scholarly journals PvB3s: Genome-wide and Transcriptome-wide Identification and Analysis Reveals the B3 Family Regulate Auxin to Resist Salt Stress at the Sprout Stage in Common Bean(P. Vulgaris L. ) .

2020 ◽  
Author(s):  
Qi Zhang ◽  
Wei-jia Li ◽  
Wen-jing Zhang ◽  
Zhen-gong Yin ◽  
Yu-xin Wang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Common Bean ◽  
Dna Sequences ◽  
Functional Characterization ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Genes Expression ◽  
Intron Structure ◽  
Auxin Content

Abstract Background: B3 gene family is a transcription factor family unique to plants, which play an important role in plant growth and development by binding specific DNA sequences. However, data on the B3 genes in the common bean and participate in many abiotic stresses especially salt stress are limited. Result: A total of encoding 100 proteins were identified in common bean. Phylogenetic analysis showed that PvB3s were classified into 4 subgroups, and these clusters were supported by several group-specific features, including exon/intron structure, MEME motifs, and predicted binding site structure. Collinearity analysis showed the connection of PvB3s in the same species and different species. The genes expression pattern showed that PvB3s expressed with a tissue-specific manner during sprout stage. Through RNA-seq and qRT-PCR analysis, it was found that there were differences in expression in extreme materials under salt stress. The determination of auxin content and the analysis of PvB3s expression in the enriched pathway showed that PvB3s would respond to auxin to enhance salt tolerance in common bean sprouting stage. Conclusion: The results provided useful and rich resources of PvB3s for the functional characterization and understanding of B3 transcription factors (TFs) in common bean, which further provides insights that PvB3s may respond to auxin to enhance salt tolerance of common bean.

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 Analysis of PEBP Genes in Dendrobium huoshanense: Unveiling the Antagonistic Functions of FT/TFL1 in Flowering Time

2021 ◽  
Vol 12 ◽  
Author(s):  
Cheng Song ◽  
Guohui Li ◽  
Jun Dai ◽  
Hui Deng
Keyword(s):  
Functional Characterization ◽  
Light Response ◽  
Pcr Analysis ◽  
Gene Expressions ◽  
Phylogeny Analysis ◽  
Medicinal Value ◽  
Genome Wide ◽  
Dendrobium Huoshanense ◽  
Flowering Regulation ◽  
Regulatory Functions

Dendrobium is a semi-shade epiphytic Orchidaceae herb with important ornamental and medicinal value. Parts of the cultivation of Dendrobium germplasm resources, as well as the identification of medicinal components, are more studied, but the functional characterization of the flowering regulation in Dendrobium plants is less reported. Here, six PEBP family genes (DhFT3, DhFT1, DhMFT, DhTFL1b, DhFT2, and DhTFL1a) were identified from the Dendrobium huoshanense genome. The chromosome-level mapping showed that these genes were sequentially distributed on chromosomes 6, 9, 15, and 17. The paralogous gene DhTFL1b corresponded to DhTFL1a, which was determined through tandem duplication. The gene structure and conserved motif of DhPEBP indicated five PEBP genes apart from DhMFT contained four exons and three introns entirely. The phylogeny analysis showed that the PEBP gene family in A. thaliana, O. sativa, Z. mays, S. lycopersicum, and P. equestris were classified into three subclades, FT, TFL, and MFT, which maintained a high homology with D. huoshanense. The conserved domain of the amino acid demonstrated that two highly conserved short motifs (DPDXP and GXHR) embed in DhPEBPs, which may contribute to the conformation of the ligand binding bag. The 86th position of DhFTs was tyrosine (Y), while the 83th and 87th of DhTFL1s belonged to histidine (H), suggesting they should have distinct functions in flowering regulation. The promoter of six DhPEBPs contained several cis-elements related to hormone induction, light response, and abiotic stress, which indicated they could be regulated by the environmental stress and endogenous signaling pathways. The qRT-PCR analysis of DhPEBPs in short-term days induced by GA indicated the gene expressions of all DhFTs were gradually increased, whereas the expression of DhTFL1 was decreased. The results implied that DhPEBPs have various regulatory functions in modulating flowering, which will provide a scientific reference for the flowering regulation of Dendrobium plants.

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 Genome-Wide Identification and Functional Characterization of the Cation Proton Antiporter (CPA) Family Related to Salt Stress Response in Radish (Raphanus sativus L.)

