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Zhang Q, Dai B, Fan M, Yang L, Li C, Hou G, Wang X, Gao H, Li J. Genome-wide profile analysis of the Hsp20 family in lettuce and identification of its response to drought stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1426719. [PMID: 39070912 PMCID: PMC11272627 DOI: 10.3389/fpls.2024.1426719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024]
Abstract
Heat shock protein 20 (Hsp20) plays a very important role in response to abiotic stressors such as drought; however, in lettuce (Lactuca sativa L.), this gene family is poorly understood. This study used bioinformatics methods to identify 36 members of the lettuce Hsp20 family, which were named LsHsp20-1~LsHsp20-36. Subcellular localization results revealed that 26 members of the LsHsp20 protein family localized to the cytoplasm and nucleus. Additionally, 15 conserved domains were identified in the LsHsp20 protein family, with the number of amino acids ranging from 8 to 50. Gene structure analysis revealed that 15 genes (41.7%) had no introns, and 20 genes (55.5%) had one intron. The proportion of the LsHsp20 secondary structure was random coil > alpha helix > extended strand > beta turn. Chromosome positioning analysis indicated that 36 genes were unevenly distributed on nine chromosomes, and four pairs of genes were collinear. The Ka/Ks ratio of the collinear genes was less than 1, indicating that purifying selection dominated during L. sativa evolution. Thirteen pairs of genes were collinear in lettuce and Arabidopsis, and 14 pairs of genes were collinear in lettuce and tomato. A total of 36 LsHsp20 proteins were divided into 12 subgroups based on phylogenetic analysis. Three types of cis-acting elements, namely, abiotic and biotic stress-responsive, plant hormone-responsive, and plant development-related elements, were identified in the lettuce LsHsp20 family. qRT-PCR was used to analyze the expression levels of 23 LsHsp20 genes that were significantly upregulated on the 7th or 14th day of drought treatment, and the expression levels of two genes (LsHsp20-12 and LsHsp20-26) were significantly increased by 153-fold and 273-fold on the 14th and 7th days of drought treatment, respectively. The results of this study provide comprehensive information for research on the LsHsp20 gene family in lettuce and lay a solid foundation for further elucidation of Hsp20 biological functions, providing valuable information on the regulatory mechanisms of the LsHsp20 family in lettuce drought resistance.
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Affiliation(s)
- Qinqin Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Bowen Dai
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Mi Fan
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Liling Yang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Chang Li
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Guangguang Hou
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiaofang Wang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Hongbo Gao
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Key Laboratory of North China Water-saving Irrigation Engineering, Hebei Agricultural University, Baoding, China
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding, China
| | - Jingrui Li
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Key Laboratory of North China Water-saving Irrigation Engineering, Hebei Agricultural University, Baoding, China
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding, China
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Song Z, Wang R, Zhang H, Tong Z, Yuan C, Li Y, Huang C, Zhao L, Wang Y, Di Y, Sui X. Comparative transcriptome analysis reveals nicotine metabolism is a critical component for enhancing stress response intensity of innate immunity system in tobacco. FRONTIERS IN PLANT SCIENCE 2024; 15:1338169. [PMID: 38595766 PMCID: PMC11003474 DOI: 10.3389/fpls.2024.1338169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/05/2024] [Indexed: 04/11/2024]
Abstract
The pyridine alkaloid nicotine acts as one of best-studied plant resistant traits in tobacco. Previous research has shown that NtERF199 and NtERF189, acting as master regulators within the NIC1 and NIC2 locus, quantitatively contribute to nicotine accumulation levels in N. tabacum. Genome editing-created Nic1(Nterf199) and Nic2 (Nterf189) double mutant provides an ideal platform for precisely dissecting the defensive role of nicotine and the connection between the nicotine biosynthetic pathway with other putative metabolic networks. Taking this advantage, we performed a comparative transcriptomic analysis to reevaluate the potential physiological and metabolic changes in response to nicotine synthesis defect by comparing the nic1nic2 and NIC1NIC2 plants. Our findings revealed that nicotine reduction could systematically diminishes the expression intensities of genes associated with stimulus perception, signal transduction and regulation, as well as secondary metabolic flux. Consequently, this global expression reduction might compromise tobacco adaptions to environmental fitness, herbivore resistances, and plant growth and development. The up-regulation of a novel set of stress-responsive and metabolic pathway genes might signify a newly established metabolic reprogramming to tradeoff the detrimental effect of nicotine loss. These results offer additional compelling evidence regarding nicotine's critical defensive role in nature and highlights the tight link between nicotine biosynthesis and gene expression levels of quantitative resistance-related genes for better environmental adaptation.
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Affiliation(s)
- Zhongbang Song
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Ruixue Wang
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hongbo Zhang
- Plant Functional Component Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Zhijun Tong
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Cheng Yuan
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Yong Li
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Changjun Huang
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Lu Zhao
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Yuehu Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yingtong Di
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xueyi Sui
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
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Zhou Y, Song R, Nevo E, Fu X, Wang X, Wang Y, Wang C, Chen J, Sun G, Sun D, Ren X. Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169679. [PMID: 38163608 DOI: 10.1016/j.scitotenv.2023.169679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
The information on how plant populations respond genetically to climate warming is scarce. Here, landscape genomic and machine learning approaches were integrated to assess genetic response of 10 wild barley (Hordeum vulgare ssp. spontaneum; WB) populations in the past and future, using whole genomic sequencing (WGS) data. The WB populations were sampled in 1980 and again in 2008. Phylogeny of accessions was roughly in conformity with sampling sites, which accompanied by admixture/introgressions. The 28-y climate warming resulted in decreased genetic diversity, increased selection pressure, and an increase in deleterious single nucleotide polymorphism (dSNP) numbers, heterozygous deleterious and total deleterious burdens for WB. Genome-environment associations identified some candidate genes belonging to peroxidase family (HORVU2Hr1G057450, HORVU4Hr1G052060 and HORVU4Hr1G057210) and heat shock protein 70 family (HORVU2Hr1G112630). The gene HORVU2Hr1G120170 identified by selective sweep analysis was under strong selection during the climate warming of the 28-y, and its derived haplotypes were fixed by WB when faced with the 28-y increasingly severe environment. Temperature variables were found to be more important than precipitation variables in influencing genomic variation, with an eco-physiological index gdd5 (growing degree-days at the baseline threshold temperature of 5 °C) being the most important determinant. Gradient forest modelling revealed higher predicted genomic vulnerability in Sede Boqer under future climate scenarios at 2041-2070 and 2071-2100. Additionally, estimates of effective population size (Ne) tracing back to 250 years indicated a forward decline in all populations over time. Our assessment about past genetic response and future vulnerability of WB under climate warming is crucial for informing conservation efforts for wild cereals and rational use strategies.
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Affiliation(s)
- Yu Zhou
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ruilian Song
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Eviator Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, 31905 Haifa, Israel
| | - Xiaoqin Fu
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaofang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yixiang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengyang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junpeng Chen
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Saint Mary's University, Halifax, NS B3H 3C3, Canada
| | - Dongfa Sun
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xifeng Ren
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Zhong L, Shi Y, Xu S, Xie S, Huang X, Li Y, Qu C, Liu J, Liao J, Huang Y, Liang Y. Heterologous overexpression of heat shock protein 20 genes of different species of yellow Camellia in Arabidopsis thaliana reveals their roles in high calcium resistance. BMC PLANT BIOLOGY 2024; 24:5. [PMID: 38163899 PMCID: PMC10759694 DOI: 10.1186/s12870-023-04686-x] [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: 06/26/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Yellow Camellia (Camellia sect. chrysantha) is a rare ornamental plant and an important germplasm resource globally. Camellia nitidissima thrives in normal acidic soils, while Camellia limonia can adapt to the calcareous soils found in karst areas. Our previous study on the karst adaptation of yellow camellias revealed that the expression levels of heat shock protein 20(HSP20) were higher in Camellia limonia than in Camellia nitidissima. However, the functions of the HSP20 gene of Camellia limonia remain unclear to data. In this study, the HSP20 genes of Camellia limonia (ClHSP20-OE lines) and Camellia. nitidissima (CnHSP20-OE lines) were cloned and overexpressed heterologously in Arabidopsis thaliana. Additionally, we overexpressed the HSP20 gene of Arabidopsis (AtHSP20-OE lines) was also overexpressed, and the T-DNA inserted mutants (athspmutant lines) were also used to determine the functions of HSP20 genes. Under high calcium stress, the chlorophyll, nitrogen, water content and humidity of leaves were increased in ClHSP20-OE lines, while those of other lines were declined. The size of the stomatal apertures, stomatal conductance, and the photosynthetic efficiency of ClHSP20-OE lines were higher than those of the other lines. However, the accumulation of H2O2 and O2- in the leaves of ClHSP20-OE lines was the lowest among all the lines. Energy spectrum scanning revealed that the percentage of calcium on the surfaces of the leaves of ClHSP20-OE lines was relatively low, while that of athspmutant lines was the highest. The ClHSP20 gene can also affected soil humidity and the contents of soil nitrogen, phosphorus, and potassium. Transcriptome analysis revealed that the expressions of FBA5 and AT5G10770 in ClHSP20-OE lines was significantly up-regulated compared to that of CnHSP20-OE lines. Compared to that of athspmutant lines, the expressions of DREB1A and AT3G30460 was significantly upregulated in AtHSP20-OE lines, and the expression of POL was down-regulated. Our findings suggest that the HSP20 gene plays a crucial role in maintained photosynthetic rate and normal metabolism by regulating the expression of key genes under high-calcium stress. This study elucidates the mechanisms underlying the karst adaptation in Camellia. limonia and provides novel insights for future research on karst plants.
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Affiliation(s)
- Lisha Zhong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China
| | - Yuxing Shi
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China
| | - Shaolei Xu
- School of Mechanical and Electrical Engineering, Guilin University of Electronic Technology, Guilin, China
| | - Sisi Xie
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China
| | - Xinhui Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China
| | - Yujie Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China
| | - Chaofan Qu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China
| | - Jianxiu Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China
| | - Jialin Liao
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China
| | - Yang Huang
- School of Mechanical and Electrical Engineering, Guilin University of Electronic Technology, Guilin, China.
| | - Yu Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China.
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Zhang C, Zhang Y, Su Z, Shen Z, Song H, Cai Z, Xu J, Guo L, Zhang Y, Guo S, Sun M, Li S, Yu M. Integrated analysis of HSP20 genes in the developing flesh of peach: identification, expression profiling, and subcellular localization. BMC PLANT BIOLOGY 2023; 23:663. [PMID: 38129812 PMCID: PMC10740231 DOI: 10.1186/s12870-023-04621-0] [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: 03/14/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Plant HSP20s are not only synthesized in response to heat stress but are also involved in plant biotic and abiotic stress resistance, normal metabolism, development, differentiation, survival, ripening, and death. Thus, HSP20 family genes play very important and diverse roles in plants. To our knowledge, HSP20 family genes in peach have not yet been characterized in detail, and little is known about their possible function in the development of red flesh in peach. RESULTS In total, 44 PpHSP20 members were identified in the peach genome in this study. Forty-four PpHSP20s were classified into 10 subfamilies, CI, CII, CIII, CV, CVI, CVII, MII, CP, ER, and Po, containing 18, 2, 2, 10, 5, 1, 1, 2, 1, and 2 proteins, respectively. Among the 44 PpHSP20 genes, 6, 4, 4, 3, 7, 11, 5, and 4 PpHSP20 genes were located on chromosomes 1 to 8, respectively. In particular, approximately 15 PpHSP20 genes were located at both termini or one terminus of each chromosome. A total of 15 tandem PpHSP20 genes were found in the peach genome, which belonged to five tandemly duplicated groups. Overall, among the three cultivars, the number of PpHSP20 genes with higher expression levels in red flesh was greater than that in yellow or white flesh. The expression profiling for most of the PpHSP20 genes in the red-fleshed 'BJ' was higher overall at the S3 stage than at the S2, S4-1, and S4-2 stages, with the S3 stage being a very important period of transformation from a white color to the gradual anthocyanin accumulation in the flesh of this cultivar. The subcellular localizations of 16 out of 19 selected PpHSP20 proteins were in accordance with the corresponding subfamily classification and naming. Additionally, to our knowledge, Prupe.3G034800.1 is the first HSP20 found in plants that has the dual targets of both the endoplasmic reticulum and nucleus. CONCLUSIONS This study provides a comprehensive understanding of PpHSP20s, lays a foundation for future analyses of the unknown function of PpHSP20 family genes in red-fleshed peach fruit and advances our understanding of plant HSP20 genes.
