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Kamolsukyeunyong W, Dabbhadatta Y, Jaiprasert A, Thunnom B, Poncheewin W, Wanchana S, Ruanjaichon V, Toojinda T, Burns P. Genome-Wide Association Analysis Identifies Candidate Loci for Callus Induction in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:2112. [PMID: 39124230 PMCID: PMC11314294 DOI: 10.3390/plants13152112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/19/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024]
Abstract
Callus induction (CI) is a critical trait for transforming desirable genes in plants. A genome-wide association study (GWAS) analysis was conducted on the rice germplasms of 110 Indica rice accessions, in which three tissue culture media, B5, MS, and N6, were used for the CI of those rice panels' mature seeds. Seven quantitative trait loci (QTLs) on rice chromosomes 2, 6, 7, and 11 affected the CI percentage in the three media. For the B5 medium, one QTL (qCI-B5-Chr6) was identified on rice chromosome 6; for the MS medium, two QTLs were identified on rice chromosomes 2 and 6 (qCI-MS-Chr2 and qCI-MS-Chr6, respectively); for the N6 medium, four QTLs were identified on rice chromosomes 6, 7, and 11 (qCI-N6-Chr6.1 and qCI-N6-Chr6.2, qCI-N6-Chr7, and qCI-N6-Chr11, respectively). Fifty-five genes were identified within the haplotype blocks corresponding to these QTLs, thirty-one of which showed haplotypes associated with different CI percentages in those media. qCI-B5-Chr6 was located in the same region as qCI-N6-Chr6.2, and the Caleosin-related family protein was also identified in this region. Analysis of the gene-based haplotype revealed the association of this gene with different CI percentages in both B5 and N6 media, suggesting that the gene may play a critical role in the CI mechanism. Moreover, several genes, including those that encode the beta-tubulin protein, zinc finger protein, RNP-1 domain-containing protein, and lysophosphatidic acid acyltransferase, were associated with different CI percentages in the N6 medium. The results of this study provide insights into the potential QTLs and candidate genes for callus induction in rice that contribute to our understanding of the physiological and biochemical processes involved in callus formation, which is an essential tool in the molecular breeding of rice.
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Affiliation(s)
- Wintai Kamolsukyeunyong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (Y.D.); (A.J.); (B.T.); (W.P.); (S.W.); (V.R.); (T.T.)
| | | | | | | | | | | | | | | | - Parichart Burns
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (Y.D.); (A.J.); (B.T.); (W.P.); (S.W.); (V.R.); (T.T.)
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Blume RY, Rabokon AM, Pydiura M, Yemets AI, Pirko YV, Blume YB. Genome-wide identification and evolution of the tubulin gene family in Camelina sativa. BMC Genomics 2024; 25:599. [PMID: 38877397 PMCID: PMC11177405 DOI: 10.1186/s12864-024-10503-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, β- and γ-subfamilies, while α- and β-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa. RESULTS We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 β- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome. CONCLUSIONS For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and β-tubulins.
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Affiliation(s)
- Rostyslav Y Blume
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine.
| | - Anastasiia M Rabokon
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Mykola Pydiura
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
- JSC "Farmak", Kyiv, 04080, Ukraine
| | - Alla I Yemets
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Yaroslav V Pirko
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Yaroslav B Blume
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
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Tan C, Nie W, Liu Y, Wang Y, Yuan Y, Liu J, Chang E, Xiao W, Jia Z. Physiological response and molecular mechanism of Quercus variabilis under cadmium stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108724. [PMID: 38744084 DOI: 10.1016/j.plaphy.2024.108724] [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: 03/26/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Heavy metal pollution is a global environmental problem, and Quercus variabilis has a stronger tolerance to Cd stress than do other species. We aimed to explore the physiological response and molecular mechanisms of Q. variabilis to Cd stress. In this study, the antioxidant enzyme activities of leaves were determined, while the photosynthetic parameters of leaves were measured using Handy PEA, and ion fluxes and DEGs in the roots were investigated using noninvasive microtest technology (NMT) and RNA sequencing techniques, respectively. Cd stress at different concentrations and for different durations affected the uptake patterns of Cd2+ and H+ by Q. variabilis and affected the photosynthetic efficiency of leaves. Moreover, there was a positive relationship between antioxidant enzyme (CAT and POD) activity and Cd concentration. Transcriptome analysis revealed that many genes, including genes related to the cell wall, glutathione metabolism, ion uptake and transport, were significantly upregulated in response to cadmium stress in Q. variabilis roots. WGCNA showed that these DEGs could be divided into eight modules. The turquoise and blue modules exhibited the strongest correlations, and the most significantly enriched pathways were the phytohormone signaling pathway and the phenylpropanoid biosynthesis pathway, respectively. These findings suggest that Q. variabilis can bolster plant tolerance by modulating signal transduction and increasing the synthesis of compounds, such as lignin, under Cd stress. In summary, Q. variabilis can adapt to Cd stress by increasing the activity of antioxidant enzymes, and regulating the fluxes of Cd2+ and H+ ions and the expression of Cd stress-related genes.
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Affiliation(s)
- Cancan Tan
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institution, Chinese Academy of Forestry, Beijing, 100091, China; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wen Nie
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institution, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yifu Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institution, Chinese Academy of Forestry, Beijing, 100091, China
| | - Ya Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yanchao Yuan
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institution, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jianfeng Liu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Ermei Chang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wenfa Xiao
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institution, Chinese Academy of Forestry, Beijing, 100091, China
| | - Zirui Jia
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China; Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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Hong MJ, Ko CS, Kim JB, Kim DY. Identification and transcriptomic profiling of salinity stress response genes in colored wheat mutant. PeerJ 2024; 12:e17043. [PMID: 38464747 PMCID: PMC10924784 DOI: 10.7717/peerj.17043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
Background Salinity is a major abiotic stress that prevents normal plant growth and development, ultimately reducing crop productivity. This study investigated the effects of salinity stress on two wheat lines: PL1 (wild type) and PL6 (mutant line generated through gamma irradiation of PL1). Results The salinity treatment was carried out with a solution consisting of a total volume of 200 mL containing 150 mM NaCl. Salinity stress negatively impacted germination and plant growth in both lines, but PL6 exhibited higher tolerance. PL6 showed lower Na+ accumulation and higher K+ levels, indicating better ion homeostasis. Genome-wide transcriptomic analysis revealed distinct gene expression patterns between PL1 and PL6 under salt stress, resulting in notable phenotypic differences. Gene ontology analysis revealed positive correlations between salt stress and defense response, glutathione metabolism, peroxidase activity, and reactive oxygen species metabolic processes, highlighting the importance of antioxidant activities in salt tolerance. Additionally, hormone-related genes, transcription factors, and protein kinases showed differential expression, suggesting their roles in the differential salt stress response. Enrichment of pathways related to flavonoid biosynthesis and secondary metabolite biosynthesis in PL6 may contribute to its enhanced antioxidant activities. Furthermore, differentially expressed genes associated with the circadian clock system, cytoskeleton organization, and cell wall organization shed light on the plant's response to salt stress. Conclusions Understanding these mechanisms is crucial for developing stress-tolerant crop varieties, improving agricultural practices, and breeding salt-resistant crops to enhance global food production and address food security challenges.
