were dissected for their LT stress response in terms of accumulation of differentially regulated proteins (DRPs). Leaf proteome analysis at three-leaf stage of maize seedlings subjected to LT stress of 6 °C for a total of 12 h duration was performed using two dimensional gel electrophoresis (2D-PAGE) followed by subsequent identification of the proteins involved. RESULTS After MALDI-TOF (Matrix-assisted laser desorption/ionization-time of flight) and bioinformatics analysis, 19 proteins were successfully identified in Gurez local, while as 10 proteins were found to get successful identification in GM6. The interesting observations from the present investigation is the identification of three novel proteins viz. threonine dehydratase biosynthetic chloroplastic, thylakoidal processing peptidase 1 chloroplastic, and nodulin-like protein, whose role in abiotic stress tolerance, in general, and LT stress, in particular, has not been reported so far. It is important to highlight here that most of LT responsive proteins including the three novel proteins were identified from Gurez local only, owing to its exceptional LT tolerance. From the protein profiles, obtained in both genotypes immediately after LT stress perception, it was inferred that stress responsive protein accumulation and their expression fashion help the Gurez local in seedling establishment and withstand unfavorable conditions as compared to GM6. This was inferred from the findings of pathway enrichment analysis like regulation of seed growth, timing of floral transition, lipid glycosylation, and aspartate family amino acid catabolic processes, besides other key stress defense mechanisms. However, in GM6, metabolic pathways enriched were found to be involved in more general processes including cell cycle DNA replication and regulation of phenylpropanoid metabolism. Furthermore, majority of the qRT-PCR results of the selected proteins demonstrated positive correlation between protein levels and transcript abundance, thereby strengthening our findings. CONCLUSIONS In conclusion, our findings reported majority of the identified proteins in Gurez local exhibiting up-regulated pattern under LT stress as compared to GM6. Furthermore, three novel proteins induced by LT stress were found in Gurez local, requiring further functional validation. Therefore, our results offer more insights for elucidating the molecular networks mediating LT stress tolerance in maize.
Collapse
Affiliation(s)
- Salika Ramazan
- Plant Molecular Biology Lab, Department of Botany, University of Kashmir, Srinagar, Kashmir, 190 006, India
| | - Nelofer Jan
- Plant Molecular Biology Lab, Department of Botany, University of Kashmir, Srinagar, Kashmir, 190 006, India
| | - Riffat John
- Plant Molecular Biology Lab, Department of Botany, University of Kashmir, Srinagar, Kashmir, 190 006, India.
| |
Collapse
|
42
|
Yan J, Qiu R, Wang K, Liu Y, Zhang W. Enhancing alfalfa resistance to Spodoptera herbivory by sequestering microRNA396 expression. PLANT CELL REPORTS 2023; 42:805-819. [PMID: 36757447 DOI: 10.1007/s00299-023-02993-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
KEY MESSAGE Sequestering microRNA396 by overexpression of MIM396 enhanced alfalfa resistance to Spodoptera litura larvae, which may be due to increased lignin content and enhanced low-molecular weight flavonoids and glucosinolates biosynthesis. Alfalfa (Medicago sativa), the most important leguminous forage crop, suffers from the outbreak of defoliator insects, especially Spodoptera litura, resulting in heavy losses in yield and forage quality. Here, we found that the expression of alfalfa microRNA396 (miR396) precursor genes and mature miR396 was significantly up-regulated in wounding treatment that simulates feeding injury by defoliator insects. To verify the function of miR396 in alfalfa resistance to insect, we generated MIM396 transgenic alfalfa plants with significantly down-regulated miR396 expression by Agrobacterium-mediated genetic transformation. The MIM396 transgenic alfalfa plants exhibited improved resistance to Spodoptera litura larvae with increased lignin content but decreased JA accumulation. Most of the miR396 putative target GRF genes were up-regulated in MIM396 transgenic lines, and responded to the wounding treatment. By RNA sequencing analysis, we found that the differentially expressed genes related to insect resistance between WT and MIM396 transgenic plants mainly clustered in biosynthesis pathways in lignin, flavonoids and glucosinolates. In addition to the phenotype of enhanced insect resistance, MIM396 transgenic plants also displayed reduced biomass yield and forage quality. Our results broaden the function of miR396 in alfalfa and provide genetic resources for studying alfalfa insect resistance.
