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Lee S, Fu F, Liao CJ, Mewa DB, Adeyanju A, Ejeta G, Lisch D, Mengiste T. Broad-spectrum fungal resistance in sorghum is conferred through the complex regulation of an immune receptor gene embedded in a natural antisense transcript. THE PLANT CELL 2022; 34:1641-1665. [PMID: 35018449 PMCID: PMC9048912 DOI: 10.1093/plcell/koab305] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/09/2021] [Indexed: 06/12/2023]
Abstract
Sorghum (Sorghum bicolor), the fifth most widely grown cereal crop globally, provides food security for millions of people. Anthracnose caused by the fungus Colletotrichum sublineola is a major disease of sorghum worldwide. We discovered a major fungal resistance locus in sorghum composed of the nucleotide-binding leucine-rich repeat receptor gene ANTHRACNOSE RESISTANCE GENE1 (ARG1) that is completely nested in an intron of a cis-natural antisense transcript (NAT) gene designated CARRIER OF ARG1 (CARG). Susceptible genotypes express CARG and two alternatively spliced ARG1 transcripts encoding truncated proteins lacking the leucine-rich repeat domains. In resistant genotypes, elevated expression of an intact allele of ARG1, attributed to the loss of CARG transcription and the presence of miniature inverted-repeat transposable element sequences, resulted in broad-spectrum resistance to fungal pathogens with distinct virulence strategies. Increased ARG1 expression in resistant genotypes is also associated with higher histone H3K4 and H3K36 methylation. In susceptible genotypes, lower ARG1 expression is associated with reduced H3K4 and H3K36 methylation and increased expression of NATs of CARG. The repressive chromatin state associated with H3K9me2 is low in CARG-expressing genotypes within the CARG exon and higher in genotypes with low CARG expression. Thus, ARG1 is regulated by multiple mechanisms and confers broad-spectrum, strong resistance to fungal pathogens.
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Affiliation(s)
| | | | - Chao-Jan Liao
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Demeke B Mewa
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Adedayo Adeyanju
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
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2
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Lei B, Chang W, Zhao H, Zhang K, Yu J, Yu S, Cai K, Zhang J, Lu K. Nitrogen application and differences in leaf number retained after topping affect the tobacco (Nicotiana tabacum) transcriptome and metabolome. BMC PLANT BIOLOGY 2022; 22:38. [PMID: 35045826 PMCID: PMC8767696 DOI: 10.1186/s12870-022-03426-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Agronomic treatments such as the application of nitrogen fertilizer and topping (removal of the inflorescence and top leaves) cause substantial changes in plant metabolism. To explore these changes, we conducted comparative transcriptomic and metabolomic analyses of leaves collected from four positions along the stem on plants exposed to two nitrogen doses and with different numbers of leaves retained after topping in tobacco (Nicotiana tabacum). RESULTS We identified 13,330 unique differentially expressed genes and 32 differentially abundant metabolites. Through RNA-seq and WGCNA analyze, we constructed 2 co-expression networks (green and blue) highly correlation to N application and leaf number retained, predicted a hub gene NtGER3 may play an important role in N metabolism related to amino acid (cysteine) through CK pathway in tobacco leaves, NtARFs may participated in modulating the auxin signal and N in bottom leaves and NtRAP2.12 as key gene involved in N regulation by ethylene pathway. What's more, our data prove C/N transformation and balance affect the "source - flow - sink" redistribution and remobilization in tobacco during growth and development process. CONCLUSIONS Overall, this comparative transcriptomics study provides novel insight into the complex molecular mechanisms underlying plant responses to different levels of nitrogen application and the number of leaves remaining after topping in plants.
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Affiliation(s)
- Bo Lei
- Molecular Genetics Key Laboratory of China Tobacco, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Wei Chang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Huina Zhao
- Molecular Genetics Key Laboratory of China Tobacco, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Jing Yu
- Molecular Genetics Key Laboratory of China Tobacco, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Kai Cai
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Jie Zhang
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China.
