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Peng Z, Rehman A, Li X, Jiang X, Tian C, Wang X, Li H, Wang Z, He S, Du X. Comprehensive Evaluation and Transcriptome Analysis Reveal the Salt Tolerance Mechanism in Semi-Wild Cotton ( Gossypium purpurascens). Int J Mol Sci 2023; 24:12853. [PMID: 37629034 PMCID: PMC10454576 DOI: 10.3390/ijms241612853] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Elevated salinity significantly threatens cotton growth, particularly during the germination and seedling stages. The utilization of primitive species of Gossypium hirsutum, specifically Gossypium purpurascens, has the potential to facilitate the restoration of genetic diversity that has been depleted due to selective breeding in modern cultivars. This investigation evaluated 45 G. purpurascens varieties and a salt-tolerant cotton variety based on 34 morphological, physiological, and biochemical indicators and comprehensive salt tolerance index values. This study effectively identified a total of 19 salt-tolerant and two salt-resistant varieties. Furthermore, transcriptome sequencing of a salt-tolerant genotype (Nayanmian-2; NY2) and a salt-sensitive genotype (Sanshagaopao-2; GP2) revealed 2776, 6680, 4660, and 4174 differentially expressed genes (DEGs) under 0.5, 3, 12, and 24 h of salt stress. Gene ontology enrichment analysis indicated that the DEGs exhibited significant enrichment in biological processes like metabolic (GO:0008152) and cellular (GO:0009987) processes. MAPK signaling, plant-pathogen interaction, starch and sucrose metabolism, plant hormone signaling, photosynthesis, and fatty acid metabolism were identified as key KEGG pathways involved in salinity stress. Among the DEGs, including NAC, MYB, WRKY, ERF, bHLH, and bZIP, transcription factors, receptor-like kinases, and carbohydrate-active enzymes were crucial in salinity tolerance. Weighted gene co-expression network analysis (WGCNA) unveiled associations of salt-tolerant genotypes with flavonoid metabolism, carbon metabolism, and MAPK signaling pathways. Identifying nine hub genes (MYB4, MYB105, MYB36, bZIP19, bZIP43, FRS2 SMARCAL1, BBX21, F-box) across various intervals offered insights into the transcriptional regulation mechanism of salt tolerance in G. purpurascens. This study lays the groundwork for understanding the important pathways and gene networks in response to salt stress, thereby providing a foundation for enhancing salt tolerance in upland cotton.
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Affiliation(s)
- Zhen Peng
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
| | - Abdul Rehman
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Xiawen Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Xuran Jiang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Chunyan Tian
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Xiaoyang Wang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Hongge Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Zhenzhen Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Shoupu He
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
| | - Xiongming Du
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
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Amin B, Atif MJ, Pan Y, Rather SA, Ali M, Li S, Cheng Z. Transcriptomic analysis of Cucumis sativus uncovers putative genes related to hormone signaling under low temperature (LT) and high humidity (HH) stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 333:111750. [PMID: 37257510 DOI: 10.1016/j.plantsci.2023.111750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
Climate change has caused changes in environmental conditions, leading to both low temperature (LT) and high humidity (HH) stress on crops worldwide. Therefore, there is a growing need to enhance our understanding of the physiological and molecular mechanisms underlying LT and HH stress tolerance in cucumbers, given the significance of climate change. The findings of this study offer a comprehensive understanding of how the transcriptome and hormone profiles of cucumbers respond to LT and HH stress. In this study, cucumber seedlings were subjected to LT and HH stress (9/5 °C day/night temperature, 95% humidity) as well as control (CK) conditions (25/18 °C day/night temperature, 80% humidity) for 24, 48, and 72 h. It was observed that the LT and HH stress caused severe damage to the morphometric traits of the plants compared to the control treatment. The concentrations of phytohormones IAA, ethylene, and GA were lower, while ABA and JA were higher during LT and HH stress at most time points. To gain insights into the molecular mechanisms underlying this stress response, RNA-sequencing was performed. The analysis revealed a total of 10,459 differentially expressed genes (DEGs) with annotated pathways. These pathways included plant hormone signal transduction, protein processing in the endoplasmic reticulum, MAPK signaling pathway, carbon fixation in photosynthetic organisms, and glycerolipid metabolism. Furthermore, 123 DEGs associated with hormone signaling pathways were identified, and their responses to LT and HH stress were thoroughly discussed. Overall, this study sheds light on the LT and HH tolerance mechanisms in cucumbers, particularly focusing on the genes involved in the LT and HH response and the signaling pathways of endogenous phytohormones.
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Affiliation(s)
- Bakht Amin
- College of Horticulture, Northwest A&F University, Yangling 712100, China; Institute of Rice Industry Technology Research, Key Laboratory of Plant Resource Conservation andGermplasm Innovation in Mountainous Region (Ministry of Education), College of AgriculturalSciences, Guizhou University, Guiyang 550025, China
| | - Muhammad Jawaad Atif
- College of Horticulture, Northwest A&F University, Yangling 712100, China; Horticultural Research Institute, National Agricultural Research Centre, Islamabad 44000, Pakistan
| | - Yupeng Pan
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Shabir A Rather
- Center for Integrative Conservation and Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Menglun 666303, Yunnan, China
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Shuju Li
- Tianjin Kerun Cucumber Research Institute, Tianjin 300192, China
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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Barqawi AA, Abulfaraj AA. Salt Stress-Related Mechanisms in Leaves of the Wild Barley Hordeum spontaneum Generated from RNA-Seq Datasets. Life (Basel) 2023; 13:1454. [PMID: 37511829 PMCID: PMC10381474 DOI: 10.3390/life13071454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
This study aims to detect salt stress-related genes and mechanisms of the wild barley Hordeum spontaneum. Among the generated RNA-Seq datasets, several regulated transcripts are influenced by levels of cellular carbon, nitrogen and oxygen. Some of the regulated genes act on photorespiration and ubiquitination processes, as well as promoting plant growth and development under salt stress. One of the genes, encoding alanine:glyoxylate aminotransferase (AGT), participates in signaling transduction and proline biosynthesis, while the gene encoding asparagine synthetase (ASN) influences nitrogen storage and transport in plants under stress. Meanwhile, the gene encoding glutamate dehydrogenase (GDH) promotes shoot and root biomass production as well as nitrate assimilation. The upregulated genes encoding alpha-aminoadipic semialdehyde synthase (AASAS) and small auxin-up RNA 40 (SAUR40) participate in the production of proline and signaling compounds, respectively, while the gene encoding E3 ubiquitin-protein ligase regulates the carbon/nitrogen-nutrient response and pathogen resistance, in addition to some physiological processes under biotic and abiotic stresses via signal transduction. The gene encoding the tetratricopeptide repeat (TPR)-domain suppressor of STIMPY (TSS) negatively regulates the carbon level in the cell. In conclusion, this study sheds light on possible molecular mechanisms underlying salt stress tolerance in wild barley that can be utilized further in genomics-based breeding programs of cultivated species.
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Affiliation(s)
- Aminah A Barqawi
- Department of Chemistry, Al-Leith University College, Umm Al-Qura University, Makkah 28434, Saudi Arabia
| | - Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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Abulfaraj AA. Relationships between some transcription factors and concordantly expressed drought stress-related genes in bread wheat. Saudi J Biol Sci 2023; 30:103652. [PMID: 37206446 PMCID: PMC10189290 DOI: 10.1016/j.sjbs.2023.103652] [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: 01/31/2023] [Revised: 03/18/2023] [Accepted: 04/09/2023] [Indexed: 05/21/2023] Open
Abstract
The challenge of climate change makes it mandatory to improve tolerance to drought stress in bread wheat (Triticum aestivum) via biotechnological approaches. Drought stress experiment was conducted followed by RNA-Seq analysis for leaves of two wheat cultivars namely Giza 168 and Gemmiza 10 with contrasting genotypes. Expression patterns of the regulated stress-related genes and concordantly expressed TFs were detected, then, validated via qPCR for two loss-of-function mutants in Arabidopsis background harboring mutated genes analogue to those in wheat. Drought-stress related genes were searched for concordantly expressed TFs and a total of eight TFs were shown to coexpress with 14 stress-related genes. Among these genes, one TF belongs to the zinc finger protein CONSTANS family and proved via qPCR to drive expression of a gene encoding a speculative TF namely zinc transporter 3-like and two other stress related genes encoding tryptophan synthase alpha chain and asparagine synthetase. Known functions of the two TFs under drought stress complement those of the two concordantly expressed stress-related genes, thus, it is likely that they are related. This study highlights the possibility to utilize metabolic engineering approaches to decipher and incorporate existing regulatory frameworks under drought stress in future breeding programs of bread wheat.
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Transcriptome Analysis of Differentially Expressed Genes Associated with Salt Stress in Cowpea ( Vigna unguiculata L.) during the Early Vegetative Stage. Int J Mol Sci 2023; 24:ijms24054762. [PMID: 36902192 PMCID: PMC10002509 DOI: 10.3390/ijms24054762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Cowpea (Vigna unguiculata (L.), 2n = 22) is a tropical crop grown in arid and semiarid regions that is tolerant to abiotic stresses such as heat and drought. However, in these regions, salt in the soil is generally not eluted by rainwater, leading to salt stress for a variety of plant species. This study was conducted to identify genes related to salt stress using the comparative transcriptome analysis of cowpea germplasms with contrasting salt tolerance. Using the Illumina Novaseq 6000 platform, 1.1 billion high-quality short reads, with a total length of over 98.6 billion bp, were obtained from four cowpea germplasms. Of the differentially expressed genes identified for each salt tolerance type following RNA sequencing, 27 were shown to exhibit significant expression levels. These candidate genes were subsequently narrowed down using reference-sequencing analysis, and two salt stress-related genes (Vigun_02G076100 and Vigun_08G125100) with single-nucleotide polymorphism (SNP) variation were selected. Of the five SNPs identified in Vigun_02G076100, one that caused significant amino acid variation was identified, while all nucleotide variations in Vigun_08G125100 was classified as missing in the salt-resistant germplasms. The candidate genes and their variation, identified in this study provide, useful information for the development of molecular markers for cowpea breeding programs.
