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Mohanty JK, Yadav A, Narnoliya L, Thakro V, Nayyar H, Dixit GP, Jha UC, Vara Prasad PV, Agarwal P, Parida SK. A Next-Generation Combinatorial Genomic Strategy Scans Genomic Loci Governing Heat Stress Tolerance in Chickpea. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39360859 DOI: 10.1111/pce.15186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 09/03/2024] [Accepted: 09/17/2024] [Indexed: 10/05/2024]
Abstract
In the wake of rising earth temperature, chickpea crop production is haunted by the productivity crisis. Chickpea, a cool season legume manifests tolerance in several agro-physiological level, which is complex quantitative in nature, and regulated by multiple genes and genetic networks. Understanding the molecular genetic basis of this tolerance and identifying key regulators can leverage chickpea breeding against heat stress. This study employed a genomics-assisted breeding strategy utilizing multi-locus GWAS to identify 10 key genomic regions linked to traits contributing to heat stress tolerance in chickpea. These loci subsequently delineated few key candidates and hub regulatory genes, such as RAD23b, CIPK25, AAE19, CK1 and WRKY40, through integrated genomics, transcriptomics and interactive analyses. The differential transcript accumulation of these identified candidates in contrasting chickpea accessions suggests their potential role in heat stress tolerance. Differential ROS accumulation along with their scavengers' transcript abundance aligning with the expression of identified candidates in the contrasting chickpea accessions persuade their regulatory significance. Additionally, their functional significance is ascertained by heterologous expression and subsequent heat stress screening. The high confidence genomic loci and the superior genes and natural alleles delineated here has great potential for swift genomic interventions to enhance heat resilience and yield stability in chickpea.
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Affiliation(s)
- Jitendra K Mohanty
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Antima Yadav
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Laxmi Narnoliya
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Virevol Thakro
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Girish P Dixit
- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
- Sustainable Intensification Innovation Lab, Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - Pinky Agarwal
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Swarup K Parida
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
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Chandra T, Jaiswal S, Tomar RS, Iquebal MA, Kumar D. Realizing visionary goals for the International Year of Millet (IYoM): accelerating interventions through advances in molecular breeding and multiomics resources. PLANTA 2024; 260:103. [PMID: 39304579 DOI: 10.1007/s00425-024-04520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
MAIN CONCLUSION Leveraging advanced breeding and multi-omics resources is vital to position millet as an essential "nutricereal resource," aligning with IYoM goals, alleviating strain on global cereal production, boosting resilience to climate change, and advancing sustainable crop improvement and biodiversity. The global challenges of food security, nutrition, climate change, and agrarian sustainability demand the adoption of climate-resilient, nutrient-rich crops to support a growing population amidst shifting environmental conditions. Millets, also referred to as "Shree Anna," emerge as a promising solution to address these issues by bolstering food production, improving nutrient security, and fostering biodiversity conservation. Their resilience to harsh environments, nutritional density, cultural significance, and potential to enhance dietary quality index made them valuable assets in global agriculture. Recognizing their pivotal role, the United Nations designated 2023 as the "International Year of Millets (IYoM 2023)," emphasizing their contribution to climate-resilient agriculture and nutritional enhancement. Scientific progress has invigorated efforts to enhance millet production through genetic and genomic interventions, yielding a wealth of advanced molecular breeding technologies and multi-omics resources. These advancements offer opportunities to tackle prevailing challenges in millet, such as anti-nutritional factors, sensory acceptability issues, toxin contamination, and ancillary crop improvements. This review provides a comprehensive overview of molecular breeding and multi-omics resources for nine major millet species, focusing on their potential impact within the framework of IYoM. These resources include whole and pan-genome, elucidating adaptive responses to abiotic stressors, organelle-based studies revealing evolutionary resilience, markers linked to desirable traits for efficient breeding, QTL analysis facilitating trait selection, functional gene discovery for biotechnological interventions, regulatory ncRNAs for trait modulation, web-based platforms for stakeholder communication, tissue culture techniques for genetic modification, and integrated omics approaches enabled by precise application of CRISPR/Cas9 technology. Aligning these resources with the seven thematic areas outlined by IYoM catalyzes transformative changes in millet production and utilization, thereby contributing to global food security, sustainable agriculture, and enhanced nutritional consequences.
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Affiliation(s)
- Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Rukam Singh Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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Shilpa, Thakur R, Prasad P. Epigenetic regulation of abiotic stress responses in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130661. [PMID: 38885816 DOI: 10.1016/j.bbagen.2024.130661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/15/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
Plants face a wide array of challenges in their environment, both from living organisms (biotic stresses) and non-living factors (abiotic stresses). Among the major abiotic stressors affecting crop plants, variations in temperature, water availability, salinity, and cold pose significant threats to crop yield and the quality of produce. Plants possess remarkable adaptability and resilience, and they employ a range of genetic and epigenetic mechanisms to respond and cope with abiotic stresses. A few crucial set of epigenetic mechanisms that support plants in their battle against these stresses includes DNA methylation and histone modifications. These mechanisms play a pivotal role in enabling plants to endure and thrive under challenging environmental conditions. The mechanisms of different epigenetic mechanisms in responding to the abiotic stresses vary. Each plant species and type of stress may trigger distinct epigenetic responses, highlighting the complexity of the plant's ability to adapt under stress conditions. This review focuses on the paramount importance of epigenetics in enhancing a plant's ability to survive and excel under various abiotic stresses. It highlights recent advancements in our understanding of the epigenetic mechanisms that contribute to abiotic stress tolerance in plants. This growing knowledge is pivotal for shaping future efforts aimed at mitigating the impact of abiotic stresses on diverse crop plants.
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Affiliation(s)
- Shilpa
- Department of Biotechnology, Dr Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India.
| | - Rajnikant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla-2, Himachal Pradesh, India
| | - Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla-2, Himachal Pradesh, India.
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Singh S, Viswanath A, Chakraborty A, Narayanan N, Malipatil R, Jacob J, Mittal S, Satyavathi TC, Thirunavukkarasu N. Identification of key genes and molecular pathways regulating heat stress tolerance in pearl millet to sustain productivity in challenging ecologies. FRONTIERS IN PLANT SCIENCE 2024; 15:1443681. [PMID: 39239194 PMCID: PMC11374647 DOI: 10.3389/fpls.2024.1443681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024]
Abstract
Pearl millet is a nutri-cereal that is mostly grown in harsh environments, making it an ideal crop to study heat tolerance mechanisms at the molecular level. Despite having a better-inbuilt tolerance to high temperatures than other crops, heat stress negatively affects the crop, posing a threat to productivity gain. Hence, to understand the heat-responsive genes, the leaf and root samples of two contrasting pearl millet inbreds, EGTB 1034 (heat tolerant) and EGTB 1091 (heat sensitive), were subjected to heat-treated conditions and generated genome-wide transcriptomes. We discovered 13,464 differentially expressed genes (DEGs), of which 6932 were down-regulated and 6532 up-regulated in leaf and root tissues. The pairwise analysis of the tissue-based transcriptome data of the two genotypes demonstrated distinctive genotype and tissue-specific expression of genes. The root exhibited a higher number of DEGs compared to the leaf, emphasizing different adaptive strategies of pearl millet. A large number of genes encoding ROS scavenging enzymes, WRKY, NAC, enzymes involved in nutrient uptake, protein kinases, photosynthetic enzymes, and heat shock proteins (HSPs) and several transcription factors (TFs) involved in cross-talking of temperature stress responsive mechanisms were activated in the stress conditions. Ribosomal proteins emerged as pivotal hub genes, highly interactive with key genes expressed and involved in heat stress response. The synthesis of secondary metabolites and metabolic pathways of pearl millet were significantly enriched under heat stress. Comparative synteny analysis of HSPs and TFs in the foxtail millet genome demonstrated greater collinearity with pearl millet compared to proso millet, rice, sorghum, and maize. In this study, 1906 unannotated DEGs were identified, providing insight into novel participants in the molecular response to heat stress. The identified genes hold promise for expediting varietal development for heat tolerance in pearl millet and similar crops, fostering resilience and enhancing grain yield in heat-prone environments.
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Affiliation(s)
- Swati Singh
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Aswini Viswanath
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Animikha Chakraborty
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Neha Narayanan
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Renuka Malipatil
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Jinu Jacob
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Shikha Mittal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Tara C Satyavathi
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
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Jin Y, Jia J, Yang Y, Zhu X, Yan H, Mao C, Najeeb A, Luo J, Sun M, Xie Z, Wang X, Huang L. DNAJ protein gene expansion mechanism in Panicoideae and PgDNAJ functional identification in pearl millet. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:149. [PMID: 38836874 DOI: 10.1007/s00122-024-04656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/21/2024] [Indexed: 06/06/2024]
Abstract
KEY MESSAGE Analyze the evolutionary pattern of DNAJ protein genes in the Panicoideae, including pearl millet, to identify and characterize the biological function of PgDNAJ genes in pearl millet. Global warming has become a major factor threatening food security and human development. It is urgent to analyze the heat-tolerant mechanism of plants and cultivate crops that are adapted to high temperature conditions. The Panicoideae are the second largest subfamily of the Poaceae, widely distributed in warm temperate and tropical regions. Many of these species have been reported to have strong adaptability to high temperature stress, such as pearl millet, foxtail millet and sorghum. The evolutionary differences in DNAJ protein genes among 12 Panicoideae species and 10 other species were identified and analyzed. Among them, 79% of Panicoideae DNAJ protein genes were associated with retrotransposon insertion. Analysis of the DNAJ protein pan-gene family in six pearl millet accessions revealed that the non-core genes contained significantly more TEs than the core genes. By identifying and analyzing the distribution and types of TEs near the DNAJ protein genes, it was found that the insertion of Copia and Gypsy retrotransposons provided the source of expansion for the DNAJ protein genes in the Panicoideae. Based on the analysis of the evolutionary pattern of DNAJ protein genes in Panicoideae, the PgDNAJ was obtained from pearl millet through identification. PgDNAJ reduces the accumulation of reactive oxygen species caused by high temperature by activating ascorbate peroxidase (APX), thereby improving the heat resistance of plants. In summary, these data provide new ideas for mining potential heat-tolerant genes in Panicoideae, and help to improve the heat tolerance of other crops.
