1
|
Wróbel A, Klichowska E, Nowak A, Nobis M. Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot. Syst Biol 2024; 73:263-278. [PMID: 38141222 PMCID: PMC11282368 DOI: 10.1093/sysbio/syad073] [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: 03/06/2023] [Revised: 11/23/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023] Open
Abstract
Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass Puccinellia pamirica and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of P. pamirica alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.
Collapse
Affiliation(s)
- Anna Wróbel
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza 11, 30-348 Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Arkadiusz Nowak
- Botanical Garden, Center for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-973 Warszawa, Poland
- Botanical Garden of the Wrocław University, Sienkiewicza 23, 50-335 Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| |
Collapse
|
2
|
Duan Y, Wang X, Jiao Y, Liu Y, Li Y, Song Y, Wang L, Tong X, Jiang Y, Wang S, Wang S. Elucidating the role of exogenous melatonin in mitigating alkaline stress in soybeans across different growth stages: a transcriptomic and metabolomic approach. BMC PLANT BIOLOGY 2024; 24:380. [PMID: 38720246 PMCID: PMC11077714 DOI: 10.1186/s12870-024-05101-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Soybean (Glycine max), a vital grain and oilseed crop, serves as a primary source of plant protein and oil. Soil salinization poses a significant threat to soybean planting, highlighting the urgency to improve soybean resilience and adaptability to saline stress. Melatonin, recently identified as a key plant growth regulator, plays crucial roles in plant growth, development, and responses to environmental stress. However, the potential of melatonin to mitigate alkali stress in soybeans and the underlying mechanisms remain unclear. RESULTS This study investigated the effects of exogenous melatonin on the soybean cultivar Zhonghuang 13 under alkaline stress. We employed physiological, biochemical, transcriptomic, and metabolomic analyses throughout both vegetative and pod-filling growth stages. Our findings demonstrate that melatonin significantly counteracts the detrimental effects of alkaline stress on soybean plants, promoting plant growth, photosynthesis, and antioxidant capacity. Transcriptomic analysis during both growth stages under alkaline stress, with and without melatonin treatment, identified 2,834 and 549 differentially expressed genes, respectively. These genes may play a vital role in regulating plant adaptation to abiotic stress. Notably, analysis of phytohormone biosynthesis pathways revealed altered expression of key genes, particularly in the ARF (auxin response factor), AUX/IAA (auxin/indole-3-acetic acid), and GH3 (Gretchen Hagen 3) families, during the early stress response. Metabolomic analysis during the pod-filling stage identified highly expressed metabolites responding to melatonin application, such as uteolin-7-O-(2''-O-rhamnosyl)rutinoside and Hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)glucoside, which helped alleviate the damage caused by alkali stress. Furthermore, we identified 183 differentially expressed transcription factors, potentially playing a critical role in regulating plant adaptation to abiotic stress. Among these, the gene SoyZH13_04G073701 is particularly noteworthy as it regulates the key differentially expressed metabolite, the terpene metabolite Hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)glucoside. WGCNA analysis identified this gene (SoyZH13_04G073701) as a hub gene, positively regulating the crucial differentially expressed metabolite of terpenoids, Hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)glucoside. Our findings provide novel insights into how exogenous melatonin alleviates alkali stress in soybeans at different reproductive stages. CONCLUSIONS Integrating transcriptomic and metabolomic approaches, our study elucidates the mechanisms by which exogenous melatonin ameliorates the inhibitory effects of alkaline stress on soybean growth and development. This occurs through modulation of biosynthesis pathways for key compounds, including terpenes, flavonoids, and phenolics. Our findings provide initial mechanistic insights into how melatonin mitigates alkaline stress in soybeans, offering a foundation for molecular breeding strategies to enhance salt-alkali tolerance in this crop.