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Affiliation(s)
- Chunhua Zhang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Yanping Zhang
- Suzhou Polytechnic Institute of Agriculture, Suzhou, Jiangsu Province, China
| | - Ziwen Su
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Zhijun Shen
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Hongfeng Song
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Zhixiang Cai
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Jianlan Xu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Lei Guo
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Yuanyuan Zhang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Shaolei Guo
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Meng Sun
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Shenge Li
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China
| | - Mingliang Yu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province, China.
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Yan W, Liu X, Wang X. The heat shock protein 20 gene family in large yellow croaker (Larimichthys crocea): Identification, phylogenetic relationships, expression analyses. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 264:106700. [PMID: 37837866 DOI: 10.1016/j.aquatox.2023.106700] [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: 08/14/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/16/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is an economically important fish in China, but its aquaculture industry has been threatened by both biotic and abiotic stressors such as hypoxia and pathogens. In the current study, hsp20 genes were identified and analyzed systematically for the first time from the genome of large yellow croaker, and their roles in hypoxia response and Aeromonas hydrophila, Pseudomonas plecoglossicida infection were investigated. Herein, 11 hsp20 genes were identified and annotated, phylogenetic analysis and selection pressure analysis showed that the hsp20 genes were evolutionarily-constrained and their function was conserved among fishes. Besides, we observed the expression patterns of the hsp20 genes under hypoxia and two pathogens' stress. In brief, seven, four, seven genes responded to hypoxia stress, A. hydrophila infection and P. plecoglossicida challenge, respectively, which indicated that they were involved in hypoxia and disease responses. Furthermore, pathogen- and time-specific pattern was observed after A. hydrophila and P. plecoglossicida infection whereas tissue-specific pattern was observed after hypoxia exposure, revealing that hsp20 genes showed differential functions in response to hypoxia and immune stress. Taken together, these results provided preliminary information for future analysis of the roles of hsp20 genes in both biotic and abiotic stress response in fish.
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Affiliation(s)
- Weijie Yan
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of marine biotechnology and Engineering, Ningbo University, China.
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Liu M, Zhao G, Huang X, Pan T, Chen W, Qu M, Ouyang B, Yu M, Shabala S. Candidate regulators of drought stress in tomato revealed by comparative transcriptomic and proteomic analyses. FRONTIERS IN PLANT SCIENCE 2023; 14:1282718. [PMID: 37936934 PMCID: PMC10627169 DOI: 10.3389/fpls.2023.1282718] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023]
Abstract
Drought is among the most common abiotic constraints of crop growth, development, and productivity. Integrating different omics approaches offers a possibility for deciphering the metabolic pathways and fundamental mechanisms involved in abiotic stress tolerance. Here, we explored the transcriptional and post-transcriptional changes in drought-stressed tomato plants using transcriptomic and proteomic profiles to determine the molecular dynamics of tomato drought stress responses. We identified 22467 genes and 5507 proteins, among which the expression of 3765 genes and 294 proteins was significantly changed under drought stress. Furthermore, the differentially expressed genes (DEGs) and differentially abundant proteins (DAPs) showed a good correlation (0.743). The results indicated that integrating different omics approaches is promising in exploring the multilayered regulatory mechanisms of plant drought resistance. Gene ontology (GO) and pathway analysis identified several GO terms and pathways related to stress resistance, including response to stress, abiotic stimulus, and oxidative stress. The plant hormone abscisic acid (ABA) plays pivotal roles in response to drought stress, ABA-response element binding factor (AREB) is a key positive regulator of ABA signaling. Moreover, our analysis indicated that drought stress increased the abscisic acid (ABA) content, which activated AREB1 expression to regulate the expression of TAS14, GSH-Px-1, and Hsp, ultimately improving tomato drought resistance. In addition, the yeast one-hybrid assay demonstrated that the AREB1 could bind the Hsp promoter to activate Hsp expression. Thus, this study involved a full-scale analysis of gene and protein expression in drought-stressed tomato, deepening the understanding of the regulatory mechanisms of the essential drought-tolerance genes in tomato.
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Affiliation(s)
- Minmin Liu
- International Research Centre for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, China
| | - Gangjun Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xin Huang
- International Research Centre for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, China
| | - Ting Pan
- International Research Centre for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, China
| | - Wenjie Chen
- International Research Centre for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, China
| | - Mei Qu
- International Research Centre for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Min Yu
- International Research Centre for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, China
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology and Department of Horticulture, Foshan University, Foshan, China
- School of Biological Science, University of Western Australia, Crawley, WA, Australia
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Muthusamy SK, Pushpitha P, Makeshkumar T, Sheela MN. Genome-wide identification and expression analysis of Hsp70 family genes in Cassava ( Manihot esculenta Crantz). 3 Biotech 2023; 13:341. [PMID: 37705861 PMCID: PMC10495308 DOI: 10.1007/s13205-023-03760-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
Hsp70 proteins function as molecular chaperones, regulating various cellular processes in plants. In this study, a genome-wide analysis led to the identification of 22 Hsp70 (MeHsp70) genes in cassava. Phylogenetic relationship studies with other Malpighiales genomes (Populus trichocarpa, Ricinus communis and Salix purpurea) classified MeHsp70 proteins into eight groups (Ia, Ib, Ic, Id, Ie, If, IIa and IIb). Promoter analysis of MeHsp70 genes revealed the presence of tissue-specific, light, biotic and abiotic stress-responsive cis-regulatory elements showing their functional importance in cassava. Meta-analysis of publically available RNA-seq transcriptome datasets showed constitutive, tissue-specific, biotic and abiotic stress-specific expression patterns among MeHsp70s in cassava. Among 22 Hsp70, six MeHsp70s viz., MecHsp70-3, MecHsp70-6, MeBiP-1, MeBiP-2, MeBiP-3 and MecpHsp70-2 displayed constitutive expression, while three MecHsp70s were induced under both drought and cold stress conditions. Five MeHsp70s, MecHsp70-7, MecHsp70-11, MecHsp70-12, MecHsp70-13, and MecHsp70-14 were induced under drought stress conditions. We predicted that 19 MeHsp70 genes are under the regulation of 24 miRNAs. This comprehensive genome-wide analysis of the Hsp70 gene family in cassava provided valuable insights into their functional roles and identified various potential Hsp70 genes associated with stress tolerance and adaptation to environmental stimuli. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03760-3.
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Affiliation(s)
- Senthilkumar K. Muthusamy
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - P. Pushpitha
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - T. Makeshkumar
- Division of Crop Protection, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - M. N. Sheela
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
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Cai H, Wang H, Zhou L, Li B, Zhang S, He Y, Guo Y, You A, Jiao C, Xu Y. Time-Series Transcriptomic Analysis of Contrasting Rice Materials under Heat Stress Reveals a Faster Response in the Tolerant Cultivar. Int J Mol Sci 2023; 24:9408. [PMID: 37298358 PMCID: PMC10253628 DOI: 10.3390/ijms24119408] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/13/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Short-term heat stress can affect the growth of rice (Oryza sativa L.) seedlings, subsequently decreasing yields. Determining the dynamic response of rice seedlings to short-term heat stress is highly important for accelerating research on rice heat tolerance. Here, we observed the seedling characteristics of two contrasting cultivars (T11: heat-tolerant and T15: heat-sensitive) after different durations of 42 °C heat stress. The dynamic transcriptomic changes of the two cultivars were monitored after 0 min, 10 min, 30 min, 1 h, 4 h, and 10 h of stress. The results indicate that several pathways were rapidly responding to heat stress, such as protein processing in the endoplasmic reticulum, glycerophospholipid metabolism, and plant hormone signal transduction. Functional annotation and cluster analysis of differentially expressed genes at different stress times indicate that the tolerant cultivar responded more rapidly and intensively to heat stress compared to the sensitive cultivar. The MAPK signaling pathway was found to be the specific early-response pathway of the tolerant cultivar. Moreover, by combining data from a GWAS and RNA-seq analysis, we identified 27 candidate genes. The reliability of the transcriptome data was verified using RT-qPCR on 10 candidate genes and 20 genes with different expression patterns. This study provides valuable information for short-term thermotolerance response mechanisms active at the rice seedling stage and lays a foundation for breeding thermotolerant varieties via molecular breeding.
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Affiliation(s)
- Haiya Cai
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (H.C.); (L.Z.); (S.Z.); (Y.H.); (Y.G.); (A.Y.)
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
| | - Hongpan Wang
- College of Agriculture, Yangtze University, Jingzhou 434025, China; (H.W.); (B.L.)
| | - Lei Zhou
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (H.C.); (L.Z.); (S.Z.); (Y.H.); (Y.G.); (A.Y.)
| | - Bo Li
- College of Agriculture, Yangtze University, Jingzhou 434025, China; (H.W.); (B.L.)
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (H.C.); (L.Z.); (S.Z.); (Y.H.); (Y.G.); (A.Y.)
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
| | - Yonggang He
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (H.C.); (L.Z.); (S.Z.); (Y.H.); (Y.G.); (A.Y.)
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
| | - Ying Guo
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (H.C.); (L.Z.); (S.Z.); (Y.H.); (Y.G.); (A.Y.)
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
| | - Aiqing You
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (H.C.); (L.Z.); (S.Z.); (Y.H.); (Y.G.); (A.Y.)
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (H.C.); (L.Z.); (S.Z.); (Y.H.); (Y.G.); (A.Y.)
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (H.C.); (L.Z.); (S.Z.); (Y.H.); (Y.G.); (A.Y.)
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
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10
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Feng H, Wu M, Wang Z, Wang X, Chen J, Yang J, Liu P. Genome-Wide Identification and Functional Analysis of NAP1 in Triticum aestivum. Genes (Basel) 2023; 14:genes14051041. [PMID: 37239401 DOI: 10.3390/genes14051041] [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: 03/08/2023] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
As a main molecular chaperone of histone H2A-H2B, nucleosome assembly protein 1 (NAP1) has been widely researched in many species. However, there is little research investigating the function of NAP1 in Triticum aestivum. To understand the capabilities of the family of NAP1 genes in wheat and the relationship between TaNAP1 genes and plant viruses, we performed comprehensive genome-wide analysis and quantitative real-time polymerase chain reaction (qRT-PCR) for testing expression profiling under hormonal and viral stresses. Our results showed that TaNAP1 was expressed at different levels in different tissues, with higher expression in tissues with high meristematic capacity, such as roots. Furthermore, the TaNAP1 family may participate in plant defense mechanisms. This study provides a systematic analysis of the NAP1 gene family in wheat and lays the foundation for further studies on the function of TaNAP1 in the response of wheat plants to viral infection.