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Bolortuya B, Kawabata S, Yamagami A, Davaapurev BO, Takahashi F, Inoue K, Kanatani A, Mochida K, Kumazawa M, Ifuku K, Jigjidsuren S, Battogtokh T, Udval G, Shinozaki K, Asami T, Batkhuu J, Nakano T. Transcriptome Analysis of Chloris virgata, Which Shows the Fastest Germination and Growth in the Major Mongolian Grassland Plant. FRONTIERS IN PLANT SCIENCE 2021; 12:684987. [PMID: 34262584 PMCID: PMC8275185 DOI: 10.3389/fpls.2021.684987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/26/2021] [Indexed: 06/13/2023]
Abstract
Plants in Mongolian grasslands are exposed to short, dry summers and long, cold winters. These plants should be prepared for fast germination and growth activity in response to the limited summer rainfall. The wild plant species adapted to the Mongolian grassland environment may allow us to explore useful genes, as a source of unique genetic codes for crop improvement. Here, we identified the Chloris virgata Dornogovi accession as the fastest germinating plant in major Mongolian grassland plants. It germinated just 5 h after treatment for germination initiation and showed rapid growth, especially in its early and young development stages. This indicates its high growth potential compared to grass crops such as rice and wheat. By assessing growth recovery after animal bite treatment (mimicked by cutting the leaves with scissors), we found that C. virgata could rapidly regenerate leaves after being damaged, suggesting high regeneration potential against grazing. To analyze the regulatory mechanism involved in the high growth potential of C. virgata, we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. Through de novo transcriptome assembly with the RNA-seq reads from whole organ samples of C. virgata at the germination stage (2 days after germination, DAG), early young development stage (8 DAG), young development stage (17 DAG), and adult development stage (28 DAG), we identified 21,589 unified transcripts (contigs) and found that 19,346 and 18,156 protein-coding transcripts were homologous to those in rice and Arabidopsis, respectively. The best-aligned sequences were annotated with gene ontology groups. When comparing the transcriptomes across developmental stages, we found an over-representation of genes involved in growth regulation in the early development stage in C. virgata. Plant development is tightly regulated by phytohormones such as brassinosteroids, gibberellic acid, abscisic acid, and strigolactones. Moreover, our transcriptome map demonstrated the expression profiles of orthologs involved in the biosynthesis of these phytohormones and their signaling networks. We discuss the possibility that C. virgata phytohormone signaling and biosynthesis genes regulate early germination and growth advantages. Comprehensive transcriptome information will provide a useful resource for gene discovery and facilitate a deeper understanding of the diversity of the regulatory systems that have evolved in C. virgata while adapting to severe environmental conditions.
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Affiliation(s)
- Byambajav Bolortuya
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | | | - Ayumi Yamagami
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Bekh-Ochir Davaapurev
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Asaka Kanatani
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Minoru Kumazawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kentaro Ifuku
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Sodnomdarjaa Jigjidsuren
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Tugsjargal Battogtokh
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Gombosuren Udval
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
| | - Javzan Batkhuu
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Takeshi Nakano
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
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Li M, Qin Y, Wang C, Wang K, Deng Z, Xu W, Xiang P, Ma LQ. Total and bioaccessible heavy metals in cabbage from major producing cities in Southwest China: health risk assessment and cytotoxicity. RSC Adv 2021; 11:12306-12314. [PMID: 35423743 PMCID: PMC8697116 DOI: 10.1039/d1ra01440d] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
Green leafy vegetables are economical and nutritious, but they may be contaminated with heavy metals. In this study, we assessed the total and bioaccessible concentrations of As, Cd, Pb and Cr in a popular vegetable cabbage (Brassica oleracea) from four major producing cities in Yunnan, Southwest China. With the mean concentrations of As, Cd, Pb and Cr being 0.24, 0.20, 0.32 and 1.28 mg kg-1, the As, Cd and Pb concentrations were within the limits of 0.2-0.5 mg kg-1 based on Chinese National Standards and the WHO/FAO, but Cr concentration was 2.6-times greater than the limit of 0.5 mg kg-1. Based on an in vitro bioaccessibility assay of the Solubility Bioaccessibility Research Consortium (SBRC), As bioaccessibility was the lowest at 11% while those of Cd, Pb and Cr were much greater at 68-87%. The estimated daily intake (EDI) of metals through cabbage ingestion was similar for children and adults. Among the four metals, only Cr's EDI at 2.29-1.87 exceeded 1 based on total and bioaccessible concentrations. The high Cr concentration at 1.28 mg kg-1 coupled with its high bioaccessibility at 67.5% makes Cr of concern in cabbage. However, human gastrointestinal cells exposed to the gastric digesta with high bioaccessible heavy metals and risky EDI, showed no obvious cytotoxicity, indicating that existing models based on total or bioaccessible heavy metals may overestimate their human health risk. Taken together, to accurately assess the human health risk of heavy metals in cabbage, both total/bioaccessible concentrations and the gastrointestinal cell responses should be considered.
