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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.
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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
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Yang Y, Ma X, Xia H, Wang L, Chen S, Xu K, Yang F, Zou Y, Wang Y, Zhu J, Li T, Luo Z, Hu S, Liao Z, Luo L, Yu S. Natural variation of Alfin-like family affects seed size and drought tolerance in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1176-1193. [PMID: 36219491 DOI: 10.1111/tpj.16003] [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: 02/10/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The Alfin-like (AL) family is a group of small plant-specific transcriptional factors involved in abiotic stresses in dicotyledon. In an early study, we found an AL gene in rice that was associated with grain yield under drought stress. However, little information is known about the AL family in rice. In this study, AL genes in the rice genome were identified, and the OsAL proteins were found to locate in the nucleus and have no transcriptional self-activation activity. The expression of the OsALs was regulated by different environmental stimulations and plant hormones. Association and domestication analysis revealed that natural variation of most OsALs was significantly associated with yield traits, drought resistance and divergence in grain size in indica and japonica rice varieties. Hap1 of OsAL7.1 and Hap7 of OsAL11 were favorable haplotypes of seed weight and germination under osmotic stress. Furthermore, osal7.1 and osal11 mutants have larger seeds and are more sensitive to abscisic acid and mannitol during germination stage. Overexpressing of OsAL7.1 and OsAL11 in rice weakened the tolerance to drought in the adult stage. Thus, our work provides informative knowledge for exploring and harnessing haplotype diversity of OsALs to improve yield stability under drought stress.
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Affiliation(s)
- Yunan Yang
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- The Research Center for Plant Functional Genes and Tissue Culture Technology of Jiangxi Agricultural University, 1101# Zhimin Avenue, Nanchang, Jiangxi, 330045, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Lei Wang
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Shoujun Chen
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Kai Xu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Fangwen Yang
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Yuqiao Zou
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Yulan Wang
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Jinmin Zhu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- The Research Center for Plant Functional Genes and Tissue Culture Technology of Jiangxi Agricultural University, 1101# Zhimin Avenue, Nanchang, Jiangxi, 330045, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Zhi Luo
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Songping Hu
- The Research Center for Plant Functional Genes and Tissue Culture Technology of Jiangxi Agricultural University, 1101# Zhimin Avenue, Nanchang, Jiangxi, 330045, China
| | - Zhigang Liao
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
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3
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Gour P, Kansal S, Agarwal P, Mishra BS, Sharma D, Mathur S, Raghuvanshi S. Variety-specific transcript accumulation during reproductive stage in drought-stressed rice. PHYSIOLOGIA PLANTARUM 2022; 174:e13585. [PMID: 34652858 DOI: 10.1111/ppl.13585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/23/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
The divergence of natural stress tolerance mechanisms between species is an intriguing phenomenon. To study it in rice, a comparative transcriptome analysis was carried out in 'heading' stage tissue (flag leaf, panicles and roots) of Nagina 22 (N22; drought-tolerant) and IR64 (drought-sensitive) plants subjected to field drought. Interestingly, N22 showed almost double the number of differentially expressed genes (DEGs) than IR64. Many DEGs colocalized within drought-related QTLs responsible for grain yield and drought tolerance and also associated with drought tolerance and critical drought-related plant traits such as leaf rolling, trehalose content, sucrose and cellulose content. Besides, co-expression analysis of the DEGs revealed several 'hub' genes known to actively regulate drought stress response. Strikingly, 1366 DEGs, including 21 'hub' genes, showed a distinct opposite regulation in the two rice varieties under similar drought conditions. Annotation of these variety-specific DEGs (VS-DEGs) revealed that they are distributed in various biological pathways. Furthermore, 103 VS-DEGs were found to physically interact with over 1300 genes, including 32 that physically interact with other VS-DEGs as well. The promoter region of these genes has sequence variations among the two rice varieties, which might be in part responsible for their unique expression pattern.