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Tashkandi M, Baz L. Function of CAZymes encoded by highly abundant genes in rhizosphere microbiome of Moringa oleifera. Saudi J Biol Sci 2023; 30:103578. [PMID: 36844641 PMCID: PMC9944558 DOI: 10.1016/j.sjbs.2023.103578] [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: 10/24/2022] [Revised: 12/21/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Metagenomic analysis referring to CAZymes (Carbohydrate-Active enZymes) of CAZy classes encoded by the most abundant genes in rhizosphere versus bulk soil microbes of the wild plant Moringa oleifera was conducted. Results indicated that microbiome signatures and corresponding CAZy datasets differ between the two soil types. CAZy class glycoside hydrolases (GH) and its α-amylase family GH13 in rhizobiome were proven to be the most abundant among CAZy classes and families. The most abundant bacteria harboring these CAZymes include phylum Actinobacteria and its genus Streptomyces and phylum Proteobacteria and its genus Microvirga. These CAZymes participate in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway "Starch and sucrose metabolism" and mainly use the "double displacement catalytic mechanism" in their reactions. We assume that microbiome of the wild plant Moringa oleifera is a good source of industrially important enzymes that act on starch hydrolysis and/or biosynthesis. In addition, metabolic engineering and integration of certain microbes of this microbiomes can also be used in improving growth of domestic plants and their ability to tolerate adverse environmental conditions.
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Affiliation(s)
- Manal Tashkandi
- Department of Biochemistry, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah, Saudi Arabia,Corresponding author.
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Nazir F, Mahajan M, Khatoon S, Albaqami M, Ashfaque F, Chhillar H, Chopra P, Khan MIR. Sustaining nitrogen dynamics: A critical aspect for improving salt tolerance in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1087946. [PMID: 36909406 PMCID: PMC9996754 DOI: 10.3389/fpls.2023.1087946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
In the current changing environment, salt stress has become a major concern for plant growth and food production worldwide. Understanding the mechanisms of how plants function in saline environments is critical for initiating efforts to mitigate the detrimental effects of salt stress. Agricultural productivity is linked to nutrient availability, and it is expected that the judicious metabolism of mineral nutrients has a positive impact on alleviating salt-induced losses in crop plants. Nitrogen (N) is a macronutrient that contributes significantly to sustainable agriculture by maintaining productivity and plant growth in both optimal and stressful environments. Significant progress has been made in comprehending the fundamental physiological and molecular mechanisms associated with N-mediated plant responses to salt stress. This review provided an (a) overview of N-sensing, transportation, and assimilation in plants; (b) assess the salt stress-mediated regulation of N dynamics and nitrogen use- efficiency; (c) critically appraise the role of N in plants exposed to salt stress. Furthermore, the existing but less explored crosstalk between N and phytohormones has been discussed that may be utilized to gain a better understanding of plant adaptive responses to salt stress. In addition, the shade of a small beam of light on the manipulation of N dynamics through genetic engineering with an aim of developing salt-tolerant plants is also highlighted.
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Affiliation(s)
- Faroza Nazir
- Department of Botany, Jamia Hamdard, New Delhi, India
| | - Moksh Mahajan
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Mohammed Albaqami
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Farha Ashfaque
- Department of Botany, Aligarh Muslim University, Aligarh, India
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Ramadan A, Alnufaei AA, Fiaz S, Khan TK, Hassan SM. Effect of salinity on ccmfn gene RNA editing of mitochondria in wild barley and uncommon types of RNA editing. Funct Integr Genomics 2023; 23:50. [PMID: 36707470 DOI: 10.1007/s10142-023-00978-5] [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: 11/10/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 01/29/2023]
Abstract
The primary function of mitochondria is cellular respiration and energy production. Cytochrome C complex is an essential complex that transports electrons in the respiratory chain between complex III and complex IV. One of this complex's main subunits is CcmFN, which is believed to be crucial for holocytochrome assembly. In wild-type plant Hordeum vulgare subsp. spontaneum, four ccmfn cDNAs are subjected to high salt stress (500 mM salinity), 0 h (or control) (GenBank accession no. ON764850), after 2 h (GenBank accession no. ON7648515), after 12 h (GenBank accession no. ON764852), and after 24 h (GenBank accession no. ON764853) and mtDNA of ccmfn gene (GenBank accession no. ON764854). Using raw data from RNA-seq, 47 sites with nucleotide and amino acid modifications were detected. There were ten different RNA editing types, with most of them are C to U. Unusual editing types in plants have also been found, such as A to C, C to A, A to G, A to U, T to A, T to C, C to G, G to C, and T to G. High levels of editing were observed in control as well as treatments of salinity stress. Amino acid changes were found in 43 sites; nearly all showed hydrophilic to hydrophilic alterations. Only C749 showed regulation under salinity stress.
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Affiliation(s)
- Ahmed Ramadan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia.
- Plant Molecular Biology Department, Agriculture Research Center (ARC), Agricultural Genetic Engineering Research Institute (AGERI), Giza, Egypt.
| | - Afnan A Alnufaei
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, University of Haripur, Haripur, Pakistan
| | - Thana K Khan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sabah M Hassan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
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Xu T, Meng S, Zhu X, Di J, Zhu Y, Yang X, Yan W. Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na +/K + balance in barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1004477. [PMID: 36777542 PMCID: PMC9910287 DOI: 10.3389/fpls.2022.1004477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/29/2022] [Indexed: 06/18/2023]
Abstract
Salt stress is one of the main abiotic stresses affecting crop yield and quality. Barley has strong salt tolerance, however, the underlying genetic basis is not fully clear, especially in the seedling stage. This study examined the ionic changes in barley core germplasms under the control and salt conditions. Genome-wide association study (GWAS) analysis revealed 54 significant SNPs from a pool of 25,342 SNPs distributed in 7 chromosomes (Chr) of the Illumina Barley 50K SNP array. These SNPs are associated with ion homeostasis traits, sodium (Na+) and potassium (K+) content, and Na+/K+ ratio representing five genomic regions on Chr 2, 4, 5, 6, and 7 in the leaves of worldwide barley accessions. And there are 3 SNP peaks located on the Chr 4, 6, and 7, which could be the "hot spots" regions for mining and identifying candidate genes for salt tolerance. Furthermore, 616 unique candidate genes were screened surrounding the significant SNPs, which are associated with transport proteins, protein kinases, binding proteins, and other proteins of unknown function. Meanwhile, transcriptomic analysis (RNA-Seq) was carried out to compare the salt-tolerant (CM72) and salt-sensitive (Gairdner) genotypes subjected to salt stress. And there was a greater accumulation of differentially expressed genes(DEGs) in Gairdner compared to CM72, mainly enriched in metabolic pathway, biosynthesis of secondary metabolites, photosynthesis, signal transduction,emphasizing the different transcriptional response in both genotypes following salt exposure. Combined GWAS and RNA-Seq analysis revealed 5 promising salt-responding genes (PGK2, BASS3, SINAT2, AQP, and SYT3) from the hot spot regions, which were verified between the salt-tolerant and salt-sensitive varieties by qRT-PCR. In all, these results provide candidate SNPs and genes responsible for salinity responding in barley, and a new idea for studying such genetic basis in similar crops.
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Shami AY, Abulfaraj AA, Refai MY, Barqawi AA, Binothman N, Tashkandi MA, Baeissa HM, Baz L, Abuauf HW, Ashy RA, Jalal RS. Abundant antibiotic resistance genes in rhizobiome of the human edible Moringa oleifera medicinal plant. Front Microbiol 2022; 13:990169. [PMID: 36187977 PMCID: PMC9524394 DOI: 10.3389/fmicb.2022.990169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/17/2022] [Indexed: 11/30/2022] Open
Abstract
Moringa oleifera (or the miracle tree) is a wild plant species widely grown for its seed pods and leaves, and is used in traditional herbal medicine. The metagenomic whole genome shotgun sequencing (mWGS) approach was used to characterize antibiotic resistance genes (ARGs) of the rhizobiomes of this wild plant and surrounding bulk soil microbiomes and to figure out the chance and consequences for highly abundant ARGs, e.g., mtrA, golS, soxR, oleC, novA, kdpE, vanRO, parY, and rbpA, to horizontally transfer to human gut pathogens via mobile genetic elements (MGEs). The results indicated that abundance of these ARGs, except for golS, was higher in rhizosphere of M. oleifera than that in bulk soil microbiome with no signs of emerging new soil ARGs in either soil type. The most highly abundant metabolic processes of the most abundant ARGs were previously detected in members of phyla Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, and Firmicutes. These processes refer to three resistance mechanisms namely antibiotic efflux pump, antibiotic target alteration and antibiotic target protection. Antibiotic efflux mechanism included resistance-nodulation-cell division (RND), ATP-binding cassette (ABC), and major facilitator superfamily (MFS) antibiotics pumps as well as the two-component regulatory kdpDE system. Antibiotic target alteration included glycopeptide resistance gene cluster (vanRO), aminocoumarin resistance parY, and aminocoumarin self-resistance parY. While, antibiotic target protection mechanism included RbpA bacterial RNA polymerase (rpoB)-binding protein. The study supports the claim of the possible horizontal transfer of these ARGs to human gut and emergence of new multidrug resistant clinical isolates. Thus, careful agricultural practices are required especially for plants used in circles of human nutrition industry or in traditional medicine.