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Affiliation(s)
- Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiyuan Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuchen Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xin Zhu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haidong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunli Mao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Atiqa Najeeb
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinchan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zheni Xie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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6
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Su R, Luo J, Wang Y, Xiao Y, Liu X, Deng H, Lu X, Chen Q, Chen G, Tang W, Zhang G. GDSL Lipase Gene HTA1 Negatively Regulates Heat Tolerance in Rice Seedlings by Regulating Reactive Oxygen Species Accumulation. Antioxidants (Basel) 2024; 13:592. [PMID: 38790697 PMCID: PMC11117967 DOI: 10.3390/antiox13050592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
High temperature is a significant environmental stress that limits plant growth and agricultural productivity. GDSL lipase is a hydrolytic enzyme with a conserved GDSL sequence at the N-terminus, which has various biological functions, such as participating in plant growth, development, lipid metabolism, and stress resistance. However, little is known about the function of the GDSL lipase gene in the heat tolerance of rice. Here, we characterized a lipase family protein coding gene HTA1, which was significantly induced by high temperature in rice. Rice seedlings in which the mutant hta1 was knocked out showed enhanced heat tolerance, whereas the overexpressing HTA1 showed more sensitivity to heat stress. Under heat stress, hta1 could reduce plant membrane damage and reactive oxygen species (ROS) levels and elevate the activity of antioxidant enzymes. Moreover, real-time quantitative PCR (RT-qPCR) analysis showed that mutant hta1 significantly activated gene expression in antioxidant enzymes, heat response, and defense. In conclusion, our results suggest that HTA1 negatively regulates heat stress tolerance by modulating the ROS accumulation and the expression of heat-responsive and defense-related genes in rice seedlings. This research will provide a valuable resource for utilizing HTA1 to improve crop heat tolerance.
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Affiliation(s)
- Rui Su
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
| | - Jingkai Luo
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
| | - Yingfeng Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
| | - Qiuhong Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
| | - Guihua Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410000, China
- State Key Laboratory of Hybrid Rice, Changsha 410000, China
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410000, China; (R.S.); (J.L.); (Y.W.); (Y.X.); (X.L.); (H.D.); (X.L.); (Q.C.); (G.C.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410000, China
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7
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Çelik S. Gene expression analysis of potato drought-responsive genes under drought stress in potato ( Solanum tuberosum L.) cultivars. PeerJ 2024; 12:e17116. [PMID: 38525286 PMCID: PMC10960530 DOI: 10.7717/peerj.17116] [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: 06/09/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
The potato (Solanum tuberosum L.), an important field crop consumed extensively worldwide, is adversely affected by abiotic stress factors especially drought. Therefore, it is vital to understand the genetic mechanism under drought stress to decrease loose of yield and quality . This trial aimed to screen drought-responsive gene expressions of potato and determine the drought-tolerant potato cultivar. The trial pattern is a completely randomized block design (CRBD) with four replications under greenhouse conditions. Four cultivars (Brooke, Orwell, Vr808, Shc909) were irrigated with four different water regimes (control and three stress conditions), and the gene expression levels of 10 potato genes were investigated. The stress treatments as follows: Control = 100% field capacity; slight drought = 75% field capacity; moderate drought = 50% field capacity, and severe drought 25% field capacity. To understand the gene expression under drought stress in potato genotypes, RT-qPCR analysis was performed and results showed that the genes most associated with drought tolerance were the StRD22 gene, MYB domain transcription factor, StERD7, Sucrose Synthase (SuSy), ABC Transporter, and StDHN1. The StHSP100 gene had the lowest genetic expression in all cultivars. Among the cultivars, the Orwell exhibited the highest expression of the StRD22 gene under drought stress. Overall, the cultivar with the highest gene expression was the Vr808, closely followed by the Brooke cultivar. As a result, it was determined that potato cultivars Orwell, Vr808, and Brooke could be used as parents in breeding programs to develop drought tolerant potato cultivars.
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Affiliation(s)
- Sadettin Çelik
- Genç Vocational School, Forestry Department, Bingol University, Bingol, Turkey
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Kumar V, Singh B, Kumar Singh R, Sharma N, Muthamilarasan M, Sawant SV, Prasad M. Histone deacetylase 9 interacts with SiHAT3.1 and SiHDA19 to repress dehydration responses through H3K9 deacetylation in foxtail millet. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1098-1111. [PMID: 37889853 DOI: 10.1093/jxb/erad425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 10/29/2023]
Abstract
Climate change inflicts several stresses on plants, of which dehydration stress severely affects growth and productivity. C4 plants possess better adaptability to dehydration stress; however, the role of epigenetic modifications underlying this trait is unclear. In particular, the molecular links between histone modifiers and their regulation remain elusive. In this study, genome-wide H3K9 acetylation (H3K9ac) enrichment using ChIP-sequencing was performed in two foxtail millet cultivars with contrasting dehydration tolerances (IC403579, cv. IC4-tolerant, and IC480117, cv. IC41-sensitive). It revealed that a histone deacetylase, SiHDA9, was significantly up-regulated in the sensitive cultivar. Further characterization indicated that SiHDA9 interacts with SiHAT3.1 and SiHDA19 to form a repressor complex. SiHDA9 might be recruited through the SiHAT3.1 recognition sequence onto the upstream of dehydration-responsive genes to decrease H3K9 acetylation levels. The silencing of SiHDA9 resulted in the up-regulation of crucial genes, namely, SiRAB18, SiRAP2.4, SiP5CS2, SiRD22, SiPIP1;4, and SiLHCB2.3, which imparted dehydration tolerance in the sensitive cultivar (IC41). Overall, the study provides mechanistic insights into SiHDA9-mediated regulation of dehydration stress response in foxtail millet.
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Affiliation(s)
- Verandra Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Babita Singh
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | | | - Samir V Sawant
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
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9
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Ceylan Y, Altunoglu YC, Horuz E. HSF and Hsp Gene Families in sunflower: a comprehensive genome-wide determination survey and expression patterns under abiotic stress conditions. PROTOPLASMA 2023; 260:1473-1491. [PMID: 37154904 DOI: 10.1007/s00709-023-01862-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Sunflowers belong to the Asteraceae family, which comprises nutrimental and economic oilseed plants. Heat shock proteins (Hsps) are protein families vital for all organisms' growth and survival. Besides the ordinary conditions, the expression of these proteins ascends during abiotic stress factors such as high temperature, salinity, and drought. Using bioinformatics approaches, the current study identified and analyzed HSF and Hsp gene family members in the sunflower (Helianthus annuus L.) plant. HSF, sHsp, Hsp40, Hsp60, Hsp70, Hsp90, and Hsp100 domains were analyzed in the sunflower genome, and 88, 72, 192, 52, 85, 49, and 148 genes were identified, respectively. The motif structures of the proteins in the same phylogenetic tree were similar, and the α-helical form was dominant in all the protein families except for sHsp. The estimated three-dimensional structure of 28 sHsp proteins was determined as β-sheets. Considering protein-protein interactions, the Hsp60-09 protein (38 interactions) was found to be the most interacting protein. The most orthologous gene pairs (58 genes) were identified between Hsp70 genes and Arabidopsis genes. The expression analysis of selected genes was performed under high temperature, drought, and high temperature-drought combined stress conditions in two sunflower cultivars. In stress conditions, gene expressions were upregulated for almost all genes in the first half and first hours at large. The expressions of HanHSF-45 and HanHsp70-29 genes were raised in two cultivars under high temperature and high temperature-drought combined stress conditions. This study presents a blueprint for subsequent research and delivers comprehensive knowledge of this vital protein domain.
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Affiliation(s)
- Yusuf Ceylan
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
- Department of Molecular Biology and Genetics, Faculty of Science, Bartın University, Bartin, Turkey
| | - Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey.
| | - Erdoğan Horuz
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
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10
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Unel NM, Baloglu MC, Altunoglu YÇ. Comprehensive investigation of cucumber heat shock proteins under abiotic stress conditions: A multi-omics survey. J Biotechnol 2023; 374:49-69. [PMID: 37517677 DOI: 10.1016/j.jbiotec.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
Heat-shock proteins (Hsps) are a family of proteins essential in preserving the vitality and functionality of proteins under stress conditions. Cucumber (Cucumis sativus) is a widely grown plant with high nutritional value and is used as a model organism in many studies. This study employed a genomics, transcriptomics, and metabolomics approach to investigate cucumbers' Hsps against abiotic stress conditions. Bioinformatics methods were used to identify six Hsp families in the cucumber genome and to characterize family members. Transcriptomics data from the Sequence Read Archive (SRA) database was also conducted to select CsHsp genes for further study. Real-time PCR was used to evaluate gene expression levels under different stress conditions, revealing that CssHsp-08 was a vital gene for resistance to stress conditions; including drought, salinity, cold, heat stresses, and ABA application. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of plant extracts revealed that amino acids accumulate in leaves under high temperatures and roots under drought, while sucrose accumulates in both tissues under applied most stress factors. The study provides valuable insights into the structure, organization, evolution, and expression profiles of the Hsp family and contributes to a better understanding of plant stress mechanisms. These findings have important implications for developing crops that can withstand environmental stress conditions better.
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Affiliation(s)
- Necdet Mehmet Unel
- Research and Application Center, Kastamonu University, Kastamonu, Turkey; Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Mehmet Cengiz Baloglu
- Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey; Sabancı University Nanotechnology Research and Application Center (SUNUM), Sabancı University, Turkey.
| | - Yasemin Çelik Altunoglu
- Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
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11
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Mezhyrova J, Martin J, Börnsen C, Dötsch V, Frangakis AS, Morgner N, Bernhard F. In vitro characterization of the phage lysis protein MS2-L. MICROBIOME RESEARCH REPORTS 2023; 2:28. [PMID: 38045926 PMCID: PMC10688784 DOI: 10.20517/mrr.2023.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 12/05/2023]
Abstract
Background: The peptide MS2-L represents toxins of the ssRNA Leviviridae phage family and consists of a predicted N-terminal soluble domain followed by a transmembrane domain. MS2-L mediates bacterial cell lysis through the formation of large lesions in the cell envelope, but further details of this mechanism as a prerequisite for applied bioengineering studies are lacking. The chaperone DnaJ is proposed to modulate MS2-L activity, whereas other cellular targets of MS2-L are unknown. Methods: Here, we provide a combined in vitro and in vivo overexpression approach to reveal molecular insights into MS2-L action and its interaction with DnaJ. Full-length MS2-L and truncated derivatives were synthesized cell-free and co-translationally inserted into nanodiscs or solubilized in detergent micelles. By native liquid bead ion desorption mass spectrometry, we demonstrate that MS2-L assembles into high oligomeric states after membrane insertion. Results: Oligomerization is directed by the transmembrane domain and is impaired in detergent environments. Studies with truncated MS2-L derivatives provide evidence that the soluble domain acts as a modulator of oligomer formation. DnaJ strongly interacts with MS2-L in membranes as well as in detergent environments. However, this interaction affects neither the MS2-L membrane insertion efficiency nor its oligomerization in nanodisc membranes. In accordance with the in vitro data, the assembly of MS2-L derivatives into large membrane located clusters was monitored by overexpression of corresponding fusions with fluorescent monitors in E. coli cells. Analysis by cryo-electron microscopy indicates that lesion formation is initiated in the outer membrane, followed by disruption of the peptidoglycan layer and disintegration of the inner membrane. Conclusion: MS2-L forms oligomeric complexes similar to the related phage toxin ΦX174-E. The oligomeric interface of both peptides is located within their transmembrane domains. We propose a potential function of the higher-order assembly of small phage toxins in membrane disintegration and cell lysis.