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Affiliation(s)
- Pratibha Gour
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Shivani Kansal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Priyanka Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Deepika Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, New Delhi, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice ( Oryza sativa L.). PLANTS 2021; 10:plants10040716. [PMID: 33917162 PMCID: PMC8067883 DOI: 10.3390/plants10040716] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 11/17/2022]
Abstract
Rice is an important grain that is the staple food for most of the world's population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Therefore, to ensure success in breeding programs for drought tolerant rice, QTLs (quantitative trait loci) of interest must be stable in a variety of plant genotypes and environments. This study identified stable QTLs in rice chromosomes in a variety of backgrounds and environments and conducted a meta-QTL analysis of stable QTLs that have been reported by previous research for use in breeding programs. A total of 653 QTLs for drought tolerance in rice from 27 genetic maps were recorded for analysis. The QTLs recorded were related to 13 traits in rice that respond to drought. Through the use of BioMercartor V4.2, a consensus map containing QTLs and molecular markers were generated using 27 genetic maps that were extracted from the previous 20 studies and meta-QTL analysis was conducted on the consensus map. A total of 70 MQTLs were identified and a total of 453 QTLs were mapped into the meta-QTL areas. Five meta-QTLs from chromosome 1 (MQTL 1.5 and MQTL 1.6), chromosome 2 (MQTL2.1 and MQTL 2.2) and chromosome 3 (MQTL 3.1) were selected for functional annotation as these regions have high number of QTLs and include many traits in rice that respond to drought. A number of genes in MQTL1.5 (268 genes), MQTL1.6 (640 genes), MQTL 2.1 (319 genes), MQTL 2.2 (19 genes) and MQTL 3.1 (787 genes) were annotated through Blast2GO. Few major proteins that respond to drought stress were identified in the meta-QTL areas which are Abscisic Acid-Insensitive Protein 5 (ABI5), the G-box binding factor 4 (GBF4), protein kinase PINOID (PID), histidine kinase 2 (AHK2), protein related to autophagy 18A (ATG18A), mitochondrial transcription termination factor (MTERF), aquaporin PIP 1-2, protein detoxification 48 (DTX48) and inositol-tetrakisphosphate 1-kinase 2 (ITPK2). These proteins are regulatory proteins involved in the regulation of signal transduction and gene expression that respond to drought stress. The meta-QTLs derived from this study and the genes that have been identified can be used effectively in molecular breeding and in genetic engineering for drought resistance/tolerance in rice.
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Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11101124. [PMID: 32987927 PMCID: PMC7650634 DOI: 10.3390/genes11101124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
Rice (Oryza sativa L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and efficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in differential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of differential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield.
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Donde R, Mohapatra S, Baksh SKY, Padhy B, Mukherjee M, Roy S, Chattopadhyay K, Anandan A, Swain P, Sahoo KK, Singh ON, Behera L, Dash SK. Identification of QTLs for high grain yield and component traits in new plant types of rice. PLoS One 2020; 15:e0227785. [PMID: 32673318 PMCID: PMC7365460 DOI: 10.1371/journal.pone.0227785] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 06/11/2020] [Indexed: 11/18/2022] Open
Abstract
A panel of 60 genotypes comprising New Plant Types (NPTs) along with indica, tropical and temperate japonica genotypes was phenotypically evaluated for four seasons in irrigated situation for grain yield per se and component traits. Twenty NPT genotypes were found promising with an average grain yield varying from 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 8% within genotypes, 68% among the genotypes within the population and 24% among the populations were observed (AMOVA). This information may help in identification of potential parents for development of transgressive segregants with very high yield. The association analysis using GLM and MLM models led to the identification of 30 and 10 SSR markers associated with 70 and 16 QTLs, respectively. Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely tiller number (qTL-6.1, qTL-11.1, qTL-4.1), panicle length (qPL-1.1, qPL-5.1, qPL-7.1, qPL-8.1), flag leaf length (qFLL-8.1, qFLL-9.1), flag leaf width (qFLW-6.2, qFLW-5.1, qFLW-8.1, qFLW-7.1), total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight (qTGW-a1.1, qTGW-a9.2, qTGW-5.1, qTGW-8.1), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se (qYLD-5.1, qYLD-6.1a, qYLD-11.1).Some of the SSRs were co-localized with more than two traits. The highest co-localization was identified with RM5709 linked to nine traits, followed by RM297 with five traits. Similarly, RM5575, RM204, RM168, RM112, RM26499 and RM22899 were also recorded to be co-localized with more than one trait and could be rated as important for marker-assisted backcross breeding programs, for pyramiding of these QTLs for important yield traits, to produce new-generation rice for prospective increment in yield potentiality and breaking yield ceiling.