Collapse
Affiliation(s)
- Yajuan Duan
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China
| | - Xianxu Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China
| | - Yan Jiao
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China
| | - Yangyang Liu
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China
| | - Yue Li
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China
| | - Yongze Song
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China
| | - Lei Wang
- School of Resources and Environment, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China
| | - Xiaohong Tong
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China
| | - Yan Jiang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China
| | - Shaodong Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China.
| | - Sui Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, PR China.
| |
Collapse
|
3
|
Wróbel A, Klichowska E, Nobis M. Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia. FRONTIERS IN PLANT SCIENCE 2024; 15:1369732. [PMID: 38693932 PMCID: PMC11061500 DOI: 10.3389/fpls.2024.1369732] [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: 01/12/2024] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
Hybridization is one of the key processes shaping lineage diversification, particularly in regions that experienced strong climate oscillations. The alpine biome with its rich history of glacial-interglacial cycles and complex patterns of species distribution shifts offers an excellent system to investigate the impact of gene flow on population dynamics and speciation, important issues for evolutionary biology and biodiversity conservation. In this study, we combined genomic data (DArTseq), chloroplast markers, and morphology to examine phylogenetic relationships and the permeability of species boundaries and their evolutionary outcomes among the alpine extremophilic species of Puccinellia (Poaceae) in the Pamir Mountains, a part of the Mountains of Central Asia biodiversity hotspot. We determined the occurrence of interspecific hybrids between P. himalaica and P. pamirica, which demonstrated almost symmetric ancestry from their parental species and did not show signals of introgression. According to our integrative revision, the natural hybrids between P. himalaica and P. pamirica should be classified as Puccinellia ×vachanica (pro species). Using approximate Bayesian computation for population history inference, we uncovered that P. himalaica hybridized with P. pamirica independently in multiple localities over the Holocene. Hybrids inherited the fine-scale genetic structure from their parental species, which developed these patterns earlier, during the Late Pleistocene. Hybridization had different consequences for the involved parental lineages, likely playing an important role in a continuing decline of P. himalaica in the Pamir Mountains over the Holocene. Our results show that P. himalaica should be considered a critically endangered species in the Pamir Mountains and could also be retreating across its entire range of distribution in High Mountain Asia. Using a comparative phylogeographic framework, we revealed the risk of extinction of a cold-adapted alpine species in a global biodiversity hotspot. This study highlights that genomics could unravel diversity trends under climate change and provides valuable evidence for conservation management.
Collapse
Affiliation(s)
- Anna Wróbel
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| |
Collapse
|
4
|
Zhou H, Shi H, Yang Y, Feng X, Chen X, Xiao F, Lin H, Guo Y. Insights into plant salt stress signaling and tolerance. J Genet Genomics 2024; 51:16-34. [PMID: 37647984 DOI: 10.1016/j.jgg.2023.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Soil salinization is an essential environmental stressor, threatening agricultural yield and ecological security worldwide. Saline soils accumulate excessive soluble salts which are detrimental to most plants by limiting plant growth and productivity. It is of great necessity for plants to efficiently deal with the adverse effects caused by salt stress for survival and successful reproduction. Multiple determinants of salt tolerance have been identified in plants, and the cellular and physiological mechanisms of plant salt response and adaption have been intensely characterized. Plants respond to salt stress signals and rapidly initiate signaling pathways to re-establish cellular homeostasis with adjusted growth and cellular metabolism. This review summarizes the advances in salt stress perception, signaling, and response in plants. A better understanding of plant salt resistance will contribute to improving crop performance under saline conditions using multiple engineering approaches. The rhizosphere microbiome-mediated plant salt tolerance as well as chemical priming for enhanced plant salt resistance are also discussed in this review.