Collapse
Affiliation(s)
- Jianping Yan
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Rumeng Qiu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kexin Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanrong Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
43
|
Fang T, Qian C, Daoura BG, Yan X, Fan X, Zhao P, Liao Y, Shi L, Chang Y, Ma XF. A novel TF molecular switch-mechanism found in two contrasting ecotypes of a psammophyte, Agriophyllum squarrosum, in regulating transcriptional drought memory. BMC PLANT BIOLOGY 2023; 23:167. [PMID: 36997861 PMCID: PMC10061855 DOI: 10.1186/s12870-023-04154-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Prior drought stress may change plants response patterns and subsequently increase their tolerance to the same condition, which can be referred to as "drought memory" and proved essential for plants well-being. However, the mechanism of transcriptional drought memory in psammophytes remains unclear. Agriophyllum squarrosum, a pioneer species on mobile dunes, is widely spread in Northern China's vast desert areas with outstanding ability of water use efficiency. Here we conducted dehydration-rehydration treatment on A. squarrosum semi-arid land ecotype AEX and arid land ecotype WW to dissect the drought memory mechanism of A. squarrosum, and to determine the discrepancy in drought memory of two contrasting ecotypes that had long adapted to water heterogeneity. RESULT Physiological traits monitoring unveiled the stronger ability and longer duration in drought memory of WW than that of AEX. A total of 1,642 and 1,339 drought memory genes (DMGs) were identified in ecotype AEX and WW, respectively. Furthermore, shared DMGs among A. squarrosum and the previously studied species depicted that drought memory commonalities in higher plants embraced pathways like primary and secondary metabolisms; while drought memory characteristics in A. squarrosum were mainly related to response to heat, high light intensity, hydrogen peroxide, and dehydration, which might be due to local adaptation to desert circumstances. Heat shock proteins (HSPs) occupied the center of the protein-protein interaction (PPI) network in drought memory transcription factors (TF), thus playing a key regulatory role in A. squarrosum drought memory. Co-expression analysis of drought memory TFs and DMGs uncovered a novel regulating module, whereby pairs of TFs might function as molecular switches in regulating DMG transforming between high and low expression levels, thus promoting drought memory reset. CONCLUSION Based on the co-expression analysis, protein-protein interaction prediction, and drought memory metabolic network construction, a novel regulatory module of transcriptional drought memory in A. squarrosum was hypothesized here, whereby recurrent drought signal is activated by primary TF switches, then amplified by secondary amplifiers, and thus regulates downstream complicated metabolic networks. The present research provided valuable molecular resources on plants' stress-resistance basis and shed light on drought memory in A. squarrosum.