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Affiliation(s)
- Ravindra Donde
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Shibani Mohapatra
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - S. K. Yasin Baksh
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Barada Padhy
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Mitadru Mukherjee
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Somnath Roy
- ICAR-NRRI, Regional Research Station (CRURRS), Hazaribagh, Jharkhand
| | | | - A. Anandan
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Padmini Swain
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | | | - Onkar Nath Singh
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
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Kaur V, Yadav SK, Wankhede DP, Pulivendula P, Kumar A, Chinnusamy V. Cloning and characterization of a gene encoding MIZ1, a domain of unknown function protein and its role in salt and drought stress in rice. PROTOPLASMA 2020; 257:475-487. [PMID: 31786672 DOI: 10.1007/s00709-019-01452-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 10/22/2019] [Indexed: 05/19/2023]
Abstract
Dwindling fresh water resources and climate change poses serious threats to rice production. Roots play crucial role in sensing water gradient and directing growth of the plant towards water through a mechanism called hydrotropism. Since very little information is available on root hydrotropism in major food crops, this study was carried out to clone and characterize an ortholog of Arabidopsis MIZU-KUSSEI1 (MIZ1) from rice. Contrasting rice genotypes for drought and salt tolerance were selected based on phenotyping for root traits. Nagina 22 and CR-262-4 were identified as most tolerant and Pusa Sugandh 5 and Pusa Basmati 1121 were identified as most susceptible varieties for both drought and salt stresses. Allele mining of MIZ1 in these varieties identified a 12 bp Indel but did not show specific allelic association with stress tolerance. Analysis of allelic variation of OsMIZ1 in 3024 rice genotypes of 3K genome lines using Rice SNP-Seek database revealed 49 InDels. Alleles with the 12 bp deletions were significantly prevalent in indica group as compared to that of japonica group. Real-time RT-PCR analysis revealed that OsMIZ1 expression levels were upregulated significantly in tolerant cv. Nagina 22 and CR-262-4 under osmotic stress, while under salt stress, it was significantly upregulated only in CR-262-4 but maintained in Nagina 22 under salt stress. However, in the roots of susceptible genotypes, OsMIZ1 expression decreased under both the stresses. These results highlight the possible involvement of OsMIZ1 in drought and salt stress tolerance in rice. Furthermore, expression studies using publically available resources showed that enhanced expression of OsMIZ1 is regulated in response to disease infections, mineral deficiency, and heavy metal stresses and is also expressed in reproductive tissues in addition to roots. These findings indicate potential involvement of MIZ1 in developmental and stress response processes in rice.
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Affiliation(s)
- Vikender Kaur
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India.
| | - Shashank K Yadav
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | | | - Pranusha Pulivendula
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Ashok Kumar
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.