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Affiliation(s)
- Ashwag Y. Shami
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science and Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Aminah A. Barqawi
- Department of Chemistry, Al-Leith University College, Umm Al Qura University, Makkah, Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Manal A. Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hanadi M. Baeissa
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science—King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haneen W. Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ruba A. Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rewaa S. Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- *Correspondence: Rewaa S. Jalal,
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12
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Liu Y, Han ZJ, Su MX, Zhang M. Transcriptomic Profile Analysis of Populus talassica × Populus euphratica Response and Tolerance under Salt Stress Conditions. Genes (Basel) 2022; 13:genes13061032. [PMID: 35741794 PMCID: PMC9222677 DOI: 10.3390/genes13061032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/31/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023] Open
Abstract
A new Populus variety with a strong salt tolerance was obtained from cross breeding P. talassica as the female parent and P. euphratica as the male parent. In order to elucidate the molecular mechanism and find out the major differentially expressed genes of salt tolerance of P. talassica × P. euphratica, after being subjected to salt stress, at 0, 200, and 400 mmol/L NaCl, the root, stem, and leaf transcriptomes (denoted as R0, S0, and L0; R200, S200, and L200; and R400, S400, and L400, respectively) of P. talassica × P. euphratica were sequenced. In total, 41,617 differentially expressed genes (DEGs) were identified in all the comparison groups with 21,603 differentially upregulated genes and 20,014 differentially downregulated genes. Gene Ontology analysis showed that DEGs were significantly enriched in biological processes that may be involved in salt stress, such as ‘cell communication’, ‘ion transport’, ‘signaling’, and signal ‘transmission’. Kyoto Encyclopedia of Genes and Genomes analysis showed that DEGs were mainly enriched in pathways of ‘plant–pathogen interaction’, ‘carbon metabolism’, and ‘plant hormone signal transmission’. The pathways and related gene information formed a basis for future research on the mechanisms of salt stress, the development of molecular markers, and the cloning of key genes in P. talassica × P. euphratica.
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Affiliation(s)
- Ying Liu
- College of Life Science and Technology, Tarim University, Alar 843300, China; (Y.L.); (M.X.S.); (M.Z.)
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China
| | - Zhan Jiang Han
- College of Life Science and Technology, Tarim University, Alar 843300, China; (Y.L.); (M.X.S.); (M.Z.)
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China
- Correspondence:
| | - Meng Xu Su
- College of Life Science and Technology, Tarim University, Alar 843300, China; (Y.L.); (M.X.S.); (M.Z.)
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China
| | - Min Zhang
- College of Life Science and Technology, Tarim University, Alar 843300, China; (Y.L.); (M.X.S.); (M.Z.)
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China
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13
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Nefissi Ouertani R, Arasappan D, Ruhlman TA, Ben Chikha M, Abid G, Mejri S, Ghorbel A, Jansen RK. Effects of Salt Stress on Transcriptional and Physiological Responses in Barley Leaves with Contrasting Salt Tolerance. Int J Mol Sci 2022; 23:5006. [PMID: 35563398 PMCID: PMC9103072 DOI: 10.3390/ijms23095006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
Salt stress negatively impacts crop production worldwide. Genetic diversity among barley (Hordeum vulgare) landraces adapted to adverse conditions should provide a valuable reservoir of tolerance genes for breeding programs. To identify molecular and biochemical differences between barley genotypes, transcriptomic and antioxidant enzyme profiles along with several morpho-physiological features were compared between salt-tolerant (Boulifa) and salt-sensitive (Testour) genotypes subjected to salt stress. Decreases in biomass, photosynthetic parameters, and relative water content were low in Boulifa compared to Testour. Boulifa had better antioxidant protection against salt stress than Testour, with greater antioxidant enzymes activities including catalase, superoxide dismutase, and guaiacol peroxidase. Transcriptome assembly for both genotypes revealed greater accumulation of differentially expressed transcripts in Testour compared to Boulifa, emphasizing the elevated transcriptional response in Testour following salt exposure. Various salt-responsive genes, including the antioxidant catalase 3, the osmoprotectant betaine aldehyde dehydrogenase 2, and the transcription factors MYB20 and MYB41, were induced only in Boulifa. By contrast, several genes associated with photosystems I and II, and light receptor chlorophylls A and B, were more repressed in Testour. Co-expression network analysis identified specific gene modules correlating with differences in genotypes and morpho-physiological traits. Overall, salinity-induced differential transcript accumulation underlies the differential morpho-physiological response in both genotypes and could be important for breeding salt tolerance in barley.
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Affiliation(s)
- Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Dhivya Arasappan
- Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA;
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
| | - Mariem Ben Chikha
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia;
| | - Samiha Mejri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Abdelwahed Ghorbel
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia; (M.B.C.); (S.M.); (A.G.)
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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14
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Transcriptome analysis of Tamarix ramosissima leaves in response to NaCl stress. PLoS One 2022; 17:e0265653. [PMID: 35358228 PMCID: PMC8970367 DOI: 10.1371/journal.pone.0265653] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/04/2022] [Indexed: 02/07/2023] Open
Abstract
Halophyte Tamarix ramosissima. Lcdcb (T. ramosissima) are known as the representative of Tamarix plants that are widely planted in salinized soil. However, molecular mechanisms towards salt tolerance and adaptation are largely rare. In this study, we carried out RNA-sequence and transcriptome analysis of T. ramosissima in response to NaCl stress, screened differentially expressed genes (DEGs) and further verified by qRT-PCR. Results showed that 105702 unigenes were spliced from the raw data of transcriptome sequencing, where 54238 unigenes were retrieved from KEGG, KOG, NR, and SwissProt. After 48 hours of NaCl treatment, the expression levels of 6374 genes were increased, and 5380 genes were decreased in leaves. After 168 hours, the expression levels of 3837 genes were up-regulated and 7808 genes were down-regulated. In particular, 8 transcription factors annotated to the KEGG Pathway were obtained, involving the WRKY and bZIP transcription family. In addition, KEGG pathway annotation showed that expression of 39 genes involved in ROS scavenging mechanisms were significantly changed, in which 21 genes were up-regulated and 18 genes were down-regulated after 48 hours as well as 15 genes were up-regulated and 24 genes were down-regulated after 168h. Simultaneously, the enzyme activities of SOD and POD were significantly enhanced under NaCl treatment, but the enzyme activity of CAT was not significantly enhanced. Moreover, WRKY, MYB and bZIP may participate in the process of salt resistance in T. ramosissima. This study provides gene resources and a theoretical basis for further molecular mechanisms of salt tolerance in T. ramosissima.
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15
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Guo W, Tzioutziou NA, Stephen G, Milne I, Calixto CPG, Waugh R, Brown JWS, Zhang R. 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA Biol 2021; 18:1574-1587. [PMID: 33345702 PMCID: PMC8594885 DOI: 10.1080/15476286.2020.1858253] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/19/2022] Open
Abstract
RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on specialized bioinformatics skills. We have developed the '3D RNA-seq' App, an R shiny App and web-based pipeline for the comprehensive analysis of RNA-seq data from any organism. It represents an easy-to-use, flexible and powerful tool for analysis of both gene and transcript-level gene expression to identify differential gene/transcript expression, differential alternative splicing and differential transcript usage (3D) as well as isoform switching from RNA-seq data. 3D RNA-seq integrates state-of-the-art differential expression analysis tools and adopts best practice for RNA-seq analysis. The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to analyse their RNA-seq data. It achieves this by operating through a user-friendly graphical interface which automates the data flow through the programs in the pipeline. The comprehensive analysis performed by 3D RNA-seq is extremely rapid and accurate, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures such as heat-maps, expression profiles and GO enrichment plots. The utility of 3D RNA-seq is illustrated by analysis of data from a time-series of cold-treated Arabidopsis plants and from dexamethasone-treated male and female mouse cortex and hypothalamus data identifying dexamethasone-induced sex- and brain region-specific differential gene expression and alternative splicing.
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Affiliation(s)
- Wenbin Guo
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
- Information and Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Nikoleta A Tzioutziou
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
| | - Gordon Stephen
- Information and Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Iain Milne
- Information and Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Cristiane PG Calixto
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
| | - John W. S. Brown
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee, UK
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16
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Guo W, Tzioutziou NA, Stephen G, Milne I, Calixto CP, Waugh R, Brown JWS, Zhang R. 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA Biol 2021. [PMID: 33345702 DOI: 10.1101/656686] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on specialized bioinformatics skills. We have developed the '3D RNA-seq' App, an R shiny App and web-based pipeline for the comprehensive analysis of RNA-seq data from any organism. It represents an easy-to-use, flexible and powerful tool for analysis of both gene and transcript-level gene expression to identify differential gene/transcript expression, differential alternative splicing and differential transcript usage (3D) as well as isoform switching from RNA-seq data. 3D RNA-seq integrates state-of-the-art differential expression analysis tools and adopts best practice for RNA-seq analysis. The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to analyse their RNA-seq data. It achieves this by operating through a user-friendly graphical interface which automates the data flow through the programs in the pipeline. The comprehensive analysis performed by 3D RNA-seq is extremely rapid and accurate, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures such as heat-maps, expression profiles and GO enrichment plots. The utility of 3D RNA-seq is illustrated by analysis of data from a time-series of cold-treated Arabidopsis plants and from dexamethasone-treated male and female mouse cortex and hypothalamus data identifying dexamethasone-induced sex- and brain region-specific differential gene expression and alternative splicing.