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Affiliation(s)
- Julija Mezhyrova
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main 60438, Germany
| | - Janosch Martin
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main 60438, Germany
| | - Clara Börnsen
- Buchmann Institute for Molecular Life Sciences & Institute of Biophysics, Goethe University, Frankfurt am Main 60438, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main 60438, Germany
| | - Achilleas Stefanos Frangakis
- Buchmann Institute for Molecular Life Sciences & Institute of Biophysics, Goethe University, Frankfurt am Main 60438, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main 60438, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main 60438, Germany
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12
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Ding X, Guo J, Lv M, Wang H, Sheng Y, Liu Y, Gai J, Yang S. The miR156b-GmSPL2b module mediates male fertility regulation of cytoplasmic male sterility-based restorer line under high-temperature stress in soybean. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37057908 PMCID: PMC10363761 DOI: 10.1111/pbi.14056] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/17/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
High-temperature (HT) stress at flowering stage causes significant damage to soybean, including pollen abortion and fertilization failure, but few genes involved in male fertility regulation under HT stress in soybean have been characterized. Here, we demonstrated that miR156b-GmSPL2b module involved in male fertility regulation of soybean cytoplasmic male sterility (CMS)-based restorer line under HT stress. Overexpression of miR156b decreased male fertility in soybean CMS-based restorer line and its hybrid F1 with CMS line under HT stress. RNA-seq analysis found that miR156b mediated male fertility regulation in soybean under HT stress by regulating the expression of pollen development and HT response related genes. Metabolomic analysis of miR156bOE revealed reduction in flavonoid content under HT stress. Integrated transcriptomic and metabolomic analysis showed that the overexpression of miR156b caused flavonoid metabolism disorder in soybean flower bud under HT stress. Knockout of GmSPL2b also decreased the thermotolerance of soybean CMS-based restorer line during flowering. Moreover, GmSPL2b turned out to be directly bounded to the promoter of GmHSFA6b. Further verification indicated that GmHSFA6b overexpression enhanced HT tolerance in Arabidopsis during flowering. Substance content and gene expression analysis revealed that miR156b-GmSPL2b may mediate reactive oxygen species clearance by regulating flavonoid metabolism, thus participating in the regulation of male fertility in soybean under HT stress. This study not only provided important progress for understanding the molecular mechanism of miR156b-GmSPL2b regulating the male fertility of soybean CMS-based restorer line under HT stress, but also provided genetic resources and theoretical basis for creating HT-tolerant strong restorer lines.
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Affiliation(s)
- Xianlong Ding
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jinfeng Guo
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Menglin Lv
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Hongjie Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ying Sheng
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ying Liu
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Junyi Gai
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture and Rural Affairs of the People's Republic of China), MOE National Innovation Platform for Soybean Bio-breeding Industry and Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
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Khan AH, Min L, Ma Y, Zeeshan M, Jin S, Zhang X. High-temperature stress in crops: male sterility, yield loss and potential remedy approaches. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:680-697. [PMID: 36221230 PMCID: PMC10037161 DOI: 10.1111/pbi.13946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 05/16/2023]
Abstract
Global food security is one of the utmost essential challenges in the 21st century in providing enough food for the growing population while coping with the already stressed environment. High temperature (HT) is one of the main factors affecting plant growth, development and reproduction and causes male sterility in plants. In male reproductive tissues, metabolic changes induced by HT involve carbohydrates, lipids, hormones, epigenetics and reactive oxygen species, leading to male sterility and ultimately reducing yield. Understanding the mechanism and genes involved in these pathways during the HT stress response will provide a new path to improve crops by using molecular breeding and biotechnological approaches. Moreover, this review provides insight into male sterility and integrates this with suggested strategies to enhance crop tolerance under HT stress conditions at the reproductive stage.
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Affiliation(s)
- Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Muhammad Zeeshan
- Guangxi Key Laboratory for Agro‐Environment and Agro‐Product Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, College of AgricultureGuanxi UniversityNanningChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
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14
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Zhao X, Yin K, Feng R, Miao R, Lin J, Cao L, Ni Y, Li W, Zhang Q. Genome-Wide Identification and Analysis of the Heat-Shock Protein Gene in L. edodes and Expression Pattern Analysis under Heat Shock. Curr Issues Mol Biol 2023; 45:614-627. [PMID: 36661527 PMCID: PMC9858218 DOI: 10.3390/cimb45010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Lentinula edodes (L. edodes), one of the most popular edible mushrooms in China, is adversely affected by high temperature. Heat shock proteins (HSPs) play a crucial role in regulating the defense responses against the abiotic stresses in L. edodes. Some HSPs in L. edodes have been described previously, but a genome-wide analysis of these proteins is still lacking. Here, the HSP genes across the entire genome of the L. edodes mushroom were identified. The 34 LeHSP genes were subsequently classified into six subfamilies according to their molecular weights and the phylogenetic analysis. Sequence analysis showed that LeHSP proteins from the same subfamily have conserved domains and one to five similar motifs. Except for Chr 5 and 9, 34 LeHSPs genes were distributed on the other eight chromosomes. Three pairs of paralogs were identified because of sequence alignment and were confirmed as arising from segmental duplication. In LeHSPs' promoters, different numbers of heat shock elements (HSEs) were predicted. The expression profiles of LeHSPs in 18N44 and 18 suggested that the thermo-tolerance of strain 18N44 might be related to high levels of LeHSPs transcript in response to heat stress. The quantitative real-time PCR (qRT-PCR) analysis of the 16 LeHSP genes in strains Le015 and Le027 verified their stress-inducible expression patterns under heat stress. Therefore, these comprehensive findings provide useful in-depth information on the evolution and function of LeHSPs and lay a theoretical foundation in breeding thermotolerant L. edodes varieties.
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Affiliation(s)
- Xu Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China
- Chengdu National Agricultural Science and Technology Center, Chengdu 610299, China
- Facility Agriculture and Equipment Research Institute, Gansu Academy of Agri-engineering Technology, Wuwei 733006, China
| | - Kaiyong Yin
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China
| | - Rencai Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China
- Chengdu National Agricultural Science and Technology Center, Chengdu 610299, China
| | - Renyun Miao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China
- Chengdu National Agricultural Science and Technology Center, Chengdu 610299, China
| | - Junbin Lin
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China
- Chengdu National Agricultural Science and Technology Center, Chengdu 610299, China
| | - Luping Cao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanqing Ni
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Wensheng Li
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, China
- Chengdu National Agricultural Science and Technology Center, Chengdu 610299, China
- Correspondence:
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15
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Zhang Y, Liu X, Su R, Xiao Y, Deng H, Lu X, Wang F, Chen G, Tang W, Zhang G. 9- cis-epoxycarotenoid dioxygenase 1 confers heat stress tolerance in rice seedling plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1092630. [PMID: 36605966 PMCID: PMC9807918 DOI: 10.3389/fpls.2022.1092630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
High temperature is one of the main constraints affecting plant growth and development. It has been reported that abscisic acid (ABA) synthesis gene 9-cis-epoxycarotenoid dioxygenase (NCED) positively regulates plant resistance to salt, cold, and drought stresses. However, little is known about the function of the NCED gene in heat tolerance of rice. Here, we found that OsNCED1 was a heat stress inducible gene. Rice seedlings overexpressing OsNCED1 showed enhanced heat tolerance with more abundant ABA content, whereas the knockout mutant osnced1 accumulated less ABA and showed more sensitive to heat stress. Under heat stress, increased expression of OsNCED1 could reduce membrane damage and reactive oxygen species (ROS) level of plants, and elevate the activity of antioxidant enzymes. Moreover, real time-quantitative PCR (RT-qPCR) analysis showed that overexpression of OsNCED1 significantly activated the expression of genes involved in antioxidant enzymes, ABA signaling pathway, heat response, and defense. Together, our results indicate that OsNCED1 positively regulates heat tolerance of rice seedling by raising endogenous ABA contents, which leads to the improved antioxidant capacity and activated expression of heat and ABA related genes.
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Affiliation(s)
- Yijin Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha, China
| | - Rui Su
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha, China
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha, China
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha, China
| | - Feng Wang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha, China
| | - Guihua Chen
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha, China
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, China
- State Key Laboratory of Hybrid Rice, Changsha, China
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha, China
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Li F, Fan K, Guo X, Liu J, Zhang K, Lu P. Genome-wide identification, molecular evolution and expression analysis of the non-specific lipid transfer protein (nsLTP) family in Setaria italica. BMC PLANT BIOLOGY 2022; 22:547. [PMID: 36443672 PMCID: PMC9703814 DOI: 10.1186/s12870-022-03921-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Foxtail millet (Setaria italica L.) is a millet species with high tolerance to stressful environments. Plant non-specific lipid transfer proteins (nsLTPs) are a kind of small, basic proteins involved in many biological processes. So far, the genome of S. italica has been fully sequenced, and a comprehensive understanding of the evolution and expression of the nsLTP family is still lacking in foxtail millet. RESULTS Forty-five nsLTP genes were identified in S. italica and clustered into 5 subfamilies except three single genes (SinsLTP38, SinsLTP7, and SinsLTP44). The proportion of SinsLTPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures. Besides, 5 SinsLTP duplication events were investigated. Both tandem and segmental duplication contributed to nsLTP expansion in S. italica, and the duplicated SinsLTPs had mainly undergone purifying selection pressure, which suggested that the function of the duplicated SinsLTPs might not diverge much. Moreover, we identified the nsLTP members in 5 other monocots, and 41, 13, 10, 4, and 1 orthologous gene pairs were identified between S. italica and S. viridis, S. bicolor, Z. mays, O. sativa, and B. distachyon, respectively. The functional divergence within the nsLTP orthologous genes might be limited. In addition, the tissue-specific expression patterns of the SinsLTPs were investigated, and the expression profiles of the SinsLTPs in response to abiotic stress were analyzed, all the 10 selected SinsLTPs were responsive to drought, salt, and cold stress. Among the selected SinsLTPs, 2 paired duplicated genes shared almost equivalent expression profiles, suggesting that these duplicated genes might retain some essential functions during subsequent evolution. CONCLUSIONS The present study provided the first systematic analysis for the phylogenetic classification, conserved domain and gene structure, expansion pattern, and expression profile of the nsLTP family in S. italica. These findings could pave a way for further comparative genomic and evolution analysis of nsLTP family in foxtail millet and related monocots, and lay the foundation for the functional analysis of the nsLTPs in S. italica.
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Affiliation(s)
- Feng Li
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China.
