scholarly journals Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 803 ◽  
Author(s):  
Umar Akram ◽  
Yuhan Song ◽  
Chengzhen Liang ◽  
Muhammad Ali Abid ◽  
Muhammad Askari ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gossypium Hirsutum ◽  
Salinity Stress ◽  
Abiotic Stresses ◽  
Functional Divergence ◽  
Gossypium Barbadense ◽  
High Expression ◽  
Functional Study ◽  
Genome Wide ◽  
A Genome

Cotton is an important economic crop affected by different abiotic stresses at different developmental stages. Salinity limits the growth and productivity of crops worldwide. Na+/H+ antiporters play a key role during the plant development and in its tolerance to salt stress. The aim of the present study was a genome-wide characterization and expression pattern analysis under the salinity stress of the sodium-proton antiporter (NHX) of Gossypium barbadense in comparison with Gossypium hirsutum. In G. barbadense, 25 NHX genes were identified on the basis of the Na+_H+ exchanger domain. All except one of the G. barbadense NHX transporters have an Amiloride motif that is a known inhibitor of Na+ ions in plants. A phylogenetic analysis inferred three classes of GbNHX genes—viz., Vac (GbNHX1, 2 and 4), Endo (GbNHX6), and PM (GbNHX7). A high number of the stress-related cis-acting elements observed in promoters show their role in tolerance against abiotic stresses. The Ka/Ks values show that the majority of GbNHX genes are subjected to strong purifying selection under the course of evolution. To study the functional divergence of G. barbadense NHX transporters, the real-time gene expression was analyzed under salt stress in the root, stem, and leaf tissues. In G. barbadense, the expression was higher in the stem, while in G. hirsutum the leaf and root showed a high expression. Moreover, our results revealed that NHX2 homologues in both species have a high expression under salinity stress at higher time intervals, followed by NHX7. The protein-protein prediction study revealed that GbNHX7 is involved in the CBL-CIPK protein interaction pathway. Our study also provided valuable information explaining the molecular mechanism of Na+ transport for the further functional study of Gossypium NHX genes.

scholarly journals Genome-wide Survey of the Dehydrin Genes in Bread Wheat (Triticum Aestivum L.) and its Relatives: Identification, Evolution and Expression Profiling Under Various Abiotic Stresses

2021 ◽  
Author(s):  
Yongchao Hao ◽  
Ming Hao ◽  
Hongwei Wang
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Abiotic Stresses ◽  
Aegilops Tauschii ◽  
Protein Structures ◽  
Interaction Network ◽  
Wheat Breeding ◽  
Functional Study ◽  
Genome Wide ◽  
A Genome

Abstract Background: Bread wheat (Triticum aestivum) is an important and fundamental cereal worldwide. With increasingly severe environmental stress, it is very important to mine stress-resistant genes for wheat breeding. Dehydrin (DHN) genes are primary candidates because they are involved in the response to many stressors. Results: Here, a genome-wide analysis of this gene family was performed on the genomes of wheat and its three relatives. A total of 55 DHN genes in Triticum aestivum, 31 in Triticum dicoccoides, 15 in Triticum urartu, and 16 in Aegilops tauschii were identified. The phylogenetic, synteny, sequence and protein structure analyses showed that the DHN genes were divided into five groups, Genes in the same group share similar conserved motifs, protein structures, and potential functions. The tandem TaDHN genes responded strongly to drought, cold and high salinity stresses, while the non-tandem genes were responded weakly to all stress conditions. Further, multiple DHN proteins cooperation maybe an important way to prevent plants from abiotic stress according to the interaction network analysis. Conclusions: Conserved, duplicated DHN genes may have played an important role in the adaptation of wheat to a variety of conditions, hence, contributing to the distribution of bread wheat as a global staple food. This research illuminates the contributions of DHN genes to abiotic stresses in Triticeae species and offers helpful information for further functional study of DHN genes in these crops.