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Affiliation(s)
- Mengying Li
- Institute of Environmental Remediation and Human Health, School of Ecology and Environment, Southwest Forestry University Kunming 650224 China
| | - Yishu Qin
- Institute of Environmental Remediation and Human Health, School of Ecology and Environment, Southwest Forestry University Kunming 650224 China
| | - Chengchen Wang
- Institute of Environmental Remediation and Human Health, School of Ecology and Environment, Southwest Forestry University Kunming 650224 China
| | - Kun Wang
- Institute of Environmental Remediation and Human Health, School of Ecology and Environment, Southwest Forestry University Kunming 650224 China
| | - Zhihua Deng
- Institute of Environmental Remediation and Human Health, School of Ecology and Environment, Southwest Forestry University Kunming 650224 China
| | - Wumei Xu
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University Kunming 650500 China
| | - Ping Xiang
- Institute of Environmental Remediation and Human Health, School of Ecology and Environment, Southwest Forestry University Kunming 650224 China
| | - Lena Q Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University Hangzhou 310058 China
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Chang W, Zhao H, Yu S, Yu J, Cai K, Sun W, Liu X, Li X, Yu M, Ali S, Zhang K, Qu C, Lei B, Lu K. Comparative transcriptome and metabolomic profiling reveal the complex mechanisms underlying the developmental dynamics of tobacco leaves. Genomics 2020; 112:4009-4022. [PMID: 32650092 DOI: 10.1016/j.ygeno.2020.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/31/2020] [Accepted: 07/02/2020] [Indexed: 12/22/2022]
Abstract
Although the leaf is the most important photosynthetic organ in most plants, many of the molecular mechanisms underlying leaf developmental dynamics remain to be explored. To better understand the transcriptional regulatory mechanisms involved in leaf development, we conducted comparative transcriptomic and metabolomic analysis of leaves from seven positions on tobacco (Nicotiana tabacum) plants. A total of 35,622 unique differentially expressed genes and 79 metabolites were identified. A time-series expression analysis detected two interesting transcriptional profiles, one comprising 10,197 genes that displayed continual up-regulation during leaf development and another comprising 4696 genes that displayed continual down-regulation. Combining these data with co-expression network results identified four important regulatory networks involved in photorespiration and the tricarboxylic acid cycle; these networks may regulate carbon/nitrogen balance during leaf development. We also found that the transcription factor NtGATA5 acts as a hub associated with C and N metabolism and chloroplast development during leaf development through regulation of phytohormones. Furthermore, we investigated the transcriptional dynamics of genes involved in the auxin, cytokinin, and jasmonic acid biosynthesis and signaling pathways during tobacco leaf development. Overall, our study greatly expands the understanding of the regulatory network controlling developmental dynamics in plant leaves.
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Affiliation(s)
- Wei Chang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Huina Zhao
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Jing Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Kai Cai
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Xumei Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Xiaodong Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Mengna Yu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Shahzad Ali
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Bo Lei
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; College of Life Sciences, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China; College of Life Sciences, Yangtze University, Jingzhou 434025, Hubei, China.