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Affiliation(s)
- Wenbin Guo
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
- Information and Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Nikoleta A Tzioutziou
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
| | - Gordon Stephen
- Information and Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Iain Milne
- Information and Computational Sciences, The James Hutton Institute, Dundee, UK
| | - Cristiane Pg Calixto
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
| | - John W S Brown
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee, UK
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17
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Razzaq A, Saleem F, Wani SH, Abdelmohsen SAM, Alyousef HA, Abdelbacki AMM, Alkallas FH, Tamam N, Elansary HO. De-novo Domestication for Improving Salt Tolerance in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:681367. [PMID: 34603347 PMCID: PMC8481614 DOI: 10.3389/fpls.2021.681367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/12/2021] [Indexed: 05/21/2023]
Abstract
Global agriculture production is under serious threat from rapidly increasing population and adverse climate changes. Food security is currently a huge challenge to feed 10 billion people by 2050. Crop domestication through conventional approaches is not good enough to meet the food demands and unable to fast-track the crop yields. Also, intensive breeding and rigorous selection of superior traits causes genetic erosion and eliminates stress-responsive genes, which makes crops more prone to abiotic stresses. Salt stress is one of the most prevailing abiotic stresses that poses severe damages to crop yield around the globe. Recent innovations in state-of-the-art genomics and transcriptomics technologies have paved the way to develop salinity tolerant crops. De novo domestication is one of the promising strategies to produce superior new crop genotypes through exploiting the genetic diversity of crop wild relatives (CWRs). Next-generation sequencing (NGS) technologies open new avenues to identifying the unique salt-tolerant genes from the CWRs. It has also led to the assembly of highly annotated crop pan-genomes to snapshot the full landscape of genetic diversity and recapture the huge gene repertoire of a species. The identification of novel genes alongside the emergence of cutting-edge genome editing tools for targeted manipulation renders de novo domestication a way forward for developing salt-tolerance crops. However, some risk associated with gene-edited crops causes hurdles for its adoption worldwide. Halophytes-led breeding for salinity tolerance provides an alternative strategy to identify extremely salt tolerant varieties that can be used to develop new crops to mitigate salinity stress.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Shabir Hussain Wani
- Division of Genetics and Plant Breeding, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Shaimaa A. M. Abdelmohsen
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Haifa A. Alyousef
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | - Fatemah H. Alkallas
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nissren Tamam
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Hosam O. Elansary
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
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18
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The first report of RNA U to C or G editing in the mitochondrial NADH dehydrogenase subunit 5 (Nad5) transcript of wild barley. Mol Biol Rep 2021; 48:6057-6064. [PMID: 34374896 DOI: 10.1007/s11033-021-06609-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Nad dehydrogenase complex in mtDNA has a significant role in cellular respiration. One of the largest subunits in the complex is subunit 5 (Nad5). METHODS AND RESULTS Four cDNAs of the Hordeum vulgare subsp. spontaneum nad5 gene have been characterized and subjected to four phases of 0.5 M salinity, at 0 h (control, accession no. MT235236), after 2 h (acc. no. MT235237), after 12 h (acc. no. MT235238) and after 24 h (acc. no. MT235239). Utilizing raw data from RNA-seq, ten RNA editing sites were reported. Seven sites have common editing from C to U in positions (C1490, C1859, C1895, C1900, C1901, C1916, C1918). A rare editing event U to C was detected in two positions (U1650 and U1652) and a novel editing event U to G was for the first time in positions nad5-U231. The highest editing level was shown in 2 and 12 h after salinity exposure. After 24 h, these edits were disrupted, possibly due to the launch of the programed cell death mechanism. However, the RNA editing in positions U1650, U1652 and U231 was fixed at all exposure times. CONCLUSIONS Although study clarified the role of salinity stress in nad5 RNA editing sites, the main achievements are first report of U to G RNA editing in plants at position U231 and first report of U to C editing in the nad5 gene at U1650 and U1652.
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19
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Nefissi Ouertani R, Arasappan D, Abid G, Ben Chikha M, Jardak R, Mahmoudi H, Mejri S, Ghorbel A, Ruhlman TA, Jansen RK. Transcriptomic Analysis of Salt-Stress-Responsive Genes in Barley Roots and Leaves. Int J Mol Sci 2021; 22:8155. [PMID: 34360920 PMCID: PMC8348758 DOI: 10.3390/ijms22158155] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
Barley is characterized by a rich genetic diversity, making it an important model for studies of salinity response with great potential for crop improvement. Moreover, salt stress severely affects barley growth and development, leading to substantial yield loss. Leaf and root transcriptomes of a salt-tolerant Tunisian landrace (Boulifa) exposed to 2, 8, and 24 h salt stress were compared with pre-exposure plants to identify candidate genes and pathways underlying barley's response. Expression of 3585 genes was upregulated and 5586 downregulated in leaves, while expression of 13,200 genes was upregulated and 10,575 downregulated in roots. Regulation of gene expression was severely impacted in roots, highlighting the complexity of salt stress response mechanisms in this tissue. Functional analyses in both tissues indicated that response to salt stress is mainly achieved through sensing and signaling pathways, strong transcriptional reprograming, hormone osmolyte and ion homeostasis stabilization, increased reactive oxygen scavenging, and activation of transport and photosynthesis systems. A number of candidate genes involved in hormone and kinase signaling pathways, as well as several transcription factor families and transporters, were identified. This study provides valuable information on early salt-stress-responsive genes in roots and leaves of barley and identifies several important players in salt tolerance.
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Affiliation(s)
- Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Dhivya Arasappan
- Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA;
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia;
| | - Mariem Ben Chikha
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Rahma Jardak
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Henda Mahmoudi
- International Center for Biosaline Agriculture, Dubai 00000, United Arab Emirates;
| | - Samiha Mejri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Abdelwahed Ghorbel
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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20
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Li H, Tang X, Yang X, Zhang H. Comprehensive transcriptome and metabolome profiling reveal metabolic mechanisms of Nitraria sibirica Pall. to salt stress. Sci Rep 2021; 11:12878. [PMID: 34145354 PMCID: PMC8213879 DOI: 10.1038/s41598-021-92317-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/09/2021] [Indexed: 02/05/2023] Open
Abstract
Nitraria sibirica Pall., a typical halophyte that can survive under extreme drought conditions and in saline-alkali environments, exhibits strong salt tolerance and environmental adaptability. Understanding the mechanism of molecular and physiological metabolic response to salt stress of plant will better promote the cultivation and use of halophytes. To explore the mechanism of molecular and physiological metabolic of N. sibirica response to salt stress, two-month-old seedlings were treated with 0, 100, and 400 mM NaCl. The results showed that the differentially expressed genes between 100 and 400 mmol L-1 NaCl and unsalted treatment showed significant enrichment in GO terms such as binding, cell wall, extemal encapsulating structure, extracellular region and nucleotide binding. KEGG enrichment analysis found that NaCl treatment had a significant effect on the metabolic pathways in N. sibirica leaves, which mainly including plant-pathogen interaction, amino acid metabolism of the beta alanine, arginine, proline and glycine metabolism, carbon metabolism of glycolysis, gluconeogenesis, galactose, starch and sucrose metabolism, plant hormone signal transduction and spliceosome. Metabolomics analysis found that the differential metabolites between the unsalted treatment and the NaCl treatment are mainly amino acids (proline, aspartic acid, methionine, etc.), organic acids (oxaloacetic acid, fumaric acid, nicotinic acid, etc.) and polyhydric alcohols (inositol, ribitol, etc.), etc. KEGG annotation and enrichment analysis showed that 100 mmol L-1 NaCl treatment had a greater effect on the sulfur metabolism, cysteine and methionine metabolism in N. sibirica leaves, while various amino acid metabolism, TCA cycle, photosynthetic carbon fixation and sulfur metabolism and other metabolic pathways have been significantly affected by 400 mmol L-1 NaCl treatment. Correlation analysis of differential genes in transcriptome and differential metabolites in metabolome have found that the genes of AMY2, BAM1, GPAT3, ASP1, CML38 and RPL4 and the metabolites of L-cysteine, proline, 4-aminobutyric acid and oxaloacetate played an important role in N. sibirica salt tolerance control. This is a further improvement of the salt tolerance mechanism of N. sibirica, and it will provide a theoretical basis and technical support for treatment of saline-alkali soil and the cultivation of halophytes.
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Affiliation(s)
- Huanyong Li
- grid.464465.10000 0001 0103 2256Research Institute of Pomology of Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaoqian Tang
- grid.216566.00000 0001 2104 9346Research Center of Saline and Alkali Land of National of Forestry and Grassland Administration, CAF, Beijing, China
| | - Xiuyan Yang
- grid.216566.00000 0001 2104 9346Research Center of Saline and Alkali Land of National of Forestry and Grassland Administration, CAF, Beijing, China
| | - Huaxin Zhang
- grid.216566.00000 0001 2104 9346Research Center of Saline and Alkali Land of National of Forestry and Grassland Administration, CAF, Beijing, China
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21
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Salt-responsive transcriptome analysis of triticale reveals candidate genes involved in the key metabolic pathway in response to salt stress. Sci Rep 2020; 10:20669. [PMID: 33244037 PMCID: PMC7691987 DOI: 10.1038/s41598-020-77686-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/10/2020] [Indexed: 12/24/2022] Open
Abstract
Triticale is tolerant of many environmental stresses, especially highly resistant to salt stress. However, the molecular regulatory mechanism of triticale seedlings under salt stress conditions is still unclear so far. In this study, a salt-responsive transcriptome analysis was conducted to identify candidate genes or transcription factors related to salt tolerance in triticale. The root of salt-tolerant triticale cultivars TW004 with salt-treated and non-salt stress at different time points were sampled and subjected to de novo transcriptome sequencing. Total 877,858 uniquely assembled transcripts were identified and most contigs were annotated in public databases including nr, GO, KEGG, eggNOG, Swiss-Prot and Pfam. 59,280, 49,345, and 85,922 differentially expressed uniquely assembled transcripts between salt treated and control triticale root samples at three different time points (C12_vs_T12, C24_vs_T24, and C48_vs_T48) were identified, respectively. Expression profile and functional enrichment analysis of DEGs found that some DEGs were significantly enriched in metabolic pathways related to salt tolerance, such as reduction–oxidation pathways, starch and sucrose metabolism. In addition, several transcription factor families that may be associated with salt tolerance were also identified, including AP2/ERF, NAC, bHLH, WRKY and MYB. Furthermore, 14 DEGs were selected to validate the transcriptome profiles via quantitative RT-PCR. In conclusion, these results provide a foundation for further researches on the regulatory mechanism of triticale seedlings adaptation to salt stress in the future.