Collapse
Affiliation(s)
- Huapeng Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Haifan Shi
- College of Grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yongqing Yang
- State Key Laboratory of Plant Environmental Resilience, China Agricultural University, Beijing 100193, China
| | - Xixian Feng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xi Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Fei Xiao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
5
|
Chen B, Liu T, Yang Z, Yang S, Chen J. PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in Sonneratia apetala. PLANTS (BASEL, SWITZERLAND) 2023; 12:3849. [PMID: 38005746 PMCID: PMC10675792 DOI: 10.3390/plants12223849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Sonneratia apetala is an essential mangrove wetland restoration tree species. Studying its molecular mechanism for salt tolerance could lay a foundation for further cultivating excellent resistant germplasm. This study used a combination of PacBio isoform sequencing (Iso-seq) and BGISEQ RNA sequencing (RNA-seq) to analyze the molecular mechanism to salt stress response of one-year-old S. apetala leaves. The growth and physiological analysis showed that physiological indexes such as growth rate, net photosynthetic rate and antioxidant enzyme activity all exhibit significant changes under salt stress. From Iso-seq, a total of 295,501 full-length transcripts, with an average length of 1418 bp, were obtained. RNA-seq produced 4712 differentially expressed genes (DEGs) as compared to a control group. Of these, 930 were identified to be co-expressed during the STEM time sequence analysis. Further, 715 and 444 co-expressed DEGs were annotated by GO and KEGG analyses, respectively. Moreover, 318 of the co-expressed DEGs were annotated as essential genes that were implicated in salt stress response of S. apetala, which were involved in transcription factors, signal transduction, hormone response, ROS homeostasis, osmotic balance, cell wall synthesis or modification. These results provide candidate targets for further characterization and offer insights into the salt-tolerant mechanism of S. apetala.
Collapse
Affiliation(s)
- Beibei Chen
- Mangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (B.C.); (T.L.); (Z.Y.); (S.Y.)
| | - Tingting Liu
- Mangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (B.C.); (T.L.); (Z.Y.); (S.Y.)
| | - Zhuanying Yang
- Mangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (B.C.); (T.L.); (Z.Y.); (S.Y.)
| | - Shaoxia Yang
- Mangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (B.C.); (T.L.); (Z.Y.); (S.Y.)
| | - Jinhui Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572019, China
| |
Collapse
|
6
|
Li R, Fu R, Li M, Song Y, Li J, Chen C, Gu Y, Liang X, Nie W, Ma L, Wang X, Zhang H, Zhang H. Transcriptome profiling reveals multiple regulatory pathways of Tamarix chinensis in response to salt stress. PLANT CELL REPORTS 2023; 42:1809-1824. [PMID: 37733273 DOI: 10.1007/s00299-023-03067-w] [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: 08/08/2023] [Accepted: 09/03/2023] [Indexed: 09/22/2023]
Abstract
KEY MESSAGE Multiple regulatory pathways of T. chinensis to salt stress were identified through transcriptome data analysis. Tamarix chinensis (Tamarix chinensis Lour.) is a typical halophyte capable of completing its life cycle in soils with medium to high salinity. However, the mechanisms underlying its resistance to high salt stress are still largely unclear. In this study, transcriptome profiling analyses in different organs of T. chinensis plants in response to salt stress were carried out. A total number of 2280, 689, and 489 differentially expressed genes (DEGs) were, respectively, identified in roots, stems, and leaves, with more DEGs detected in roots than in stems and leaves. Gene Ontology (GO) term analysis revealed that they were significantly enriched in "biological processes" and "molecular functions". Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that "Beta-alanine metabolism" was the most differentially enriched pathway in roots, stems, and leaves. In pair-to-pair comparison of the most differentially enriched pathways, a total of 14 pathways, including 5 pathways in roots and leaves, 6 pathways in roots and stems, and 3 pathways in leaves and stems, were identified. Furthermore, genes encoding transcription factor, such as bHLH, bZIP, HD-Zip, MYB, NAC, WRKY, and genes associated with oxidative stress, starch and sucrose metabolism, and ion homeostasis, were differentially expressed with distinct organ specificity in roots, stems, and leaves. Our findings in this research provide a novel approach for exploring the salt tolerance mechanism of halophytes and identifying new gene targets for the genetic breeding of new plant cultivars with improved resistance to salt stress.
Collapse
Affiliation(s)
- Ruxia Li
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Rao Fu
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Meng Li
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Yanjing Song
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Junlin Li
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Chuanjie Chen
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Yinyu Gu
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Xiaoyan Liang
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Wenjing Nie
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Lan Ma
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Xiangyu Wang
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China
| | - Haiyang Zhang
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China.
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China.
| | - Hongxia Zhang
- Yantai Engineering Research Center for Plant Stem Cell Targeted Breeding, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China.