scholarly journals Polyamine and Ethylene pathways crosstalk revisited on a genome wide and gene function scale

2019 ◽  
Author(s):  
BLAISE PASCAL MUVUNYI ◽  
Fan Wu ◽  
Qi Yan ◽  
Gisele Kanzana ◽  
Yufei Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Tolerance ◽  
Abiotic Stresses ◽  
Primary Root ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Regulatory Elements ◽  
Pathway Gene ◽  
Genome Wide ◽  
A Genome

Abstract Background Polyamine and ethylene biosynthesis pathway genes are widely involved in the regulation of plant abiotic stresses. For their biosynthesis, both pathways require the same precursor, Synthase Adenosyl Methionine (SAM) enzyme. Whether they function as competitors or collaborators to regulate plant abiotic stress tolerance is still an elusive topic. Genome wide analysis of Cleistogenes songorica polyamine and ethylene pathway gene families was conducted to study their evolutionary relationship. And, using Arabidopsis plants transformed with a polyamine gene SAMDC2 from C. songorica, the expression of key genes from both pathways, and other previously well-studied stress responsive genes was investigated under salt or drought stress. Further, the ABA’s role on this interaction salt stress was also studied. Results 17 polyamine, 12 ethylene and 6 SAM biosynthesis related genes were identified at genome wide level in C. songorica. Phylogenetic analysis revealed close evolutionary similarities between gene families from both pathways. Also, analysis of cis regulatory elements indicated that SAM family genes promoters were rich into both ABA and ethylene related cis regulatory elements. Transcriptomic analysis, qRT-PCR validation, and confirmation using transgenic Arabidopsis showed that polyamine and ethylene key pathway genes can be concurrently expressed during abiotic stresses. Arabidopsis plants expressing a polyamine gene CsSAMDC2 driven by RD29A showed an improved drought and salt stress tolerance, and an increased expression of key polyamine and ethylene pathway genes. These plants maintained higher chlorophyll content and photosynthetic capacity. Morphological analysis of transgenic seedlings showed that leaves of these lines exhibited a more compact architecture following salt stress exposure. Application of ABA on transgenic lines under salt stress further improved the expression of polyamine and ethylene pathway genes. Further, lateral and primary root development were found improved during salt stress and ABA treatments. Interestingly, the expression of ethylene pathway genes was not reversed by exogenous ABA during salt stress treatment. Conclusion In silico and gene functional analysis assays revealed potential evolutionary and functional similarities between polyamine and ethylene pathway gene families. Such findings imply a synergetic interaction between polyamine and ethylene pathways, and the significant role of ABA on this crosstalk.

scholarly journals Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Teame Gereziher MEHARI ◽  
Yanchao XU ◽  
Richard Odongo MAGWANGA ◽  
Muhammad Jawad UMER ◽  
Joy Nyangasi KIRUNGU ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gossypium Hirsutum ◽  
Abiotic Stresses ◽  
Substitution Rate ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

scholarly journals Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Peng Xu ◽  
Qi Guo ◽  
Shan Meng ◽  
Xianggui Zhang ◽  
Zhenzhen Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Cotton Production ◽  
Fresh Matter ◽  
Salt Stress Response ◽  
Genome Wide ◽  
A Genome

Abstract Background Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (−log10p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

scholarly journals Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

2020 ◽  
Author(s):  
Peng Xu ◽  
Qi Guo ◽  
Shan Meng ◽  
Xianggui Zhang ◽  
Zhenzhen Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Cotton Production ◽  
Fresh Matter ◽  
Salt Stress Response ◽  
Genome Wide ◽  
A Genome

Abstract Background: Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results: In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on two years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (-log10p>4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions: These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

scholarly journals In-silico genome wide analysis of Mitogen activated protein kinase kinase kinase gene family in C. sinensis