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Affiliation(s)
- Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk-do, Korea
| | - Chan Seop Ko
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk-do, Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk-do, Korea
| | - Dae Yeon Kim
- Plant Resources, Kongju National University, Yesan-eup, Chungnam, South Korea
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Zhu F, Cheng H, Guo J, Bai S, Liu Z, Huang C, Shen J, Wang K, Yang C, Guan Q. Vegetative cell wall protein OsGP1 regulates cell wall mediated soda saline-alkali stress in rice. PeerJ 2024; 12:e16790. [PMID: 38436004 PMCID: PMC10908258 DOI: 10.7717/peerj.16790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/21/2023] [Indexed: 03/05/2024] Open
Abstract
Plant growth and development are inhibited by the high levels of ions and pH due to soda saline-alkali soil, and the cell wall serves as a crucial barrier against external stresses in plant cells. Proteins in the cell wall play important roles in plant cell growth, morphogenesis, pathogen infection and environmental response. In the current study, the full-length coding sequence of the vegetative cell wall protein gene OsGP1 was characterized from Lj11 (Oryza sativa longjing11), it contained 660 bp nucleotides encoding 219 amino acids. Protein-protein interaction network analysis revealed possible interaction between CESA1, TUBB8, and OsJ_01535 proteins, which are related to plant growth and cell wall synthesis. OsGP1 was found to be localized in the cell membrane and cell wall. Furthermore, overexpression of OsGP1 leads to increase in plant height and fresh weight, showing enhanced resistance to saline-alkali stress. The ROS (reactive oxygen species) scavengers were regulated by OsGP1 protein, peroxidase and superoxide dismutase activities were significantly higher, while malondialdehyde was lower in the overexpression line under stress. These results suggest that OsGP1 improves saline-alkali stress tolerance of rice possibly through cell wall-mediated intracellular environmental homeostasis.
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Affiliation(s)
- Fengjin Zhu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Huihui Cheng
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Jianan Guo
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Shuomeng Bai
- Aulin College, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Ziang Liu
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Chunxi Huang
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Jiayi Shen
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Kai Wang
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Chengjun Yang
- College of Forestry, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Qingjie Guan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang Province, China
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Kumar S, Chakraborty S, Chakraborty N. Dehydration-responsive cytoskeleton proteome of rice reveals reprograming of key molecular pathways to mediate metabolic adaptation and cell survival. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108359. [PMID: 38237420 DOI: 10.1016/j.plaphy.2024.108359] [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: 09/29/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/16/2024]
Abstract
The plant cytoskeletal proteins play a key role that control cytoskeleton dynamics, contributing to crucial biological processes such as cell wall morphogenesis, stomatal conductance and abscisic acid accumulation in repercussion to water-deficit stress or dehydration. Yet, it is still completely unknown which specific biochemical processes and regulatory mechanisms the cytoskeleton uses to drive dehydration tolerance. To better understand the role of cytoskeleton, we developed the dehydration-responsive cytoskeletal proteome map of a resilient rice cultivar. Initially, four-week-old rice plants were exposed to progressive dehydration, and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical indices. The organelle fractionation in conjunction with label-free quantitative proteome analysis led to the identification of 955 dehydration-responsive cytoskeletal proteins (DRCPs). To our knowledge, this is the first report of a stress-responsive plant cytoskeletal proteome, representing the largest inventory of cytoskeleton and cytoskeleton-associated proteins. The DRCPs were apparently involved in a wide array of intra-cellular molecules transportation, organelles positioning, cytoskeleton organization followed by different metabolic processes including amino acid metabolism. These findings presented open a unique view on global regulation of plant cytoskeletal proteome is intimately linked to cellular metabolic rewiring of adaptive responses, and potentially confer dehydration tolerance, especially in rice, and other crop species, in general.