Collapse
Affiliation(s)
- Tingzhou Fang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chaoju Qian
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
| | - Bachir Goudia Daoura
- Department of Biology, Faculty of Sciences and Technology, Dan Dicko Dankoulodo University, POBox 465, Maradi, Niger
| | - Xia Yan
- Key Laboratory of Eco-hydrology of Inland River Basin, Northwest Institute of Eco- Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000 China
| | - Xingke Fan
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
| | - Pengshu Zhao
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuqiu Liao
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Liang Shi
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuxiao Chang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Science, Shenzhen, 518000 China
| | - Xiao-Fei Ma
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000 China
| |
Collapse
|
44
|
Wang Q, Li S, Xu C, Hua A, Wang C, Xiong Y, Deng Q, Chen X, Yang T, Wan J, Ding ZY, Zhang BX, Yang X, Li Z. A novel lonidamine derivative targeting mitochondria to eliminate cancer stem cells by blocking glutamine metabolism. Pharmacol Res 2023; 190:106740. [PMID: 36958408 DOI: 10.1016/j.phrs.2023.106740] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/25/2023]
Abstract
Cancer stem cells (CSCs) have been blamed as the main culprit of tumor initiation, progression, metastasis, chemoresistance, and recurrence. However, few anti-CSCs agents have achieved clinical success so far. Here we report a novel derivative of lonidamine (LND), namely HYL001, which selectively and potently inhibits CSCs by targeting mitochondria, with 380-fold and 340-fold lower IC50 values against breast cancer stem cells (BCSCs) and hepatocellular carcinoma stem cells (HCSCs), respectively, compared to LND. Mechanistically, we reveal that HYL001 downregulates glutaminase (GLS) expression to block glutamine metabolism, blunt tricarboxylic acid cycle, and amplify mitochondrial oxidative stress, leading to apoptotic cell death. Therefore, HYL001 displays significant antitumor activity in vivo, both as a single agent and combined with paclitaxel. Furthermore, HYL001 represses CSCs of fresh tumor tissues derived from liver cancer patients. This study provides critical implications for CSCs biology and development of potent anti-CSCs drugs.
Collapse
Affiliation(s)
- Qiang Wang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Shiyou Li
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Chen Xu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Ao Hua
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Chong Wang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yuxuan Xiong
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Qingyuan Deng
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Xiang Chen
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Tian Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Jiangling Wan
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Ze-Yang Ding
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Bi-Xiang Zhang
- Hepatic Surgery Center and Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China; Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China; Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medical, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China; GBA Research Innovation Institute for Nanotechnology, Guangdong, 510530, P. R. China; Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Zifu Li
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China; Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China; Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medical, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China; Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China; Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China.
| |
Collapse
|
45
|
Fan R, Zhu C, Qiu D, Mao G, Mueller-Roeber B, Zeng J. Integrated transcriptomic and metabolomic analyses reveal key genes controlling flavonoid biosynthesis in Citrus grandis 'Tomentosa' fruits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:210-221. [PMID: 36724705 DOI: 10.1016/j.plaphy.2023.01.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/01/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
As a well-recognized traditional Chinese medicine (TCM), immature fruits of Citrus grandis 'Tomentosa' (CGT) serve to cure chronic cough in humans. Specialized metabolites including flavonoids may have contribute to this curing effect. Knowledge about the molecular mechanisms underlying flavonoid biosynthesis in 'Tomentosa' fruits will, therefore, support the breeding of varieties with improved medicinal properties. Hence, we profiled the transcriptomes and metabolites of the fruits of two contrasting C. grandis varieties, namely 'Zheng-Mao' ('ZM') used in TCM production, and a locally cultivated pomelo, namely 'Guang-Qing' ('GQ'), at four developmental stages. A total of 39 flavonoids, including 14 flavanone/flavone, 5 isoflavonoids, 12 flavonols, and 6 anthocyanins, were identified, and 16 of which were quantitatively determined in the fruits of the two varieties. We found that 'ZM' fruits contain more flavonoids than 'GQ'. Specifically, rhoifolin levels were significantly higher in 'ZM' than in 'GQ'. We annotated 31,510 genes, including 1,387 previously unknown ones, via transcriptome sequencing of 'ZM' and 'GQ.' A total of 646 genes were found to be differentially expressed between 'ZM' and 'GQ' throughout at all four fruit developmental stages, indicating that they are robust expression markers for future breeding programs. Weighted gene co-expression network analysis identified 18 modules. Combined transcriptional and metabolic analysis revealed 25 genes related to flavonoid biosynthesis and 16 transcriptional regulators (MYBs, bHLHs, WD40) that may be involved in the flavonoids biosynthesis in C. grandis 'Tomentosa' fruits.
Collapse
Affiliation(s)
- Ruiyi Fan
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
| | - Congyi Zhu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
| | - Diyang Qiu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
| | - Genlin Mao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
| | - Bernd Mueller-Roeber
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Golm, Germany; Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd., 4000, Plovdiv, Bulgaria.
| | - Jiwu Zeng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, China.
| |
Collapse
|
46
|
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.