2020 ◽  
Vol 21 (21) ◽  
pp. 8262
Author(s):  
Yan Wang ◽  
Jiali Ying ◽  
Yang Zhang ◽  
Liang Xu ◽  
Wanting Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Functional Characterization ◽  
Plant Stress ◽  
Positive Function ◽  
Yellow Mosaic Virus ◽  
Ph Homeostasis ◽  
Salt Stress Response ◽  
Expression Levels ◽  
Genome Wide ◽  
Genome Level

The CPA (cation proton antiporter) family plays an essential role during plant stress tolerance by regulating ionic and pH homeostasis of the cell. Radish fleshy roots are susceptible to abiotic stress during growth and development, especially salt stress. To date, CPA family genes have not yet been identified in radish and the biological functions remain unclear. In this study, 60 CPA candidate genes in radish were identified on the whole genome level, which were divided into three subfamilies including the Na+/H+ exchanger (NHX), K+ efflux antiporter (KEA), and cation/H+ exchanger (CHX) families. In total, 58 of the 60 RsCPA genes were localized to the nine chromosomes. RNA-seq. data showed that 60 RsCPA genes had various expression levels in the leaves, roots, cortex, cambium, and xylem at different development stages, as well as under different abiotic stresses. RT–qPCR analysis indicated that all nine RsNHXs genes showed up regulated trends after 250 mM NaCl exposure at 3, 6, 12, and 24h. The RsCPA31 (RsNHX1) gene, which might be the most important members of the RsNHX subfamily, exhibited obvious increased expression levels during 24h salt stress treatment. Heterologous over-and inhibited-expression of RsNHX1 in Arabidopsis showed that RsNHX1 had a positive function in salt tolerance. Furthermore, a turnip yellow mosaic virus (TYMV)-induced gene silence (VIGS) system was firstly used to functionally characterize the candidate gene in radish, which showed that plant with the silence of endogenous RsNHX1 was more susceptible to the salt stress. According to our results we provide insights into the complexity of the RsCPA gene family and a valuable resource to explore the potential functions of RsCPA genes in radish.

scholarly journals Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

Rice ◽  
2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Chen Liu ◽  
Kai Chen ◽  
Xiuqin Zhao ◽  
Xiaoqian Wang ◽  
Congcong Shen ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Grain Yield ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Field Conditions ◽  
Genome Wide Association ◽  
Saline Stress ◽  
Rice Breeding ◽  
Genome Wide

Abstract Background Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages. Results Large phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms “biological processes” and “molecular function” with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions. Conclusions Using high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.

scholarly journals Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa (Medicago sativa L.)

2020 ◽  
Vol 21 (9) ◽  
pp. 3361
Author(s):  
Cesar Augusto Medina ◽  
Charles Hawkins ◽  
Xiang-Ping Liu ◽  
Michael Peel ◽  
Long-Xi Yu
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Prediction Models ◽  
Genome Wide Association ◽  
Support Vector ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Allele Dosage ◽  
Mean Square Errors

Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.

scholarly journals RsSOS1 Responding to Salt Stress Might Be Involved in Regulating Salt Tolerance by Maintaining Na+ Homeostasis in Radish (Raphanus sativus L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 458
Author(s):  
Wanting Zhang ◽  
Jingxue Li ◽  
Junhui Dong ◽  
Yan Wang ◽  
Liang Xu ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Functional Characterization ◽  
Vital Role ◽  
Salt Stress Response ◽  
Reading Frame ◽  
Yield And Quality

Radish is a kind of moderately salt-sensitive vegetable. Salt stress seriously decreases the yield and quality of radish. The plasma membrane Na+/H+ antiporter protein Salt Overly Sensitive 1 (SOS1) plays a crucial role in protecting plant cells against salt stress, but the biological function of the RsSOS1 gene in radish remains to be elucidated. In this study, the RsSOS1 gene was isolated from radish genotype ‘NAU-TR17’, and contains an open reading frame of 3414 bp encoding 1137 amino acids. Phylogenetic analysis showed that RsSOS1 had a high homology with BnSOS1, and clustered together with Arabidopsis plasma membrane Na+/H+ antiporter (AtNHX7). The result of subcellular localization indicated that the RsSOS1 was localized in the plasma membrane. Furthermore, RsSOS1 was strongly induced in roots of radish under 150 mmol/L NaCl treatment, and its expression level in salt-tolerant genotypes was significantly higher than that in salt-sensitive ones. In addition, overexpression of RsSOS1 in Arabidopsis could significantly improve the salt tolerance of transgenic plants. Meanwhile, the transformation of RsSOS1△999 could rescue Na+ efflux function of AXT3 yeast. In summary, the plasma membrane Na+/H+ antiporter RsSOS1 plays a vital role in regulating salt-tolerance of radish by controlling Na+ homeostasis. These results provided useful information for further functional characterization of RsSOS1 and facilitate clarifying the molecular mechanism underlying salt stress response in radish.

scholarly journals Generation of New Salt-Tolerant Wheat Lines and Transcriptomic Exploration of the Responsive Genes to Ethylene and Salt Stress