- Yantai Key Laboratory for Evaluation and Utilization of Silkworm Functional Substances, Shandong Institute of Sericulture, 21 Zhichubei Road, Yantai, 264001, Shandong Province, China.
- 3The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China.
| |
Collapse
|
7
|
Ghanmi S, Smith MA, Zaidi I, Drira M, Graether SP, Hanin M. Isolation and molecular characterization of an FSK 2-type dehydrin from Atriplex halimus. PHYTOCHEMISTRY 2023:113783. [PMID: 37406790 DOI: 10.1016/j.phytochem.2023.113783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
Dehydrins form the group II LEA protein family and are known to play multiple roles in plant stress tolerance and enzyme protection. They harbor a variable number of conserved lysine rich motifs (K-segments) and may also contain three additional conserved motifs (Y-, F- and S-segments). In this work, we report the isolation and characterization of an FSK2-type dehydrin from the halophytic species Atriplex halimus, which we designate as AhDHN1. In silico analysis of the protein sequence revealed that AhDHN1 contains large number of hydrophilic residues, and is predicted to be intrinsically disordered. In addition, it has an FSK2 architecture with one F-segment, one S-segment, and two K-segments. The expression analysis showed that the AhDHN1 transcript is induced by salt and water stress treatments in the leaves of Atriplex seedlings. Moreover, circular dichroism spectrum performed on recombinant AhDHN1 showed that the dehydrin lacks any secondary structure, confirming its intrinsic disorder nature. However, there is a gain of α-helicity in the presence of membrane-like SDS micelles. In vitro assays revealed that AhDHN1 is able to effectively protect enzymatic activity of the lactate dehydrogenase against cold, heat and dehydration stresses. Our findings strongly suggest that AhDHN1 can be involved in the adaptation mechanisms of halophytes to adverse environments.
Collapse
Affiliation(s)
- Siwar Ghanmi
- Plant Physiology & Functional Genomics Research Unit, Institute of Biotechnology, University of Sfax, 3038 Sfax, Tunisia
| | - Margaret A Smith
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Ikram Zaidi
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, BP "1177", University of Sfax, 3018 Sfax, Tunisia
| | - Marwa Drira
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, BP "1177", University of Sfax, 3018 Sfax, Tunisia
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Moez Hanin
- Plant Physiology & Functional Genomics Research Unit, Institute of Biotechnology, University of Sfax, 3038 Sfax, Tunisia.
| |
Collapse
|
8
|
Shelake RM, Kadam US, Kumar R, Pramanik D, Singh AK, Kim JY. Engineering drought and salinity tolerance traits in crops through CRISPR-mediated genome editing: Targets, tools, challenges, and perspectives. PLANT COMMUNICATIONS 2022; 3:100417. [PMID: 35927945 PMCID: PMC9700172 DOI: 10.1016/j.xplc.2022.100417] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/07/2022] [Accepted: 07/27/2022] [Indexed: 05/10/2023]
Abstract
Prolonged periods of drought triggered by climate change hamper plant growth and cause substantial agricultural yield losses every year. In addition to drought, salinity is one of the major abiotic stresses that severely affect crop health and agricultural production. Plant responses to drought and salinity involve multiple processes that operate in a spatiotemporal manner, such as stress sensing, perception, epigenetic modifications, transcription, post-transcriptional processing, translation, and post-translational changes. Consequently, drought and salinity stress tolerance are polygenic traits influenced by genome-environment interactions. One of the ideal solutions to these challenges is the development of high-yielding crop varieties with enhanced stress tolerance, together with improved agricultural practices. Recently, genome-editing technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR) tools, have been effectively applied to elucidate how plants deal with drought and saline environments. In this work, we aim to portray that the combined use of CRISPR-based genome engineering tools and modern genomic-assisted breeding approaches are gaining momentum in identifying genetic determinants of complex traits for crop improvement. This review provides a synopsis of plant responses to drought and salinity stresses at the morphological, physiological, and molecular levels. We also highlight recent advances in CRISPR-based tools and their use in understanding the multi-level nature of plant adaptations to drought and salinity stress. Integrating CRISPR tools with modern breeding approaches is ideal for identifying genetic factors that regulate plant stress-response pathways and for the introgression of beneficial traits to develop stress-resilient crops.