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China.
| | - Kai Fan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xuhu Guo
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China
| | - Jianxia Liu
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China
| | - Kun Zhang
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China
| | - Ping Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Li M, Tang T, Yuan F, Zhang Y, Li F, Liu F. Protective effects of small heat shock proteins in Daphnia magna against heavy metal exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157565. [PMID: 35907523 DOI: 10.1016/j.scitotenv.2022.157565] [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: 04/25/2022] [Revised: 07/08/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Daphnia magna is one of the most commonly used model organisms to assess toxicity of heavy metal and other xenobiotics. However, the lack of knowledge about important stress-resistant molecules limits our understanding of the alteration of phenotypic and physiological traits of D. magna upon stress exposures. In this study, we focused on a chaperone family of small heat shock protein (sHSP) that has been found in archaea, bacteria and eukaryotes and plays an important role in stress tolerance. A total of eleven sHSP genes (termed DmsHSP1 - DmsHSP11) were identified from the D. magna genome, whose expression profiles during exposure to heavy metal (Cd2+, Cu2+ and Zn2+) and a few other potential pollutants were evaluated via qRT-PCR and RNA-Seq analysis. The results highlighted the predominant role of DmsHSP1 with the highest basal expression level in adults and robust upregulation upon exposure to heavy metals (Cu2+ > Cd2+ > Zn2+). In vivo, recombinant protein rDmsHSP1-21 and rDmsHSP11-12.8 could not only prevent model substrates agglutination induced by heavy metals or reducer dithiotreitol (DTT), but also protect tissue proteins and enzymes from denaturation and inactivation caused by heavy metals or high temperature. Ectopically expression of DmsHSP1-21 or DmsHSP11-12.8 in E. coli conferred host enhanced resistance against various abiotic stresses including Cd2+, Cu2+ and phenazine methosulfate (PMS). Knockdown of DmsHSP1-21 by RNAi, but not for DmsHSP11-12.8, significantly increased the vulnerability of D. magna to heavy metal exposure. Our work provides systematic information on the evolution and function of sHSPs in D. magna and leads to important insights into the mechanisms by which D. magna survive in adverse environments.
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Affiliation(s)
- Muyi Li
- Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Ting Tang
- Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Fengyu Yuan
- Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Yuming Zhang
- Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Fengchao Li
- Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Fengsong Liu
- Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding 071002, China.
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18
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SiHSFA2e regulated expression of SisHSP21.9 maintains chloroplast proteome integrity under high temperature stress. Cell Mol Life Sci 2022; 79:580. [DOI: 10.1007/s00018-022-04611-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/06/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
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19
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Fernandes I, Paulo OS, Marques I, Sarjkar I, Sen A, Graça I, Pawlowski K, Ramalho JC, Ribeiro-Barros AI. Salt Stress Tolerance in Casuarina glauca: Insights from the Branchlets Transcriptome. PLANTS (BASEL, SWITZERLAND) 2022; 11:2942. [PMID: 36365395 PMCID: PMC9658546 DOI: 10.3390/plants11212942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Climate change and the accelerated rate of population growth are imposing a progressive degradation of natural ecosystems worldwide. In this context, the use of pioneer trees represents a powerful approach to reverse the situation. Among others, N2-fixing actinorhizal trees constitute important elements of plant communities and have been successfully used in land reclamation at a global scale. In this study, we have analyzed the transcriptome of the photosynthetic organs of Casuarina glauca (branchlets) to unravel the molecular mechanisms underlying salt stress tolerance. For that, C. glauca plants supplied either with chemical nitrogen (KNO3+) or nodulated by Frankia (NOD+) were exposed to a gradient of salt concentrations (200, 400, and 600 mM NaCl) and RNA-Seq was performed. An average of ca. 25 million clean reads was obtained for each group of plants, corresponding to 86,202 unigenes. The patterns of differentially expressed genes (DEGs) clearly separate two groups: (i) control- and 200 mM NaCl-treated plants, and (ii) 400 and 600 mM NaCl-treated plants. Additionally, although the number of total transcripts was relatively high in both plant groups, the percentage of significant DEGs was very low, ranging from 6 (200 mM NaCl/NOD+) to 314 (600 mM NaCl/KNO3+), mostly involving down-regulation. The vast majority of up-regulated genes was related to regulatory processes, reinforcing the hypothesis that some ecotypes of C. glauca have a strong stress-responsive system with an extensive set of constitutive defense mechanisms, complemented by a tight mechanism of transcriptional and post-transcriptional regulation. The results suggest that the robustness of the stress response system in C. glauca is regulated by a limited number of genes that tightly regulate detoxification and protein/enzyme stability, highlighting the complexity of the molecular interactions leading to salinity tolerance in this species.
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Affiliation(s)
- Isabel Fernandes
- Computational Biology and Population Genomics Group, cE3c–Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, cE3c–Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Isabel Marques
- Forest Research Centre (CEF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Indrani Sarjkar
- Bioinformatics Facility, University of North Bengal, Siliguri 734013, India
| | - Arnab Sen
- Bioinformatics Facility, University of North Bengal, Siliguri 734013, India
| | - Inês Graça
- Forest Research Centre (CEF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - José C. Ramalho
- Forest Research Centre (CEF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal
| | - Ana I. Ribeiro-Barros
- Forest Research Centre (CEF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal
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20
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Arora H, Singh RK, Sharma S, Sharma N, Panchal A, Das T, Prasad A, Prasad M. DNA methylation dynamics in response to abiotic and pathogen stress in plants. PLANT CELL REPORTS 2022; 41:1931-1944. [PMID: 35833989 DOI: 10.1007/s00299-022-02901-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
DNA methylation is a dynamic epigenetic mechanism that plays a significant role in gene expression and also maintains chromatin stability. The process is conserved in both plants and animals, and crucial for development and stress responses. Differential DNA methylation during adverse environmental conditions or pathogen attack facilitates the selective expression of defense-related genes. Both stress-induced DNA hypomethylation and hypermethylation play beneficial roles in activating the defense response. These DNA marks may be carried to the next generation making the progenies 'primed' for abiotic and biotic stress responses. Over the recent years, rapid advancements in the area of high throughput sequencing have enabled the detection of methylation status at genome levels in several plant species. Epigenotyping offers an alternative tool to plant breeders in addition to conventional markers for the selection of the desired offspring. In this review, we briefly discuss the mechanism of DNA methylation, recent understanding of DNA methylation-mediated gene regulation during abiotic and biotic stress responses, and stress memory in plants.
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Affiliation(s)
- Heena Arora
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shambhavi Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Institute of Life Sciences, NALCO Nagar, Bhubaneswar, 751023, India
| | - Anurag Panchal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Tuhin Das
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.
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21
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Liu D, Cui Y, Zhao Z, Zhang J, Li S, Liu Z. Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet ( Setaria italica (L.) P. Beauv.). ROYAL SOCIETY OPEN SCIENCE 2022; 9:220953. [PMID: 36249327 PMCID: PMC9532984 DOI: 10.1098/rsos.220953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
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Affiliation(s)
- Dan Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crop Sciences, Tianjin Academy of Agricultural Sciences, Tianjin, People's Republic of China
| | - Yanjiao Cui
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Zilong Zhao
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Jing Zhang
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Suying Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Zhengli Liu
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
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22
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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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23
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Yaashikaa PR, Kumar PS, Jeevanantham S, Saravanan R. A review on bioremediation approach for heavy metal detoxification and accumulation in plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 301:119035. [PMID: 35196562 DOI: 10.1016/j.envpol.2022.119035] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/30/2022] [Accepted: 02/17/2022] [Indexed: 05/21/2023]
Abstract
Nowadays, the accumulation of toxic heavy metals in soil and water streams is considered a serious environmental problem that causes various harmful effects on plants and animals. Phytoremediation is an effective, green, and economical bioremediation approach by which the harmful heavy metals in the contaminated ecosystem can be detoxified and accumulated in the plant. Hyperaccumulators exude molecules called transporters that carry and translocate the heavy metals present in the soil to different plant parts. The hyperaccumulator plant genes can confine higher concentrations of toxic heavy metals in their tissues. The efficiency of phytoremediation relies on various parameters such as soil properties (pH and soil type), organic matters in soil, heavy metal type, nature of rhizosphere, characteristics of rhizosphere microflora, etc. The present review comprehensively discusses the toxicity effect of heavy metals on the environment and different phytoremediation mechanisms for the transport and accumulation of heavy metals from polluted soil. This review gave comprehensive insights into plants tolerance for the higher heavy metal concentration their responses for heavy metal accumulation and the different mechanisms involved for heavy metal tolerance. The current status and the characteristic features that need to be improved in the phytoremediation process are also reviewed in detail.
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Affiliation(s)
- P R Yaashikaa
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India.
| | - S Jeevanantham
- Department of Biotechnology, Rajalakshmi Engineering College, Chennai, 602105, India
| | - R Saravanan
- Department of Mechanical Engineering, Universidad de Tarapacá, Arica, Chile
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24
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Saeed F, Chaudhry UK, Bakhsh A, Raza A, Saeed Y, Bohra A, Varshney RK. Moving Beyond DNA Sequence to Improve Plant Stress Responses. Front Genet 2022; 13:874648. [PMID: 35518351 PMCID: PMC9061961 DOI: 10.3389/fgene.2022.874648] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023] Open
Abstract
Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.
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Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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25
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Nouraei S, Mia MS, Liu H, Turner NC, Yan G. Transcriptome Analyses of Near Isogenic Lines Reveal Putative Drought Tolerance Controlling Genes in Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:857829. [PMID: 35422827 PMCID: PMC9005202 DOI: 10.3389/fpls.2022.857829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/24/2022] [Indexed: 05/08/2023]
Abstract
Drought stress, especially at the grain-filling stage, is a major constraint for wheat production. Drought tolerance is a complex trait controlled by a large array of genes and pathways. This study conducted gene expression profiling on two pairs of near-isogenic lines (NILs) for an important qDSI.4B.1 QTL conferring drought tolerance on the short arm of chromosome 4B in wheat. Analysis showed 1,614 genome-wide differentially expressed genes (DEGs) between the tolerant and susceptible isolines in both NIL pairs. Six common DEGs were found between NIL1 and NIL2 at both 7 and 14 days after stress induction, with two of them having single nucleotide polymorphism (SNP) variants. These six genes that were confirmed by quantitative real-time PCR (qRT-PCR) expression analysis are considered candidate genes for drought tolerance mediated by qDSI.4B.1 QTL with their main contributions to gene regulation, cell elongation, protein quality control, secondary metabolism, and hormone signaling. These six candidate genes and the highest number of DEGs and variants (SNPs/indels) were located between 49 and 137 Mbp of 4BS, making this interval the most probable location for the qDSI.4B.1 locus. Additionally, 765 and 84 DEGs were detected as responsive genes to drought stress in tolerant and susceptible isolines, respectively. According to gene ontology (GO), protein phosphorylation, oxidation reduction, and regulation of transcription were top biological processes involved in the drought response and tolerance. These results provide insights into stress responses regulated by the 4BS locus and have identified candidate genes and genetic markers that can be used for fine mapping of the qDSI.4B.1 locus and, ultimately, in wheat breeding programs for drought tolerance.