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Affiliation(s)
- Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Kim P, Mahboob S, Nguyen HT, Eastman S, Fiala O, Sousek M, Gaussoin RE, Brungardt JL, Jackson-Ziems TA, Roston R, Alfano JR, Clemente TE, Guo M. Characterization of Soybean Events with Enhanced Expression of the Microtubule-Associated Protein 65-1 (MAP65-1). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:62-71. [PMID: 37889205 DOI: 10.1094/mpmi-09-23-0134-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Microtubule-associated protein 65-1 (MAP65-1) protein plays an essential role in plant cellular dynamics through impacting stabilization of the cytoskeleton by serving as a crosslinker of microtubules. The role of MAP65-1 in plants has been associated with phenotypic outcomes in response to various environmental stresses. The Arabidopsis MAP65-1 (AtMAP65-1) is a known virulence target of plant bacterial pathogens and is thus a component of plant immunity. Soybean events were generated that carry transgenic alleles for both AtMAP65-1 and GmMAP65-1, the soybean AtMAP65-1 homolog, under control of cauliflower mosaic virus 35S promoter. Both AtMAP65-1 and GmMAP65-1 transgenic soybeans are more resistant to challenges by the soybean bacterial pathogen Pseudomonas syringae pv. glycinea and the oomycete pathogen Phytophthora sojae, but not the soybean cyst nematode, Heterodera glycines. Soybean plants expressing AtMAP65-1 and GmMAP65-1 also display a tolerance to the herbicide oryzalin, which has a mode of action to destabilize microtubules. In addition, GmMAP65-1-expressing soybean plants show reduced cytosol ion leakage under freezing conditions, hinting that ectopic expression of GmMAP65-1 may enhance cold tolerance in soybean. Taken together, overexpression of AtMAP65-1 and GmMAP65-1 confers tolerance of soybean plants to various biotic and abiotic stresses. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Panya Kim
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Samira Mahboob
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Hanh T Nguyen
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Samuel Eastman
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Olivia Fiala
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Matthew Sousek
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Roch E Gaussoin
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Jae L Brungardt
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Tamra A Jackson-Ziems
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Rebecca Roston
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - James R Alfano
- Center for Plant Science Innovation and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A. (deceased)
| | - Tom Elmo Clemente
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Ming Guo
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
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Abdelmoneim MS, Hafez EE, Dawood MFA, Hammad SF, Ghazy MA. Toxicity of bisphenol A and p-nitrophenol on tomato plants: Morpho-physiological, ionomic profile, and antioxidants/defense-related gene expression studies. Biomol Concepts 2024; 15:bmc-2022-0049. [PMID: 38924751 DOI: 10.1515/bmc-2022-0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Bisphenol A (BPA) and p-nitrophenol (PNP) are emerging contaminants of soils due to their wide presence in agricultural and industrial products. Thus, the present study aimed to integrate morpho-physiological, ionic homeostasis, and defense- and antioxidant-related genes in the response of tomato plants to BPA or PNP stress, an area of research that has been scarcely studied. In this work, increasing the levels of BPA and PNP in the soil intensified their drastic effects on the biomass and photosynthetic pigments of tomato plants. Moreover, BPA and PNP induced osmotic stress on tomato plants by reducing soluble sugars and soluble proteins relative to control. The soil contamination with BPA and PNP treatments caused a decline in the levels of macro- and micro-elements in the foliar tissues of tomatoes while simultaneously increasing the contents of non-essential micronutrients. The Fourier transform infrared analysis of the active components in tomato leaves revealed that BPA influenced the presence of certain functional groups, resulting in the absence of some functional groups, while on PNP treatment, there was a shift observed in certain functional groups compared to the control. At the molecular level, BPA and PNP induced an increase in the gene expression of polyphenol oxidase and peroxidase, with the exception of POD gene expression under BPA stress. The expression of the thaumatin-like protein gene increased at the highest level of PNP and a moderate level of BPA without any significant effect of both pollutants on the expression of the tubulin (TUB) gene. The comprehensive analysis of biochemical responses in tomato plants subjected to BPA and PNP stress illustrates valuable insights into the mechanisms underlying tolerance to these pollutants.
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Affiliation(s)
- Mahmoud S Abdelmoneim
- Biotechnology program, Basic and Applied Science Institute, Egypt-Japan University of Science and Technology (E-JUST), 21934, New Borg El-Arab City, Alexandrina, Egypt
- Botany and Microbiology Department, Faculty of Science, Assiut University, 71515, Assiut, Egypt
| | - Elsayed E Hafez
- Plant Protection and Bimolecular Diagnosis Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), 21934, New Borg El-Arab city, Alexandrina, Egypt
| | - Mona F A Dawood
- Botany and Microbiology Department, Faculty of Science, Assiut University, 71515, Assiut, Egypt
| | - Sherif F Hammad
- Pharm D program, Egypt-Japan University of Science and Technology (E-JUST), 21934, New Borg El-Arab City, Alexandrina, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Helwan University, 11795, Ain Helwan, Cairo, Egypt
| | - Mohamed A Ghazy
- Biotechnology program, Basic and Applied Science Institute, Egypt-Japan University of Science and Technology (E-JUST), 21934, New Borg El-Arab City, Alexandrina, Egypt
- Biochemistry Department, Faculty of Science, Ain Shams University, 11566, Cairo, Egypt
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Guo H, Zhang G, Zhou M, Wan M, Zhu B, Yang Z, Zeng D, Zeng Z. Whole genome doubling-induced the enrichment of H3K27me3 in genes carrying specific TEs in Aegilops tauschii. Front Genet 2023; 14:1241201. [PMID: 37560386 PMCID: PMC10407559 DOI: 10.3389/fgene.2023.1241201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023] Open
Abstract
Polyploidization plays important roles in the evolution and breeding of the common wheat. Aegilops tauschii, the D-genome progenitor of the common wheat, provides a valuable pool of resistance genes to multiple diseases. Extensive studies focus on the exploration of these genes for wheat improvement. However, few studies have unveiled alternations on genome-wide expression pattern and histone modifications induced by whole-genome doubling (WGD) process. In this study, we conducted transcriptome analysis for the diploid and tetraploid Ae. taushcii lines using the leaf and root tissues. Both lines tend to display similar tissue-specific pattern. Interestingly, we found that TEs located in genic regions were depleted of the repressive histone mark H3K27me3, whereas their adjacent chromatin was enriched with H3K27me3. The tetraploid line exhibited higher levels of H3K27me3 in those regions than the diploid line, particularly for genic regions associated with TEs of the long interspersed nuclear elements (LINEs), CACTA, PIF/Harbinger, Tc1/Mariner and unclassed DNA transposon. Surprisingly, the expression levels of these TEs cognate genes were negatively associated with the levels of H3K27me3 between the tetraploid and diploid lines, suggesting the five types of TEs located within genic regions might be involved in the regulation of the ploidy-related gene expression, possibly through differential enrichment of H3K27me3 in the genic regions. These findings will help to understand the potential role of specific types of TEs on transcription in response to WGD.
