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Jin X, Ackah M, Acheampong A, Zhang Q, Wang L, Lin Q, Qiu C, Zhao W. Genome-Wide Identification of Candidate Genes Associated with Heat Stress in Mulberry ( Morus alba L.). Curr Issues Mol Biol 2023; 45:4151-4167. [PMID: 37232733 DOI: 10.3390/cimb45050264] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023] Open
Abstract
Mulberry (Morus alba L.) is an economically important plant for the silk industry and has the possibility of contributing immensely to Chinese pharmacopeia because of its health benefits. Domesticated silkworms feed only on mulberry leaves, meaning that the worms' survival depends on the mulberry tree. Mulberry production is threatened by climate change and global warming. However, the regulatory mechanisms of mulberry responses to heat are poorly understood. We performed transcriptome analysis of high-temperature-stressed (42 °C) M. alba seedlings using RNA-Seq technologies. A total of 703 differentially expressed genes (DEGs) were discovered from 18,989 unigenes. Among these, 356 were up-regulated, and 347 were down-regulated. KEGG analysis revealed that most DEGs were enriched in valine, leucine and isoleucine degradation, and in starch and sucrose metabolism, alpha-linolenic acid metabolism, carotenoid biosynthesis and galactose metabolism, among others. In addition, TFs such as the NAC, HSF, IAA1, MYB, AP2, GATA, WRKY, HLH and TCP families were actively involved in response to high temperatures. Moreover, we used RT-qPCR to confirm the expression changes of eight genes under heat stress observed in the RNA-Seq analysis. This study provides M. alba transcriptome profiles under heat stress and provides theoretical bases to researchers for better understanding mulberry heat response mechanisms and breeding heat-tolerant mulberry plants.
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Affiliation(s)
- Xin Jin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Michael Ackah
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Adolf Acheampong
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Qiaonan Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Lei Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Qiang Lin
- Guangxi Sericultural Research Institute, Guangxi Zhuang Autonomous Regin, Nanning 530007, China
| | - Changyu Qiu
- Guangxi Sericultural Research Institute, Guangxi Zhuang Autonomous Regin, Nanning 530007, China
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
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Wang J, Gao C, Li L, Cao W, Dong R, Ding X, Zhu C, Chu Z. Transgenic RXLR Effector PITG_15718.2 Suppresses Immunity and Reduces Vegetative Growth in Potato. Int J Mol Sci 2019; 20:ijms20123031. [PMID: 31234322 PMCID: PMC6627464 DOI: 10.3390/ijms20123031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 01/25/2023] Open
Abstract
Phytophthora infestans causes the severe late blight disease of potato. During its infection process, P. infestans delivers hundreds of RXLR (Arg-x-Leu-Arg, x behalf of any one amino acid) effectors to manipulate processes in its hosts, creating a suitable environment for invasion and proliferation. Several effectors interact with host proteins to suppress host immunity and inhibit plant growth. However, little is known about how P. infestans regulates the host transcriptome. Here, we identified an RXLR effector, PITG_15718.2, which is upregulated and maintains a high expression level throughout the infection. Stable transgenic potato (Solanum tuberosum) lines expressing PITG_15718.2 show enhanced leaf colonization by P. infestans and reduced vegetative growth. We further investigated the transcriptional changes between three PITG_15718.2 transgenic lines and the wild type Désirée by using RNA sequencing (RNA-Seq). Compared with Désirée, 190 differentially expressed genes (DEGs) were identified, including 158 upregulated genes and 32 downregulated genes in PITG_15718.2 transgenic lines. Eight upregulated and nine downregulated DEGs were validated by real-time RT-PCR, which showed a high correlation with the expression level identified by RNA-Seq. These DEGs will help to explore the mechanism of PITG_15718.2-mediated immunity and growth inhibition in the future.
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Affiliation(s)
- Jiao Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- Shandong Provincial Key Laboratory of Vegetable Disease and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China.
| | - Cungang Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
| | - Long Li
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
| | - Weilin Cao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- College of Life Science, Shandong Agricultural University, Tai'an, 271018, China.
| | - Ran Dong
- Shandong Provincial Key Laboratory of Vegetable Disease and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China.
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- Shandong Provincial Key Laboratory of Vegetable Disease and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China.
| | - Changxiang Zhu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- College of Life Science, Shandong Agricultural University, Tai'an, 271018, China.