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Wang X, Gong C, Zhao Y, Shen L. Transcriptome and Resistance-Related Genes Analysis of Botrytis cinerea B05.10 Strain to Different Selective Pressures of Cyprodinil and Fenhexamid. Front Microbiol 2018; 9:2591. [PMID: 30425701 PMCID: PMC6218599 DOI: 10.3389/fmicb.2018.02591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/11/2018] [Indexed: 01/10/2023] Open
Abstract
The pathogen Botrytis cinerea is a very dangerous pathogen that infects many economically important crops such as grape, strawberry, tomato, and eggplant. Cyprodinil, a pyrimidine amine fungicide, and fenhexamid, an amide fungicide, are new reagents for controlling gray mold with special efficacy. It is necessary to understand the change trends in the toxicological and physiological characteristics of B. cinerea with successive selective pressures of cyprodinil and fenhexamid to elongate the serving life of these fungicides for effective disease control. The toxicities of cyprodinil and fenhexamid at successive concentrations of EC25, EC50 and EC75 on B. cinerea strain BO5.10 were assayed along with mycelial growth-inhibition capacity. The results showed that the EC50 value of the cyprodinil-treated F27 strain increased approximately 18-fold, whereas of which in the fenhexamid-treated F27 strain increased only 3-fold compared with that of the F0 strain. The conductivities and glycerinum contents of the strains resistant to cyprodinil and fenhexamid were obviously enhanced; in contrast, the oxalic acid contents were decreased compared with those in the F0 strain. The transcriptomes of the F27 control (T01), cyprodinil-treated (T02) and fenhexamid- treated (T03) strains were analyzed, and the expression levels of functional genes in the T02 and T03 strains were significantly increased compared with those in the T01 strain; these results were further validated using qRT-PCR. The results indicated that the relative expression of two genes encoding mixed-functional oxidases (MFOs) BC1G_16062 and BC1G_16084, two genes encoding transmembrane proteins BC1G_12366 and BC1G_13768, two genes encoding Zinc finger proteins BC1G_13764 and BC1G_10483,one gene encoding citrate synthase enzyme BC1G_09151, one gene encoding gluconolactonase BC1G_15612 in the T02 and T03 strains and one gene encoding lysophospholipids enzyme BC1G_04893 in the T3 strain increased substantially compared with that in the T1 strain (P < 0.01). Functional prediction analysis of upregulated gene expression and structural verification was also performed, and the results showed that BC1G_10483 was a ZnF_C2HC transcriptional regulator interacting with the Sp1 element of these genes to respond to the pressures from cyprodinil and fenhexamid. Our results could contribute to a better understanding of the resistance mechanism of B. cinerea against cyprodinil and fenhexamid.
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Wang G, Weng L, Li M, Xiao H. Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato. Int J Mol Sci 2017; 18:E475. [PMID: 28257093 PMCID: PMC5372491 DOI: 10.3390/ijms18030475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/07/2017] [Accepted: 02/13/2017] [Indexed: 12/27/2022] Open
Abstract
Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops.
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Affiliation(s)
- Guixiang Wang
- University of Chinese Academy of Sciences, 19A Yuquan Rd., Beijing 100049, China.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
| | - Lin Weng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
| | - Meng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
| | - Han Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
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A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus. Sci Rep 2016; 6:36452. [PMID: 27811979 PMCID: PMC5095561 DOI: 10.1038/srep36452] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/14/2016] [Indexed: 01/02/2023] Open
Abstract
Harvest index (HI), the ratio of seed mass to total biomass of the aboveground plant parts, is an important trait for harvestable yield of crops. Unfortunately, HI of Brassica napus is lower than that of other economically important crops. To identify candidate genes associated with high HI, a genome-wide association study of HI and four HI-related traits was conducted with 520 B. napus accessions cultivated in both Yunnan and Chongqing. We detected 294 single nucleotide polymorphisms significantly associated with the abovementioned traits, including 79 SNPs that affected two or more traits. Differentially expressed genes between extremely high- and low-HI accessions were identified in 8 tissues at two cultivated regions. Combination of linkage disequilibrium and transcriptome analyses revealed 33 functional candidate genes located within the confidence intervals of significant SNPs associated with more than one trait, such as SHOOT GRAVITROPISM 5 (Bna.SGR5), ATP-CITRATE LYASE A-3 (Bna.ACLA-3) and CAROTENOID CLEAVAGE DIOXYGENASE 1 (Bna.CCD1), their orthologs in the Arabidopsis thaliana have been shown to play key roles in photosynthesis, inflorescence, and silique development. Our results provide insight into the molecular mechanisms underlying establishment of high-HI B. napus and lay a foundation for characterization of candidate genes aimed at developing high-HI B. napus varieties.