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Affiliation(s)
- Hongwei Guo
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Guoyan Zhang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Min Zhou
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Min Wan
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Bo Zhu
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Deying Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
| | - Zixian Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
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Zhao Q, Shen W, Gu Y, Hu J, Ma Y, Zhang X, Du Y, Zhang Y, Du J. Exogenous melatonin mitigates saline-alkali stress by decreasing DNA oxidative damage and enhancing photosynthetic carbon metabolism in soybean (Glycine max [L.] Merr.) leaves. PHYSIOLOGIA PLANTARUM 2023; 175:e13983. [PMID: 37616002 DOI: 10.1111/ppl.13983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/25/2023] [Accepted: 07/17/2023] [Indexed: 08/25/2023]
Abstract
Saline-alkali stress (SS) is a common abiotic stress affecting crop cultivation worldwide, seriously inhibiting plant growth and biomass accumulation. Melatonin has been proven to relieve the inhibition of multiple abiotic stresses on plant growth. Therefore, soybean cultivars Heihe 49 (HH49, SS-tolerant) and Henong 95 (HN95, SS-sensitive) were pot-cultured in SS soil and then treated with 300 μM melatonin at the V1 stage, when the first trifoliate leaves were fully unfolded, to investigate if melatonin has an effect on SS. SS increased reactive oxygen species (ROS) accumulation in soybean leaves and thereby induced DNA oxidative damage. In addition, SS retarded cell growth and decreased the mesophyll cell size, chloroplast number, photosynthetic pigment content, which further reduced the light energy capture and electron transport rate in soybean leaves, and affected carbohydrate accumulation and metabolism. However, melatonin treatment reduced SS-induced ROS accumulation in the soybean leaves by increasing antioxidant content and oxidase activity. Effective removal of ROS reduced SS-induced DNA oxidative damage in the soybean leaf genome, which was represented by decreased random-amplified polymorphic DNA polymorphism, 8-hydroxy-20-deoxyguanine content, and relative density of apurinic/apyrimidinic-sites. Melatonin treatment also increased the volume of mesophyll cells, the numbers of chloroplast and starch grains, the contents of chlorophyll a and b and carotenoids in soybean seedling leaves treated with SS, thereby increasing the efficiency of effective light capture and electron transfer and improving photosynthesis. Subsequently, carbohydrate accumulation and metabolism in soybean leaves under SS were improved by melatonin treatment, which contributes to providing basic substances and energy for cell growth and metabolism, ultimately improving soybean SS tolerance.
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Affiliation(s)
- Qiang Zhao
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, PR China
- Research Center of Saline and Alkali Land Improvement Engineering Technology in Heilongjiang Province, Daqing, PR China
| | - Wanzheng Shen
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, PR China
| | - Yanhua Gu
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, PR China
| | - Jiachen Hu
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, PR China
| | - Yue Ma
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, PR China
| | - Xinlin Zhang
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, PR China
| | - Yanli Du
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, PR China
| | - Yuxian Zhang
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, PR China
- National Coarse Cereals Engineering Research Center, Daqing, PR China
| | - Jidao Du
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, PR China
- Research Center of Saline and Alkali Land Improvement Engineering Technology in Heilongjiang Province, Daqing, PR China
- National Coarse Cereals Engineering Research Center, Daqing, PR China
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11
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Karumanchi AR, Sivan P, Kummari D, Rajasheker G, Kumar SA, Reddy PS, Suravajhala P, Podha S, Kishor PBK. Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor. PLANTS (BASEL, SWITZERLAND) 2023; 12:2400. [PMID: 37446963 DOI: 10.3390/plants12132400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
Roots from salt-susceptible ICSR-56 (SS) sorghum plants display metaxylem elements with thin cell walls and large diameter. On the other hand, roots with thick, lignified cell walls in the hypodermis and endodermis were noticed in salt-tolerant CSV-15 (ST) sorghum plants. The secondary wall thickness and number of lignified cells in the hypodermis have increased with the treatment of sodium chloride stress to the plants (STN). Lignin distribution in the secondary cell wall of sclerenchymatous cells beneath the lower epidermis was higher in ST leaves compared to the SS genotype. Casparian thickenings with homogenous lignin distribution were observed in STN roots, but inhomogeneous distribution was evident in SS seedlings treated with sodium chloride (SSN). Higher accumulation of K+ and lower Na+ levels were noticed in ST compared to the SS genotype. To identify the differentially expressed genes among SS and ST genotypes, transcriptomic analysis was carried out. Both the genotypes were exposed to 200 mM sodium chloride stress for 24 h and used for analysis. We obtained 70 and 162 differentially expressed genes (DEGs) exclusive to SS and SSN and 112 and 26 DEGs exclusive to ST and STN, respectively. Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis unlocked the changes in metabolic pathways in response to salt stress. qRT-PCR was performed to validate 20 DEGs in each SSN and STN sample, which confirms the transcriptomic results. These results surmise that anatomical changes and higher K+/Na+ ratios are essential for mitigating salt stress in sorghum apart from the genes that are differentially up- and downregulated in contrasting genotypes.
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Affiliation(s)
- Appa Rao Karumanchi
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 209, India
| | - Pramod Sivan
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Albanova University Center, SE-10691 Stockholm, Sweden
| | - Divya Kummari
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - G Rajasheker
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - S Anil Kumar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research (Deemed to Be University), Guntur 522 213, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | | | - Sudhakar Podha
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 209, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India
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12
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Hsiao AS, Huang JY. Microtubule Regulation in Plants: From Morphological Development to Stress Adaptation. Biomolecules 2023; 13:biom13040627. [PMID: 37189374 DOI: 10.3390/biom13040627] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/09/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023] Open
Abstract
Microtubules (MTs) are essential elements of the eukaryotic cytoskeleton and are critical for various cell functions. During cell division, plant MTs form highly ordered structures, and cortical MTs guide the cell wall cellulose patterns and thus control cell size and shape. Both are important for morphological development and for adjusting plant growth and plasticity under environmental challenges for stress adaptation. Various MT regulators control the dynamics and organization of MTs in diverse cellular processes and response to developmental and environmental cues. This article summarizes the recent progress in plant MT studies from morphological development to stress responses, discusses the latest techniques applied, and encourages more research into plant MT regulation.