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Affiliation(s)
- Huimin Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Mila Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Ziqiong Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xia Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Peng Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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11
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Licaj I, Di Meo MC, Fiorillo A, Samperna S, Marra M, Rocco M. Comparative Analysis of the Response to Polyethylene Glycol-Simulated Drought Stress in Roots from Seedlings of "Modern" and "Ancient" Wheat Varieties. PLANTS (BASEL, SWITZERLAND) 2023; 12:428. [PMID: 36771510 PMCID: PMC9921267 DOI: 10.3390/plants12030428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Durum wheat is widely cultivated in the Mediterranean, where it is the basis for the production of high added-value food derivatives such as pasta. In the next few years, the detrimental effects of global climate change will represent a serious challenge to crop yields. For durum wheat, the threat of climate change is worsened by the fact that cultivation relies on a few genetically uniform, elite varieties, better suited to intensive cultivation than "traditional" ones but less resistant to environmental stress. Hence, the renewed interest in "ancient" traditional varieties are expected to be more tolerant to environmental stress as a source of genetic resources to be exploited for the selection of useful agronomic traits such as drought tolerance. The aim of this study was to perform a comparative analysis of the effect and response of roots from the seedlings of two durum wheat cultivars: Svevo, a widely cultivated elite variety, and Saragolla, a traditional variety appreciated for its organoleptic characteristics, to Polyethylene glycol-simulated drought stress. The effect of water stress on root growth was analyzed and related to biochemical data such as hydrogen peroxide production, electrolyte leakage, membrane lipid peroxidation, proline synthesis, as well as to molecular data such as qRT-PCR analysis of drought responsive genes and proteomic analysis of changes in the protein repertoire of roots from the two cultivars.
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Affiliation(s)
- Ilva Licaj
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Maria Chiara Di Meo
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Anna Fiorillo
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy
| | - Simone Samperna
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy
| | - Mauro Marra
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy
| | - Mariapina Rocco
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
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12
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Govindasamy P, Muthusamy SK, Bagavathiannan M, Mowrer J, Jagannadham PTK, Maity A, Halli HM, G. K. S, Vadivel R, T. K. D, Raj R, Pooniya V, Babu S, Rathore SS, L. M, Tiwari G. Nitrogen use efficiency-a key to enhance crop productivity under a changing climate. FRONTIERS IN PLANT SCIENCE 2023; 14:1121073. [PMID: 37143873 PMCID: PMC10151540 DOI: 10.3389/fpls.2023.1121073] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/20/2023] [Indexed: 05/06/2023]
Abstract
Nitrogen (N) is an essential element required for the growth and development of all plants. On a global scale, N is agriculture's most widely used fertilizer nutrient. Studies have shown that crops use only 50% of the applied N effectively, while the rest is lost through various pathways to the surrounding environment. Furthermore, lost N negatively impacts the farmer's return on investment and pollutes the water, soil, and air. Therefore, enhancing nitrogen use efficiency (NUE) is critical in crop improvement programs and agronomic management systems. The major processes responsible for low N use are the volatilization, surface runoff, leaching, and denitrification of N. Improving NUE through agronomic management practices and high-throughput technologies would reduce the need for intensive N application and minimize the negative impact of N on the environment. The harmonization of agronomic, genetic, and biotechnological tools will improve the efficiency of N assimilation in crops and align agricultural systems with global needs to protect environmental functions and resources. Therefore, this review summarizes the literature on nitrogen loss, factors affecting NUE, and agronomic and genetic approaches for improving NUE in various crops and proposes a pathway to bring together agronomic and environmental needs.
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Affiliation(s)
- Prabhu Govindasamy
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Senthilkumar K. Muthusamy
- Division of Crop Improvement, Indian Council of Agricultural Research (ICAR)-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - Muthukumar Bagavathiannan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Jake Mowrer
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | | | - Aniruddha Maity
- Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Hanamant M. Halli
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Sujayananad G. K.
- Crop Protection, Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulse Research, Kanpur, India
| | - Rajagopal Vadivel
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Das T. K.
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rishi Raj
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Vijay Pooniya
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Subhash Babu
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sanjay Singh Rathore
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Muralikrishnan L.
- Division of Agricultural Extension, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gopal Tiwari
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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13
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Hu Y, Li M, Hu Y, Han D, Wei J, Zhang T, Guo J, Shi L. Wild soybean salt tolerance metabolic model: Assessment of storage protein mobilization in cotyledons and C/N balance in the hypocotyl/root axis. PHYSIOLOGIA PLANTARUM 2023; 175:e13863. [PMID: 36688582 DOI: 10.1111/ppl.13863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/19/2022] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Salt stress has become one of the main factors limiting crop yield in recent years. The post-germinative growth is most sensitive to salt stress in soybean. In this study, cultivated and wild soybeans were used for an integrated metabonomics and transcriptomics analysis to determine whether wild soybean can resist salt stress by maintaining the mobilization of stored substances in cotyledons and the balance of carbon and nitrogen in the hypocotyl/root axis (HRA). Compared with wild soybean, the growth of cultivated soybean was significantly inhibited during the post-germinative growth period under salt stress. Integrating analysis found that the breakdown products of proteins, such as glutamate, glutamic acid, aspartic acid, and asparagine, increased significantly in wild soybean cotyledons. Asparagine synthase and fumarate hydratase genes and genes encoding HSP20 family proteins were specifically upregulated. In wild soybean HRA, levels of glutamic acid, aspartic acid, asparagine, citric acid, and succinic acid increased significantly, and the glutamate decarboxylase gene and the gene encoding carbonic anhydrase in nitrogen metabolism were significantly upregulated. The metabolic model indicated that wild soybean enhanced the decomposition of stored proteins and the transport of amino acids to the HRA in cotyledons and the GABA shunt to maintain carbon and nitrogen balance in the HRA to resist salt stress. This study provided a theoretical basis for cultivating salt-tolerant soybean varieties and opened opportunities for the development of sustainable agricultural practices.
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Affiliation(s)
- Yunan Hu
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Mingxia Li
- School of Life Sciences, ChangChun Normal University, Changchun, China
| | - Yongjun Hu
- School of Life Sciences, ChangChun Normal University, Changchun, China
| | - Defu Han
- School of Life Sciences, ChangChun Normal University, Changchun, China
| | - Jian Wei
- School of Life Sciences, ChangChun Normal University, Changchun, China
| | - Tao Zhang
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Jixun Guo
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Lianxuan Shi
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
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14
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Vu AT, Utsumi Y, Utsumi C, Tanaka M, Takahashi S, Todaka D, Kanno Y, Seo M, Ando E, Sako K, Bashir K, Kinoshita T, Pham XH, Seki M. Ethanol treatment enhances drought stress avoidance in cassava (Manihot esculenta Crantz). PLANT MOLECULAR BIOLOGY 2022; 110:269-285. [PMID: 35969295 DOI: 10.1007/s11103-022-01300-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
External application of ethanol enhances tolerance to high salinity, drought, and heat stress in various plant species. However, the effects of ethanol application on increased drought tolerance in woody plants, such as the tropical crop "cassava," remain unknown. In the present study, we analyzed the morphological, physiological, and molecular responses of cassava plants subjected to ethanol pretreatment and subsequent drought stress treatment. Ethanol pretreatment induced a slight accumulation of abscisic acid (ABA) and stomatal closure, resulting in a reduced transpiration rate, higher water content in the leaves during drought stress treatment and the starch accumulation in leaves. Transcriptomic analysis revealed that ethanol pretreatment upregulated the expression of ABA signaling-related genes, such as PP2Cs and AITRs, and stress response and protein-folding-related genes, such as heat shock proteins (HSPs). In addition, the upregulation of drought-inducible genes during drought treatment was delayed in ethanol-pretreated plants compared with that in water-pretreated control plants. These results suggest that ethanol pretreatment induces stomatal closure through activation of the ABA signaling pathway, protein folding-related response by activating the HSP/chaperone network and the changes in sugar and starch metabolism, resulting in increased drought avoidance in plants.
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Affiliation(s)
- Anh Thu Vu
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Yoshinori Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Chikako Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Satoshi Takahashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Daisuke Todaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuri Kanno
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mitsunori Seo
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Eigo Ando
- Department of Biological Sciences, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Kaori Sako
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, 631-8505, Japan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Department of Life Sciences, Lahore University of Management Sciences, Lahore, Pakistan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Xuan Hoi Pham
- Agricultural Genetics Institute, Pham Van Dong Road, Bac Tu Lie District, Ha Noi, Vietnam
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan.
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15
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Barreto P, Koltun A, Nonato J, Yassitepe J, Maia IDG, Arruda P. Metabolism and Signaling of Plant Mitochondria in Adaptation to Environmental Stresses. Int J Mol Sci 2022; 23:ijms231911176. [PMID: 36232478 PMCID: PMC9570015 DOI: 10.3390/ijms231911176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
The interaction of mitochondria with cellular components evolved differently in plants and mammals; in plants, the organelle contains proteins such as ALTERNATIVE OXIDASES (AOXs), which, in conjunction with internal and external ALTERNATIVE NAD(P)H DEHYDROGENASES, allow canonical oxidative phosphorylation (OXPHOS) to be bypassed. Plant mitochondria also contain UNCOUPLING PROTEINS (UCPs) that bypass OXPHOS. Recent work revealed that OXPHOS bypass performed by AOXs and UCPs is linked with new mechanisms of mitochondrial retrograde signaling. AOX is functionally associated with the NO APICAL MERISTEM transcription factors, which mediate mitochondrial retrograde signaling, while UCP1 can regulate the plant oxygen-sensing mechanism via the PRT6 N-Degron. Here, we discuss the crosstalk or the independent action of AOXs and UCPs on mitochondrial retrograde signaling associated with abiotic stress responses. We also discuss how mitochondrial function and retrograde signaling mechanisms affect chloroplast function. Additionally, we discuss how mitochondrial inner membrane transporters can mediate mitochondrial communication with other organelles. Lastly, we review how mitochondrial metabolism can be used to improve crop resilience to environmental stresses. In this respect, we particularly focus on the contribution of Brazilian research groups to advances in the topic of mitochondrial metabolism and signaling.
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Affiliation(s)
- Pedro Barreto
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista, Botucatu 18618-970, Brazil
| | - Alessandra Koltun
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, Brazil
| | - Juliana Nonato
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, Brazil
| | - Juliana Yassitepe
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, Brazil
- Embrapa Agricultura Digital, Campinas 13083-886, Brazil
| | - Ivan de Godoy Maia
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista, Botucatu 18618-970, Brazil
| | - Paulo Arruda
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Correspondence:
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16
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Wang H, Dong Z, Chen J, Wang M, Ding Y, Xue Q, Liu W, Niu Z, Ding X. Genome-wide identification and expression analysis of the Hsp20, Hsp70 and Hsp90 gene family in Dendrobium officinale. FRONTIERS IN PLANT SCIENCE 2022; 13:979801. [PMID: 36035705 PMCID: PMC9399769 DOI: 10.3389/fpls.2022.979801] [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: 06/28/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Dendrobium officinale, an important orchid plant with great horticultural and medicinal values, frequently suffers from abiotic or biotic stresses in the wild, which may influence its well-growth. Heat shock proteins (Hsps) play essential roles in the abiotic stress response of plants. However, they have not been systematically investigated in D. officinale. Here, we identified 37 Hsp20 genes (DenHsp20s), 43 Hsp70 genes (DenHsp70s) and 4 Hsp90 genes (DenHsp90s) in D. officinale genome. These genes were classified into 8, 4 and 2 subfamilies based on phylogenetic analysis and subcellular predication, respectively. Sequence analysis showed that the same subfamily members have relatively conserved gene structures and similar protein motifs. Moreover, we identified 33 pairs of paralogs containing 30 pairs of tandem duplicates and 3 pairs of segmental duplicates among these genes. There were 7 pairs in DenHsp70s under positive selection, which may have important functions in helping cells withstand extreme stress. Numerous gene promoter sequences contained stress and hormone response cis-elements, especially light and MeJA response elements. Under MeJA stress, DenHsp20s, DenHsp70s and DenHsp90s responded to varying degrees, among which DenHsp20-5,6,7,16 extremely up-regulated, which may have a strong stress resistance. Therefore, these findings could provide useful information for evolutional and functional investigations of Hsp20, Hsp70 and Hsp90 genes in D. officinale.