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Hu R, Zhu X, Xiang S, Zhan Y, Zhu M, Yin H, Zhou Q, Zhu L, Zhang X, Liu Z. Comparative transcriptome analysis revealed the genotype specific cold response mechanism in tobacco. Biochem Biophys Res Commun 2016; 469:535-41. [PMID: 26692485 DOI: 10.1016/j.bbrc.2015.12.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 12/22/2022]
Abstract
Cold stress is a major adverse environmental factor that affects plant growth, development, productivity and quality. In the present study, comparative genome-wide transcriptome analysis on two tobacco (Nicotiana tobacum L.) cultivars, cold-tolerant NC567 and cold-sensitive Taiyan8, was performed using RNA-seq technology. After the first assembly, total length of unigenes is from 101,308,644 to 123,781,795 bp, the N50 length is from 1357 to 1475 bp, and 152,688 unigenes in NC567 and 144,160 unigenes in Taiyan8 were identified, respectively. Functional classification of cold-responsive (COR) genes showed that the genes involved in cell wall metabolism, transcription factors, ubiquitin-proteasome system (UPS) and signaling are over-represented, and the COR genes are specifically induced during cold stress in NC567. Pathway analysis revealed the significant enrichment of the COR genes in plant circadian clock. Taken together, the present study suggested the positive roles of the highly induced expression of the COR genes and the conserved mechanism of circadian clock related genes in tobacco response to cold stress, and provided some valuable genes for crop improvement to cope with cold stress.
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Affiliation(s)
- Risheng Hu
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China
| | - Xianxin Zhu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Shipeng Xiang
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Youguo Zhan
- Kunming Municipal Tobacco Company, Kunming, 650000, China
| | - Mingdong Zhu
- Hunan Rice Research Institute, Changsha, 410125, China
| | - Hanqi Yin
- Shanghai Biotechnology Corporation, Shanghai, 201203, China
| | - Qingming Zhou
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Lieshu Zhu
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Xianwen Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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Fukushima A, Nakamura M, Suzuki H, Yamazaki M, Knoch E, Mori T, Umemoto N, Morita M, Hirai G, Sodeoka M, Saito K. Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling. FRONTIERS IN PLANT SCIENCE 2016; 7:1883. [PMID: 28066454 PMCID: PMC5167740 DOI: 10.3389/fpls.2016.01883] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/29/2016] [Indexed: 05/07/2023]
Abstract
The genus Physalis in the Solanaceae family contains several species of benefit to humans. Examples include P. alkekengi (Chinese-lantern plant, hôzuki in Japanese) used for medicinal and for decorative purposes, and P. peruviana, also known as Cape gooseberry, which bears an edible, vitamin-rich fruit. Members of the Physalis genus are a valuable resource for phytochemicals needed for the development of medicines and functional foods. To fully utilize the potential of these phytochemicals we need to understand their biosynthesis, and for this we need genomic data, especially comprehensive transcriptome datasets for gene discovery. We report the de novo assembly of the transcriptome from leaves of P. alkekengi and P. peruviana using Illumina RNA-seq technologies. We identified 75,221 unigenes in P. alkekengi and 54,513 in P. peruviana. All unigenes were annotated with gene ontology (GO), Enzyme Commission (EC) numbers, and pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We classified unigenes encoding enzyme candidates putatively involved in the secondary metabolism and identified more than one unigenes for each step in terpenoid backbone- and steroid biosynthesis in P. alkekengi and P. peruviana. To measure the variability of the withanolides including physalins and provide insights into their chemical diversity in Physalis, we also analyzed the metabolite content in leaves of P. alkekengi and P. peruviana at five different developmental stages by liquid chromatography-mass spectrometry. We discuss that comprehensive transcriptome approaches within a family can yield a clue for gene discovery in Physalis and provide insights into their complex chemical diversity. The transcriptome information we submit here will serve as an important public resource for further studies of the specialized metabolism of Physalis species.