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13
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Zhou S, Luo Q, Nie Z, Wang C, Zhu W, Hong Y, Zhao J, Pei B, Ma W. CRK41 Modulates Microtubule Depolymerization in Response to Salt Stress in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1285. [PMID: 36986973 PMCID: PMC10051889 DOI: 10.3390/plants12061285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
The pivotal role of cysteine-rich receptor-like kinases (CRKs) in modulating growth, development, and responses to stress has been widely acknowledged in Arabidopsis. However, the function and regulation of CRK41 has remained unclear. In this study, we demonstrate that CRK41 is critical for modulating microtubule depolymerization in response to salt stress. The crk41 mutant exhibited increased tolerance, while overexpression of CRK41 led to hypersensitivity to salt. Further analysis revealed that CRK41 interacts directly with the MAP kinase3 (MPK3), but not with MPK6. Inactivation of either MPK3 or MPK6 could abrogate the salt tolerance of the crk41 mutant. Upon NaCl treatment, microtubule depolymerization was heightened in the crk41 mutant, yet alleviated in the crk41mpk3 and crk41mpk6 double mutants, indicating that CRK41 suppresses MAPK-mediated microtubule depolymerizations. Collectively, these results reveal that CRK41 plays a crucial role in regulating microtubule depolymerization triggered by salt stress through coordination with MPK3/MPK6 signalling pathways, which are key factors in maintaining microtubule stability and conferring salt stress resistance in plants.
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Affiliation(s)
- Sa Zhou
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (S.Z.)
| | - Qiuling Luo
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (S.Z.)
| | - Zhiyan Nie
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (S.Z.)
| | - Changhui Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (S.Z.)
| | - Wenkang Zhu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (S.Z.)
| | - Yingxiang Hong
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (S.Z.)
| | - Jun Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Baolei Pei
- College of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China
| | - Wenjian Ma
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; (S.Z.)
- Qilu Institute of Technology, Jinan 250200, China
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14
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Characteristics of Root Cells during In Vitro Rhizogenesis under Action of NaCl in Two Tomato Genotypes Differing in Salt Tolerance. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2023. [DOI: 10.3390/ijpb14010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Understanding the mechanisms of plant salt tolerance as a complex trait is an integral part of many studies, the results of which have been used in the breeding process. The aim of this study was to compare the root response of two tomato (Solanum lycopersicum L.) genotypes (breeding line YaLF and cultivar Recordsmen) differing in salt tolerance. Rhizogenesis was induced in tomato shoots in vitro with different concentrations of NaCl in the culture medium. A number of morphobiological and cytological parameters were evaluated at the organ, tissue, and cellular levels for possible use in a comprehensive assessment of genotypes for salt tolerance. The influence of NaCl caused disruption of the cell cycle and redistribution of cells in the phases of the cell cycle. An increase in the degree of vacuolization was shown in cv Recordsmen at 75 and 150 mM NaCl and in the YaLF line at 150 mM NaCl. Under salt action, an increase/decrease in the length of cells such as columella cells (both genotypes) and epidermal cells (in cv Recordsmen at 75 and 150 mM NaCl) was shown. Differences between genotypes were demonstrated by changes in the area of the central cylinder and primary root cortex cells, as well as by changes of the Snucleolus/Snucleus ratio in these cells. Transmission electron microscopy (TEM) showed the modification of the chromatin structure in the root cells of these genotypes. Various cytoskeletal disorders were revealed in interphase cells of the tomato root of cv Recordsmen and the YaLF line by immunofluorescent staining under saline conditions. These morphometric and cytological parameters can be used for a comparative evaluation of genotypes differing in salt tolerance in a comprehensive assessment of varieties.
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15
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Kumar S, Jeevaraj T, Yunus MH, Chakraborty S, Chakraborty N. The plant cytoskeleton takes center stage in abiotic stress responses and resilience. PLANT, CELL & ENVIRONMENT 2023; 46:5-22. [PMID: 36151598 DOI: 10.1111/pce.14450] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Stress resilience behaviours in plants are defensive mechanisms that develop under adverse environmental conditions to promote growth, development and yield. Over the past decades, improving stress resilience, especially in crop species, has been a focus of intense research for global food security and economic growth. Plants have evolved specific mechanisms to sense external stress and transmit information to the cell interior and generate appropriate responses. Plant cytoskeleton, comprising microtubules and actin filaments, takes a center stage in stress-induced signalling pathways, either as a direct target or as a signal transducer. In the past few years, it has become apparent that the function of the plant cytoskeleton and other associated proteins are not merely limited to elementary processes of cell growth and proliferation, but they also function in stress response and resilience. This review summarizes recent advances in the role of plant cytoskeleton and associated proteins in abiotic stress management. We provide a thorough overview of the mechanisms that plant cells employ to withstand different abiotic stimuli such as hypersalinity, dehydration, high temperature and cold, among others. We also discuss the crucial role of the plant cytoskeleton in organellar positioning under the influence of high light intensity.
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Affiliation(s)
- Sunil Kumar
- Stress Biology, National Institute of Plant Genome Research, New Delhi, India
| | - Theboral Jeevaraj
- Stress Biology, National Institute of Plant Genome Research, New Delhi, India
| | - Mohd H Yunus
- Stress Biology, National Institute of Plant Genome Research, New Delhi, India
| | - Subhra Chakraborty
- Stress Biology, National Institute of Plant Genome Research, New Delhi, India
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16
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Qin D, Liu G, Liu R, Wang C, Xu F, Xu Q, Ling Y, Dong G, Peng Y, Ge S, Guo G, Dong J, Li C. Positional cloning identified HvTUBULIN8 as the candidate gene for round lateral spikelet (RLS) in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:7. [PMID: 36656367 PMCID: PMC9852219 DOI: 10.1007/s00122-023-04272-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Map-based cloning, subcellular localization, virus-induced-gene-silencing and transcriptomic analysis reveal HvTUB8 as a candidate gene with pleiotropic effects on barley spike and leaf development via ethylene and chlorophyll metabolism. Barley lateral spikelet morphology and grain shape play key roles in grain physical quality and yield. Several genes and QTLs for these traits have been cloned or fine mapped previously. Here, we report the phenotypic and genotypic analysis of a barley mutant with round lateral spikelet (rls) from cv. Edamai 934. rls had round lateral spikelet, short but round grain, shortened awn, thick glume and dark green leaves. Histocytologic and ultrastructural analysis revealed that the difference of grain shape of rls was caused by change of cell arrangement in glume, and the dark leaf color resulted from enlarged chloroplast. HvTUBULIN8 (HvTUB8) was identified as the candidate gene for rls by combination of RNA-Seq, map-based-cloning, virus-induced-gene-silencing (VIGS) and protein subcellular location. A single G-A substitution at the third exon of HvTUB8 resulted in change of Cysteine 354 to tyrosine. Furthermore, the mutant isoform Hvtub8 could be detected in both nucleus and cytoplasm, whereas the wild-type protein was only in cytoplasm and granular organelles of wheat protoplasts. Being consistent with the rare phenotype, the "A" allele of HvTUB8 was only detected in rls, but not in a worldwide barley germplasm panel with 400 accessions. VIGS confirmed that HvTUB8 was essential to maintain spike integrity. RNA-Seq results suggested that HvTUB8 may control spike morphogenesis via ethylene homeostasis and signaling, and control leaf color through chlorophyll metabolism. Collectively, our results support HvTUB8 as a candidate gene for barley spike and leaf morphology and provide insight of a novel mechanism of it in barley development.