Collapse
Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Ulhas Sopanrao Kadam
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Ritesh Kumar
- Department of Agronomy & Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Anil Kumar Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea.
| |
Collapse
|
9
|
Szymańska S, Lis MI, Piernik A, Hrynkiewicz K. Pseudomonas stutzeri and Kushneria marisflavi Alleviate Salinity Stress-Associated Damages in Barley, Lettuce, and Sunflower. Front Microbiol 2022; 13:788893. [PMID: 35350624 PMCID: PMC8957930 DOI: 10.3389/fmicb.2022.788893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Soil salinity is one of the most important abiotic factors limiting plant productivity. The aim of this study was to determine the effect of selected halotolerant plant growth-promoting endophytes (PGPEs, Pseudomonas stutzeri ISE12 and Kushneria marisflavi CSE9) on the growth parameters of barley (Hordeum vulgare), lettuce (Lactuca sativa), and sunflower (Helianthus annuus) cultivated under salt stress conditions. A negative effect of two higher tested salinities (150 and 300 mM NaCl) was observed on the growth parameters of all investigated plants, including germination percentage and index (decreasing compared to the non-saline control variant in the ranges 5.3-91.7 and 13.6-90.9%, respectively), number of leaves (2.2-39.2%), fresh weight (24.2-81.6%); however, differences in salt stress tolerance among the investigated crops were observed (H. annuus > H. vulgare > L. sativa). Our data showed that the most crucial traits affected by endophyte inoculation under salt stress were chlorophyll concentration, leaf development, water storage, root development, and biomass accumulation. Thus, the influence of endophytes was species specific. K. marisflavi CSE9 promoted the growth of all tested plant species and could be considered a universal PGPEs for many plant genotypes cultivated under saline conditions (e.g., increasing of fresh weight compared to the non-inoculated control variant of barley, lettuce, and sunflower in the ranges 11.4-246.8, 118.9-201.2, and 16.4-77.7%, respectively). P. stutzeri ISE12 stimulated growth and mitigated salinity stress only in the case of barley. Bioaugmentation of crops with halotolerant bacterial strains can alleviate salt stress and promote plant growth; however, the selection of compatible strains and the verification of universal plant stress indicators are the key factors.
Collapse
Affiliation(s)
- Sonia Szymańska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Marta Izabela Lis
- Department of Geobotany and Landscape Planning, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Agnieszka Piernik
- Department of Geobotany and Landscape Planning, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| |
Collapse
|
10
|
The Halophyte Dehydrin Sequence Landscape. Biomolecules 2022; 12:biom12020330. [PMID: 35204830 PMCID: PMC8869203 DOI: 10.3390/biom12020330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/04/2022] Open
Abstract
Dehydrins (DHNs) belong to the LEA (late embryogenesis abundant) family group II, that comprise four conserved motifs (the Y-, S-, F-, and K-segments) and are known to play a multifunctional role in plant stress tolerance. Based on the presence and order of these segments, dehydrins are divided into six subclasses: YnSKn, FnSKn, YnKn, SKn, Kn, and KnS. DHNs are rarely studied in halophytes, and their contribution to the mechanisms developed by these plants to survive in extreme conditions remains unknown. In this work, we carried out multiple genomic analyses of the conservation of halophytic DHN sequences to discover new segments, and examine their architectures, while comparing them with their orthologs in glycophytic plants. We performed an in silico analysis on 86 DHN sequences from 10 halophytic genomes. The phylogenetic tree showed that there are different distributions of the architectures among the different species, and that FSKn is the only architecture present in every plant studied. It was found that K-, F-, Y-, and S-segments are highly conserved in halophytes and glycophytes with a few modifications, mainly involving charged amino acids. Finally, expression data collected for three halophytic species (Puccinillia tenuiflora, Eutrema salsugenium, and Hordeum marinum) revealed that many DHNs are upregulated by salt stress, and the intensity of this upregulation depends on the DHN architecture.