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
- College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
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Shi J, Yan B, Lou X, Ma H, Ruan S. Comparative transcriptome analysis reveals the transcriptional alterations in heat-resistant and heat-sensitive sweet maize (Zea mays L.) varieties under heat stress. BMC PLANT BIOLOGY 2017; 17:26. [PMID: 28122503 PMCID: PMC5267381 DOI: 10.1186/s12870-017-0973-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/10/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Despite the heat-related physiology and heat-shock proteins in maize have been extensively studied, little is known about the transcriptome profiling of how the maize varieties with different genotypes responding to high temperatures. Seedling mortality of Xiantian 5 (XT) is significantly lower than that of Zhefengtian (ZF) when exposed to high temperature (42 °C for 6 h) and followed by a recovery growth (25 °C for one week). Therefore, we performed a transcriptome analysis using the total RNA extracted from the leaves of XT and ZF that were previously subjected to heat stress at 42 °C for 0 h, 0.5 h, and 3 h, respectively. RESULTS A total of 516 commonly up-regulated and 1,261 commonly down-regulated genes were identified among XT/ZF, XT0.5/ZF0.5 and XT3/ZF3 using transcriptome analysis. Gene Ontology classification of the 516 up-regulated genes showed that their encoded proteins were significantly assigned to 18 cellular components, and were classified into 9 functional categories, and were involved in 9 biological processes. Most of proteins encoded by up-regulated genes were localized in chloroplast and its structural components, and involved in multiple biological processes associated with photosynthesis, indicating that these chloroplast proteins play an important role in increasing heat tolerance in sweet maize. While the proteins encoded by 1,261 down-regulated genes were significantly assigned to 31 cellular components, and were classified into 3 functional categories, and were involved in 9 biological processes. Interestingly, these proteins were involved in a series of biological processes from gene expression to translation, suggesting that lowering these processes may contribute to improved heat resistance in sweet maize. The up-regulated genes were identified to be involved in 36 distinct metabolic pathways, of which the most significant ones was secondary metabolite biosynthetic pathway. While the down-regulated genes were identified to be involved in 23 distinct metabolic pathways, of which the most significant ones were found in ribosome. Quantitative real-time PCR analysis demonstrated that 5 genes involved in the biosynthesis of secondary metabolites and photosynthesis in XT have higher abundance than those in ZF, whereas 5 ribosome genes in XT showed lower abundance than those in ZF. In addition, heat-tolerant sweet maize may keep at lower growth level than heat-sensitive one through dowregulating expression of genes related to zeatin and brassinosteroid biosynthesis to better regulate heat stress responses. CONCLUSIONS Comparative transcriptomic profiling reveals transcriptional alterations in heat-resistant and heat-sensitive sweet maize varieties under heat stress, which provides a new insight into underlying molecular mechanism of maize in response to heat stress.
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Affiliation(s)
- Jiang Shi
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 People’s Republic of China
| | - Baiyuan Yan
- Jiande seed management station, Hangzhou, 311600 People’s Republic of China
| | - Xuping Lou
- Xianshan Institute of Agricultural Sciences, Hangzhou, 330100 People’s Republic of China
| | - Huasheng Ma
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 People’s Republic of China
| | - Songlin Ruan
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 People’s Republic of China
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 People’s Republic of China
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Chen Y, Chen C, Tan Z, Liu J, Zhuang L, Yang Z, Huang B. Functional Identification and Characterization of Genes Cloned from Halophyte Seashore Paspalum Conferring Salinity and Cadmium Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:102. [PMID: 26904068 PMCID: PMC4746305 DOI: 10.3389/fpls.2016.00102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/19/2016] [Indexed: 05/25/2023]
Abstract
Salinity-affected and heavy metal-contaminated soils limit the growth of glycophytic plants. Identifying genes responsible for superior tolerance to salinity and heavy metals in halophytes has great potential for use in developing salinity- and Cd-tolerant glycophytes. The objective of this study was to identify salinity- and Cd-tolerance related genes in seashore paspalum (Paspalum vaginatum), a halophytic perennial grass species, using yeast cDNA expression library screening method. Based on the Gateway-compatible vector system, a high-quality entry library was constructed, which contained 9.9 × 10(6) clones with an average inserted fragment length of 1.48 kb representing a 100% full-length rate. The yeast expression libraries were screened in a salinity-sensitive and a Cd-sensitive yeast mutant. The screening yielded 32 salinity-tolerant clones harboring 18 salinity-tolerance genes and 20 Cd-tolerant clones, including five Cd-tolerance genes. qPCR analysis confirmed that most of the 18 salinity-tolerance and five Cd-tolerance genes were up-regulated at the transcript level in response to salinity or Cd stress in seashore paspalum. Functional analysis indicated that salinity-tolerance genes from seashore paspalum could be involved mainly in photosynthetic metabolism, antioxidant systems, protein modification, iron transport, vesicle traffic, and phospholipid biosynthesis. Cd-tolerance genes could be associated with regulating pathways that are involved in phytochelatin synthesis, HSFA4-related stress protection, CYP450 complex, and sugar metabolism. The 18 salinity-tolerance genes and five Cd-tolerance genes could be potentially used as candidate genes for genetic modification of glycophytic grass species to improve salinity and Cd tolerance and for further analysis of molecular mechanisms regulating salinity and Cd tolerance.