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Affiliation(s)
- Dandan Qin
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Gang Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Rui Liu
- Wuhan Polytechnic University, Wuhan, 430023, Hubei, China
| | - Chunchao Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fuchao Xu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Qing Xu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
| | - Guoqing Dong
- Wuhan Polytechnic University, Wuhan, 430023, Hubei, China
| | - Yanchun Peng
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Shuangtao Ge
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Ganggang Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Dong
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Chengdao Li
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Western Australia, WA, 6150, Australia.
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17
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Liu Z, Hu Y, Du A, Yu L, Fu X, Wu C, Lu L, Liu Y, Wang S, Huang W, Tu S, Ma X, Li H. Cell Wall Matrix Polysaccharides Contribute to Salt-Alkali Tolerance in Rice. Int J Mol Sci 2022; 23:ijms232315019. [PMID: 36499349 PMCID: PMC9735747 DOI: 10.3390/ijms232315019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
Salt-alkali stress threatens the resilience to variable environments and thus the grain yield of rice. However, how rice responds to salt-alkali stress at the molecular level is poorly understood. Here, we report isolation of a novel salt-alkali-tolerant rice (SATR) by screening more than 700 germplasm accessions. Using 93-11, a widely grown cultivar, as a control, we characterized SATR in response to strong salt-alkali stress (SSAS). SATR exhibited SSAS tolerance higher than 93-11, as indicated by a higher survival rate, associated with higher peroxidase activity and total soluble sugar content but lower malonaldehyde accumulation. A transcriptome study showed that cell wall biogenesis-related pathways were most significantly enriched in SATR relative to 93-11 upon SSAS. Furthermore, higher induction of gene expression in the cell wall matrix polysaccharide biosynthesis pathway, coupled with higher accumulations of hemicellulose and pectin as well as measurable physio-biochemical adaptive responses, may explain the strong SSAS tolerance in SATR. We mapped SSAS tolerance to five genomic regions in which 35 genes were candidates potentially governing SSAS tolerance. The 1,4-β-D-xylan synthase gene OsCSLD4 in hemicellulose biosynthesis pathway was investigated in details. The OsCSLD4 function-disrupted mutant displayed reduced SSAS tolerance, biomass and grain yield, whereas the OsCSLD4 overexpression lines exhibited increased SSAS tolerance. Collectively, this study not only reveals the potential role of cell wall matrix polysaccharides in mediating SSAS tolerance, but also highlights applicable value of OsCSLD4 and the large-scale screening system in developing SSAS-tolerant rice.
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Affiliation(s)
- Zhijian Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongzhi Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China
| | - Anping Du
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Lan Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China
| | - Xingyue Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cuili Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China
| | - Longxiang Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangxuan Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songhu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weizao Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Shengbin Tu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinrong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- Correspondence:
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18
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Guo H, Xiong X, Wang Y, Tian H, Zhang S, Geng G. Integrative proteomic and physiological analyses of the molecular response to dessication-stress in Auricularia fibrillifera. FRONTIERS IN PLANT SCIENCE 2022; 13:995810. [PMID: 36212373 PMCID: PMC9532602 DOI: 10.3389/fpls.2022.995810] [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: 07/16/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Drought stress is one of the main factors influencing the growth and development of an organism. Auricularia fibrillifera has strong dessication resistance. In A. fibrillifera under dessication-stress, the melanin content of fruiting bodies elevated significantly by >10-fold compared with the control. Folate content also increased sharply but decreased significantly after rehydration, and amino acid and biotin levels increased by 40.11 and 22.14%, respectively. In proteomic analysis, 1,572 and 21 differentially abundant proteins (DAPs) were identified under dessication-stress and rehydration, respectively. A large number of DAPs were annotated in "amino acid metabolism," "carbohydrate metabolism," and "translation" pathways, and the DAPs related to osmotic regulation and antioxidant enzymes were significantly increased in abundance. Transcriptome-proteome association analysis showed that most DAPs (30) were annotated in the "biosynthesis of antibiotics" pathway. DAPs and corresponding differentially expressed genes were all up-regulated in the "biotin biosynthesis" pathway and associated with "folate biosynthesis" and "phenylalanine, tyrosine, and tryptophan biosynthesis." In the analysis of protein-protein interactions, the DAPs annotated in the "phenylalanine, tyrosine, and tryptophan biosynthesis" pathway had the strongest interactions with other DAPs. These enriched pathways could enhance amino acid, folate, biotin, and melanin levels during desiccation stress, which is consistent with the physiological data (amino acid, folate, biotin, and melanin contents). In addition, many DAPs related to the cytoskeleton were significantly increased in abundance under dessication-stress. Physiological and transcriptome data were in agreement with proteomic results. This work provides valuable insight into the dessication-tolerant mechanisms of A. fibrillifera.
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19
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Mo C, Wu Z, Shang X, Shi P, Wei M, Wang H, Xiao L, Cao S, Lu L, Zeng W, Yan H, Kong Q. Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana. DNA Res 2022; 29:6663990. [PMID: 35961033 PMCID: PMC9397507 DOI: 10.1093/dnares/dsac030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/10/2022] [Indexed: 12/03/2022] Open
Abstract
Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigour and cold-adaption but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana with length of 978.59 Mb and scaffold N50 of 80.18 Mb. Comparative genomics analysis showed that P. montana possesses smaller genome size than that of P. thomsonii owing to less repeat sequences and duplicated genes. A total of 6,548 and 4,675 variety-specific gene families were identified in P. montana and P. thomsonii, respectively. The identified variety-specific and expanded/contracted gene families related to biosynthesis of bioactive metabolites and microtubules are likely the causes for the different characteristics of metabolism and cold-adaption of P. montana and P. thomsonii. Moreover, a graphic genome was constructed based on 11 P. montana accessions. Total 92 structural variants were identified and most of which are related to stimulus-response. In conclusion, the chromosome-level and graphic genomes of P. montana will not only facilitate the studies of evolution and metabolic regulation, but also promote the breeding of Pueraria.