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22
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Abulfaraj AA. Stepwise signal transduction cascades under salt stress in leaves of wild barley (Hordeum spontaneum). BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1807408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Aala Abdulaziz Abulfaraj
- Department of Biological Sciences, Science and Arts College, King Abdulaziz University, Jeddah, Saudi Arabia
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23
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Ramadan AM. Salinity effects on nad3 gene RNA editing of wild barley mitochondria. Mol Biol Rep 2020; 47:3857-3865. [PMID: 32358688 DOI: 10.1007/s11033-020-05475-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/25/2020] [Indexed: 12/30/2022]
Abstract
Nad complex plays a very important role during cellular respiration. nad3 (nad dehydrogenase subunit 3) is one of the biggest subunits in this complex. Four cDNAs of nad3 gene were characterized in Hordeum vulgare subsp. spontaneum at exposed to four periods of 500 mM salinity, 0 h or control (accession no. MN066165), after 2 h (accession no. MN066166), after 12 h (accession no. MN066167) and after 24 h (accession no. MN066168) using RNA-seq raw data. Seventeen RNA editing sites were found in positions (or nucleotide nos. C5, C39, C44, C61, C62, C79, C80, C147, C185, C190, C191, C208, C209, C275, C317, C344, C349) within the nad3 coding region. These alterations represent differential editing at four exposure times. The maximum editing rate was revealed 2 and 12 h after salinity exposure. However, these edits were disrupted after 24 h probably due to the initiation of program cell death machinery. We found that RNA editing not only improved protein function but also may improve codon bias by altering the nucleotide without any change in amino acid. Characterization of pentatricopeptide repeat-containing protein At4g13650 (PPRSp1) in wild barley helped us to understand the behavior of editing sites C190 and C191 under salinity. Position - 6 in cis-element upstream editing sites of C155, C190 and C191 may be vital to the editing process in these sites by PPRSp1 protein. The differential editing of this gene under salinity led to a relationship between RNA editing and cellular respiration regulation.
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Affiliation(s)
- Ahmed M Ramadan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia. .,Department of Plant Molecular Biology, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
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24
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Liu L, Wang B, Liu D, Zou C, Wu P, Wang Z, Wang Y, Li C. Transcriptomic and metabolomic analyses reveal mechanisms of adaptation to salinity in which carbon and nitrogen metabolism is altered in sugar beet roots. BMC PLANT BIOLOGY 2020; 20:138. [PMID: 32245415 PMCID: PMC7118825 DOI: 10.1186/s12870-020-02349-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 03/23/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Beta vulgaris L. is one of the main sugar-producing crop species and is highly adaptable to saline soil. This study explored the alterations to the carbon and nitrogen metabolism mechanisms enabling the roots of sugar beet seedlings to adapt to salinity. RESULTS The ionome, metabolome, and transcriptome of the roots of sugar beet seedlings were evaluated after 1 day (short term) and 7 days (long term) of 300 mM Na+ treatment. Salt stress caused reactive oxygen species (ROS) damage and ion toxicity in the roots. Interestingly, under salt stress, the increase in the Na+/K+ ratio compared to the control ratio on day 7 was lower than that on day 1 in the roots. The transcriptomic results showed that a large number of differentially expressed genes (DEGs) were enriched in various metabolic pathways. A total of 1279 and 903 DEGs were identified on days 1 and 7, respectively, and were mapped mainly to 10 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most of the genes were involved in carbon metabolism and amino acid (AA) biosynthesis. Furthermore, metabolomic analysis revealed that sucrose metabolism and the activity of the tricarboxylic acid (TCA) cycle increased in response to salt stress. After 1 day of stress, the content of sucrose decreased, whereas the content of organic acids (OAs) such as L-malic acid and 2-oxoglutaric acid increased. After 7 days of salt stress, nitrogen-containing metabolites such as AAs, betaine, melatonin, and (S)-2-aminobutyric acid increased significantly. In addition, multiomic analysis revealed that the expression of the gene encoding xanthine dehydrogenase (XDH) was upregulated and that the expression of the gene encoding allantoinase (ALN) was significantly downregulated, resulting in a large accumulation of allantoin. Correlation analysis revealed that most genes were significantly related to only allantoin and xanthosine. CONCLUSIONS Our study demonstrated that carbon and nitrogen metabolism was altered in the roots of sugar beet plants under salt stress. Nitrogen metabolism plays a major role in the late stages of salt stress. Allantoin, which is involved in the purine metabolic pathway, may be a key regulator of sugar beet salt tolerance.
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Affiliation(s)
- Lei Liu
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang China
| | - Bin Wang
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang China
| | - Dan Liu
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang China
| | - Chunlei Zou
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang China
| | - Peiran Wu
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang China
| | - Ziyang Wang
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang China
| | - Yubo Wang
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang China
| | - Caifeng Li
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang China
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25
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Zou C, Liu D, Wu P, Wang Y, Gai Z, Liu L, Yang F, Li C, Guo G. Transcriptome analysis of sugar beet (Beta vulgaris L.) in response to alkaline stress. PLANT MOLECULAR BIOLOGY 2020; 102:645-657. [PMID: 32040759 DOI: 10.1007/s11103-020-00971-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 01/18/2020] [Indexed: 05/20/2023]
Abstract
RNA-seq was used to analyze the transcriptional changes in sugar beet (Beta vulgaris L.) triggered by alkaline solution to elucidate the molecular mechanism underlying alkaline tolerance in sugar beet. Several differentially expressed genes related to stress tolerance were identified. Our results provide a valuable resource for the breeding of new germplasms with high alkaline tolerance. Alkalinity is a highly stressful environmental factor that limits plant growth and production. Sugar beet own the ability to acclimate to various abiotic stresses, especially salt and alkaline stress. Although substantial previous studies on response of sugar beet to saline stress has been conducted, the expressions of alkali-responsive genes in sugar beet have not been comprehensively investigated. In this study, we conducted transcriptome analysis of leaves in sugar beet seedlings treated with alkaline solutions for 0 day (control, C), 3 days (short-term alkaline treatment, ST) and 7 days (long-term alkaline treatment, LT). The clean reads were obtained and assembled into 25,507 unigenes. Among them, 975 and 383 differentially expressed genes (DEGs) were identified in the comparison groups ST_vs_C and LT_vs_C, respectively. Gene ontology (GO) analysis revealed that oxidation-reduction process and lipid metabolic process were the most enriched GO term among the DEGs in ST_vs_C and LT_vs_C, respectively. According to Kyoto Encyclopedia of Genes and Genomes pathway, carbon fixation in photosynthetic organisms pathway were significantly enriched under alkaline stress. Besides, expression level of genes encoding D-3-phosphoglycerate dehydrogenase 1, glutamyl-tRNA reductase 1, fatty acid hydroperoxide lyase, ethylene-insensitive protein 2, metal tolerance protein 11 and magnesium-chelatase subunit ChlI, etc., were significantly altered under alkaline stress. Additionally, among the DEGs, 136 were non-annotated genes and 24 occurred with differential alternative splicing. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in sugar beet.
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Affiliation(s)
- Chunlei Zou
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Dan Liu
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Peiran Wu
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Yubo Wang
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Zhijia Gai
- Jiamusi Branch, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Lei Liu
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Fangfang Yang
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Caifeng Li
- College of Agronomy, Northeast Agricultural University, Harbin, China.
| | - Guanghao Guo
- College of Agronomy, Northeast Agricultural University, Harbin, China
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26
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Tack DC, Su Z, Yu Y, Bevilacqua PC, Assmann SM. Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis. RNA (NEW YORK, N.Y.) 2020; 26:492-511. [PMID: 31937672 PMCID: PMC7075263 DOI: 10.1261/rna.072850.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/13/2020] [Indexed: 05/22/2023]
Abstract
Little is known concerning the effects of abiotic factors on in vivo RNA structures. We applied Structure-seq to assess the in vivo mRNA structuromes of Arabidopsis thaliana under salinity stress, which negatively impacts agriculture. Structure-seq utilizes dimethyl sulfate reactivity to identify As and Cs that lack base-pairing or protection. Salt stress refolded transcripts differentially in root versus shoot, evincing tissue specificity of the structurome. Both tissues exhibited an inverse correlation between salt stress-induced changes in transcript reactivity and changes in abundance, with stress-related mRNAs showing particular structural dynamism. This inverse correlation is more pronounced in mRNAs wherein the mean reactivity of the 5'UTR, CDS, and 3'UTR concertedly change under salinity stress, suggesting increased susceptibility to abundance control mechanisms in transcripts exhibiting this phenomenon, which we name "concordancy." Concordant salinity-induced increases in reactivity were notably observed in photosynthesis genes, thereby implicating mRNA structural loss in the well-known depression of photosynthesis by salt stress. Overall, changes in secondary structure appear to impact mRNA abundance, molding the functional specificity of the transcriptome under stress.