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0258657
Author(s):  
Abhirup Paul ◽  
Anurag P. Srivastava ◽  
Shreya Subrahmanya ◽  
Guoxin Shen ◽  
Neelam Mishra
Keyword(s):  
Protein Kinase ◽  
Regulatory Elements ◽  
Stress Factors ◽  
Mitogen Activated Protein Kinase ◽  
Functional Study ◽  
Functional Domain ◽  
Genome Wide ◽  
A Genome ◽  
Mitogen Activated Protein ◽  
Protein Kinase Kinase

Mitogen activated protein kinase kinase kinase (MAPKKK) form the upstream component of MAPK cascade. It is well characterized in several plants such as Arabidopsis and rice however the knowledge about MAPKKKs in tea plant is largely unknown. In the present study, MAPKKK genes of tea were obtained through a genome wide search using Arabidopsis thaliana as the reference genome. Among 59 candidate MAPKKK genes in tea, 17 genes were MEKK-like, 31 genes were Raf-like and 11 genes were ZIK- like. Additionally, phylogenetic relationships were established along with structural analysis, which includes gene structure, its location as well as conserved motifs, cis-acting regulatory elements and functional domain signatures that were systematically examined. Also, on the basis of one orthologous gene found between tea and Arabidopsis, functional interaction was carried out in C. sinensis based on an Arabidopsis association model. The expressional profiles indicated major involvement of MAPKKK genes from tea in response to various abiotic stress factors. Taken together, this study provides the targets for additional inclusive identification, functional study, and provides comprehensive knowledge for a better understanding of the MAPKKK cascade regulatory network in C. sinensis.

scholarly journals Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10617
Author(s):  
Jie Li ◽  
Xinhao Liu ◽  
Qingmei Wang ◽  
Junyan Sun ◽  
Dexian He
Keyword(s):  
Gene Family ◽  
Seed Development ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Seed Formation ◽  
Aphid Infestation ◽  
Genome Wide ◽  
A Genome ◽  
Cystatin Family

To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions.

scholarly journals Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Yuzhu Huo ◽  
Wangdan Xiong ◽  
Kunlong Su ◽  
Yu Li ◽  
Yawen Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Panicum Virgatum ◽  
Expression Profiles ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

scholarly journals A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 829 ◽  
Author(s):  
Muhammad Yasir ◽  
Shoupu He ◽  
Gaofei Sun ◽  
Xiaoli Geng ◽  
Zhaoe Pan ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Stress Tolerance ◽  
Salinity Stress ◽  
Upland Cotton ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Salinity Stress Tolerance

Millions of hectares of land are too saline to produce economically valuable crop yields. Salt tolerance in cotton is an imperative approach for improvement in response to ever-increasing soil salinization. Little is known about the genetic basis of salt tolerance in cotton at the seedling stage. To address this issue, a genome-wide association study (GWAS) was conducted on a core collection of a genetically diverse population of upland cotton (Gossypium hirsutum L.) comprising of 419 accessions, representing various geographic origins, including China, USA, Pakistan, the former Soviet Union, Chad, Australia, Brazil, Mexico, Sudan, and Uganda. Phenotypic evaluation of 7 traits under control (0 mM) and treatment (150 mM) NaCl conditions depicted the presence of broad natural variation in the studied population. The association study was carried out with the efficient mixed-model association eXpedited software package. A total of 17,264 single-nucleotide polymorphisms (SNPs) associated with different salinity stress tolerance related traits were found. Twenty-three candidate SNPs related to salinity stress-related traits were selected. Final key SNPs were selected based on the r2 value with nearby SNPs in a linkage disequilibrium (LD) block. Twenty putative candidate genes surrounding SNPs, A10_95330133 and D10_61258588, associated with leaf relative water content, RWC_150, and leaf fresh weight, FW_150, were identified, respectively. We further validated the expression patterns of twelve candidate genes with qRT-PCR, which revealed different expression levels in salt-tolerant and salt-sensitive genotypes. The results of our GWAS provide useful knowledge about the genetic control of salt tolerance at the seedling stage, which could assist in elucidating the genetic and molecular mechanisms of salinity stress tolerance in cotton plants.

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