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Affiliation(s)
- Hongman Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobium, Nanjing, China
| | - Zuqi Dong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobium, Nanjing, China
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Jianbing Chen
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Meng Wang
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Yuting Ding
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobium, Nanjing, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobium, Nanjing, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobium, Nanjing, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobium, Nanjing, China
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17
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BAG9 Confers Thermotolerance by Regulating Cellular Redox Homeostasis and the Stability of Heat Shock Proteins in Solanum lycopersicum. Antioxidants (Basel) 2022; 11:antiox11081467. [PMID: 36009189 PMCID: PMC9404849 DOI: 10.3390/antiox11081467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
The Bcl-2-associated athanogene (BAG) family, a group of co-chaperones that share conservative domains in flora and fauna, is involved in plant growth, development, and stress tolerance. However, the function of tomato BAG genes on thermotolerance remains largely unknown. Herein, we found that the expression of BAG9 was induced during heat stress in tomato plants. Knockout of the BAG9 gene by CRISPR/Cas9 reduced, while its overexpression increased thermotolerance in tomato plants as reflected by the phenotype, photosynthesis rate, and membrane peroxidation. Heat-induced reactive oxygen species and oxidative/oxidized proteins were further increased in bag9 mutants and were normalized in BAG9 overexpressing plants. Furthermore, the activities of antioxidant enzymes, ascorbic acid (AsA)/dehydroascorbic acid (DHA), and reduced glutathione (GSH)/oxidized glutathione (GSSG) were reduced in bag9 mutants and were increased in BAG9 overexpressing plants under heat stress. Additionally, BAG9 interacted with Hsp20 proteins in vitro and in vivo. Accumulation of Hsp proteins induced by heat showed a reduction in bag9 mutants; meanwhile, it was increased in BAG9 overexpressing plants. Thus, BAG9 played a crucial role in response to heat stress by regulating cellular redox homeostasis and the stability of heat shock proteins.
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18
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Huang Y, Liu J, Li J, Sun M, Duan Y. The heat shock protein 20 gene editing suppresses mycelial growth of Botryosphaeria dothidea and decreases its pathogenicity to postharvest apple fruits. Front Microbiol 2022; 13:930012. [PMID: 35966691 PMCID: PMC9363843 DOI: 10.3389/fmicb.2022.930012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Apple ring rot caused by Botryosphaeria dothidea is an essential and prevalent disease in the apple orchard in China. Our previous study demonstrated that dimethyl trisulfide (DT) from Chinese leek (Allium tuberosum) significantly suppressed the mycelial growth of B. dothidea and inhibited the incidence of apple ring rot postharvest. However, the mechanism underlying the inhibitory role of DT against B. dothidea is not fully understood. Comparing the control and the DT-treated B. dothidea mycelial transcriptomes revealed that heat shock protein 20 (Hsp20) strongly responded to DT treatment. This study identified four Hsp20 genes throughout the B. dothidea genome (BdHsp20_1-4). Each BdHsp20 gene had a conserved ACD with a variable N-terminal region and a short C-terminal extension. The segmental duplication event has contributed to the expansion of the BdHsp20 gene family. Compared to the wild-type strain, the CRISPR/Cas9 gene-edited BdHsp20 mutant (ΔBdHsp20) decreased the mycelial growth by 55.95% and reduced the disease symptom in postharvest apple fruit by 96.34%. However, the BdHsp20 complemented strain (ΔBdHsp20_C) significantly restored the growth and pathogenicity, which suggested that the BdHsp20 gene was closely involved in the growth and pathogenicity of B. dothidea. This study would accelerate the exploration of the molecular mechanism of the inhibitory effect of DT against B. dothidea and also provide new insights for the management of apple ring rot disease.
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Affiliation(s)
- Yonghong Huang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
- *Correspondence: Yonghong Huang
| | - Junping Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Jinghui Li
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Meng Sun
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Yanxin Duan
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
- Yanxin Duan
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Wu J, Gao T, Hu J, Zhao L, Yu C, Ma F. Research advances in function and regulation mechanisms of plant small heat shock proteins (sHSPs) under environmental stresses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:154054. [PMID: 35202686 DOI: 10.1016/j.scitotenv.2022.154054] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 05/27/2023]
Abstract
Plants respond to various stresses by triggering the expression of genes that encode proteins involved in plant growth, fruit ripening, cellular protein homeostasis, and tolerance systems. sHSPs, a subfamily of heat shock proteins (HSPs), can be expressed in plants to inhibit abnormal aggregation of proteins and protect normal proteins by interacting with folding target proteins, protect cell integrity, and improve resistance under various adverse conditions. Thus, sHSPs have significant influences on seed germination and plant development. In this review, the classification, structure, and functions of sHSP family members in plants are systematically summarized, with emphasis on their roles in promoting fruit ripening and plant growth by reducing the accumulation of ROS, improving the survival rate of plants and the antioxidant activity, and protecting photosynthesis under biotic and abiotic stresses. Meanwhile, the production and regulatory mechanisms of sHSPs are described in detail. Heat shock factors, long non-coding RNA (lncRNAs), microRNA (miRNAs), and FK506 binding proteins are related to the production process of sHSPs. Molecular chaperone complex HSP70/100, plastidic proteins, and abscisic acid (ABA) are involved in the regulatory mechanisms of sHSPs. Besides, scientific efforts and practices for improving plant stress resistance have carried out the constitutive expression of sHSPs in transgenic plants in recent years. It is a powerful path for inducing the protective mechanisms of plants under various stresses. Therefore, exploring the role of sHSPs in the plant defense system paves a way for comprehensively unraveling plant tolerance in response to biotic and abiotic stress.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China.
| | - Tian Gao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Jianing Hu
- Dalian Neusoft University of Information, Dalian 116032, People's Republic of China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Chang Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China.
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20
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Sun Y, Hu D, Xue P, Wan X. Identification of the DcHsp20 gene family in carnation (Dianthus caryophyllus) and functional characterization of DcHsp17.8 in heat tolerance. PLANTA 2022; 256:2. [PMID: 35624182 DOI: 10.1007/s00425-022-03915-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/11/2022] [Indexed: 05/09/2023]
Abstract
33 heat shock protein 20 (Hsp20) genes were identified from the carnation genome whose expression were altered by abiotic stresses. DcHsp17.8 may function to improve the heat resistance of Arabidopsis. Heat shock proteins 20 (Hsp20s) mainly function as molecular chaperones that play crucial roles in relieving abiotic stresses such as heat stress. In this study, we identified and characterized 33 DcHsp20 genes from the carnation genome that were classified into 9 subfamilies. Gene structure analysis showed that 25 DcHsp20 genes contained 1 intron whilst the remaining 8 DcHsp20 genes did not contain introns. Motif analysis found that DcHsp20 proteins were relatively conserved. Cis-regulatory elements analysis of the Hsp20 promoters revealed a number of cis-regulatory elements that regulate growth and development, hormone and stress responses. Gene expression analysis revealed that DcHsp20 genes had multiple response patterns to heat stress. The largest range of induction occurred in DcHsp17.8 after 1 h of heat stress. Under cold stress, or treatment with saline or abscisic acid, the expression of most DcHsp20 genes was inhibited. To further understand the function of DcHsp20 genes in response to heat stress, we overexpressed DcHsp17.8 in Arabidopis and the plants showed improved heat tolerance, O2- and H2O2 activities and photosynthetic capacity with reduced relative electrolyte leakage and malondialdehyde content. Gene expression analysis revealed that DcHsp17.8 modulated the expression of genes involved in antioxidant enzyme synthesis. Our data provided a solid foundation for the further detailed study of DcHsp20 genes.
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Affiliation(s)
- Yuying Sun
- College of Landscape and Forestry, Qingdao Agricultural University, No.100, Changcheng Road, Chengyang District, Qingdao, 266109, Shandong, People's Republic of China
| | - Diandian Hu
- College of Landscape and Forestry, Qingdao Agricultural University, No.100, Changcheng Road, Chengyang District, Qingdao, 266109, Shandong, People's Republic of China
| | - Pengcheng Xue
- College of Landscape and Forestry, Qingdao Agricultural University, No.100, Changcheng Road, Chengyang District, Qingdao, 266109, Shandong, People's Republic of China
| | - Xueli Wan
- College of Landscape and Forestry, Qingdao Agricultural University, No.100, Changcheng Road, Chengyang District, Qingdao, 266109, Shandong, People's Republic of China.
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21
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Influence of Seed Quality Stimulation in “Khao Dawk Mali 105” Rough Rice during the Deterioration Period Using an Automatic Soaking and Germination Accelerator Unit and Infrared Radiation Treatment. AGRIENGINEERING 2022. [DOI: 10.3390/agriengineering4020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
This study aimed to improve the seed quality during the deterioration period of rough rice (Oryza sativa L.), cultivar ‘Khoa Dawk Mali 105’ (KDML 105), using an automatic soaking and germination accelerator unit (ASGA) together with stimulation via infrared radiation treatment (IRT) to stimulate seed quality (germination rate and γ-aminobutyric acid (GABA) content). This study used a general full factorial design, and the independent variables were the storage period (10, 11 and 12 months), methods of germinated rough rice preparation (conventional method (CM) and an automatic soaking and germination accelerator unit (ASGA)), and stimulation with IRT. The initial grain moisture content did not exceed 14% (wet basis (wb)). The germination rate of the rough rice by CM and ASGA with stimulation with IRT was significantly higher than non-stimulated rice, by 6.56 and 8.11%, respectively, in each storage period. The GABA contents of the germinated rough rice using CM and ASGA stimulated with IRT were significantly higher than ungerminated rough rice, by 19.52 and 21.24% (10 months), respectively; 16.36 and 23.58% (11 months), respectively; and 69.88 and 67.69% (12 months), respectively.
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22
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Ramakrishna G, Singh A, Kaur P, Yadav SS, Sharma S, Gaikwad K. Genome wide identification and characterization of small heat shock protein gene family in pigeonpea and their expression profiling during abiotic stress conditions. Int J Biol Macromol 2022; 197:88-102. [PMID: 34902444 DOI: 10.1016/j.ijbiomac.2021.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/26/2022]
Abstract
Small heat shock proteins as large multigene family are present ubiquitously among Archaea to Eukaryota. The sHSPs are molecular chaperones that maintain the proper protein folding and disaggregation of denatured proteins during stress conditions. In the present study, out of identified 38 sHSPs in the pigeonpea genome, the 20 are distributed across seven chromosomes while the remaining are located on unassembled scaffolds. These Cc_sHSPs are classified into 16 subfamilies. The cytoplasmic class-II is the largest sub-family with five Cc_sHSPs. The gene structure analysis revealed that Cc_sHSP genes specifically containing no or very few introns. The promoter analysis revealed the presence of various cis-acting elements responsible for developmental, biotic, and abiotic stress specific-induction of Cc_sHSPs. A total of one segmental duplication and four tandem duplication events are identified for Cc_sHSPs. The qRT-PCR based expression analysis of all 38 Cc_sHSP genes was conducted for diverse abiotic stress conditions. The Cc_sHSP genes are highly induced by heat, drought, cold, and salt stresses indicating a key role in mitigating the various abiotic stress responses. The divergence time of paralogous Cc_sHSPs ranged from 8.66 to 191.82 MYA. The present study can be a strong basis for the functional characterization of Cc_sHSPs.