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Affiliation(s)
- David C Tack
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Spectrum Health Office of Research, Grand Rapids, Michigan 49503, USA
| | - Zhao Su
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Yunqing Yu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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27
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Yousefirad S, Soltanloo H, Ramezanpour SS, Zaynali Nezhad K, Shariati V. The RNA-seq transcriptomic analysis reveals genes mediating salt tolerance through rapid triggering of ion transporters in a mutant barley. PLoS One 2020; 15:e0229513. [PMID: 32187229 PMCID: PMC7080263 DOI: 10.1371/journal.pone.0229513] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/09/2020] [Indexed: 12/23/2022] Open
Abstract
Considering the complex nature of salinity tolerance mechanisms, the use of isogenic lines or mutants possessing the same genetic background albeit different tolerance to salinity is a suitable method for reduction of analytical complexity to study these mechanisms. In the present study, whole transcriptome analysis was evaluated using RNA-seq method between a salt-tolerant mutant line "M4-73-30" and its wild-type "Zarjou" cultivar at seedling stage after six hours of exposure to salt stress (300 mM NaCl). Transcriptome sequencing yielded 20 million reads for each genotype. A total number of 7116 transcripts with differential expression were identified, 1586 and 1479 of which were obtained with significantly increased expression in the mutant and the wild-type, respectively. In addition, the families of WRKY, ERF, AP2/EREBP, NAC, CTR/DRE, AP2/ERF, MAD, MIKC, HSF, and bZIP were identified as the important transcription factors with specific expression in the mutant genotype. The RNA-seq results were confirmed at several time points using qRT-PCR for some important salt-responsive genes. In general, the results revealed that the mutant accumulated higher levels of sodium ion in the root and decreased its transfer to the shoot. Also, the mutant increased the amount of potassium ion leading to the maintenance a high ratio [K+]/[Na+] in the shoot compared to its wild-type via fast stomata closure and consequently transpiration reduction under the salt stress. Moreover, a reduction in photosynthesis and respiration was observed in the mutant, resulting in utilization of the stored energy and the carbon for maintaining the plant tissues, which is considered as a mechanism of salt tolerance in plants. Up-regulation of catalase, peroxidase, and ascorbate peroxidase genes has resulted in higher accumulation of H2O2 in the wild-type compared to the mutant. Therefore, the wild-type initiated rapid ROS signals which led to less oxidative scavenging in comparison with the mutant. The mutant increased expression in the ion transporters and the channels related to the salinity to maintain the ion homeostasis. In overall, the results demonstrated that the mutant responded better to the salt stress under both osmotic and ionic stress phases and lower damage was observed in the mutant compared to its wild-type under the salt stress.
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Affiliation(s)
- Sareh Yousefirad
- Department of Plant Breeding and Plant Biotechnolgy, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Golestan, Iran
| | - Hassan Soltanloo
- Department of Plant Breeding and Plant Biotechnolgy, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Golestan, Iran
| | - Seyedeh Sanaz Ramezanpour
- Department of Plant Breeding and Plant Biotechnolgy, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Golestan, Iran
| | - Khalil Zaynali Nezhad
- Department of Plant Breeding and Plant Biotechnolgy, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Golestan, Iran
| | - Vahid Shariati
- Department of Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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28
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Zhang L, Wang Y, Zhang Q, Jiang Y, Zhang H, Li R. Overexpression of HbMBF1a, encoding multiprotein bridging factor 1 from the halophyte Hordeum brevisubulatum, confers salinity tolerance and ABA insensitivity to transgenic Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2020; 102:1-17. [PMID: 31655970 PMCID: PMC6976555 DOI: 10.1007/s11103-019-00926-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/13/2019] [Indexed: 05/11/2023]
Abstract
HbMBF1a was isolated and characterized in H. brevisubulatum, and overexpressed HbMBF1a could enhance the salt tolerance and ABA insensitivity in Arabidopsis thaliana. The transcript levels of stress-responsive genes were significantly increased in the transgenic lines under salt and ABA conditions. Salinity is an abiotic stress that considerably affects plant growth, yield, and distribution. Hordeum brevisubulatum is a halophyte that evolved to become highly tolerant to salinity. Multiprotein bridging factor 1 (MBF1) is a transcriptional coactivator and an important regulator of stress tolerance. In this study, we isolated and characterized HbMBF1a based on the transcriptome data of H. brevisubulatum grown under saline conditions. We overexpressed HbMBF1a in Arabidopsis thaliana and compared the phenotypes of the transgenic lines and the wild-type in response to stresses. The results indicated that HbMBF1a expression was induced by salt and ABA treatments during the middle and late stages. The overexpression of HbMBF1a in A. thaliana resulted in enhanced salt tolerance and ABA insensitivity. More specifically, the enhanced salt tolerance manifested as the increased seed germination and seedling growth and development. Similarly, under ABA treatments, the cotyledon greening rate and seedling root length were higher in the HbMBF1a-overexpressing lines, suggesting the transgenic plants were better adapted to high exogenous ABA levels. Furthermore, the transcript levels of stress-responsive genes were significantly increased in the transgenic lines under salt and ABA conditions. Thus, HbMBF1a is a positive regulator of salt and ABA responses, and the corresponding gene may be useful for producing transgenic plants that are salt tolerant and/or ABA insensitive, with few adverse effects. This study involved a comprehensive analysis of HbMBF1a. The results may provide the basis and insight for the application of MBF1 family genes for developing stress-tolerant crops.
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Affiliation(s)
- Lili Zhang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Yunxiao Wang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Qike Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024 China
| | - Ying Jiang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Haiwen Zhang
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
| | - Ruifen Li
- Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, 100097 China
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29
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Chen Z, Zhao X, Hu Z, Leng P. Nitric oxide modulating ion balance in Hylotelephium erythrostictum roots subjected to NaCl stress based on the analysis of transcriptome, fluorescence, and ion fluxes. Sci Rep 2019; 9:18317. [PMID: 31797954 PMCID: PMC6892800 DOI: 10.1038/s41598-019-54611-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022] Open
Abstract
Soil salinization is one of the main stress factors that affect both growth and development of plants. Hylotelephium erythrostictum exhibits strong resistance to salt, but the underlying genetic mechanisms remain unclear. In this study, hydroponically cultured seedlings of H. erythrostictum were exposed to 200 mM NaCl. RNA-Seq was used to determine root transcriptomes at 0, 5, and 10 days, and potential candidate genes with differential expression were analyzed. Transcriptome sequencing generated 89.413 Gb of raw data, which were assembled into 111,341 unigenes, 82,081 of which were annotated. Differentially expressed genes associated to Na+ and K+ transport, Ca2+ channel, calcium binding protein, and nitric oxide (NO) biosynthesis had high expression levels in response to salt stress. An increased fluorescence intensity of NO indicated that it played an important role in the regulation of the cytosolic K+/Na+ balance in response to salt stress. Exogenous NO donor and NO biosynthesis inhibitors significantly increased and decreased the Na+ efflux, respectively, thus causing the opposite effect for K+ efflux. Moreover, under salt stress, exogenous NO donors and NO biosynthesis inhibitors enhanced and reduced Ca2+ influx, respectively. Combined with Ca2+ reagent regulation of Na+ and K+ fluxes, this study identifies how NaCl-induced NO may function as a signaling messenger that modulates the K+/Na+ balance in the cytoplasm via the Ca2+ signaling pathway. This enhances the salt resistance in H. erythrostictum roots.
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Affiliation(s)
- Zhixin Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Xueqi Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Zenghui Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China.
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing, 102206, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China.
| | - Pingsheng Leng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China.
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing, 102206, China.
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30
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Zhu M, Xie H, Wei X, Dossa K, Yu Y, Hui S, Tang G, Zeng X, Yu Y, Hu P, Wang J. WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice. Genes (Basel) 2019; 10:E719. [PMID: 31533315 PMCID: PMC6771013 DOI: 10.3390/genes10090719] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/07/2019] [Accepted: 09/11/2019] [Indexed: 12/21/2022] Open
Abstract
Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties.
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Affiliation(s)
- Mingdong Zhu
- Hunan Agricultural University, Changsha 410128, China.
- Hunan Rice Research Institute, Changsha 410125, China.
| | - Hongjun Xie
- Hunan Rice Research Institute, Changsha 410125, China.
| | - Xiangjin Wei
- China National Rice Research Institute, Hangzhou 311401, China.
| | - Komivi Dossa
- Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China.
| | - Yaying Yu
- Hunan Agricultural University, Changsha 410128, China.
| | - Suozhen Hui
- Hunan Agricultural University, Changsha 410128, China.
| | - Guohua Tang
- Hunan Rice Research Institute, Changsha 410125, China.
| | - Xiaoshan Zeng
- Hunan Rice Research Institute, Changsha 410125, China.
| | - Yinghong Yu
- Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Peisong Hu
- China National Rice Research Institute, Hangzhou 311401, China.
| | - Jianlong Wang
- Hunan Agricultural University, Changsha 410128, China.
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Zhang C, Luo W, Li Y, Zhang X, Bai X, Niu Z, Zhang X, Li Z, Wan D. Transcriptomic Analysis of Seed Germination Under Salt Stress in Two Desert Sister Species ( Populus euphratica and P. pruinosa). Front Genet 2019; 10:231. [PMID: 30967895 PMCID: PMC6442517 DOI: 10.3389/fgene.2019.00231] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/04/2019] [Indexed: 11/13/2022] Open
Abstract
As a major abiotic stress, soil salinity limits seed germination and plant growth, development and production. Seed germination is highly related not only to the seedlings survival rate but also subsequent vegetative growth. Populus euphratica and P. pruinosa are closely related species that show a distinguished adaptability to salinity stress. In this study, we performed an integrative transcriptome analyses of three seed germination phases from P. euphratica and P. pruinosa under salt stress. A two-dimensional data set of this study provides a comprehensive view of the dynamic biochemical processes that underpin seed germination and salt tolerance. Our analysis identified 12831 differentially expressed genes (DEGs) for seed germination processes and 8071 DEGs for salt tolerance in the two species. Furthermore, we identified the expression profiles and main pathways in each growth phase. For seed germination, a large number of DEGs, including those involved in energy production and hormonal regulation pathways, were transiently and specifically induced in the late phase. In the comparison of salt tolerance between the two species, the flavonoid and brassinosteroid pathways were significantly enriched. More specifically, in the flavonoid pathway, FLS and F3'5'H exhibited significant differential expression. In the brassinosteroid pathway, the expression levels of DWF4, BR6OX2 and ROT3 were notably higher in P. pruinosa than in P. euphratica. Our results describe transcript dynamics and highlight secondary metabolite pathways involved in the response to salt stress during the seed germination of two desert poplars.