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Affiliation(s)
| | | | - Xiaohong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Pingli Shi
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Minghua Wei
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiyan Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Liuying Lu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Wendan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Huabing Yan
- To whom correspondence should be addressed. Tel. 86-13877165487. (H.Y.); Tel. 86-18942928088. (Q.K.)
| | - Qiusheng Kong
- To whom correspondence should be addressed. Tel. 86-13877165487. (H.Y.); Tel. 86-18942928088. (Q.K.)
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20
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Liu Z, Østerlund I, Ruhnow F, Cao Y, Huang G, Cai W, Zhang J, Liang W, Nikoloski Z, Persson S, Zhang D. Fluorescent cytoskeletal markers reveal associations between the actin and microtubule cytoskeleton in rice cells. Development 2022; 149:275467. [DOI: 10.1242/dev.200415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/09/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Rice (Oryza sativa) is one of our main food crops, feeding ∼3.5 billion people worldwide. An increasing number of studies note the importance of the cytoskeleton, including actin filaments and microtubules, in rice development and environmental responses. Yet, reliable in vivo cytoskeleton markers are lacking in rice, which limits our knowledge of cytoskeletal functions in living cells. Therefore, we generated bright fluorescent marker lines of the actin and microtubule cytoskeletons in rice, suitable for live-cell imaging in a wide variety of rice tissues. Using these lines, we show that actin bundles and microtubules engage and co-function during pollen grain development, how the cytoskeletal components are coordinated during root cell development, and that the actin cytoskeleton is robust and facilitates microtubule responses during salt stress. Hence, we conclude that our cytoskeletal marker lines, highlighted by our findings of cytoskeletal associations and dynamics, will substantially further future investigations in rice biology.
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Affiliation(s)
- Zengyu Liu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Isabella Østerlund
- University of Copenhagen 2 Department of Plant and Environmental Sciences (PLEN) , , 1870 Frederiksberg , Denmark
- Max Planck Institute of Molecular Plant Physiology 3 Systems Biology and Mathematical Modelling , , Am Mühlenberg 1, 14476 Potsdam-Golm , Germany
| | - Felix Ruhnow
- University of Copenhagen 2 Department of Plant and Environmental Sciences (PLEN) , , 1870 Frederiksberg , Denmark
| | - Yiran Cao
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Wenguo Cai
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Jiao Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology 3 Systems Biology and Mathematical Modelling , , Am Mühlenberg 1, 14476 Potsdam-Golm , Germany
| | - Staffan Persson
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
- University of Copenhagen 2 Department of Plant and Environmental Sciences (PLEN) , , 1870 Frederiksberg , Denmark
- Copenhagen Plant Science Center (CPSC) 4 , , 1870 Frederiksberg , Denmark
- University of Copenhagen 4 , , 1870 Frederiksberg , Denmark
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
- School of Agriculture, Food, and Wine 5 , , Waite Campus, Urrbrae, SA 5064 , Australia
- University of Adelaide 5 , , Waite Campus, Urrbrae, SA 5064 , Australia
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21
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Acidic and Alkaline Conditions Affect the Growth of Tree Peony Plants via Altering Photosynthetic Characteristics, Limiting Nutrient Assimilation, and Impairing ROS Balance. Int J Mol Sci 2022; 23:ijms23095094. [PMID: 35563483 PMCID: PMC9099645 DOI: 10.3390/ijms23095094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 12/04/2022] Open
Abstract
Exposure to acidic and alkaline conditions were found to cause the excess accumulation of reactive oxygen species in tree peony, thereby causing damage and inhibiting plant growth and development. The activities of antioxidant enzymes were also found to be significantly up-regulated, especially under alkaline conditions; this explained why tree peony is better adapted to alkaline than to acidic conditions. Through pairwise comparisons, 144 differentially expressed genes (DEGs) associated with plant growth, photosynthesis, and stress were identified. The DEGs related to stress were up-regulated, whereas the remaining DEGs were almost all down-regulated after acid and alkaline treatments. The nutrient assimilation was greatly inhibited. Chlorophyll synthesis genes were suppressed, and chlorophyll content was reduced. The development and structures of stomata and chloroplasts and the transcription of related genes were also influenced. Among photosynthesis-related DEGs, electron transport chains were the most sensitive. The suppressed expression of photosynthesis genes and the reduced light-harvesting capacity, together with the impairment of chloroplasts and stomata, finally led to a sharp decrease in the net photosynthetic rate. Carbohydrate accumulation and plant biomass were also reduced. The present study provides a theoretical basis for the response mechanisms of tree peony to adverse pH conditions and enriches knowledge of plant adaptation to alkaline conditions.
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22
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Plant Responses and Tolerance to Salt Stress: Physiological and Molecular Interventions. Int J Mol Sci 2022; 23:ijms23094810. [PMID: 35563198 PMCID: PMC9103774 DOI: 10.3390/ijms23094810] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 02/05/2023] Open
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23
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Hao Z, Ma S, Liang L, Feng T, Xiong M, Lian S, Zhu J, Chen Y, Meng L, Li M. Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network. Int J Mol Sci 2022; 23:ijms23074016. [PMID: 35409377 PMCID: PMC8999833 DOI: 10.3390/ijms23074016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 01/24/2023] Open
Abstract
Drought and salinity stresses are significant abiotic factors that limit rice yield. Exploring the co-response mechanism to drought and salt stress will be conducive to future rice breeding. A total of 1748 drought and salt co-responsive genes were screened, most of which are enriched in plant hormone signal transduction, protein processing in the endoplasmic reticulum, and the MAPK signaling pathways. We performed gene-coding sequence haplotype (gcHap) network analysis on nine important genes out of the total amount, which showed significant differences between the Xian/indica and Geng/japonica population. These genes were combined with related pathways, resulting in an interesting mechanistic draft called the ‘gcHap-network pathway’. Meanwhile, we collected a lot of drought and salt breeding varieties, especially the introgression lines (ILs) with HHZ as the parent, which contained the above-mentioned nine genes. This might imply that these ILs have the potential to improve the tolerance to drought and salt. In this paper, we focus on the relationship of drought and salt co-response gene gcHaps and their related pathways using a novel angle. The haplotype network will be helpful to explore the desired haplotypes that can be implemented in haplotype-based breeding programs.