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Affiliation(s)
- G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Anupam Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Parampreet Kaur
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; School of Organic Farming, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Sunishtha S Yadav
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
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23
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Sidibé A, Charles MT, Lucier JF, Xu Y, Beaulieu C. Preharvest UV-C Hormesis Induces Key Genes Associated With Homeostasis, Growth and Defense in Lettuce Inoculated With Xanthomonas campestris pv. vitians. FRONTIERS IN PLANT SCIENCE 2022; 12:793989. [PMID: 35111177 PMCID: PMC8801786 DOI: 10.3389/fpls.2021.793989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Preharvest application of hormetic doses of ultraviolet-C (UV-C) generates beneficial effects in plants. In this study, within 1 week, four UV-C treatments of 0.4 kJ/m2 were applied to 3-week-old lettuce seedlings. The leaves were inoculated with a virulent strain of Xanthomonas campestris pv. vitians (Xcv) 48 h after the last UV-C application. The extent of the disease was tracked over time and a transcriptomic analysis was performed on lettuce leaf samples. Samples of lettuce leaves, from both control and treated groups, were taken at two different times corresponding to T2, 48 h after the last UV-C treatment and T3, 24 h after inoculation (i.e., 72 h after the last UV-C treatment). A significant decrease in disease severity between the UV-C treated lettuce and the control was observed on days 4, 8, and 14 after pathogen inoculation. Data from the transcriptomic study revealed, that in response to the effect of UV-C alone and/or UV-C + Xcv, a total of 3828 genes were differentially regulated with fold change (|log2-FC|) > 1.5 and false discovery rate (FDR) < 0.05. Among these, of the 2270 genes of known function 1556 were upregulated and 714 were downregulated. A total of 10 candidate genes were verified by qPCR and were generally consistent with the transcriptomic results. The differentially expressed genes observed in lettuce under the conditions of the present study were associated with 14 different biological processes in the plant. These genes are involved in a series of metabolic pathways associated with the ability of lettuce treated with hormetic doses of UV-C to resume normal growth and to defend themselves against potential stressors. The results indicate that the hormetic dose of UV-C applied preharvest on lettuce in this study, can be considered as an eustress that does not interfere with the ability of the treated plants to carry on a set of key physiological processes namely: homeostasis, growth and defense.
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Affiliation(s)
- Amadou Sidibé
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Marie Thérèse Charles
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | | | - Yanqun Xu
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, Hangzhou, China
| | - Carole Beaulieu
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
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24
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Wang X, Zheng Y, Chen B, Zhi C, Qiao L, Liu C, Pan Y, Cheng Z. Genome-wide identification of small heat shock protein (HSP20) homologs in three cucurbit species and the expression profiles of CsHSP20s under several abiotic stresses. Int J Biol Macromol 2021; 190:827-836. [PMID: 34492251 DOI: 10.1016/j.ijbiomac.2021.08.222] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/22/2022]
Abstract
Small heat shock protein (HSP20) genes play important roles in biological processes of plants. In this study, a total of 47 CsHSP20 genes, 45 CmHSP20 genes, and 47 ClHSP20 genes were genome-wide identified by 'hmmsearch' and BLASTP using the latest versions of cucumber, melon, and watermelon genomes, respectively. According to the phylogenetic relationships and predicted subcellular localizations, HSP20s of these three cucurbit species were divided into 8 subfamilies (CI-CIV, CP, ER, M, and PX), in which some HSP20s were closely related with each other based on the collinearity analysis. Specific expression patterns of CsHSP20s were checked in 10 different tissues of cucumber plants. RNA-seq analysis of transcript levels, combined with cis-acting elements and GO enrichment analysis suggested that CsHSP20s were responsive to several different types of abiotic stresses, including chilling, temperature and photoperiod, high temperature and high humidity, and salinity. In conclusion, results of this work not only provided valuable information for exploring the regulating mechanisms of CsHSP20s in responding to abiotic stresses in cucumber, but also shed light on the potentially evolutional relations among cucumber, melon, and watermelon from a perspective of comparative genomics that specified on HSP20 gene families.
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Affiliation(s)
- Xi'ao Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Yujie Zheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Birong Chen
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Chengchen Zhi
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Lijun Qiao
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Ce Liu
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Yupeng Pan
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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25
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Cui F, Taier G, Wang X, Wang K. Genome-Wide Analysis of the HSP20 Gene Family and Expression Patterns of HSP20 Genes in Response to Abiotic Stresses in Cynodon transvaalensis. Front Genet 2021; 12:732812. [PMID: 34567082 PMCID: PMC8455957 DOI: 10.3389/fgene.2021.732812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
African bermudagrass (Cynodon transvaalensis Burtt-Davy) is an important warm-season turfgrass and forage grass species. Heat shock protein 20 (HSP20) is a diverse, ancient, and important protein family. To date, HSP20 genes have not been characterized genome-widely in African bermudagrass. Here, we confirmed 41 HSP20 genes in African bermudagrass genome. On the basis of the phylogenetic tree and cellular locations, the HSP20 proteins were classified into 12 subfamilies. Motif composition was consistent with the phylogeny. Moreover, we identified 15 pairs of paralogs containing nine pairs of tandem duplicates and six pairs of WGD/segmental duplicates of HSP20 genes. Unsurprisingly, the syntenic genes revealed that African bermudagrass had a closer evolutionary relationship with monocots (maize and rice) than dicots (Arabidopsis and soybean). The expression patterns of HSP20 genes were identified with the transcriptome data under abiotic stresses. According to the expression profiles, HSP20 genes could be clustered into three groups (Groups I, II, and III). Group I was the largest, and these genes were up-regulated in response to heat stress as expected. In Group II, one monocot-specific HSP20, CtHSP20-14 maintained higher expression levels under optimum temperature and low temperature, but not high temperature. Moreover, a pair of WGD/segmental duplicates CtHSP20-9 and CtHSP20-10 were among the most conserved HSP20s across different plant species, and they seemed to be positively selected in response to extreme temperatures during evolution. A total of 938 cis-elements were captured in the putative promoters of HSP20 genes. Almost half of the cis-elements were stress responsive, indicating that the expression pattern of HSP20 genes under abiotic stresses might be largely regulated by the cis-elements. Additionally, three-dimensional structure simulations and protein-protein interaction networks were incorporated to resolve the function mechanism of HSP20 proteins. In summary, the findings fulfilled the HSP20 family analysis and could provide useful information for further functional investigations of the specific HSP20s (e.g., CtHSP20-9, CtHSP20-10, and CtHSP20-14) in African bermudagrass.
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Affiliation(s)
- Fengchao Cui
- Department of Turfgrass Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Geli Taier
- Department of Turfgrass Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Kehua Wang
- Department of Turfgrass Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, China
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26
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Yu X, Mo Z, Tang X, Gao T, Mao Y. Genome-wide analysis of HSP70 gene superfamily in Pyropia yezoensis (Bangiales, Rhodophyta): identification, characterization and expression profiles in response to dehydration stress. BMC PLANT BIOLOGY 2021; 21:435. [PMID: 34560838 PMCID: PMC8464122 DOI: 10.1186/s12870-021-03213-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/14/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Individual family members have been analyzed in previous studies, but there has not yet been a comprehensive analysis of the HSP70 gene family in Pyropia yezoensis. RESULTS We investigated 15 putative HSP70 genes in Py. yezoensis. These genes were classified into two sub-families, denoted as DnaK and Hsp110. In each sub-family, there was relative conservation of the gene structure and motif. Synteny-based analysis indicated that seven and three PyyHSP70 genes were orthologous to HSP70 genes in Pyropia haitanensis and Porphyra umbilicalis, respectively. Most PyyHSP70s showed up-regulated expression under different degrees of dehydration stress. PyyHSP70-1 and PyyHSP70-3 were expressed in higher degrees compared with other PyyHSP70s in dehydration treatments, and then expression degrees somewhat decreased in rehydration treatment. Subcellular localization showed PyyHSP70-1-GFP and PyyHSP70-3-GFP were in the cytoplasm and nucleus/cytoplasm, respectively. Similar expression patterns of paired orthologs in Py. yezoensis and Py. haitanensis suggest important roles for HSP70s in intertidal environmental adaptation during evolution. CONCLUSIONS These findings provide insight into the evolution and modification of the PyyHSP70 gene family and will help to determine the functions of the HSP70 genes in Py. yezoensis growth and development.
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Affiliation(s)
- Xinzi Yu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- College of Marine Life Sciences , Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zhaolan Mo
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- College of Marine Life Sciences , Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xianghai Tang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- College of Marine Life Sciences , Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Tian Gao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- College of Marine Life Sciences , Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Yunxiang Mao
- Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Hainan Tropical Ocean University), Ministry of Education, Sanya, 572022, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Park M, Choi W, Shin SY, Moon H, Lee D, Gho YS, Jung KH, Jeon JS, Shin C. Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice ( Oryza sativa L.) by Transcriptome and Small RNAome Analyses. FRONTIERS IN PLANT SCIENCE 2021; 12:727302. [PMID: 34421977 PMCID: PMC8377729 DOI: 10.3389/fpls.2021.727302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/19/2021] [Indexed: 06/02/2023]
Abstract
Pre-harvest sprouting (PHS) is one of the primary problems associated with seed dormancy in rice (Oryza sativa L.). It causes yield loss and reduces grain quality under unpredictable humid conditions at the ripening stage, thus affecting the economic value of the rice crop. To resolve this issue, understanding the molecular mechanism underlying seed dormancy in rice is important. Recent studies have shown that seed dormancy is affected by a large number of genes associated with plant hormone regulation. However, understanding regarding the effect of heat stress on seed dormancy and plant hormones is limited. This study compared the transcriptome and small RNAome of the seed embryo and endosperm of two contrasting japonica rice accessions, PHS susceptible (with low seed dormancy) and PHS resistant (with high seed dormancy), at three different maturation stages. We found that 9,068 genes and 35 microRNAs (miRNAs) were differentially expressed in the embryo, whereas 360 genes were differentially expressed in the endosperm. Furthermore, we identified and verified the candidate genes associated with seed dormancy and heat stress-related responses in rice using quantitative real-time PCR. We newly discovered eight hormone-related genes, four heat shock protein-related genes, and two miRNAs potentially involved in PHS. These findings provide a strong foundation for understanding the dynamics of transcriptome and small RNAome of hormone- and heat stress-related genes, which affect PHS during seed maturation.
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Affiliation(s)
- Minsu Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, South Korea
| | - Woochang Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Sang-Yoon Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Hongman Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Dowhan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yun-Shil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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Jeyasri R, Muthuramalingam P, Satish L, Pandian SK, Chen JT, Ahmar S, Wang X, Mora-Poblete F, Ramesh M. An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10071472. [PMID: 34371676 PMCID: PMC8309266 DOI: 10.3390/plants10071472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 05/06/2023]
Abstract
Abiotic stresses (AbS), such as drought, salinity, and thermal stresses, could highly affect the growth and development of plants. For decades, researchers have attempted to unravel the mechanisms of AbS for enhancing the corresponding tolerance of plants, especially for crop production in agriculture. In the present communication, we summarized the significant factors (atmosphere, soil and water) of AbS, their regulations, and integrated omics in the most important cereal crops in the world, especially rice, wheat, sorghum, and maize. It has been suggested that using systems biology and advanced sequencing approaches in genomics could help solve the AbS response in cereals. An emphasis was given to holistic approaches such as, bioinformatics and functional omics, gene mining and agronomic traits, genome-wide association studies (GWAS), and transcription factors (TFs) family with respect to AbS. In addition, the development of omics studies has improved to address the identification of AbS responsive genes and it enables the interaction between signaling pathways, molecular insights, novel traits and their significance in cereal crops. This review compares AbS mechanisms to omics and bioinformatics resources to provide a comprehensive view of the mechanisms. Moreover, further studies are needed to obtain the information from the integrated omics databases to understand the AbS mechanisms for the development of large spectrum AbS-tolerant crop production.
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Affiliation(s)
- Rajendran Jeyasri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
| | - Pandiyan Muthuramalingam
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641062, India
| | - Lakkakula Satish
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Shunmugiah Karutha Pandian
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 81148, Taiwan;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile;
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an 716000, China;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile;
- Correspondence: (F.M.-P.); (M.R.)
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, India; (R.J.); (P.M.); (L.S.); (S.K.P.)
- Correspondence: (F.M.-P.); (M.R.)