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Wen X, Wang J, Zhang D, Wang Y. A Gene Regulatory Network Controlled by BpERF2 and BpMYB102 in Birch under Drought Conditions. Int J Mol Sci 2019; 20:ijms20123071. [PMID: 31234595 PMCID: PMC6627136 DOI: 10.3390/ijms20123071] [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: 05/07/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022] Open
Abstract
Gene expression profiles are powerful tools for investigating mechanisms of plant stress tolerance. Betula platyphylla (birch) is a widely distributed tree, but its drought-tolerance mechanism has been little studied. Using RNA-Seq, we identified 2917 birch genes involved in its response to drought stress. These drought-responsive genes include the late embryogenesis abundant (LEA) family, heat shock protein (HSP) family, water shortage-related and ROS-scavenging proteins, and many transcription factors (TFs). Among the drought-induced TFs, the ethylene responsive factor (ERF) and myeloblastosis oncogene (MYB) families were the most abundant. BpERF2 and BpMYB102, which were strongly induced by drought and had high transcription levels, were selected to study their regulatory networks. BpERF2 and BpMYB102 both played roles in enhancing drought tolerance in birch. Chromatin immunoprecipitation combined with qRT-PCR indicated that BpERF2 regulated genes such as those in the LEA and HSP families, while BpMYB102 regulated genes such as Pathogenesis-related Protein 1 (PRP1) and 4-Coumarate:Coenzyme A Ligase 10 (4CL10). Multiple genes were regulated by both BpERF2 and BpMYB102. We further characterized the function of some of these genes, and the genes that encode Root Primordium Defective 1 (RPD1), PRP1, 4CL10, LEA1, SOD5, and HSPs were found to be involved in drought tolerance. Therefore, our results suggest that BpERF2 and BpMYB102 serve as transcription factors that regulate a series of drought-tolerance genes in B. platyphylla to improve drought tolerance.
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Affiliation(s)
- Xuejing Wen
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China.
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jingxin Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.
| | - Daoyuan Zhang
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China.
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China.
| | - Yucheng Wang
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China.
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China.
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9
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Phule AS, Barbadikar KM, Maganti SM, Seguttuvel P, Subrahmanyam D, Babu MBBP, Kumar PA. RNA-seq reveals the involvement of key genes for aerobic adaptation in rice. Sci Rep 2019; 9:5235. [PMID: 30918284 PMCID: PMC6437204 DOI: 10.1038/s41598-019-41703-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 03/01/2019] [Indexed: 12/24/2022] Open
Abstract
Adaptation of rice to the aerobic condition is needed to cope with the water scarcity as well as to ensure sustainable yield in future. To understand the molecular mechanisms responsible for aerobic adaptation in rice, we performed RNA-seq analysis of root and shoot i.e. developing panicle tissues at panicle initiation stage in two cultivars adapted to aerobic (CR Dhan 202) and traditional transplanted anaerobic (BPT 5204) conditions. The RNA-seq data emanated from 1.65 billion clean reads with approximately 37 million reads per sample. The number of differentially expressed transcripts was higher in the root than that in the shoot under both aerobic and anaerobic conditions. The transcription factors viz. MADS4, MADS5, MADS6, MADS7, MADS15 and transporters involved in sugar (SWEET3A) and nutrient uptake (PHT1;6, MDR-like ABC and vacuolar iron transporter homolog 2) were highly and uniquely expressed in the aerobic adapted cultivar (AAC) CR Dhan 202 under aerobic condition indicating their role in adaptation. The hormones such as ethylene and abscisic acid might be significantly involved in imparting aerobic adaptation. The higher expression of root related genes in the AAC under aerobic conditions suggests the involvement and sensitivity of roots to the water limiting condition. The metabolic activities are also more pronounced in the roots which impart rigorous plant establishment under the aerobic condition. The presence of alternative splice variants in the transcripts viz. Tetratrico peptide repeat (TPR) domain containing protein and GOLDEN2-LIKE1 (GLK1) additionally confirms that post transcriptional regulation is also crucial for aerobic adaptation. The QTLs related to root traits and stress tolerance harboring the uniquely expressed genes, which were identified in the present study can be deployed in molecular breeding programs to develop elite, high yielding aerobic rice cultivars.
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Affiliation(s)
- Amol S Phule
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Hyderabad, 30, India
| | - Kalyani M Barbadikar
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - Sheshu Madhav Maganti
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - P Seguttuvel
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - D Subrahmanyam
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - M B B Prasad Babu
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - Polumetla A Kumar
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India.
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Mohd Ikmal A, Nurasyikin Z, Kumar A, Noraziyah AAS. Evaluation of morpho-physiological traits of MRQ74 pyramided lines with drought yield QTLs. EUPHYTICA 2018; 214:98. [DOI: 10.1007/s10681-018-2178-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/13/2018] [Indexed: 09/02/2023]
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