Collapse
|
11
|
Mao Y, Yin Y, Cui X, Wang H, Su X, Qin X, Liu Y, Hu Y, Shen X. Homologous Cloning of Potassium Channel Genes From the Superior Apple Rootstock Line 12-2, Which is Tolerant to Apple Replant Disease. Front Genet 2022; 13:803160. [PMID: 35154275 PMCID: PMC8826240 DOI: 10.3389/fgene.2022.803160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Potassium channels are important ion channels that are responsible for the absorption of potassium in the plant nutrient uptake system. In this study, we used homologous molecular cloning to obtain 8 K+ channel genes from the superior apple rootstock line 12-2 (self-named): MsAKT1-1, MsKAT3-2, MsKAT1-3, MsK2P3-4, MsK2P3-5, MsK2P5-6, MsK2P3-7, and MsK2P3-8. Their lengths varied from 942 bp (MsK2P5-6) to 2625 bp (MsAKT1-1), and the number of encoded amino acids varied from 314 (MsK2P5-6) to 874 (MsAKT1-1). Subcellular localization predictions showed that MsAKT1-1, MsKAT3-2, and MsKAT1-3 were localized on the plasma membrane, and MsK2P3-4, MsK2P3-5, MsK2P5-6, MsK2P3-7, and MsK2P3-8 were localized on the vacuole and plasma membrane. The 8 K+ channel proteins contained α helices, extended strands, β turns, and random coils. MsKAT1-3 had four transmembrane structures, MsKAT3-2 had six, and the other six K+ channel genes had five. Protein structure domain analysis showed that MsAKT1-1 contained nine protein domains, followed by MsKAT3-2 with four, MsKAT1-3 with three, and the other five two-pore domain K+ channel proteins with two. Semi-quantitative RT-PCR detection of the K+ channel genes showed that their expression levels were high in roots. qRT-PCR analysis showed that the relative expression levels of the 8 genes changed after exposure to ARD stress. The above results provide a theoretical basis for further research on the functions of potassium channel genes in 12-2 and a scientific basis for the breeding of ARD-resistant rootstock.
Collapse
Affiliation(s)
- Yunfei Mao
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yijun Yin
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xueli Cui
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Haiyan Wang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - XiaFei Su
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xin Qin
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yangbo Liu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Yanli Hu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiang Shen
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| |
Collapse
|
12
|
Hussain T, Asrar H, Zhang W, Gul B, Liu X. Combined Transcriptome and Proteome Analysis to Elucidate Salt Tolerance Strategies of the Halophyte Panicum antidotale Retz. FRONTIERS IN PLANT SCIENCE 2021; 12:760589. [PMID: 34804096 PMCID: PMC8598733 DOI: 10.3389/fpls.2021.760589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/05/2021] [Indexed: 05/24/2023]
Abstract
Panicum antidotale, a C4 monocot, has the potential to reclaim saline and drylands and to be utilized as fodder and forage. Its adaptability to survive saline stress has been proven with eco-physiological and biochemical studies. However, little is known about its molecular mechanisms of salt tolerance. In this study, an integrated transcriptome and proteome analysis approach, based on RNA sequencing and liquid chromatography tandem mass spectrometry (LC-MS/MS), was used to identify the said mechanisms. Plants were treated with control (0 mM), low (100 mM), and high (300 mM) sodium chloride (NaCl) treatments to distinguish beneficial and toxic pathways influencing plant biomass. The results indicated differential expression of 3,179 (1,126 upregulated/2,053 downregulated) and 2,172 (898 upregulated/1,274 downregulated) genes (DEGs), and 514 (269 upregulated/245 downregulated) and 836 (494 upregulated/392 downregulated) proteins (DEPs) at 100 and 300 mM NaCl, respectively. Among these, most upregulated genes and proteins were involved in salt resistance strategies such as proline biosynthesis, the antioxidant defense system, ion homeostasis, and sugar accumulation at low salinity levels. On the other hand, the expression of several genes and proteins involved in the respiratory process were downregulated, indicating the inability of plants to meet their energy demands at high salinity levels. Moreover, the impairments in photosynthesis were also evident with the reduced expression of genes regulating the structure of photosystems and increased expression of abscisic acid (ABA) mediated pathways which limits stomatal gas exchange. Similarly, the disturbance in fatty acid metabolism and activation of essential ion transport blockers damaged the integrity of the cell membrane, which was also evident with enhanced malondialdehyde (MDA). Overall, the analysis of pathways revealed that the plant optimal performance at low salinity was related to enhanced metabolism, antioxidative defense, cell growth, and signaling pathways, whereas high salinity inhibited biomass accumulation by altered expression of numerous genes involved in carbon metabolism, signaling, transcription, and translation. The data provided the first global analysis of the mechanisms imparting salt stress tolerance of any halophyte at transcriptome and proteome levels.