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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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CaHSP18.1a, a Small Heat Shock Protein from Pepper (Capsicum annuum L.), Positively Responds to Heat, Drought, and Salt Tolerance. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7050117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pepper is a thermophilic crop, shallow-rooted plant that is often severely affected by abiotic stresses such as heat, salt, and drought. The growth and development of pepper is seriously affected by adverse stresses, resulting in decreases in the yield and quality of pepper crops. Small heat shock proteins (s HSPs) play a crucial role in protecting plant cells against various stresses. A previous study in our laboratory showed that the expression level of CaHSP18.1a was highly induced by heat stress, but the function and mechanism of CaHSP18.1a responding to abiotic stresses is not clear. In this study, we first analyzed the expression of CaHSP18.1a in the thermo-sensitive B6 line and thermo-tolerant R9 line and demonstrated that the transcription of CaHSP18.1a was strongly induced by heat stress, salt, and drought stress in both R9 and B6, and that the response is more intense and earlier in the R9 line. In the R9 line, the silencing of CaHSP18.1a decreased resistance to heat, drought, and salt stresses. The silencing of CaHSP18.1a resulted in significant increases in relative electrolyte leakage (REL) and malonaldehyde (MDA) contents, while total chlorophyll content decreased under heat, salt, and drought stresses. Overexpression analyses of CaHSP18.1a in transgenic Arabidopsis further confirmed that CaHSP18.1a functions positively in resistance to heat, drought, and salt stresses. The transgenic Arabidopsis had higherchlorophyll content and activities of superoxide dismutase, catalase, and ascorbate peroxidase than the wild type (WT). However, the relative conductivity and MDA content were decreased in transgenic Arabidopsis compared to the wild type (WT). We further showed that the CaHSP18.1a protein is localized to the cell membrane. These results indicate CaHSP18.1a may act as a positive regulator of responses to abiotic stresses.
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Wang H, Chen JG, Chang Y. Identification, Expression, and Interaction Analysis of Ovate Family Proteins in Populus trichocarpa Reveals a Role of PtOFP1 Regulating Drought Stress Response. FRONTIERS IN PLANT SCIENCE 2021; 12:650109. [PMID: 33959141 PMCID: PMC8095670 DOI: 10.3389/fpls.2021.650109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Ovate family proteins (OFPs) are a family of plant growth regulators that play diverse roles in many aspects of physiological processes. OFPs have been characterized in various plant species including tomato, Arabidopsis, and rice. However, little is known about OFPs in woody species. Here, a total of 30 PtOFP genes were identified from the genome of Populus trichocarpa and were further grouped into four subfamilies based on their sequence similarities. Gene expression analysis indicated that some members of the PtOFP gene family displayed tissue/organ-specific patterns. Analysis of cis-acting elements in the promoter as well as gene expression by hormone treatment revealed putative involvement of PtOFPs in hormonal response. Furthermore, PtOFP1 (Potri.006G107700) was further experimentally demonstrated to act as a transcriptional repressor. Yeast two-hybrid assay showed physical interactions of PtOFP1 with other proteins, which suggests that they might function in various cellular processes by forming protein complexes. In addition, overexpression of PtOFP1 in Arabidopsis conferred enhanced tolerance to PEG-induced drought stress at seedling stage, as well as a higher survival rate than the wild type at mature stage. These results provide a systematic analysis of the Populus OFP gene family and lay a foundation for functional characterization of this gene family.
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Affiliation(s)
- Hemeng Wang
- Northeast Agricultural University, Harbin, China
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ying Chang
- Northeast Agricultural University, Harbin, China
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Elhadi GMI, Kamal NM, Gorafi YSA, Yamasaki Y, Takata K, Tahir ISA, Itam MO, Tanaka H, Tsujimoto H. Exploitation of Tolerance of Wheat Kernel Weight and Shape-Related Traits from Aegilops tauschii under Heat and Combined Heat-Drought Stresses. Int J Mol Sci 2021; 22:1830. [PMID: 33673217 PMCID: PMC7917938 DOI: 10.3390/ijms22041830] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/25/2022] Open
Abstract
Kernel weight and shape-related traits are inherited stably and increase wheat yield. Narrow genetic diversity limits the progress of wheat breeding. Here, we evaluated kernel weight and shape-related traits and applied genome-wide association analysis to a panel of wheat multiple synthetic derivative (MSD) lines. The MSD lines harbored genomic fragments from Aegilops tauschii. These materials were grown under optimum conditions in Japan, as well as under heat and combined heat-drought conditions in Sudan. We aimed to explore useful QTLs for kernel weight and shape-related traits under stress conditions. These can be useful for enhancing yield under stress conditions. MSD lines possessed remarkable genetic variation for all traits under all conditions, and some lines showed better performance than the background parent Norin 61. We identified 82 marker trait associations (MTAs) under the three conditions; most of them originated from the D genome. All of the favorable alleles originated from Ae. tauschii. For the first time, we identified markers on chromosome 5D associated with a candidate gene encoding a RING-type E3 ubiquitin-protein ligase and expected to have a role in regulating wheat seed size. Our study provides important knowledge for the improvement of wheat yield under optimum and stress conditions. The results emphasize the importance of Ae. tauschii as a gene reservoir for wheat breeding.
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Affiliation(s)
- Gamila Mohamed Idris Elhadi
- United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan; (G.M.I.E.); (M.O.I.)
| | - Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
- Wheat Research Program, Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan;
| | - Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
- Wheat Research Program, Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan;
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
| | - Kanenori Takata
- National Agriculture and Food Research Organization, Fukuyama 721-8514, Japan;
| | - Izzat S. A. Tahir
- Wheat Research Program, Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan;
| | - Michel O. Itam
- United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan; (G.M.I.E.); (M.O.I.)
| | - Hiroyuki Tanaka
- Faculty of Agriculture, Tottori University, Tottori 680-8550, Japan;
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
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Zhang K, He S, Sui Y, Gao Q, Jia S, Lu X, Jia L. Genome-Wide Characterization of HSP90 Gene Family in Cucumber and Their Potential Roles in Response to Abiotic and Biotic Stresses. Front Genet 2021; 12:584886. [PMID: 33613633 PMCID: PMC7889589 DOI: 10.3389/fgene.2021.584886] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/14/2021] [Indexed: 11/29/2022] Open
Abstract
Heat shock protein 90 (HSP90) possesses critical functions in plant developmental control and defense reactions. The HSP90 gene family has been studied in various plant species. However, the HSP90 gene family in cucumber has not been characterized in detail. In this study, a total of six HSP90 genes were identified from the cucumber genome, which were distributed to five chromosomes. Phylogenetic analysis divided the cucumber HSP90 genes into two groups. The structural characteristics of cucumber HSP90 members in the same group were similar but varied among different groups. Synteny analysis showed that only one cucumber HSP90 gene, Csa1G569290, was conservative, which was not collinear with any HSP90 gene in Arabidopsis and rice. The other five cucumber HSP90 genes were collinear with five Arabidopsis HSP90 genes and six rice HSP90 genes. Only one pair of paralogous genes in the cucumber HSP90 gene family, namely one pair of tandem duplication genes (Csa1G569270/Csa1G569290), was detected. The promoter analysis showed that the promoters of cucumber HSP90 genes contained hormone, stress, and development-related cis-elements. Tissue-specific expression analysis revealed that only one cucumber HSP90 gene Csa3G183950 was highly expressed in tendril but low or not expressed in other tissues, while the other five HSP90 genes were expressed in all tissues. Furthermore, the expression levels of cucumber HSP90 genes were differentially induced by temperature and photoperiod, gibberellin (GA), downy mildew, and powdery mildew stimuli. Two cucumber HSP90 genes, Csa1G569270 and Csa1G569290, were both differentially expressed in response to abiotic and biotic stresses, which means that these two HSP90 genes play important roles in the process of cucumber growth and development. These findings improve our understanding of cucumber HSP90 family genes and provide preliminary information for further studies of cucumber HSP90 gene functions in plant growth and development.
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Affiliation(s)
- Kaijing Zhang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Shuaishuai He
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yihu Sui
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Qinghai Gao
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Shuangshuang Jia
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Xiaomin Lu
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Li Jia
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
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The Chloroplastic Small Heat Shock Protein Gene KvHSP26 Is Induced by Various Abiotic Stresses in Kosteletzkya virginica. Int J Genomics 2021; 2021:6652445. [PMID: 33623779 PMCID: PMC7875624 DOI: 10.1155/2021/6652445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/03/2021] [Accepted: 01/15/2021] [Indexed: 01/16/2023] Open
Abstract
Small heat shock proteins (sHSPs) are a group of chaperone proteins existed in all organisms. The functions of sHSPs in heat and abiotic stress responses in many glycophyte plants have been studied. However, their possible roles in halophyte plants are still largely known. In this work, a putative sHSP gene KvHSP26 was cloned from K. virginica. Bioinformatics analyses revealed that KvHSP26 encoded a chloroplastic protein with the typical features of sHSPs. Amino acid sequence alignment and phylogenetic analysis demonstrated that KvHSP26 shared 30%-77% homology with other sHSPs from Arabidopsis, cotton, durian, salvia, and soybean. Quantitative real-time PCR (qPCR) assays exhibited that KvHSP26 was constitutively expressed in different tissues such as leaves, stems, and roots, with a relatively higher expression in leaves. Furthermore, expression of KvHSP26 was strongly induced by salt, heat, osmotic stress, and ABA in K. virginica. All these results suggest that KvHSP26 encodes a new sHSP, which is involved in multiple abiotic stress responses in K. virginica, and it has a great potential to be used as a candidate gene for the breeding of plants with improved tolerances to various abiotic stresses.
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Identification and development of novel salt-responsive candidate gene based SSRs (cg-SSRs) and MIR gene based SSRs (mir-SSRs) in bread wheat (Triticum aestivum). Sci Rep 2021; 11:2210. [PMID: 33500485 PMCID: PMC7838269 DOI: 10.1038/s41598-021-81698-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/03/2020] [Indexed: 01/30/2023] Open
Abstract
Salt stress adversely affects the global wheat production and productivity. To improve salinity tolerance of crops, identification of robust molecular markers is highly imperative for development of salt-tolerant cultivars to mimic yield losses under saline conditions. In this study, we mined 171 salt-responsive genes (including 10 miRNAs) from bread wheat genome using the sequence information of functionally validated salt-responsive rice genes. Salt-stress, tissue and developmental stage-specific expression analysis of RNA-seq datasets revealed the constitutive as well as the inductive response of salt-responsive genes in different tissues of wheat. Fifty-four genotypes were phenotyped for salt stress tolerance. The stress tolerance index of the genotypes ranged from 0.30 to 3.18. In order to understand the genetic diversity, candidate gene based SSRs (cg-SSRs) and MIR gene based SSRs (miR-SSRs) were mined from 171 members of salt-responsive genes of wheat and validated among the contrasting panels of 54 tolerant as well as susceptible wheat genotypes. Among 53 SSR markers screened, 10 cg-SSRs and 8 miR-SSRs were found to be polymorphic. Polymorphic information content between the wheat genotypes ranged from 0.07 to 0.67, indicating the extant of wide genetic variation among the salt tolerant and susceptible genotypes at the DNA level. The genetic diversity analysis based on the allelic data grouped the wheat genotypes into three separate clusters of which single group encompassing most of the salt susceptible genotypes and two of them containing salt tolerance and moderately salt tolerance wheat genotypes were in congruence with penotypic data. Our study showed that both salt-responsive genes and miRNAs based SSRs were more diverse and can be effectively used for diversity analysis. This study reports the first extensive survey on genome-wide analysis, identification, development and validation of salt-responsive cg-SSRs and miR-SSRs in wheat. The information generated in the present study on genetic divergence among genotypes having a differential response to salt will help in the selection of suitable lines as parents for developing salt tolerant cultivars in wheat.