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Affiliation(s)
- Yu Chen
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Chuanming Chen
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Zhiqun Tan
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Jun Liu
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Lili Zhuang
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Zhimin Yang
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers, The State University of New JerseyNew Brunswick, NJ, USA
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Goyer A, Hamlin L, Crosslin JM, Buchanan A, Chang JH. RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection. BMC Genomics 2015; 16:472. [PMID: 26091899 PMCID: PMC4475319 DOI: 10.1186/s12864-015-1666-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/29/2015] [Indexed: 11/21/2022] Open
Abstract
Background Potato virus Y (PVY) is one of the most important plant viruses affecting potato production. The interactions between potato and PVY are complex and the outcome of the interactions depends on the potato genotype, the PVY strain, and the environmental conditions. A potato cultivar can induce resistance to a specific PVY strain, yet be susceptible to another. How a single potato cultivar responds to PVY in both compatible and incompatible interactions is not clear. Results In this study, we used RNA-sequencing (RNA-Seq) to investigate and compare the transcriptional changes in leaves of potato upon inoculation with PVY. We used two potato varieties: Premier Russet, which is resistant to the PVY strain O (PVYO) but susceptible to the strain NTN (PVYNTN), and Russet Burbank, which is susceptible to all PVY strains that have been tested. Leaves were inoculated with PVYO or PVYNTN, and samples were collected 4 and 10 h post inoculation (hpi). A larger number of differentially expressed (DE) genes were found in the compatible reactions compared to the incompatible reaction. For all treatments, the majority of DE genes were down-regulated at 4 hpi and up-regulated at 10 hpi. Gene Ontology enrichment analysis showed enrichment of the biological process GO term “Photosynthesis, light harvesting” specifically in PVYO-inoculated Premier Russet leaves, while the GO term “nucleosome assembly” was largely overrepresented in PVYNTN-inoculated Premier Russet leaves and PVYO-inoculated Russet Burbank leaves but not in PVYO-inoculated Premier Russet leaves. Fewer genes were DE over 4-fold in the incompatible reaction compared to the compatible reactions. Amongst these, five genes were DE only in PVYO-inoculated Premier Russet leaves, and all five were down-regulated. These genes are predicted to encode for a putative ABC transporter, a MYC2 transcription factor, a VQ-motif containing protein, a non-specific lipid-transfer protein, and a xyloglucan endotransglucosylase-hydroxylase. Conclusions Our results show that the incompatible and compatible reactions in Premier Russet shared more similarities, in particular during the initial response, than the compatible reactions in the two different hosts. Our results identify potential key processes and genes that determine the fate of the reaction, compatible or incompatible, between PVY and its host. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1666-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aymeric Goyer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA. .,Hermiston Agricultural Research and Extension Center, Hermiston, OR, USA. .,Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
| | | | | | - Alex Buchanan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA. .,Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
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Aulakh SS, Veilleux RE, Tang G, Flinn BS. Characterization of a potato activation-tagged mutant, nikku, and its partial revertant. PLANTA 2015; 241:1481-1495. [PMID: 25772042 DOI: 10.1007/s00425-015-2272-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
A potato mutant with a strong stress-response phenotype, and a partial mutant revertant, were characterized. Gene expression patterns and DNA cytosine methylation varied between these and wild-type, indicating a role for DNA cytosine methylation changes in the gene expression and visible phenotypes. Morphological and molecular studies were conducted to compare potato cv. Bintje, a Bintje activation-tagged mutant (nikku), and nikku revertant phenotype plants. Morphological studies revealed that nikku plants exhibited an extremely dwarf phenotype, had small hyponastic leaves, were rootless, and infrequently produced small tubers compared to wild-type Bintje. The overall phenotype was suggestive of a constitutive stress response, which was further supported by the greater expression level of several stress-responsive genes in nikku. Unlike the nikku mutant, the revertant exhibited near normal shoot elongation, larger leaves and consistent rooting. The reversion appeared partial, and was not the result of a loss of 35S enhancer copies from the original nikku mutant. Southern blot analyses indicated the presence of a single T-DNA insertion on chromosome 12 in the mutant. Gene expression studies comparing Bintje, nikku and revertant phenotype plants indicated transcriptional activation/repression of several genes flanking both sides of the insertion in the mutant, suggesting that activation tagging had pleiotropic effects in nikku. In contrast, gene expression levels for many, but not all, of the same genes in the revertant were similar to Bintje, indicating some reversion at the gene expression level as well. DNA methylation studies indicated differences in cytosine methylation status of the 35S enhancers between the nikku mutant and its revertant. In addition, global DNA cytosine methylation varied between Bintje, the nikku mutant and the revertant, suggesting involvement in gene expression changes, as well as mutant phenotype.
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