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Affiliation(s)
- Sina Nouraei
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Md Sultan Mia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Department of Primary Industries and Regional Development, Northam, WA, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Neil C. Turner
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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Liu J, Zhang L, Huang L, Yang T, Ma J, Yu T, Zhu W, Zhang Z, Tang J. Uncovering the Gene Regulatory Network of Maize Hybrid ZD309 under Heat Stress by Transcriptomic and Metabolomic Analysis. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050677. [PMID: 35270147 PMCID: PMC8912342 DOI: 10.3390/plants11050677] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 05/21/2023]
Abstract
Maize is an important cereal crop but is sensitive to heat stress, which significantly restricts its grain yield. To explore the molecular mechanism of maize heat tolerance, a heat-tolerant hybrid ZD309 and its parental lines (H39_1 and M189) were subjected to heat stress, followed by transcriptomic and metabolomic analyses. After six-day-heat treatment, the growth of ZD309 and its parental lines were suppressed, showing dwarf stature and rolled leaf compared with the control plants. ZD309 exhibited vigorous growth; however, M189 displayed superior heat tolerance. By transcriptomic and metabolomic analysis, hundreds to thousands of differentially expressed genes (DEGs) and metabolites (DEMs) were identified. Notably, the female parent H39 shares more DEGs and DEMs with the hybrid ZD309, indicating more genetic gain derived from the female instead of the male. A total of 299 heat shock genes detected among three genotypes were greatly aggregated in sugar transmembrane transporter activity, plasma membrane, photosynthesis, protein processing in the endoplasmic reticulum, cysteine, and methionine metabolism. A total of 150 heat-responsive metabolites detected among three genotypes were highly accumulated, including jasmonic acid, amino acids, sugar, flavonoids, coumarin, and organic acids. Integrating transcriptomic and metabolomic assays revealed that plant hormone signal transduction, cysteine, and methionine metabolism, and α-linolenic acid metabolism play crucial roles in heat tolerance in maize. Our research will be facilitated to identify essential heat tolerance genes in maize, thereby contributing to breeding heat resistance maize varieties.
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Affiliation(s)
- Jingbao Liu
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Linna Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Lu Huang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Tianxiao Yang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA;
| | - Juan Ma
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Ting Yu
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Weihong Zhu
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Zhanhui Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- Correspondence: (Z.Z.); (J.T.)
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- Correspondence: (Z.Z.); (J.T.)
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27
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Biniaz Y, Tahmasebi A, Afsharifar A, Tahmasebi A, Poczai P. Meta-Analysis of Common and Differential Transcriptomic Responses to Biotic and Abiotic Stresses in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2022; 11:502. [PMID: 35214836 PMCID: PMC8877356 DOI: 10.3390/plants11040502] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Environmental stresses adversely affect crop growth and yield, resulting in major losses to plants. These stresses occur simultaneously in nature, and we therefore conducted a meta-analysis in this study to identify differential and shared genes, pathways, and transcriptomic mechanisms involved in Arabidopsis response to biotic and abiotic stresses. The results showed a total of 436/21 significant up-/downregulated differentially expressed genes (DEGs) in response to biotic stresses, while 476 and 71 significant DEGs were respectively up- and downregulated in response to abiotic stresses in Arabidopsis thaliana. In addition, 21 DEGs (2.09%) were commonly regulated in response to biotic and abiotic stresses. Except for WRKY45 and ATXTH22, which were respectively up-/down- and down-/upregulated in response to biotic and abiotic stresses, other common DEGs were upregulated in response to all biotic and abiotic treatments. Moreover, the transcription factors (TFs) bHLH, MYB, and WRKY were the common TFs in response to biotic and abiotic stresses. In addition, ath-miR414 and ath-miR5658 were identified to be commonly expressed in response to both biotic and abiotic stresses. The identified common genes and pathways during biotic and abiotic stresses may provide potential candidate targets for the development of stress resistance breeding programs and for the genetic manipulation of crop plants.
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Affiliation(s)
- Yaser Biniaz
- Plant Virology Research Center, Faculty of Agriculture, Shiraz University, Shiraz 7144113131, Iran; (Y.B.); (A.A.)
| | - Aminallah Tahmasebi
- Department of Agriculture, Minab Higher Education Center, University of Hormozgan, Bandar Abbas 7916193145, Iran;
- Plant Protection Research Group, University of Hormozgan, Bandar Abbas 7916193145, Iran
| | - Alireza Afsharifar
- Plant Virology Research Center, Faculty of Agriculture, Shiraz University, Shiraz 7144113131, Iran; (Y.B.); (A.A.)
| | - Ahmad Tahmasebi
- Institute of Biotechnology, Faculty of Agriculture, Shiraz University, Shiraz 7144113131, Iran;
| | - Péter Poczai
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, FI-00065 Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), P.O. Box 4, H-9731 Kőszeg, Hungary
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28
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Chaudhry S, Sidhu GPS. Climate change regulated abiotic stress mechanisms in plants: a comprehensive review. PLANT CELL REPORTS 2022; 41:1-31. [PMID: 34351488 DOI: 10.1007/s00299-021-02759-5] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/18/2021] [Indexed: 05/20/2023]
Abstract
Global climate change is identified as a major threat to survival of natural ecosystems. Climate change is a dynamic, multifaceted system of alterations in environmental conditions that affect abiotic and biotic components of the world. It results in alteration in environmental conditions such as heat waves, intensity of rainfall, CO2 concentration and temperature that lead to rise in new pests, weeds and pathogens. Climate change is one of the major constraints limiting plant growth and development worldwide. It impairs growth, disturbs photosynthesis, and reduces physiological responses in plants. The variations in global climate have gained the attention of researchers worldwide, as these changes negatively affect the agriculture by reducing crop productivity and food security. With this background, this review focuses on the effects of elevated atmospheric CO2 concentration, temperature, drought and salinity on the morphology, physiology and biochemistry of plants. Furthermore, this paper outlines an overview on the reactive oxygen species (ROS) production and their impact on the biochemical and molecular status of plants with increased climatic variations. Also additionally, different tolerance strategies adopted by plants to combat environmental adversities have been discussed.
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Affiliation(s)
- Smita Chaudhry
- Institute of Environmental Studies, Kurukshetra University, Kurukshetra, Haryana, 136119, India
- Centre for Applied Biology in Environment Sciences, Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | - Gagan Preet Singh Sidhu
- Centre for Applied Biology in Environment Sciences, Kurukshetra University, Kurukshetra, Haryana, 136119, India.
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Hezema YS, Shukla MR, Goel A, Ayyanath MM, Sherif SM, Saxena PK. Rootstocks Overexpressing StNPR1 and StDREB1 Improve Osmotic Stress Tolerance of Wild-Type Scion in Transgrafted Tobacco Plants. Int J Mol Sci 2021; 22:8398. [PMID: 34445105 PMCID: PMC8395105 DOI: 10.3390/ijms22168398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/24/2022] Open
Abstract
In grafted plants, the movement of long-distance signals from rootstocks can modulate the development and function of the scion. To understand the mechanisms by which tolerant rootstocks improve scion responses to osmotic stress (OS) conditions, mRNA transport of osmotic responsive genes (ORGs) was evaluated in a tomato/potato heterograft system. In this system, Solanum tuberosum was used as a rootstock and Solanum lycopersicum as a scion. We detected changes in the gene expression levels of 13 out of the 21 ORGs tested in the osmotically stressed plants; of these, only NPR1 transcripts were transported across the graft union under both normal and OS conditions. Importantly, OS increased the abundance of StNPR1 transcripts in the tomato scion. To examine mRNA mobility in transgrafted plants, StNPR1 and StDREB1 genes representing the mobile and non-mobile transcripts, respectively, were overexpressed in tobacco (Nicotiana tabacum). The evaluation of transgenic tobacco plants indicated that overexpression of these genes enhanced the growth and improved the physiological status of transgenic plants growing under OS conditions induced by NaCl, mannitol and polyethylene glycol (PEG). We also found that transgenic tobacco rootstocks increased the OS tolerance of the WT-scion. Indeed, WT scions on transgenic rootstocks had higher ORGs transcript levels than their counterparts on non-transgenic rootstocks. However, neither StNPR1 nor StDREB1 transcripts were transported from the transgenic rootstock to the wild-type (WT) tobacco scion, suggesting that other long-distance signals downstream these transgenes could have moved across the graft union leading to OS tolerance. Overall, our results signify the importance of StNPR1 and StDREB1 as two anticipated candidates for the development of stress-resilient crops through transgrafting technology.
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Affiliation(s)
- Yasmine S. Hezema
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (Y.S.H.); (M.R.S.); (A.G.); (M.M.A.)
- Department of Horticulture, Damanhour University, Damanhour 22713, El-Beheira, Egypt
| | - Mukund R. Shukla
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (Y.S.H.); (M.R.S.); (A.G.); (M.M.A.)
| | - Alok Goel
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (Y.S.H.); (M.R.S.); (A.G.); (M.M.A.)
| | - Murali M. Ayyanath
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (Y.S.H.); (M.R.S.); (A.G.); (M.M.A.)
| | - Sherif M. Sherif
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA 22602, USA
| | - Praveen K. Saxena
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (Y.S.H.); (M.R.S.); (A.G.); (M.M.A.)
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Singh RK, Prasad M. Delineating the epigenetic regulation of heat and drought response in plants. Crit Rev Biotechnol 2021; 42:548-561. [PMID: 34289772 DOI: 10.1080/07388551.2021.1946004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Being sessile in nature, plants cannot overlook the incursion of unfavorable environmental conditions, including heat and drought. Heat and drought severely affect plant growth, development, reproduction and therefore productivity which poses a severe threat to global food security. Plants respond to these hostile environmental circumstances by rearranging their genomic and molecular architecture. One such modification commonly known as epigenetic changes involves the perishable to inheritable changes in DNA or DNA-binding histone proteins leading to modified chromatin organization. Reversible epigenetic modifications include DNA methylation, exchange of histone variants, histone methylation, histone acetylation, ATP-dependent nucleosome remodeling, and others. These modifications are employed to regulate the spatial and temporal expression of genes in response to external stimuli or specific developmental requirements. Understanding the epigenetic regulation of stress-related gene expression in response to heat and drought would commence manifold avenues for crop improvement through molecular breeding or biotechnological approaches.