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Affiliation(s)
- Caihua Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenchun Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yanda Li
- Computer Science and Engineering Department, University of California, San Diego, La Jolla, CA, United States
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiaotao Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiao Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhijun Li
- Xinjiang Production & Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Sciences, Tarim University, Xinjiang, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
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Ma Y, Liu M, Stiller J, Liu C. A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. BMC Genomics 2019; 20:12. [PMID: 30616511 PMCID: PMC6323845 DOI: 10.1186/s12864-018-5357-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/09/2018] [Indexed: 11/12/2022] Open
Abstract
Background It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications. Results In this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones. Conclusions We demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication. Electronic supplementary material The online version of this article (10.1186/s12864-018-5357-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanling Ma
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Miao Liu
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.,Crop Research Institute of Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jiri Stiller
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture & Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
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Ramadan AM, Azeiz AA, Baabad S, Hassanein S, Gadalla NO, Hassan S, Algandaby M, Bakr S, Khan T, Abouseadaa HH, Ali HM, Al-Ghamdi A, Osman G, Edris S, Eissa H, Bahieldin A. Control of β-sitosterol biosynthesis under light and watering in desert plant Calotropis procera. Steroids 2019; 141:1-8. [PMID: 30414421 DOI: 10.1016/j.steroids.2018.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/23/2018] [Accepted: 11/02/2018] [Indexed: 01/13/2023]
Abstract
Most scientific studies on Calotropis procera refer to the plant as an important source of pharmaceutical compounds and its valuable benefits in medicine. One of the most important substances in this plant is the potential immunostimulant β-sitosterol (BS) that acts in improving human health. This study focused on the effects of lighting before and after irrigation on the BS accumulation pathway namely steroid biosynthesis. Studying the enzymes in BS biosynthetic pathway indicated the upregulation at dawn and predusk of the SMT2 and SMO2 genes encoding sterol methyltransferase 2 and methylsterol monooxygenase, two key enzymes in BS accumulation in C. procera. The results almost indicated no regulation at the different time points of the CYP710A gene encoding sterol 22-desaturase, an enzyme that acts in depleting β-sitosterol towards the biosynthesis of stigmasterol. RNA-Seq data was validated via quantitative RT-PCR and results were positive. The data of ultra-performance liquid chromatography-tandem mass spectrometry analysis with regard to BS accumulation also aligned with those of RNA-Seq analysis. We focused on the effects of light before and after watering on BS accumulation in C. procera. Our results show that BS accumulation is high at dawn in both dehydrated and well-watered condition. While, the BS was dramatically decrease at midday in well-watered plants. This increase/decrease in BS content is correlated with rates of expression of SMT 2 gene. This gene is a key convertor between the different branches in the cardiac glycoside biosynthesis. Accordingly, it could be suggested that BS (or one of the descendent product) may play an important role in C. procera tolerance to drought/light intensity conditions.
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Affiliation(s)
- Ahmed M Ramadan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Plant Molecular Biology Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
| | - Ahmed Abdel Azeiz
- College of Biotechnology, Misr University for Science and Technology (MUST), 6th October City, Egypt
| | - Saeed Baabad
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sameh Hassanein
- College of Biotechnology, Misr University for Science and Technology (MUST), 6th October City, Egypt; Bioinformatics Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center(ARC), Giza, Egypt
| | - Nour O Gadalla
- Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia; Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Sabah Hassan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Mardi Algandaby
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Salwa Bakr
- Department of Clinical Pathology, Hematology, College of Medicine, Fayoum University, Fayoum, Egypt; College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Thana Khan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Heba H Abouseadaa
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Hani Mohammed Ali
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Areej Al-Ghamdi
- Physics Department, Faculty of Science, Jeddah University, Jeddah, Saudi Arabia
| | - Gamal Osman
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia; Department of Microbial genetics, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
| | - Sherif Edris
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Hala Eissa
- Plant Molecular Biology Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt; College of Biotechnology, Misr University for Science and Technology (MUST), 6th October City, Egypt
| | - Ahmed Bahieldin
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
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Liu Q, Tang J, Wang W, Zhang Y, Yuan H, Huang S. Transcriptome analysis reveals complex response of the medicinal/ornamental halophyte Iris halophila Pall. to high environmental salinity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 165:250-260. [PMID: 30199796 DOI: 10.1016/j.ecoenv.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/28/2018] [Accepted: 09/01/2018] [Indexed: 05/25/2023]
Abstract
The remediation and subsequent use of saline-alkaline land are of great significance to ecological environment construction and sustainable agricultural development. Iris halophila Pall. is a salt-tolerant medicinal and ornamental plant, which has good application prospects in the ecological construction of saline-alkaline land; therefore, study of the molecular mechanisms of salt tolerance in I. halophila has important theoretical and practical value. To evaluate the molecular mechanism of the response of I. halophila to salt toxicity, I. halophila seedlings were treated with salt (300 mM NaCl) and subjected to deep RNA sequencing. The clean reads were obtained and assembled into 297,188 unigenes. Among them, 1120 and 100 salt-responsive genes were identified in I. halophila shoots and roots, respectively. Among them, the key flavonoid and lignin biosynthetic genes, hormone signaling genes, sodium/potassium ion transporter genes, and transcription factors were analyzed and summarized. Quantitative reverse-transcription PCR analysis strengthened the reliability of the RNA sequencing results. This work provides an overview of the transcriptomic responses to salt toxicity in I. halophila and identifies the responsive genes that may contribute to its reduced salt toxicity. These results lay an important foundation for further study of the molecular mechanisms of salt tolerance in I. halophila and related species.
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Affiliation(s)
- Qingquan Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Jun Tang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Weilin Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Yongxia Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Haiyan Yuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Suzhen Huang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China.
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Gairola S, Al Shaer KI, Al Harthi EK, Mosa KA. Strengthening desert plant biotechnology research in the United Arab Emirates: a viewpoint. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:521-533. [PMID: 30042610 PMCID: PMC6041242 DOI: 10.1007/s12298-018-0551-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/19/2018] [Accepted: 05/08/2018] [Indexed: 05/09/2023]
Abstract
The biotechnology of desert plants is a vast subject. The main applications in this broad field of study comprises of plant tissue culture, genetic engineering, molecular markers and others. Biotechnology applications have the potential to address biodiversity conservation as well as agricultural, medicinal, and environmental issues. There is a need to increase our knowledge of the genetic diversity through the use of molecular genetics and biotechnological approaches in desert plants in the Arabian Gulf region including those in the United Arab Emirates (UAE). This article provides a prospective research for the study of UAE desert plant diversity through DNA fingerprinting as well as understanding the mechanisms of both abiotic stress resistance (including salinity, drought and heat stresses) and biotic stress resistance (including disease and insect resistance). Special attention is given to the desert halophytes and their utilization to alleviate the salinity stress, which is one of the major challenges in agriculture. In addition, symbioses with microorganisms are thought to be hypothesized as important components of desert plant survival under stressful environmental conditions. Thus, factors shaping the diversity and functionality of plant microbiomes in desert ecosystems are also emphasized in this article. It is important to establish a critical mass for biotechnology research and applications while strengthening the channels for collaboration among research/academic institutions in the area of desert plant biotechnology.
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Affiliation(s)
- Sanjay Gairola
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Khawla I. Al Shaer
- Plant Molecular Biology and Biotechnology Laboratory, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Eman K. Al Harthi
- Plant Molecular Biology and Biotechnology Laboratory, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Kareem A. Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
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Qiu L, Feng J, Dai Y, Chang S. Biosorption of strontium ions from simulated high-level liquid waste by living Saccharomyces cerevisiae. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:17194-17206. [PMID: 29651726 DOI: 10.1007/s11356-018-1662-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
In this study, the Saccharomyces cerevisiae (S. cerevisiae) was modified by γ-ray. The RNA-seq results reflect that the high γ-ray energies could change some gene fragments, such as deletion, recombination, and mutation. The biosorption of strontium ions (Sr2+) to different types of S. cerevisiae (S. cerevisiae (K-0), modified S. cerevisiae (Y-7), and non-living S. cerevisiae (H-K)) from the simulated high-level liquid waste (S-HLLW) was assessed at different experimental conditions. The sorption experimental results show that, under an appropriate condition, γ-ray radiation can enhance its biosorption capacity slightly of Sr2+ to S. cerevisiae. The maximum metal uptake and efficiency of Y-7 under S-HLLW were 11.656 mg g-1 and 37.91% at 32 h (wet weight), respectively. They decreased to 9.46 mg g-1 and 30.76% under radiation conditions. SEM-EDX and TEM analysis indicates that Sr2+ was adsorbed both on the cellular surface and the inner parts of the cells. Our experimental results fit well to the Langmuir and Freundlich model isotherms (r2 > 0.94), and the maximum biosorption capacity values reached qmax > 24.74 mg g-1 at 32 °C. Negative values of ΔG0 and positive values of ΔH0 were observed, indicating the spontaneous and endothermic nature of Sr2+ biosorption on modified S. cerevisiae. The biosorption kinetics follow a pseudo-second-order equation at 32 °C (r2 > 0.94). The desorption efficiency of Sr2+ adsorbed onto Y-7 was 7.65 ± 0.52%, 76.51 ± 2.13%, and 65.62 ± 2.42% by deionized water, 1 M HCl, and 0.1 M EDTA-Na, respectively. However, they were lower than H-K (18.82, 83.32, and 73.32%). Our findings demonstrate that living S. cerevisiae (Y-7) is a promising sorbent material for the treatment of radioactive process streams.