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- *Correspondence: Atsushi Fukushima, Kazuki Saito,
| | - Michimi Nakamura
- Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Hideyuki Suzuki
- Department of Biotechnology Research, Kazusa DNA Research InstituteChiba, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Eva Knoch
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Naoyuki Umemoto
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Masaki Morita
- Synthetic Organic Chemistry Laboratory, RIKENSaitama, Japan
| | - Go Hirai
- Synthetic Organic Chemistry Laboratory, RIKENSaitama, Japan
- RIKEN Center for Sustainable Resource ScienceSaitama, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKENSaitama, Japan
- RIKEN Center for Sustainable Resource ScienceSaitama, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
- *Correspondence: Atsushi Fukushima, Kazuki Saito,
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11
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Qu C, Fu F, Liu M, Zhao H, Liu C, Li J, Tang Z, Xu X, Qiu X, Wang R, Lu K. Comparative Transcriptome Analysis of Recessive Male Sterility (RGMS) in Sterile and Fertile Brassica napus Lines. PLoS One 2015; 10:e0144118. [PMID: 26656530 PMCID: PMC4675519 DOI: 10.1371/journal.pone.0144118] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/15/2015] [Indexed: 11/24/2022] Open
Abstract
The recessive genetic male sterility (RGMS) system plays a key role in the production of hybrid varieties in self-pollinating B. napus plants, and prevents negative cytoplasmic effects. However, the complete molecular mechanism of the male sterility during male-gametogenesis in RGMS remains to be determined. To identify transcriptomic changes that occur during the transition to male sterility in RGMS, we examined the male sterile line WSLA and male fertile line WSLB, which are near-isogenic lines (NILs) differing only in the fertility trait. We evaluated the phenotypic features and sterility stage using anatomical analysis. Comparative RNA sequencing analysis revealed that 3,199 genes were differentially expressed between WSLA and WSLB. Many of these genes are mainly involved in biological processes related to flowering, including pollen tube development and growth, pollen wall assembly and modification, and pollen exine formation and pollination. The transcript profiles of 93 genes associated with pollen wall and anther development were determined by quantitative RT-PCR in different flower parts, and classified into the following three major clades: 1) up-regulated in WSLA plants; 2) down-regulated in WSLA plants; and 3) down-regulated in buds, but have a higher expression in stigmas of WSLA than in WSLB. A subset of genes associated with sporopollenin accumulation were all up-regulated in WSLA. An excess of sporopollenin results in defective pollen wall formation, which leads to male sterility in WSLA. Some of the genes identified in this study are candidates for future research, as they could provide important insight into the molecular mechanisms underlying RGMS in WSLA.
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Affiliation(s)
- Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.,Food and Bioproduct science, University of Saskatchewan, 51 Campus Drive, S7N 5A8, Saskatoon, SK, Canada
| | - Fuyou Fu
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, S7N 02X, Saskatoon SK, Canada
| | - Miao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China
| | - Chuan Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China
| | - Zhanglin Tang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China
| | - Xiao Qiu
- Food and Bioproduct science, University of Saskatchewan, 51 Campus Drive, S7N 5A8, Saskatoon, SK, Canada
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China
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12
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Abstract
The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.
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Reddy MM, Ulaganathan K. Nitrogen Nutrition, Its Regulation and Biotechnological Approaches to Improve Crop Productivity. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/ajps.2015.618275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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