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Affiliation(s)
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
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Mukesh Sankar S, Tara Satyavathi C, Barthakur S, Singh SP, Bharadwaj C, Soumya SL. Differential Modulation of Heat-Inducible Genes Across Diverse Genotypes and Molecular Cloning of a sHSP From Pearl Millet [ Pennisetum glaucum (L.) R. Br.]. FRONTIERS IN PLANT SCIENCE 2021; 12:659893. [PMID: 34335644 PMCID: PMC8324246 DOI: 10.3389/fpls.2021.659893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/08/2021] [Indexed: 05/09/2023]
Abstract
The survival, biomass, and grain yield of most of the crops are negatively influenced by several environmental stresses. The present study was carried out by using transcript expression profiling for functionally clarifying the role of genes belonging to a small heat shock protein (sHSP) family in pearl millet under high-temperature stress. Transcript expression profiling of two high-temperature-responsive marker genes, Pgcp70 and PgHSF, along with physio-biochemical traits was considered to screen out the best contrasting genotypes among the eight different pearl millet inbred lines in the seedling stage. Transcript expression pattern suggested the existence of differential response among different genotypes upon heat stress in the form of accumulation of heat shock-responsive gene transcripts. Genotypes, such as WGI 126, TT-1, TT-6, and MS 841B, responded positively toward high-temperature stress for the transcript accumulation of both Pgcp70 and PgHSF and also indicated a better growth under heat stress. PPMI-69 showed the least responsiveness to transcript induction; moreover, it supports the membrane stability index (MSI) data for scoring thermotolerance, thereby suggesting the efficacy of transcript expression profiling as a molecular-based screening technique for the identification of thermotolerant genes and genotypes at particular crop growth stages. The contrasting genotypes, such as PPMI-69 (thermosusceptible) and WGI-126 and TT-1 (thermotolerant), are further utilized for the characterization of thermotolerance behavior of sHSP by cloning a PgHSP16.97 from the thermotolerant cv. WGI-126. In addition, the investigation was extended for the identification and characterization of 28 different HSP20 genes through a genome-wide search in the pearl millet genome and an understanding of their expression pattern using the RNA-sequencing (RNA-Seq) data set. The outcome of the present study indicated that transcript profiling can be a very useful technique for high-throughput screening of heat-tolerant genotypes in the seedling stage. Also, the identified PgHSP20s genes can provide further insights into the molecular regulation of pearl millet stress tolerance, thereby bridging them together to fight against the unpredicted nature of abiotic stress.
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Affiliation(s)
- S. Mukesh Sankar
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - C. Tara Satyavathi
- Indian Council of Agricultural Research-All India Coordinated Research Project on Pearl Millet (AICPMIP), Jodhpur, India
| | - Sharmistha Barthakur
- Functional Genomics, Indian Council of Agricultural Research-National Institute for Plant Biotechnology (NIPB), New Delhi, India
| | - Sumer Pal Singh
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - C. Bharadwaj
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - S. L. Soumya
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
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Nagaraju M, Kumar A, Jalaja N, Rao DM, Kishor PBK. Functional Exploration of Chaperonin (HSP60/10) Family Genes and their Abiotic Stress-induced Expression Patterns in Sorghum bicolor. Curr Genomics 2021; 22:137-152. [PMID: 34220300 PMCID: PMC8188580 DOI: 10.2174/1389202922666210324154336] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 01/05/2021] [Accepted: 01/22/2021] [Indexed: 11/30/2022] Open
Abstract
Background Sorghum, the C4 dry-land cereal, important for food, fodder, feed and fuel, is a model crop for abiotic stress tolerance with smaller genome size, genetic diversity, and bio-energy traits. The heat shock proteins/chaperonin 60s (HSP60/Cpn60s) assist the plastid proteins, and participate in the folding and aggregation of proteins. However, the functions of HSP60s in abiotic stress tolerance in Sorghum remain unclear. Methods Genome-wide screening and in silico characterization of SbHSP60s were carried out along with tissue and stress-specific expression analysis. Results A total of 36 HSP60 genes were identified in Sorghum bicolor. They were subdivided into 2 groups, the HSP60 and HSP10 co-chaperonins encoded by 30 and 6 genes, respectively. The genes are distributed on all the chromosomes, chromosome 1 being the hot spot with 9 genes. All the HSP60s were found hydrophilic and highly unstable. The HSP60 genes showed a large number of introns, the majority of them with more than 10. Among the 12 paralogs, only 1 was tandem and the remaining 11 segmental, indicating their role in the expansion of SbHSP60s. Majority of the SbHSP60 genes expressed uniformly in leaf while a moderate expression was observed in the root tissues, with the highest expression displayed by SbHSP60-1. From expression analysis, SbHSP60-3 for drought, SbHSP60-9 for salt, SbHSP60-9 and 24 for heat and SbHSP60-3, 9 and SbHSP10-2 have been found implicated for cold stress tolerance and appeared as the key regulatory genes. Conclusion This work paves the way for the utilization of chaperonin family genes for achieving abiotic stress tolerance in plants.
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Affiliation(s)
- M Nagaraju
- Department of Genetics, Osmania University, Hyderabad 500 007, India.,Biochemistry Division, National Institute of Nutrition (ICMR), Hyderabad 500 007, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Silk Park, Prem Nagar, Dehradun 248 007, India
| | - N Jalaja
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur 522 213, Andhra Pradesh, India
| | - D Manohar Rao
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - P B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur 522 213, Andhra Pradesh, India
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Panzade KP, Kale SS, Chavan NR, Hatzade B. Genome-wide analysis of Hsp70 and Hsp100 gene families in Ziziphus jujuba. Cell Stress Chaperones 2021; 26:341-353. [PMID: 33184780 PMCID: PMC7925773 DOI: 10.1007/s12192-020-01179-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
The Ziziphus species are naturally tolerant to a range of abiotic stresses. Therefore, it is expected that they are an enriched source of genes conferring stress tolerance. Heat shock proteins (Hsps) play a significant role in plants in imparting tolerance against abiotic stress conditions. To get an insight into potential Hsp function in Ziziphus, we performed a genome-wide analysis and expression study of Hsp70 and Hsp100 gene families in Ziziphus jujuba. We identified 21 and 6 genes of the ZjHsp70 and ZjHsp100 families, respectively. Physiochemical properties, chromosomal location, gene structure, motifs, and protein domain organization were analysed for structural and functional characterization. We identified the contribution of tandem and segmental gene duplications in expansions of ZjHsp70s and ZjHsp100s in Z. jujuba. Promoter analysis suggested that ZjHsp70s and ZjHsp100s perform diverse functions related to abiotic stress. Furthermore, expression analyses revealed that most of the Z. jujuba Hsp genes are differentially expressed in response to heat, drought, and salinity stress. Our analyses suggested ZjHsp70-3, ZjHsp70-5, ZjHsp70-6, ZjHsp70-16, ZjHsp70-17, ZjHsp70-20, ZjHsp100-1, ZjHsp100-2, and ZjHsp100-3 are potential candidates for further functional analysis and with regard to breeding new more resilient strains. The present analysis laid the foundation for understanding the molecular mechanism of Hsps70 and Hsp100 gene families regulating abiotic stress tolerance in Z. jujuba.
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Affiliation(s)
- Kishor Prabhakar Panzade
- Division of Molecular Biology and Biotechnology, Indian Agriculture Research Institute, New Delhi, 110012 India
| | - Sonam S. Kale
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431007 India
| | - Narendra R. Chavan
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431007 India
| | - Bhupal Hatzade
- Department of Plant Biotechnology, Ajeet Seeds Pvt. Ltd., Aurangabad, 431133 India
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Farooq MA, Hong Z, Islam F, Noor Y, Hannan F, Zhang Y, Ayyaz A, Mwamba TM, Zhou W, Song W. Comprehensive proteomic analysis of arsenic induced toxicity reveals the mechanism of multilevel coordination of efficient defense and energy metabolism in two Brassica napus cultivars. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111744. [PMID: 33396070 DOI: 10.1016/j.ecoenv.2020.111744] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 05/19/2023]
Abstract
Arsenic (As) a non-essential element is of particular concern with respect to harmful effects on plant metabolism. While extensive studies have been conducted on the physiological responses of plants to increase As concentrations, however, molecular differences elucidating species-specific changes remain largely unknown. In the present experiment, two oilseed Brassica napus (B. napus) cultivars, ZS758 and ZD622, were treated by elevated As concentration. Their responses to the As stress have been investigated through pulse amplitude modulated fluorometer and isobaric tags based proteomic (iTRAQ) analysis. The chlorophyll fluorescence attributes showed that As stress significantly decrease the photochemical efficiency of photosystem II (PSII) and photosystem I (PSI) as well as the comparatively closed stomata observed under scanning electron microscopy (SEM). In this study, 65 proteins displayed increased abundance and 52 down-regulated were found in the control vs As comparison in cultivar ZS758, while 44 up and 67 down-regulated proteins were found in the control vs As comparison in ZD622. Metabolic pathways, followed by ribosome and biosynthesis of secondary metabolites were the dominant functional annotation categories among the differentially expressed protein (DEPs). Many genes involved in primary metabolism, stress and defense were found to be As-responsive DEPs and/or DEPs between these two cultivars. Based on these results, a schematic description of key processes involved in As tolerance in ZS758 and ZD622 is proposed, which suggests that higher tolerance in ZS758 depends on a multilevel coordination of efficient defense and energy metabolism. Real-time quantitative PCR supported the expression patterns of several genes encoding a protein similar to their corresponding DEPs. In addition, these findings could shed light in unraveling the molecular mechanisms of B. napus exposed to As stress and provide or improve essential understandings in the development of advanced B. napus cultivars against As resistance.
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Affiliation(s)
- Muhammad Ahsan Farooq
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Zheyuan Hong
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Faisal Islam
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Yamna Noor
- Department of Botany, The Women University, Multan 60000, Pakistan
| | - Fakhir Hannan
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Yan Zhang
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Ahsan Ayyaz
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Theodore M Mwamba
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Weijun Zhou
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Wenjian Song
- Agricultural Technology Extension Center, Zhejiang University, Hangzhou 310058, China.
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Singh RK, Muthamilarasan M, Prasad M. Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement. J Biotechnol 2021; 327:64-73. [PMID: 33422569 DOI: 10.1016/j.jbiotec.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 10/22/2022]
Abstract
'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi 110067, India.