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Sharma P, Mehta G, Shefali, Muthusamy SK, Singh SK, Singh GP. Development and validation of heat-responsive candidate gene and miRNA gene based SSR markers to analysis genetic diversity in wheat for heat tolerance breeding. Mol Biol Rep 2021; 48:381-393. [PMID: 33389541 DOI: 10.1007/s11033-020-06059-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Being a major staple food crop of the world, wheat provides nutritional food security to the global populations. Heat stress is a major abiotic stress that adversely affects wheat production throughout the world including Indo-Gangatic Plains (IGP) where four wheat growing countries viz., India, Bangladesh, Nepal and Pakistan produce 42% of the total wheat production. Therefore, identification of heat stress responsive molecular markers is imperative to marker assisted breeding programs. Information about trait specific gene based SSRs is available but there is lack of information on SSRs from non-coding regions. In the present study, we developed 177 heat-responsive gene-based SSRs (cg-SSR) and MIR gene-based SSR (miRNA-SSR) markers from wheat genome for assessing genetic diversity analysis of thirty- six contrasting wheat genotypes for heat tolerance. Of the 177 SSR loci, 144 yielded unambiguous and repeatable amplicons, however, thirty-seven were found polymorphic among the 36 wheat genotypes. The polymorphism information content (PIC) of primers used in this study ranged from 0.03-0.73, with a mean of 0.35. Number of alleles produced per primer varied from 2 to 6, with a mean of 2.58. The UPGMA dendrogram analysis grouped all wheat genotypes into four clusters. The markers developed in this study has potential application in the MAS based breeding programs for developing heat tolerant wheat cultivars and genetic diversity analysis of wheat germplasm. Identification of noncoding region based SSRs will be fruitful for identification of trait specific wheat germplasm.
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Affiliation(s)
- Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India.
| | - Geetika Mehta
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Shefali
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Senthilkumar K Muthusamy
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India.,ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
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Shi P, Zhou J, Song H, Wu Y, Lan L, Tang X, Ma Z, Vossbrinck CR, Vossbrinck B, Zhou Z, Xu J. Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress. Ecol Evol 2020; 10:13427-13438. [PMID: 33304549 PMCID: PMC7713975 DOI: 10.1002/ece3.6946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 01/12/2023] Open
Abstract
The geographic and biological diversity of China has resulted in the differential adaptation of the eastern honeybee, Apis cerana, to these varied habitats. A. cerana were collected from 14 locations in China. Their genomes were sequenced, and nucleotide polymorphisms were identified at more than 9 million sites. Both STRUCTURE and principal component analysis placed the bees into seven groups. Phylogenomic analysis groups the honeybees into many of the same clusters with high bootstrap values (91%-100%). Populations from Tibet and South Yunnan are sister taxa and together represent the earliest diverging lineage included in this study. We propose that the evolutionary origin of A. cerana in China was in the southern region of Yunnan Province and expanded from there into the southeastern regions and into the northeastern mountain regions. The Cold-Temperate West Sichuan Plateau and Tropical Diannan populations were compared to identify genes under adaptive selection in these two habitats. Pathway enrichment analysis showing genes under selection, including the Hippo signaling pathway, GABAergic pathway, and trehalose-phosphate synthase, indicates that most genes under selection pressure are involved in the process of signal transduction and energy metabolism. qRT-PCR analysis reveals that one gene under selection, the AcVIAAT gene, involved in the GABAergic pathway, is responding to cold temperature stress. Through homologous recombination, we show that the AcVIAAT gene is able to replace the CNAG_01904 gene in the fungus Cryptococcus neoformans and that it makes the fungus less sensitive to conditions of oxidative stress and variations in temperature. Our results contribute to our understanding of the evolutionary origin of A. cerana in China and the molecular basis of environmental adaptation.
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Affiliation(s)
- Peng Shi
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Jun Zhou
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Huali Song
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Yujuan Wu
- State Key Laboratory of Silkworm Genome BiologySouthwest UniversityChongqingChina
| | - Lan Lan
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Xiangyou Tang
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Zhengang Ma
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Charles R. Vossbrinck
- Department of Environmental ScienceConnecticut Agricultural Experiment StationNew HavenCTUSA
| | | | - Zeyang Zhou
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
- State Key Laboratory of Silkworm Genome BiologySouthwest UniversityChongqingChina
| | - Jinshan Xu
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
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Comparative analysis of developing grain transcriptome reveals candidate genes and pathways improving GPC in wheat lines derived from wild emmer. J Appl Genet 2020; 62:17-25. [PMID: 33063291 DOI: 10.1007/s13353-020-00588-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/18/2020] [Accepted: 09/30/2020] [Indexed: 10/23/2022]
Abstract
The grain protein content (GPC) in modern wheat is inherently low. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, 2n = 4x = 28, AABB) gene pool harbors wide genotypic variations in GPC. However, the characterization of candidate genes associated with high GPC is a challenge due to the complex characteristic of this trait. In the current study, we performed RNA-seq analysis on developing grains of wild emmer genotype D1, common wheat CN16, and their hexaploid wide hybrid BAd107-4 with contrasting GPC. We have found a total of 39,795 expressed genes on chromosomes A and B, of which 24,152 were shared between D1, CN16, and BAd107-4. From 1744 differentially expressed genes (DEGs), 1203 were downregulated and 541 were upregulated in the high GPC (D1+BAd107-4) compared with low GPC (CN16) groups. The majority of DEGs were associated with protein processing in endoplasmic reticulum, starch and sucrose metabolism, galactose metabolism, and protein export pathways. Expression levels of nine randomly selected genes were verified by qRT-PCR, which was consistent with the transcriptome data. The present database will help us to understand the potential regulation networks underlying wheat grain protein accumulation and provide the foundation for simultaneous improvement of grain protein content and yield in wheat breeding programs.
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Wen X, Ding Y, Tan Z, Wang J, Zhang D, Wang Y. Identification and characterization of cadmium stress-related LncRNAs from Betula platyphylla. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110601. [PMID: 32900439 DOI: 10.1016/j.plantsci.2020.110601] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Cadmium (Cd) is one of the most serious global environmental pollutants, which inhibits plant growth and interferes with their physiological processes. However, there have been few studies on the involvement of long noncoding RNAs (lncRNAs) in Cd tolerance. In the present study, we identified the lncRNAs from Betula platyphylla (birch) that respond to Cd stress. Thirty lncRNAs that were differentially expressed under Cd treatment were identified, including 16 upregulated and 14 downregulated lncRNAs. Nine differentially regulated lncRNAs were selected for further characterization. These lncRNAs were transiently overexpressed in birch plants to determine their roles in Cd tolerance. Among them, two lncRNAs conferred Cd tolerance and two induced sensitivity to Cd stress. We further determined the Cd tolerance of four target genes of the lncRNAs involved in Cd tolerance, including l-lactate dehydrogenase A (LDHA),heat shock protein (HSP18.1), yellow stripe-like protein (YSL9), and H/ACA ribonucleoprotein complex subunit 2-like protein (HRCS2L). Among them, HSP18.1 and LDHA showed improved tolerance to Cd stress, whereas the other two genes did not appear to be involved in Cd tolerance. These results suggested that lncRNAs can up- or downregulate their target genes to improve Cd tolerance. These results increase our understanding of lncRNA-mediated Cd tolerance.
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Affiliation(s)
- Xuejing Wen
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.
| | - Yu Ding
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zilong Tan
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jingxin Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.
| | - Yucheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.
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Mao L, Deng M, Jiang S, Zhu H, Yang Z, Yue Y, Zhao K. Characterization of the DREBA4-Type Transcription Factor (SlDREBA4), Which Contributes to Heat Tolerance in Tomatoes. FRONTIERS IN PLANT SCIENCE 2020; 11:554520. [PMID: 33101326 PMCID: PMC7554514 DOI: 10.3389/fpls.2020.554520] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/11/2020] [Indexed: 06/09/2023]
Abstract
Dehydration-responsive element binding (DREB) transcription factors play crucial regulatory roles in abiotic stress. The only DREB transcription factor in tomato (Solanum lycopersicum), SlDREBA4 (Accession No. MN197531), which was determined to be a DREBA4 subfamily member, was isolated from cv. Microtom using high-temperature-induced digital gene expression (DGE) profiling technology. The constitutive expression of SlDREBA4 was detected in different tissues of Microtom plants. In addition to responding to high temperature, SlDREBA4 was up-regulated after exposure to abscisic acid (ABA), cold, drought and high-salt conditions. Transgenic overexpression and silencing systems revealed that SlDREBA4 could alter the resistance of transgenic Microtom plants to heat stress by altering the content of osmolytes and stress hormones, and the activities of antioxidant enzymes at the physiologic level. Moreover, SlDREBA4 regulated the downstream gene expression of many heat shock proteins (Hsp), as well as calcium-binding protein enriched in the pathways of protein processing in endoplasmic reticulum (ko04141) and plant-pathogen interaction (ko04626) at the molecular level. SlDREBA4 also induces the expression of biosynthesis genes in jasmonic acid (JA), salicylic acid (SA), and ethylene (ETH), and specifically binds to the DRE elements (core sequence, A/GCCGAC) of the Hsp genes downstream from SlDREBA4. This study provides new genetic resources and rationales for tomato heat-tolerance breeding and the heat-related regulatory mechanisms of DREBs.
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Affiliation(s)
| | | | | | | | | | | | - Kai Zhao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
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41
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Al Khateeb W, Muhaidat R, Alahmed S, Al Zoubi MS, Al-Batayneh KM, El-Oqlah A, Abo Gamar M, Hussein E, Aljabali AA, Alkaraki AK. Heat shock proteins gene expression and physiological responses in durum wheat ( Triticum durum) under salt stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1599-1608. [PMID: 32801489 PMCID: PMC7415065 DOI: 10.1007/s12298-020-00850-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/29/2020] [Accepted: 07/10/2020] [Indexed: 05/13/2023]
Abstract
Salt stress is a major abiotic stress causing adverse effects on plant growth and development. The aim of this study was to investigate the effect of NaCl stress on growth, stress indicator parameters (lipid peroxidation, chlorophyll content and proline content), yield, and the expression of heat shock proteins genes (Hsp17.8, Hsp26.3, Hsp70 and Hsp101) of five Jordanian durum wheat (Triticum durum) landraces. Plants were irrigated with tap water as control or 200 mM NaCl. Significant differences among the 5 Triticum durum landraces in terms of growth parameters, stress indicator parameters, and expression of heat shock proteins genes were observed. Salt stressed landraces demonstrated decreased growth, increased levels of stress indicator parameters, and upregulation in Hsp17.8, Hsp26.3, Hsp70 and Hsp101 expression. Landraces T11 and M23 showed the highest growth, lowest levels of stress indicator parameters, and high expression of heat shock protein genes under NaCl stress. Whereas, J2 and A8 landraces showed the lowest growth, highest levels of stress indicator parameters and low expression of heat shock protein genes under NaCl stress. In conclusion, NaCl stress caused significant reduction in growth parameters, increased level of lipid peroxidation and proline content and upregulation in heat shock proteins gene expression levels. Growth, stress indicator parameters and gene expression results suggest that T11 and M23 landraces are the most NaCl stress tolerant landraces and could be used to enhance the gene pool in wheat breeding programs.