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Affiliation(s)
- Liang Qiu
- Department of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, People's Republic of China
| | - Jundong Feng
- Department of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, People's Republic of China.
| | - Yaodong Dai
- Department of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, People's Republic of China
| | - Shuquan Chang
- Department of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, People's Republic of China
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Ashoub A, Müller N, Jiménez-Gómez JM, Brüggemann W. Prominent alterations of wild barley leaf transcriptome in response to individual and combined drought acclimation and heat shock conditions. PHYSIOLOGIA PLANTARUM 2018; 163:18-29. [PMID: 29111595 DOI: 10.1111/ppl.12667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Under field conditions, drought and heat stress typically happen simultaneously and their negative impact on the agricultural production is expected to increase worldwide under the climate change scenario. In this study, we performed RNA-sequencing analysis on leaves of wild barley (Hordeum spontaneum) originated from the northern coastal region of Egypt following individual drought acclimation (DA) and heat shock (HS) treatments and their combination (CS, combined stresses) to distinguish the unique and shared differentially expressed genes (DEG). Results indicated that the number of unique genes that were differentially expressed following HS treatment exceeded the number of those expressed following DA. In addition, the number of genes that were uniquely differentially expressed in response to CS treatment exceeded the number of those of shared responses to individual DA and HS treatments. These results indicate a better adaptation of the Mediterranean wild barley to drought conditions when compared with heat stress. It also manifests that the wild barley response to CS tends to be unique rather than common. Annotation of DEG showed that metabolic processes were the most influenced biological function in response to the applied stresses.
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Affiliation(s)
- Ahmed Ashoub
- Institute of Ecology, Evolution, and Diversity, Johann Wolfgang Goethe-University Frankfurt, Frankfurt am Main, Germany
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Niels Müller
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - José M Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Wolfgang Brüggemann
- Institute of Ecology, Evolution, and Diversity, Johann Wolfgang Goethe-University Frankfurt, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
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38
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Physiological and Transcriptomic Responses of Chinese Cabbage (Brassica rapa L. ssp. Pekinensis) to Salt Stress. Int J Mol Sci 2017; 18:ijms18091953. [PMID: 28895882 PMCID: PMC5618602 DOI: 10.3390/ijms18091953] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/18/2017] [Accepted: 09/04/2017] [Indexed: 11/17/2022] Open
Abstract
Salt stress is one of the major abiotic stresses that severely impact plant growth and development. In this study, we investigated the physiological and transcriptomic responses of Chinese cabbage “Qingmaye” to salt stress, a main variety in North China. Our results showed that the growth and photosynthesis of Chinese cabbage were significantly inhibited by salt treatment. However, as a glycophyte, Chinese cabbage could cope with high salinity; it could complete an entire life cycle at 100 mM NaCl. The high salt tolerance of Chinese cabbage was achieved by accumulating osmoprotectants and by maintaining higher activity of antioxidant enzymes. Transcriptomic responses were analyzed using the digital gene expression profiling (DGE) technique after 12 h of treatment by 200 mM NaCl. A total of 1235 differentially expressed genes (DEGs) including 740 up- and 495 down-regulated genes were identified. Functional annotation analyses showed that the DEGs were related to signal transduction, osmolyte synthesis, transcription factors, and antioxidant proteins. Taken together, this study contributes to our understanding of the mechanism of salt tolerance in Chinese cabbage and provides valuable information for further improvement of salt tolerance in Chinese cabbage breeding programs.
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De Novo Transcriptome Characterization, Gene Expression Profiling and Ionic Responses of Nitraria sibirica Pall. under Salt Stress. FORESTS 2017. [DOI: 10.3390/f8060211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Hajrah NH, Obaid AY, Atef A, Ramadan AM, Arasappan D, Nelson CA, Edris S, Mutwakil MZ, Alhebshi A, Gadalla NO, Makki RM, Al-Kordy MA, El-Domyati FM, Sabir JSM, Khiyami MA, Hall N, Bahieldin A, Jansen RK. Transcriptomic analysis of salt stress responsive genes in Rhazya stricta. PLoS One 2017; 12:e0177589. [PMID: 28520766 PMCID: PMC5433744 DOI: 10.1371/journal.pone.0177589] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/29/2017] [Indexed: 11/24/2022] Open
Abstract
Rhazya stricta is an evergreen shrub that is widely distributed across Western and South Asia, and like many other members of the Apocynaceae produces monoterpene indole alkaloids that have anti-cancer properties. This species is adapted to very harsh desert conditions making it an excellent system for studying tolerance to high temperatures and salinity. RNA-Seq analysis was performed on R. stricta exposed to severe salt stress (500 mM NaCl) across four time intervals (0, 2, 12 and 24 h) to examine mechanisms of salt tolerance. A large number of transcripts including genes encoding tetrapyrroles and pentatricopeptide repeat (PPR) proteins were regulated only after 12 h of stress of seedlings grown in controlled greenhouse conditions. Mechanisms of salt tolerance in R. stricta may involve the upregulation of genes encoding chaperone protein Dnaj6, UDP-glucosyl transferase 85a2, protein transparent testa 12 and respiratory burst oxidase homolog protein b. Many of the highly-expressed genes act on protecting protein folding during salt stress and the production of flavonoids, key secondary metabolites in stress tolerance. Other regulated genes encode enzymes in the porphyrin and chlorophyll metabolic pathway with important roles during plant growth, photosynthesis, hormone signaling and abiotic responses. Heme biosynthesis in R. stricta leaves might add to the level of salt stress tolerance by maintaining appropriate levels of photosynthesis and normal plant growth as well as by the participation in reactive oxygen species (ROS) production under stress. We speculate that the high expression levels of PPR genes may be dependent on expression levels of their targeted editing genes. Although the results of PPR gene family indicated regulation of a large number of transcripts under salt stress, PPR actions were independent of the salt stress because their RNA editing patterns were unchanged.
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Affiliation(s)
- Nahid H. Hajrah
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Abdullah Y. Obaid
- Department of Chemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Ahmed Atef
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Ahmed M. Ramadan
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
| | - Dhivya Arasappan
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Charllotte A. Nelson
- Centre of Genomic Research, Institute for Integrative Biology, Crown Street, Liverpool, United Kingdom
| | - Sherif Edris
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Mohammed Z. Mutwakil
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Alawia Alhebshi
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Nour O. Gadalla
- Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Rania M. Makki
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Madgy A. Al-Kordy
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Fotouh M. El-Domyati
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Jamal S. M. Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Mohammad A. Khiyami
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Neil Hall
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- The Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ahmed Bahieldin
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Robert K. Jansen
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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Zhang H, Mittal N, Leamy LJ, Barazani O, Song B. Back into the wild-Apply untapped genetic diversity of wild relatives for crop improvement. Evol Appl 2017; 10:5-24. [PMID: 28035232 PMCID: PMC5192947 DOI: 10.1111/eva.12434] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/07/2016] [Indexed: 12/18/2022] Open
Abstract
Deleterious effects of climate change and human activities, as well as diverse environmental stresses, present critical challenges to food production and the maintenance of natural diversity. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enables them to thrive in marginal lands. However, considering the diverse interactions between crops and environmental factors, it is surprising that evolutionary principles have been underexploited in addressing these food and environmental challenges. Compared with domesticated cultivars, crop wild relatives (CWRs) have been challenged in natural environments for thousands of years and maintain a much higher level of genetic diversity. In this review, we highlight the significance of CWRs for crop improvement by providing examples of CWRs that have been used to increase biotic and abiotic stress resistance/tolerance and overall yield in various crop species. We also discuss the surge of advanced biotechnologies, such as next-generation sequencing technologies and omics, with particular emphasis on how they have facilitated gene discovery in CWRs. We end the review by discussing the available resources and conservation of CWRs, including the urgent need for CWR prioritization and collection to ensure continuous crop improvement for food sustainability.
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Affiliation(s)
- Hengyou Zhang
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Neha Mittal
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Larry J. Leamy
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Oz Barazani
- The Institute for Plant SciencesIsrael Plant Gene BankAgricultural Research OrganizationBet DaganIsrael
| | - Bao‐Hua Song
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
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Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley. Sci Rep 2016; 6:32586. [PMID: 27585856 PMCID: PMC5009332 DOI: 10.1038/srep32586] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/03/2016] [Indexed: 11/15/2022] Open
Abstract
Producing sufficient food for nine billion people by 2050 will be constrained by soil salinity, especially in irrigated systems. To improve crop yield, greater understanding of the genetic control of traits contributing to salinity tolerance in the field is needed. Here, we exploit natural variation in exotic germplasm by taking a genome-wide association approach to a new nested association mapping population of barley called HEB-25. The large population (1,336 genotypes) allowed cross-validation of loci, which, along with two years of phenotypic data collected from plants irrigated with fresh and saline water, improved statistical power. We dissect the genetic architecture of flowering time under high salinity and we present genes putatively affecting this trait and salinity tolerance. In addition, we identify a locus on chromosome 2H where, under saline conditions, lines homozygous for the wild allele yielded 30% more than did lines homozygous for the Barke allele. Introgressing this wild allele into elite cultivars could markedly improve yield under saline conditions.
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