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Genetic and genomic resources, and breeding for accelerating improvement of small millets: current status and future interventions. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00322-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AbstractCurrent agricultural and food systems encourage research and development on major crops, neglecting regionally important minor crops. Small millets include a group of small- seeded cereal crops of the grass family Poaceae. This includes finger millet, foxtail millet, proso millet, barnyard millet, kodo millet, little millet, teff, fonio, job’s tears, guinea millet, and browntop millet. Small millets are an excellent choice to supplement major staple foods for crop and dietary diversity because of their diverse adaptation on marginal lands, less water requirement, lesser susceptibility to stresses, and nutritional superiority compared to major cereal staples. Growing interest among consumers about healthy diets together with climate-resilient features of small millets underline the necessity of directing more research and development towards these crops. Except for finger millet and foxtail millet, and to some extent proso millet and teff, other small millets have received minimal research attention in terms of development of genetic and genomic resources and breeding for yield enhancement. Considerable breeding efforts were made in finger millet and foxtail millet in India and China, respectively, proso millet in the United States of America, and teff in Ethiopia. So far, five genomes, namely foxtail millet, finger millet, proso millet, teff, and Japanese barnyard millet, have been sequenced, and genome of foxtail millet is the smallest (423-510 Mb) while the largest one is finger millet (1.5 Gb). Recent advances in phenotyping and genomics technologies, together with available germplasm diversity, could be utilized in small millets improvement. This review provides a comprehensive insight into the importance of small millets, the global status of their germplasm, diversity, promising germplasm resources, and breeding approaches (conventional and genomic approaches) to accelerate climate-resilient and nutrient-dense small millets for sustainable agriculture, environment, and healthy food systems.
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Genomic dissection and expression analysis of stress-responsive genes in C4 panicoid models, Setaria italica and Setaria viridis. J Biotechnol 2020; 318:57-67. [DOI: 10.1016/j.jbiotec.2020.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 02/02/2023]
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Kumar A, Sharma S, Chunduri V, Kaur A, Kaur S, Malhotra N, Kumar A, Kapoor P, Kumari A, Kaur J, Sonah H, Garg M. Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L. Sci Rep 2020; 10:7858. [PMID: 32398647 PMCID: PMC7217896 DOI: 10.1038/s41598-020-64746-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 04/01/2020] [Indexed: 12/02/2022] Open
Abstract
Heat shock proteins (HSPs) have a significant role in protein folding and are considered as prominent candidates for development of heat-tolerant crops. Understanding of wheat HSPs has great importance since wheat is severely affected by heat stress, particularly during the grain filling stage. In the present study, efforts were made to identify HSPs in wheat and to understand their role during plant development and under different stress conditions. HSPs in wheat genome were first identified by using Position-Specific Scoring Matrix (PSSMs) of known HSP domains and then also confirmed by sequence homology with already known HSPs. Collectively, 753 TaHSPs including 169 TaSHSP, 273 TaHSP40, 95 TaHSP60, 114 TaHSP70, 18 TaHSP90 and 84 TaHSP100 were identified in the wheat genome. Compared with other grass species, number of HSPs in wheat was relatively high probably due to the higher ploidy level. Large number of tandem duplication was identified in TaHSPs, especially TaSHSPs. The TaHSP genes showed random distribution on chromosomes, however, there were more TaHSPs in B and D sub-genomes as compared to the A sub-genome. Extensive computational analysis was performed using the available genomic resources to understand gene structure, gene expression and phylogentic relationship of TaHSPs. Interestingly, apart from high expression under heat stress, high expression of TaSHSP was also observed during seed development. The study provided a list of candidate HSP genes for improving thermo tolerance during developmental stages and also for understanding the seed development process in bread wheat.
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Affiliation(s)
- Ashish Kumar
- South Asian University, Chankyapuri, New Delhi, 110021, India
| | - Saloni Sharma
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Venkatesh Chunduri
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Amandeep Kaur
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Satinder Kaur
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Nikhil Malhotra
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Aman Kumar
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Payal Kapoor
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Anita Kumari
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | | | - Humira Sonah
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India.
| | - Monika Garg
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India.
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Chang YN, Zhu C, Jiang J, Zhang H, Zhu JK, Duan CG. Epigenetic regulation in plant abiotic stress responses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:563-580. [PMID: 31872527 DOI: 10.1111/jipb.12901] [Citation(s) in RCA: 226] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/20/2020] [Indexed: 05/18/2023]
Abstract
In eukaryotic cells, gene expression is greatly influenced by the dynamic chromatin environment. Epigenetic mechanisms, including covalent modifications to DNA and histone tails and the accessibility of chromatin, create various chromatin states for stress-responsive gene expression that is important for adaptation to harsh environmental conditions. Recent studies have revealed that many epigenetic factors participate in abiotic stress responses, and various chromatin modifications are changed when plants are exposed to stressful environments. In this review, we summarize recent progress on the cross-talk between abiotic stress response pathways and epigenetic regulatory pathways in plants. Our review focuses on epigenetic regulation of plant responses to extreme temperatures, drought, salinity, the stress hormone abscisic acid, nutrient limitations and ultraviolet stress, and on epigenetic mechanisms of stress memory.
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Affiliation(s)
- Ya-Nan Chang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jing Jiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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Wei Y, Liu W, Hu W, Yan Y, Shi H. The chaperone MeHSP90 recruits MeWRKY20 and MeCatalase1 to regulate drought stress resistance in cassava. THE NEW PHYTOLOGIST 2020; 226:476-491. [PMID: 31782811 DOI: 10.1111/nph.16346] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/23/2019] [Indexed: 05/25/2023]
Abstract
The 90 kDa heat shock protein (HSP90) is widely involved in various developmental processes and stress responses in plants. However, the molecular chaperone HSP90-constructed protein complex and its function in cassava remain elusive. In this study, we report that HSP90 is essential for drought stress resistance in cassava by regulating abscisic acid (ABA) and hydrogen peroxide (H2 O2 ) using two specific protein inhibitors of HSP90 (geldanamycin (GDA) and radicicol (RAD)). Among 10 MeHSP90s, the transcript of MeHSP90.9 is largely induced during drought stress. Further investigation identifies MeWRKY20 and MeCatalase1 as MeHSP90.9-interacting proteins. MeHSP90.9-, MeWRKY20-, or MeCatalase1-silenced plants through virus-induced gene silencing display drought sensitivity in cassava, indicating that they are important to drought stress response. MeHSP90.9 can promote the direct transcriptional activation of MeWRKY20 on the W-box element of MeNCED5 promoter, encoding a key enzyme in ABA biosynthesis. Moreover, MeHSP90.9 positively regulates the activity of MeCatalase1, and MeHSP90.9-silenced cassava leaves accumulate more H2 O2 under drought stress. Taken together, we demonstrate that the MeHSP90.9 chaperone complex is a regulator of drought stress resistance in cassava.
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Affiliation(s)
- Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
| | - Wen Liu
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/ Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China
| | - Yu Yan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, China
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Haq SU, Khan A, Ali M, Gai WX, Zhang HX, Yu QH, Yang SB, Wei AM, Gong ZH. Knockdown of CaHSP60-6 confers enhanced sensitivity to heat stress in pepper (Capsicum annuum L.). PLANTA 2019; 250:2127-2145. [PMID: 31606756 DOI: 10.1007/s00425-019-03290-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/26/2019] [Indexed: 05/24/2023]
Abstract
HSP60 gene family in pepper was analyzed through bioinformatics along with transcriptional regulation against multiple abiotic and hormonal stresses. Furthermore, the knockdown of CaHSP60-6 increased sensitivity to heat stress. The 60 kDa heat shock protein (HSP60) also known as chaperonin (cpn60) is encoded by multi-gene family that plays an important role in plant growth, development and in stress response as a molecular chaperone. However, little is known about the HSP60 gene family in pepper (Capsicum annuum L.). In this study, 16 putative pepper HSP60 genes were identified through bioinformatic tools. The phylogenetic tree revealed that eight of the pepper HSP60 genes (50%) clustered into group I, three (19%) into group II, and five (31%) into group III. Twelve (75%) CaHSP60 genes have more than 10 introns, while only a single gene contained no introns. Chromosomal mapping revealed that the tandem and segmental duplication events occurred in the process of evolution. Gene ontology enrichment analysis predicted that CaHSP60 genes were responsible for protein folding and refolding in an ATP-dependent manner in response to various stresses in the biological processes category. Multiple stress-related cis-regulatory elements were found in the promoter region of these CaHSP60 genes, which indicated that these genes were regulated in response to multiple stresses. Tissue-specific expression was studied under normal conditions and induced under 2 h of heat stress measured by RNA-Seq data and qRT-PCR in different tissues (roots, stems, leaves, and flowers). The data implied that HSP60 genes play a crucial role in pepper growth, development, and stress responses. Fifteen (93%) CaHSP60 genes were induced in both, thermo-sensitive B6 and thermo-tolerant R9 lines under heat treatment. The relative expression of nine representative CaHSP60 genes in response to other abiotic stresses (cold, NaCl, and mannitol) and hormonal applications [ABA, methyl jasmonate (MeJA), and salicylic acid (SA)] was also evaluated. Knockdown of CaHSP60-6 increased the sensitivity to heat shock treatment as documented by a higher relative electrolyte leakage, lipid peroxidation, and reactive oxygen species accumulation in silenced pepper plants along with a substantial lower chlorophyll content and antioxidant enzyme activity. These results suggested that HSP60 might act as a positive regulator in pepper defense against heat and other abiotic stresses. Our results provide a basis for further functional analysis of HSP60 genes in pepper.
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Affiliation(s)
- Saeed Ul Haq
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qing-Hui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, People's Republic of China
| | - Sheng-Bao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, People's Republic of China
| | - Ai-Min Wei
- Tianjin Vegetable Research Center, Tianjin, 300192, People's Republic of China
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, 300384, People's Republic of China.
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Molecular evolution and structural variations in nuclear encoded chloroplast localized heat shock protein 26 (sHSP26) from genetically diverse wheat species. Comput Biol Chem 2019; 83:107144. [PMID: 31751884 DOI: 10.1016/j.compbiolchem.2019.107144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 07/01/2019] [Accepted: 10/05/2019] [Indexed: 11/20/2022]
Abstract
Heat shock proteins are an important class of molecular chaperones known to impart tolerance under high temperature stress. sHSP26, a member of small heat shock protein subfamily is specifically involved in protecting plant's photosynthetic machinery. The present study aimed at identifying and characterizing sequence and structural variations in sHSP26 from genetically diverse progenitor and non-progenitor species of wheat. In silico analysis identified three paralogous copies of TaHSP26 to reside on short arm of chromosome 4A while one homeologue each was localized on long arm of chromosome 4B and 4D of cultivated bread wheat. Wild DD-genome donor Aegilops tauschii carried an additional sHSP26 gene (AET4Gv20569400) which was absent in the cultivated DD genome of bread wheat. In vitro amplification of this novel gene in wild accessions of Ae. tauschii and synthetic hexaploid wheat but not in cultivated bread wheat validated this finding. Further, significant length polymorphism could be identified in exon1 from diverse sHSP26 sequences. Multiple sequence alignment of procured sequences revealed numerous sSNPs and nsSNPs. D3A, P125 L, Q242 K were designated as homeolog specific- while A49 G as non-progenitor specific amino acid replacements. A 9-bp indel in TmHSP26-1(GA) translated into a deletion of SPM amino acid segment in chloroplast specific conserved consensus region III. High degree of divergence in nucleotide sequence between cultivated and wild species appeared in the form of higher ω values (Ka/Ks >1) indicating positive selection during the course of evolution. Phylogenetic analysis elucidated ancestral relationships between wheat sHSP26 proteins and orthologous proteins across plant kingdom. Overall, data mining approach may be employed as an effective pre-breeding strategy to identify and mobilize novel stress responsive genes and distinct allelic variants from wider germplasm collections of wheat to enhance climate resilience of present day elite wheat cultivars.