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Affiliation(s)
- Zhiqi Hao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sai Ma
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lunping Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Mengyuan Xiong
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Shangshu Lian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jingyan Zhu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Yanjun Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lijun Meng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Correspondence: (L.M.); (M.L.)
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Correspondence: (L.M.); (M.L.)
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Kumar S, Lande NV, Barua P, Pareek A, Chakraborty S, Chakraborty N. Proteomic dissection of rice cytoskeleton reveals the dominance of microtubule and microfilament proteins, and novel components in the cytoskeleton-bound polysome. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:75-86. [PMID: 34861586 DOI: 10.1016/j.plaphy.2021.11.037] [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: 09/16/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The plant cytoskeleton persistently undergoes remodeling to achieve its roles in supporting cell division, differentiation, cell expansion and organelle transport. However, the links between cell metabolism and cytoskeletal networks, particularly how the proteinaceous components execute such processes remain poorly understood. We investigated the cytoskeletal proteome landscape of rice to gain better understanding of such events. Proteins were extracted from highly enriched cytoskeletal fraction of four-week-old rice seedlings, and the purity of the fraction was stringently monitored. A total of 2577 non-redundant proteins were identified using both gel-based and gel-free approaches, which constitutes the most comprehensive dataset, thus far, for plant cytoskeleton. The data set includes both microtubule and microfilament-associated proteins and their binding proteins comprising hypothetical as well as novel cytoskeletal proteins. Further, various in-silico analyses were performed, and the proteins were functionally classified on the basis of their gene ontology. The catalogued proteins were validated through their sequence analysis. Extensive comparative analysis of our dataset with the non-redundant set of cytoskeletal proteins across plant species affirms unique as well as overlapping candidates. Together, these findings unveil new insights of how cytoskeletons undergo dynamic remodeling in rice to drive seedling development processes in rapidly changing in planta environment.
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Affiliation(s)
- Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nilesh Vikram Lande
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Pragya Barua
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akanksha Pareek
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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25
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Gutierrez N, Torres AM. QTL dissection and mining of candidate genes for Ascochyta fabae and Orobanche crenata resistance in faba bean (Vicia faba L.). BMC PLANT BIOLOGY 2021; 21:551. [PMID: 34809555 PMCID: PMC8607628 DOI: 10.1186/s12870-021-03335-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Ascochyta blight caused by Ascochyta fabae Speg. and broomrape (Orobanche crenata) are among the economically most significant pathogens of faba bean. Several QTLs conferring resistance against the two pathogens have been identified and validated in different genetic backgrounds. The aim of this study was to saturate the most stable QTLs for ascochyta and broomrape resistance in two Recombinant Inbred Line (RIL) populations, 29H x Vf136 and Vf6 x Vf136, to identify candidate genes conferring resistance against these two pathogens. RESULTS We exploited the synteny between faba bean and the model species Medicago truncatula by selecting a set of 219 genes encoding putative WRKY transcription factors and defense related proteins falling within the target QTL intervals, for genotyping and marker saturation in the two RIL populations. Seventy and 50 of the candidate genes could be mapped in 29H x Vf136 and Vf6 x Vf136, respectively. Besides the strong reduction of the QTL intervals, the mapping process allowed replacing previous dominant and pedigree-specific RAPD flanking markers with robust and transferrable SNP markers, revealing promising candidates for resistance against the two pathogens. CONCLUSIONS Although further efforts in association mapping and expression studies will be required to corroborate the candidate genes for resistance, the fine-mapping approach proposed here increases the genetic resolution of relevant QTL regions and paves the way for an efficient deployment of useful alleles for faba bean ascochyta and broomrape resistance through marker-assisted breeding.
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Affiliation(s)
- Natalia Gutierrez
- Área de Genómica y Biotecnología, IFAPA-Centro Alameda del Obispo, Apdo 3092, E-14080, Córdoba, Spain.
| | - Ana M Torres
- Área de Genómica y Biotecnología, IFAPA-Centro Alameda del Obispo, Apdo 3092, E-14080, Córdoba, Spain
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26
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Abstract
Salt stress causes several damaging effects in plant cells. These commonly observed effects are the results of oxidative, osmotic, and toxic stresses. To ensure normal growth and development of tissues, the cellular compartments of multicellular plants have a unique system that provides the specified parameters of growth and differentiation. The cell shape and the direction of division support the steady development of the organism, the habit, and the typical shape of the organs and the whole plant. When dividing, daughter cells evenly or unevenly distribute the components of cytoplasm. Factors such as impaired osmotic regulation, exposure to toxic compounds, and imbalance in the antioxidant system cause disorders associated with the moving of organelles, distribution transformations of the endoplasmic reticulum, and the vacuolar compartment. In some cases, one can observe a different degree of plasmolysis manifestation, local changes in the density of cytoplasm. Together, these processes can cause disturbances in the direction of cell division, the formation of a phragmoplast, the formation of nuclei of daughter cells, and a violation of their fine structural organization. These processes are often accompanied by significant damage to the cytoskeleton, the formation of nonspecific structures formed by proteins of the cytoskeleton. The consequences of these processes can lead to the death of some cells or to a significant change in their morphology and properties, deformation of newly formed tissues and organs, and changes in the plant phenotype. Thus, as a result of significant violations of the cytoskeleton, causing critical destabilization of the symmetric distribution of the cell content, disturbances in the distribution of chromosomes, especially in polyploid cells, may occur, resulting in the appearance of micronuclei. Hence, the asymmetry of a certain component of the plant cell is a marker of susceptibility to abiotic damage.
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