Collapse
|
47
|
Marques I, Fernandes I, Paulo OS, Batista D, Lidon FC, Partelli F, DaMatta FM, Ribeiro-Barros AI, Ramalho JC. Overexpression of Water-Responsive Genes Promoted by Elevated CO 2 Reduces ROS and Enhances Drought Tolerance in Coffea Species. Int J Mol Sci 2023; 24:ijms24043210. [PMID: 36834624 PMCID: PMC9966387 DOI: 10.3390/ijms24043210] [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: 11/24/2022] [Revised: 01/23/2023] [Accepted: 01/29/2023] [Indexed: 02/10/2023] Open
Abstract
Drought is a major constraint to plant growth and productivity worldwide and will aggravate as water availability becomes scarcer. Although elevated air [CO2] might mitigate some of these effects in plants, the mechanisms underlying the involved responses are poorly understood in woody economically important crops such as Coffea. This study analyzed transcriptome changes in Coffea canephora cv. CL153 and C. arabica cv. Icatu exposed to moderate (MWD) or severe water deficits (SWD) and grown under ambient (aCO2) or elevated (eCO2) air [CO2]. We found that changes in expression levels and regulatory pathways were barely affected by MWD, while the SWD condition led to a down-regulation of most differentially expressed genes (DEGs). eCO2 attenuated the impacts of drought in the transcripts of both genotypes but mostly in Icatu, in agreement with physiological and metabolic studies. A predominance of protective and reactive oxygen species (ROS)-scavenging-related genes, directly or indirectly associated with ABA signaling pathways, was found in Coffea responses, including genes involved in water deprivation and desiccation, such as protein phosphatases in Icatu, and aspartic proteases and dehydrins in CL153, whose expression was validated by qRT-PCR. The existence of a complex post-transcriptional regulatory mechanism appears to occur in Coffea explaining some apparent discrepancies between transcriptomic, proteomic, and physiological data in these genotypes.
Collapse
Affiliation(s)
- Isabel Marques
- Plant-Environment Interactions and Biodiversity Lab (PlantStress & Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Isabel Fernandes
- cE3c—Center for Ecology, Evolution and Environmental Changes and CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Octávio S. Paulo
- cE3c—Center for Ecology, Evolution and Environmental Changes and CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Dora Batista
- Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Fernando C. Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal
| | - Fábio Partelli
- Centro Universitário do Norte do Espírito Santo (CEUNES), Departmento Ciências Agrárias e Biológicas (DCAB), Universidade Federal Espírito Santo (UFES), São Mateus 29932-540, ES, Brazil
| | - Fábio M. DaMatta
- Departamento de Biologia Vegetal, Universidade Federal Viçosa (UFV), Viçosa 36570-900, MG, Brazil
| | - Ana I. Ribeiro-Barros
- Plant-Environment Interactions and Biodiversity Lab (PlantStress & Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal
- Correspondence: (A.I.R.-B.); or (J.C.R.)
| | - José C. Ramalho
- Plant-Environment Interactions and Biodiversity Lab (PlantStress & Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal
- Correspondence: (A.I.R.-B.); or (J.C.R.)
| |
Collapse
|
48
|
Yang C, Xia L, Fu M, Chen Y, Kong X, Zhang S. DNA methylation-mediated phenylpropane and starch metabolism causes male poplars to be more tolerant to nitrogen deficiency than females. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 195:144-154. [PMID: 36638604 DOI: 10.1016/j.plaphy.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Nitrogen (N) is an essential nutrient for plant growth and development. Dioecious plants, especially perennial plants, are often faced with a shortage of N supply in nature. Poplar is one of the most important dioecious and perennials species. Due to the different ecological functions, female and male poplars adopt different adaptation strategies to N limitation. However, the regulation in epigenetic mechanism is poorly understood on sexes. Here, the integrative analysis of whole-genome bisulfite sequencing (WGBS), RNA sequencing, and plant physiological analysis on female and male Populus cathayana were performed. We found that N deficiency reprograms methylation in both sexes, and the CG and CHH methylation types played critical roles in female and male poplars, respectively. Induced by DNA methylation, N-deficient males had a stronger phenylpropanoid synthesis pathway and less anthocyanin accumulation than females, which not only strengthened the N cycle but also reduced the defense cost of males. In addition, compared with male poplars, females accumulated more starch to expend excess energy under N limited condition. Additionally, DNA methylation also mediated hormone signalling involved in anthocyanin synthesis and starch metabolism. Therefore, our study reveals new molecular evidences that male poplars are more tolerant to N deficiency than females, which provides a reference for ecological adaptability of forest trees.