Collapse
Affiliation(s)
- Tabassum Hussain
- Chinese Academy of Sciences Engineering Laboratory for Efficient Utilization of Saline Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Dr. M. Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan
| | - Hina Asrar
- Dr. M. Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan
| | - Wensheng Zhang
- Chinese Academy of Sciences Engineering Laboratory for Efficient Utilization of Saline Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Bilquees Gul
- Dr. M. Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan
| | - Xiaojing Liu
- Chinese Academy of Sciences Engineering Laboratory for Efficient Utilization of Saline Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| |
Collapse
|
13
|
Rahman MM, Mostofa MG, Keya SS, Siddiqui MN, Ansary MMU, Das AK, Rahman MA, Tran LSP. Adaptive Mechanisms of Halophytes and Their Potential in Improving Salinity Tolerance in Plants. Int J Mol Sci 2021; 22:ijms221910733. [PMID: 34639074 PMCID: PMC8509322 DOI: 10.3390/ijms221910733] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/18/2022] Open
Abstract
Soil salinization, which is aggravated by climate change and inappropriate anthropogenic activities, has emerged as a serious environmental problem, threatening sustainable agriculture and future food security. Although there has been considerable progress in developing crop varieties by introducing salt tolerance-associated traits, most crop cultivars grown in saline soils still exhibit a decline in yield, necessitating the search for alternatives. Halophytes, with their intrinsic salt tolerance characteristics, are known to have great potential in rehabilitating salt-contaminated soils to support plant growth in saline soils by employing various strategies, including phytoremediation. In addition, the recent identification and characterization of salt tolerance-related genes encoding signaling components from halophytes, which are naturally grown under high salinity, have paved the way for the development of transgenic crops with improved salt tolerance. In this review, we aim to provide a comprehensive update on salinity-induced negative effects on soils and plants, including alterations of physicochemical properties in soils, and changes in physiological and biochemical processes and ion disparities in plants. We also review the physiological and biochemical adaptation strategies that help halophytes grow and survive in salinity-affected areas. Furthermore, we illustrate the halophyte-mediated phytoremediation process in salinity-affected areas, as well as their potential impacts on soil properties. Importantly, based on the recent findings on salt tolerance mechanisms in halophytes, we also comprehensively discuss the potential of improving salt tolerance in crop plants by introducing candidate genes related to antiporters, ion transporters, antioxidants, and defense proteins from halophytes for conserving sustainable agriculture in salinity-prone areas.
Collapse
Affiliation(s)
- Md. Mezanur Rahman
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA; (M.M.R.); (S.S.K.)
| | - Mohammad Golam Mostofa
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA; (M.M.R.); (S.S.K.)
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
- Correspondence: (M.G.M.); (L.S.-P.T.); Tel.: +1-806-5007763 (M.G.M.); +1-806-8347829 (L.S.-P.T.)
| | - Sanjida Sultana Keya
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA; (M.M.R.); (S.S.K.)
| | - Md. Nurealam Siddiqui
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Md. Mesbah Uddin Ansary
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh;
| | - Ashim Kumar Das
- Department of Agroforestry and Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh; (A.K.D.); (M.A.R.)
| | - Md. Abiar Rahman
- Department of Agroforestry and Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh; (A.K.D.); (M.A.R.)
| | - Lam Son-Phan Tran
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA; (M.M.R.); (S.S.K.)
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
- Correspondence: (M.G.M.); (L.S.-P.T.); Tel.: +1-806-5007763 (M.G.M.); +1-806-8347829 (L.S.-P.T.)
| |
Collapse
|