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ul Haq S, Khan A, Ali M, Khattak AM, Gai WX, Zhang HX, Wei AM, Gong ZH. Heat Shock Proteins: Dynamic Biomolecules to Counter Plant Biotic and Abiotic Stresses. Int J Mol Sci 2019; 20:E5321. [PMID: 31731530 PMCID: PMC6862505 DOI: 10.3390/ijms20215321] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Due to the present scenario of climate change, plants have to evolve strategies to survive and perform under a plethora of biotic and abiotic stresses, which restrict plant productivity. Maintenance of plant protein functional conformation and preventing non-native proteins from aggregation, which leads to metabolic disruption, are of prime importance. Plant heat shock proteins (HSPs), as chaperones, play a pivotal role in conferring biotic and abiotic stress tolerance. Moreover, HSP also enhances membrane stability and detoxifies the reactive oxygen species (ROS) by positively regulating the antioxidant enzymes system. Additionally, it uses ROS as a signal to molecules to induce HSP production. HSP also enhances plant immunity by the accumulation and stability of pathogenesis-related (PR) proteins under various biotic stresses. Thus, to unravel the entire plant defense system, the role of HSPs are discussed with a special focus on plant response to biotic and abiotic stresses, which will be helpful in the development of stress tolerance in plant crops.
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Affiliation(s)
- Saeed ul Haq
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
- Department of Horticulture, University of Agriculture Peshawar, Peshawar 25130, Pakistan;
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Abdul Mateen Khattak
- Department of Horticulture, University of Agriculture Peshawar, Peshawar 25130, Pakistan;
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Ai-Min Wei
- Tianjin Vegetable Research Center, Tianjin 300192, China;
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
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Nagaraju M, Reddy PS, Kumar SA, Kumar A, Rajasheker G, Rao DM, Kavi Kishor PB. Genome-wide identification and transcriptional profiling of small heat shock protein gene family under diverse abiotic stress conditions in Sorghum bicolor (L.). Int J Biol Macromol 2019; 142:822-834. [PMID: 31622710 DOI: 10.1016/j.ijbiomac.2019.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 10/02/2019] [Indexed: 11/24/2022]
Abstract
The small heat shock proteins (sHsps/Hsp20s) are the molecular chaperones that maintain proper folding, trafficking and disaggregation of proteins under diverse abiotic stress conditions. In the present investigation, a genome-wide scan revealed the presence of a total of 47 sHsps in Sorghum bicolor (SbsHsps), distributed across 10 subfamilies, the major subfamily being P (plastid) group with 17 genes. Chromosomes 1 and 3 appear as the hot spot regions for SbsHsps, and majority of them were found acidic, hydrophilic, unstable and intron less. Interestingly, promoter analysis indicated that they are associated with both biotic and abiotic stresses, as well as plant development. Sorghum sHsps exhibited 15 paralogous and 20 orthologous duplications. Expression analysis of 15 genes selected from different subfamilies showed high transcript levels in roots and leaves implying that they are likely to participate in the developmental processes. SbsHsp genes were highly induced by diverse abiotic stresses inferring their critical role in mediating the environmental stress responses. Gene expression data revealed that SbsHsp-02 is a candidate gene expressed in all the tissues under varied stress conditions tested. Our results contribute to the understanding of the complexity of SbsHsp genes and help to analyse them further for functional validation.
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Affiliation(s)
- M Nagaraju
- Department of Genetics, Osmania University, Hyderabad 500 007, India; Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad 500 007, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - S Anil Kumar
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun 248 007, India
| | - G Rajasheker
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - D Manohar Rao
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
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Singh RK, Shweta S, Muthamilarasan M, Rani R, Prasad M. Study on aquaporins of Setaria italica suggests the involvement of SiPIP3;1 and SiSIP1;1 in abiotic stress response. Funct Integr Genomics 2019; 19:587-596. [PMID: 30759293 DOI: 10.1007/s10142-018-00653-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 11/26/2022]
Abstract
Aquaporins are versatile proteins involved in several biological as well as molecular functions, and they have been extensively studied in various plant systems. Increasing evidences indicate their role in biotic and abiotic stresses, and therefore, studying these proteins in a naturally stress-tolerant crop would provide further insights into the roles of this important protein family. Given this, the present study was performed in foxtail millet (Setaria italica), a model plant for studying biofuel, stress tolerance, and C4 photosynthetic traits. The study identified 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), and 3 small basic intrinsic proteins (SIPs) in foxtail millet. The identified proteins and their corresponding genes were characterized using in silico approaches such as chromosomal localization, analysis of gene and protein properties, phylogenetic analysis, promoter analysis, and RNA-seq-derived expression profiling. The candidate genes identified through these analyses were studied for their expression in response to abiotic stresses (dehydration, salinity, and heat) as well as hormone treatments (abscisic acid, methyl jasmonate, and salicylic acid) in two contrasting cultivars of foxtail millet. The study showed that SiPIP3;1 and SiSIP1;1 were differentially expressed in both the cultivars in response to stress and hormone treatments. Overexpression of these genes in a heterologous yeast system also demonstrated that the transgenic cells were able to tolerate dehydration as well as salt stress which suggests the involvement of these proteins in the tolerance mechanism. Overall, the present study provides insights into structure and organization of the aquaporin gene family in foxtail millet and highlights the potential candidate genes for further functional characterizations.
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Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shweta Shweta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | - Rekha Rani
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Chen B, Feder ME, Kang L. Evolution of heat-shock protein expression underlying adaptive responses to environmental stress. Mol Ecol 2018; 27:3040-3054. [PMID: 29920826 DOI: 10.1111/mec.14769] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/03/2018] [Accepted: 06/07/2018] [Indexed: 12/27/2022]
Abstract
Heat-shock proteins (Hsps) and their cognates are primary mitigators of cell stress. With increasingly severe impacts of climate change and other human modifications of the biosphere, the ability of the heat-shock system to affect evolutionary fitness in environments outside the laboratory and to evolve in response is topic of growing importance. Since the last major reviews, several advances have occurred. First, demonstrations of the heat-shock response outside the laboratory now include many additional taxa and environments. Many of these demonstrations are only correlative, however. More importantly, technical advances in "omic" quantification of nucleic acids and proteins, genomewide association analysis, and manipulation of genes and their expression have enabled the field to move beyond correlation. Several consequent advances are already evident: The pathway from heat-shock gene expression to stress tolerance in nature can be extremely complex, mediated through multiple biological processes and systems, and even multiple species. The underlying genes are more numerous, diverse and variable than previously appreciated, especially with respect to their regulatory variation and epigenetic changes. The impacts and limitations (e.g., due to trade-offs) of natural selection on these genes have become more obvious and better established. At last, as evolutionary capacitors, Hsps may have distinctive impacts on the evolution of other genes and ecological consequences.
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Affiliation(s)
- Bing Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Martin E Feder
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Mishra D, Shekhar S, Singh D, Chakraborty S, Chakraborty N. Heat Shock Proteins and Abiotic Stress Tolerance in Plants. REGULATION OF HEAT SHOCK PROTEIN RESPONSES 2018. [DOI: 10.1007/978-3-319-74715-6_3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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48
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Pandey G, Yadav CB, Sahu PP, Muthamilarasan M, Prasad M. Salinity induced differential methylation patterns in contrasting cultivars of foxtail millet (Setaria italica L.). PLANT CELL REPORTS 2017; 36:759-772. [PMID: 27999979 DOI: 10.1007/s00299-016-2093-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/07/2016] [Indexed: 05/18/2023]
Abstract
Genome-wide methylation analysis of foxtail millet cultivars contrastingly differing in salinity tolerance revealed DNA demethylation events occurring in tolerant cultivar under salinity stress, eventually modulating the expression of stress-responsive genes. Reduced productivity and significant yield loss are the adverse effects of environmental conditions on physiological and biochemical pathways in crop plants. In this context, understanding the epigenetic machinery underlying the tolerance traits in a naturally stress tolerant crop is imperative. Foxtail millet (Setaria italica) is known for its better tolerance to abiotic stresses compared to other cereal crops. In the present study, methylation-sensitive amplified polymorphism (MSAP) technique was used to quantify the salt-induced methylation changes in two foxtail millet cultivars contrastingly differing in their tolerance levels to salt stress. The study highlighted that the DNA methylation level was significantly reduced in tolerant cultivar compared to sensitive cultivar. A total of 86 polymorphic MSAP fragments were identified, sequenced and functionally annotated. These fragments showed sequence similarity to several genes including ABC transporter, WRKY transcription factor, serine threonine-protein phosphatase, disease resistance, oxidoreductases, cell wall-related enzymes and retrotransposon and transposase like proteins, suggesting salt stress-induced methylation in these genes. Among these, four genes were chosen for expression profiling which showed differential expression pattern between both cultivars of foxtail millet. Altogether, the study infers that salinity stress induces genome-wide DNA demethylation, which in turn, modulates expression of corresponding genes.
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Affiliation(s)
- Garima Pandey
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Chandra Bhan Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Pranav Pankaj Sahu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | | | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India.
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Acharya BR, Roy Choudhury S, Estelle AB, Vijayakumar A, Zhu C, Hovis L, Pandey S. Optimization of Phenotyping Assays for the Model Monocot Setaria viridis. FRONTIERS IN PLANT SCIENCE 2017; 8:2172. [PMID: 29312412 PMCID: PMC5743732 DOI: 10.3389/fpls.2017.02172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/11/2017] [Indexed: 05/02/2023]
Abstract
Setaria viridis (green foxtail) is an important model plant for the study of C4 photosynthesis in panicoid grasses, and is fast emerging as a system of choice for the study of plant development, domestication, abiotic stress responses and evolution. Basic research findings in Setaria are expected to advance research not only in this species and its close relative S. italica (foxtail millet), but also in other panicoid grasses, many of which are important food or bioenergy crops. Here we report on the standardization of multiple growth and development assays for S. viridis under controlled conditions, and in response to several phytohormones and abiotic stresses. We optimized these assays at three different stages of the plant's life: seed germination and post-germination growth using agar plate-based assays, early seedling growth and development using germination pouch-based assays, and adult plant growth and development under environmentally controlled growth chambers and greenhouses. These assays will be useful for the community to perform large scale phenotyping analyses, mutant screens, comparative physiological analysis, and functional characterization of novel genes of Setaria or other related agricultural crops. Precise description of various growth conditions, effective treatment conditions and description of the resultant phenotypes will help expand the use of S. viridis as an effective model system.
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