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Affiliation(s)
- Wesam Al Khateeb
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, 21163 Jordan
| | - Riyadh Muhaidat
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, 21163 Jordan
| | - Sanaa Alahmed
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, 21163 Jordan
| | - Mazhar S. Al Zoubi
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | - Khalid M. Al-Batayneh
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, 21163 Jordan
| | - Ahmad El-Oqlah
- Department of Biology, Faculty of Science, Jerash University, Jerash, Jordan
| | - Mohammad Abo Gamar
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, 21163 Jordan
| | - Emad Hussein
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, 21163 Jordan
- Department of Food Science and Human Nutrition, A’Sharqiyah University, Ibra, Oman
| | - Alaa A. Aljabali
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan
| | - Almuthanna K. Alkaraki
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, 21163 Jordan
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Waters ER, Vierling E. Plant small heat shock proteins - evolutionary and functional diversity. THE NEW PHYTOLOGIST 2020; 227:24-37. [PMID: 32297991 DOI: 10.1111/nph.16536] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/21/2020] [Indexed: 05/22/2023]
Abstract
Small heat shock proteins (sHSPs) are an ubiquitous protein family found in archaea, bacteria and eukaryotes. In plants, as in other organisms, sHSPs are upregulated by stress and are proposed to act as molecular chaperones to protect other proteins from stress-induced damage. sHSPs share an 'α-crystallin domain' with a β-sandwich structure and a diverse N-terminal domain. Although sHSPs are 12-25 kDa polypeptides, most assemble into oligomers with ≥ 12 subunits. Plant sHSPs are particularly diverse and numerous; some species have as many as 40 sHSPs. In angiosperms this diversity comprises ≥ 11 sHSP classes encoding proteins targeted to the cytosol, nucleus, endoplasmic reticulum, chloroplasts, mitochondria and peroxisomes. The sHSPs underwent a lineage-specific gene expansion, diversifying early in land plant evolution, potentially in response to stress in the terrestrial environment, and expanded again in seed plants and again in angiosperms. Understanding the structure and evolution of plant sHSPs has progressed, and a model for their chaperone activity has been proposed. However, how the chaperone model applies to diverse sHSPs and what processes sHSPs protect are far from understood. As more plant genomes and transcriptomes become available, it will be possible to explore theories of the evolutionary pressures driving sHSP diversification.
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Affiliation(s)
- Elizabeth R Waters
- Biology Department, San Diego State University, San Diego, CA, 92182, USA
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
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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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Ma Q, Shi C, Su C, Liu Y. Complementary analyses of the transcriptome and iTRAQ proteome revealed mechanism of ethylene dependent salt response in bread wheat (Triticum aestivum L.). Food Chem 2020; 325:126866. [PMID: 32387982 DOI: 10.1016/j.foodchem.2020.126866] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/13/2020] [Accepted: 04/18/2020] [Indexed: 12/11/2022]
Abstract
In order to clarify the ethylene dependent salt response mechanism in wheat, 2-week-old wheat seedlings of cultivar 'Qingmai 6' treated with water, sodium chloride (NaCl), NaCl and ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), and NaCl and ethylene signaling inhibitor 1-methylcyclopropene (1-MCP) were collected and analyzed by transcriptional sequencing and isobaric tags for relative and absolute quantitation (iTRAQ) proteomics. At least 1140 proteins and 73,401 genes were identified, and proteins including ribosomal proteins (RPs), nucleoside diphosphate kinases (CDPKs), transaldolases (TALs), beta-glucosidases (BGLUs), phosphoenlpyruvate carboxylases (PEPCs), superoxide dismutases (SODs), and 6-phosphogluconate dehydrogenases (6-PGDHs) were significantly differently expressed. These genes and proteins revealed that ethylene dependent salt response through RPs activation, chaperones synthesis, the reactive oxygen species (ROS) scavenging, and carbohydrate metabolites pathway. Our results provided transcriptomics and proteomics information with respect to the molecular mechanisms of ethylene regualted salt response.
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Affiliation(s)
- Qian Ma
- College of Life Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Changhai Shi
- College of Agriculture, Qingdao Agricultural University, Qingdao 266109, China
| | - Chunxue Su
- College of Life Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Yiguo Liu
- College of Agriculture, Qingdao Agricultural University, Qingdao 266109, China.
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45
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Guo LM, Li J, He J, Liu H, Zhang HM. A class I cytosolic HSP20 of rice enhances heat and salt tolerance in different organisms. Sci Rep 2020; 10:1383. [PMID: 31992813 PMCID: PMC6987133 DOI: 10.1038/s41598-020-58395-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/13/2020] [Indexed: 01/07/2023] Open
Abstract
Small heat shock proteins (sHSPs) have been thought to function as chaperones, protecting their targets from denaturation and aggregation when organisms are subjected to various biotic and abiotic stresses. We previously reported an sHSP from Oryza sativa (OsHSP20) that homodimerizes and forms granules within the cytoplasm but its function was unclear. We now show that OsHSP20 transcripts were significantly up-regulated by heat shock and high salinity but not by drought. A recombinant protein was purified and shown to inhibit the thermal aggregation of the mitochondrial malate dehydrogenase (MDH) enzyme in vitro, and this molecular chaperone activity suggested that OsHSP20 might be involved in stress resistance. Heterologous expression of OsHSP20 in Escherichia coli or Pichia pastoris cells enhanced heat and salt stress tolerance when compared with the control cultures. Transgenic rice plants constitutively overexpressing OsHSP20 and exposed to heat and salt treatments had longer roots and higher germination rates than those of control plants. A series of assays using its truncated mutants showed that its N-terminal arm plus the ACD domain was crucial for its homodimerization, molecular chaperone activity in vitro, and stress tolerance in vivo. The results supported the viewpoint that OsHSP20 could confer heat and salt tolerance by its molecular chaperone activity in different organisms and also provided a more thorough characterization of HSP20-mediated stress tolerance in O. sativa.
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Affiliation(s)
- Liu-Ming Guo
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Jing Li
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jing He
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Han Liu
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.,College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Heng-Mu Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China. .,College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, China.
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Parveen A, Mustafa SH, Yadav P, Kumar A. Applications of Machine Learning in miRNA Discovery and Target Prediction. Curr Genomics 2020; 20:537-544. [PMID: 32581642 PMCID: PMC7290058 DOI: 10.2174/1389202921666200106111813] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 11/28/2022] Open
Abstract
MicroRNA (miRNA) is a small non-coding molecule that is involved in gene regulation and RNA silencing by complementary on their targets. Experimental methods for target prediction can be time-consuming and expensive. Thus, the application of the computational approach is implicated to enlighten these complications with experimental studies. However, there is still a need for an optimized approach in miRNA biology. Therefore, machine learning (ML) would initiate a new era of research in miRNA biology towards potential diseases biomarker. In this article, we described the application of ML approaches in miRNA discovery and target prediction with functions and future prospective. The implementation of a new era of computational methodologies in this direction would initiate further advanced levels of discoveries in miRNA.
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Affiliation(s)
- Alisha Parveen
- 1Institute of Medical Bioinformatics and Systems Medicine Medical Center, Faculty of Medicine, Albert-Ludwigs University of Freiburg, 79110Freiburg, Germany; 2Department of Computer Engineering, Zakir Husain College of Engineering and Technology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India; 3Department of Bioscience and Bio- engineering, Indian Institute of Technology, Jodhpur, India; 4Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; 5Manipal Academy of Higher Education (MAHE), Manipal576104, Karnataka, India
| | - Syed H Mustafa
- 1Institute of Medical Bioinformatics and Systems Medicine Medical Center, Faculty of Medicine, Albert-Ludwigs University of Freiburg, 79110Freiburg, Germany; 2Department of Computer Engineering, Zakir Husain College of Engineering and Technology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India; 3Department of Bioscience and Bio- engineering, Indian Institute of Technology, Jodhpur, India; 4Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; 5Manipal Academy of Higher Education (MAHE), Manipal576104, Karnataka, India
| | - Pankaj Yadav
- 1Institute of Medical Bioinformatics and Systems Medicine Medical Center, Faculty of Medicine, Albert-Ludwigs University of Freiburg, 79110Freiburg, Germany; 2Department of Computer Engineering, Zakir Husain College of Engineering and Technology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India; 3Department of Bioscience and Bio- engineering, Indian Institute of Technology, Jodhpur, India; 4Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; 5Manipal Academy of Higher Education (MAHE), Manipal576104, Karnataka, India
| | - Abhishek Kumar
- 1Institute of Medical Bioinformatics and Systems Medicine Medical Center, Faculty of Medicine, Albert-Ludwigs University of Freiburg, 79110Freiburg, Germany; 2Department of Computer Engineering, Zakir Husain College of Engineering and Technology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India; 3Department of Bioscience and Bio- engineering, Indian Institute of Technology, Jodhpur, India; 4Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; 5Manipal Academy of Higher Education (MAHE), Manipal576104, Karnataka, India
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Wang X, Li Z, Liu B, Zhou H, Elmongy MS, Xia Y. Combined Proteome and Transcriptome Analysis of Heat-Primed Azalea Reveals New Insights Into Plant Heat Acclimation Memory. FRONTIERS IN PLANT SCIENCE 2020; 11:1278. [PMID: 32973837 PMCID: PMC7466565 DOI: 10.3389/fpls.2020.01278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/05/2020] [Indexed: 05/21/2023]
Abstract
Plants can obtain superinduction of defense against unpredictable challenges based on prior acclimation, but the mechanisms involved in the acclimation memory are little known. The objective of this study was to characterize mechanisms of heat acclimation memory in Rhododendron hainanense, a thermotolerant wild species of azalea. Pretreatment of a 2-d recovery (25/18°C, day/night) after heat acclimation (37°C, 1 h) (AR-pt) did not weaken but enhanced acquired thermotolerance in R. hainanense with less damaged phenotype, net photosynthetic rate, and membrane stability than non-acclimation pretreated (NA-pt) plants. Combined transcriptome and proteome analysis revealed that a lot of heat-responsive genes still maintained high protein abundance rather than transcript level after the 2-d recovery. Photosynthesis-related genes were highly enriched and most decreased under heat stress (HS: 42°C, 1 h) with a less degree in AR-pt plants compared to NA-pt. Sustainably accumulated chloroplast-localized heat shock proteins (HSPs), Rubisco activase 1 (RCA1), beta-subunit of chaperonin-60 (CPN60β), and plastid transcriptionally active chromosome 5 (pTAC5) in the recovery period probably provided equipped protection of AR-pt plants against the subsequent HS, with less damaged photochemical efficiency and chloroplast structure. In addition, significant higher levels of RCA1 transcripts in AR-pt compared to NA-pt plants in early stage of HS showed a more important role of RCA1 than other chaperonins in heat acclimation memory. The novel heat-induced RCA1, rather than constitutively expressed RCA2 and RCA3, showed excellent thermostability after long-term HS (LHS: 42/35°C, 7 d) and maintained balanced Rubisco activation state in photosynthetic acclimation. This study provides new insights into plant heat acclimation memory and indicates candidate genes for genetic modification and molecular breeding in thermotolerance improvement.
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Affiliation(s)
- Xiuyun Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zheng Li
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bing Liu
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hong Zhou
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mohamed S. Elmongy
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Department of Vegetable and Floriculture, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Yiping Xia,
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48
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Altunoğlu YÇ, Keleş M, Can TH, Baloğlu MC. Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses. ACTA ACUST UNITED AC 2019; 43:404-419. [PMID: 31892809 PMCID: PMC6911259 DOI: 10.3906/biy-1907-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Heat shock protein (Hsp) gene family members in the watermelon genome were identified and characterized by bioinformatics analysis. In addition, expression profiles of genes under combined drought and heat stress conditions were experimentally analyzed. In the watermelon genome, 39 genes belonging to the sHsp family, 101 genes belonging to the Hsp40 family, 23 genes belonging to the Hsp60 family, 12 genes belonging to the Hsp70 family, 6 genes belonging to the Hsp90 family, and 102 genes belonging to the Hsp100 family were found. It was also observed that the proteins in the same cluster in the phylogenetic trees had similar motif patterns. When the estimated 3-dimensional structures of the Hsp proteins were examined, it was determined that the α-helical structure was dominant in almost all families. The most orthologous relationship appeared to be between watermelon, soybean, and poplar in the ClaHsp gene families. For tissue-specific gene expression analysis under combined stress conditions, expression analysis of one representative Hsp gene each from root, stem, leaf, and shoot tissues was performed by real-time PCR. A significant increase was detected usually at 30 min in almost all tissues. This study provides extensive information for watermelon Hsps, and can enhance our knowledge about the relationships between Hsp genes and combined stresses.
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Affiliation(s)
- Yasemin Çelik Altunoğlu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu Turkey
| | - Merve Keleş
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu Turkey
| | - Tevfik Hasan Can
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu Turkey
| | - Mehmet Cengiz Baloğlu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu Turkey
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49
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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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50
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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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