Collapse
Affiliation(s)
- Congcong Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Linchao Xia
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Mingyue Fu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yao Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xiangge Kong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Sheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| |
Collapse
|
49
|
Berdugo-Cely JA, Céron-Lasso MDS, Yockteng R. Phenotypic and molecular analyses in diploid and tetraploid genotypes of Solanum tuberosum L. reveal promising genotypes and candidate genes associated with phenolic compounds, ascorbic acid contents, and antioxidant activity. FRONTIERS IN PLANT SCIENCE 2023; 13:1007104. [PMID: 36743552 PMCID: PMC9889998 DOI: 10.3389/fpls.2022.1007104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/08/2022] [Indexed: 06/18/2023]
Abstract
Potato tubers contain biochemical compounds with antioxidant properties that benefit human health. However, the genomic basis of the production of antioxidant compounds in potatoes has largely remained unexplored. Therefore, we report the first genome-wide association study (GWAS) based on 4488 single nucleotide polymorphism (SNP) markers and the phenotypic evaluation of Total Phenols Content (TPC), Ascorbic Acid Content (AAC), and Antioxidant Activity (AA) traits in 404 diverse potato genotypes (84 diploids and 320 tetraploids) conserved at the Colombian germplasm bank that administers AGROSAVIA. The concentration of antioxidant compounds correlated to the skin tuber color and ploidy level. Especially, purple-blackish tetraploid tubers had the highest TPC (2062.41 ± 547.37 mg GAE), while diploid pink-red tubers presented the highest AA (DDPH: 14967.1 ± 4687.79 μmol TE; FRAP: 2208.63 ± 797.35 mg AAE) and AAC (4.52 mg ± 0.68 AA). The index selection allowed us to choose 20 promising genotypes with the highest values for the antioxidant compounds. Genome Association mapping identified 58 SNP-Trait Associations (STAs) with single-locus models and 28 Quantitative Trait Nucleotide (QTNs) with multi-locus models associated with the evaluated traits. Among models, eight STAs/QTNs related to TPC, AAC, and AA were detected in common, flanking seven candidate genes, from which four were pleiotropic. The combination in one population of diploid and tetraploid genotypes enabled the identification of more genetic associations. However, the GWAS analysis implemented independently in populations detected some regions in common between diploids and tetraploids not detected in the mixed population. Candidate genes have molecular functions involved in phenolic compounds, ascorbic acid biosynthesis, and antioxidant responses concerning plant abiotic stress. All candidate genes identified in this study can be used for further expression analysis validation and future implementation in marker-assisted selection pre-breeding platforms targeting fortified materials. Our study further revealed the importance of potato germplasm conserved in national genebanks, such as AGROSAVIA's, as a valuable genetic resource to improve existing potato varieties.
Collapse
Affiliation(s)
- Jhon A. Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Turipaná, Km 13 vía Montería-Cereté, Montería, Córdoba, Colombia
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
| | - María del Socorro Céron-Lasso
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, Paris, France
| |
Collapse
|
50
|
Li Q, Shen H, Yuan S, Dai X, Yang C. miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2023; 13:1094459. [PMID: 36714724 PMCID: PMC9875070 DOI: 10.3389/fpls.2022.1094459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.
Collapse
Affiliation(s)
- Qian Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Heng Shen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shoujuan Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xigang Dai
- School of Life Sciences, Jianghan University/Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|