2020 ◽  
Author(s):  
Qian Ma ◽  
Huajian Zhou ◽  
Xinying Sui ◽  
Chunxue Su ◽  
Yanchong Yu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Agricultural Land ◽  
Carotenoid Biosynthesis ◽  
Pcr Analysis ◽  
Salt Tolerant ◽  
Ethylene Response ◽  
The World ◽  
Antenna Proteins ◽  
Wheat Lines

Abstract Background: Wheat (Triticum aestivum L.) is a staple crop in the world, but is only moderately salt tolerant. However, salt stress affects one-fifth of irrigated agricultural land in the world, it is of great importance to cultivate salt-tolerant varieties to improve the global wheat production. Results: In this study, over 90,000 wheat seeds of cultivar ‘Luyuan502’ were mutated by EMS, and 2000 salt-tolerant lines were harvested from salinized field. By analysis of ethylene sensitivity, salt related physiological factors, and preliminary crop yield, 12 salt-tolerant wheat lines with high production were selected among the crop plants. Transcriptome analysis indicated that a large number of the transcripts levels were significantly altered, mainly based on antenna proteins involved in photosynthesis, biosynthesis of secondary metabolites, cyanoamino acid metabolism, carotenoid biosynthesis, thiamine metabolism, and cutin, suberine and wax biosynthesis pathways including CABs, PERs/PODs, BGLUs, CYP707s, and ZEPs. qRT-PCR analysis revealed that the expressions of salt-related genes in the wheat lines were mostly higher than the wild type, and salt stress can significantly increase the expression levels of the ethylene-related genes in the wheat lines. Based on transcriptomic data, nine novel wheat ERFs were identified and analyzed, and it is suggested that they may play important roles in mediation of ethylene response and salt tolerance.Conclusion: Salt-tolerant wheat mutant lines with ethylene insensitivity were obtained from screen of a wheat EMS-mutagenized pool. Transcriptome data showed that the mutant plants exhibit significant alterations in the antenna proteins involved in various biological processes. Expression analysis suggests that ERFs may mediate ethylene response and salt tolerance of the wheat lines.

scholarly journals Overexpression of Grapevine VvIAA18 Gene Enhanced Salt Tolerance in Tobacco

2020 ◽  
Vol 21 (4) ◽  
pp. 1323 ◽  
Author(s):  
Wei Li ◽  
Changxi Dang ◽  
Yuxiu Ye ◽  
Zunxin Wang ◽  
Laibao Hu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Transgenic Plants ◽  
Transgenic Tobacco ◽  
Transcriptional Activation ◽  
Late Embryogenesis Abundant Protein ◽  
Pcr Analysis ◽  
Vitis Vinifera L ◽  
Transgenic Tobacco Plants ◽  
Tobacco Plants

In plants, auxin/indoleacetic acid (Aux/IAA) proteins are transcriptional regulators that regulate developmental process and responses to phytohormones and stress treatments. However, the regulatory functions of the Vitis vinifera L. (grapevine) Aux/IAA transcription factor gene VvIAA18 have not been reported. In this study, the VvIAA18 gene was successfully cloned from grapevine. Subcellular localization analysis in onion epidermal cells indicated that VvIAA18 was localized to the nucleus. Expression analysis in yeast showed that the full length of VvIAA18 exhibited transcriptional activation. Salt tolerance in transgenic tobacco plants and Escherichia. coli was significantly enhanced by VvIAA18 overexpression. Real-time quantitative PCR analysis showed that overexpression of VvIAA18 up-regulated the salt stress-responsive genes, including pyrroline-5-carboxylate synthase (NtP5CS), late embryogenesis abundant protein (NtLEA5), superoxide dismutase (NtSOD), and peroxidase (NtPOD) genes, under salt stress. Enzymatic analyses found that the transgenic plants had higher SOD and POD activities under salt stress. Meanwhile, component analysis showed that the content of proline in transgenic plants increased significantly, while the content of hydrogen peroxide (H2O2) and malondialdehyde (MDA) decreased significantly. Based on the above results, the VvIAA18 gene is related to improving the salt tolerance of transgenic tobacco plants. The VvIAA18 gene has the potential to be applied to enhance plant tolerance to abiotic stress.

scholarly journals Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yanchao Yuan ◽  
Huixian Xing ◽  
Wenguan Zeng ◽  
Jialing Xu ◽  
Lili Mao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Upland Cotton ◽  
Differentially Expressed ◽  
Genome Wide Association ◽  
Rna Seq ◽  
Salt Tolerant ◽  
Genome Wide ◽  
Germination Stage

Abstract Background Salinity is a major abiotic stress seriously hindering crop yield. Development and utilization of tolerant varieties is the most economical way to address soil salinity. Upland cotton is a major fiber crop and pioneer plant on saline soil and thus its genetic architecture underlying salt tolerance should be extensively explored. Results In this study, genome-wide association analysis and RNA sequencing were employed to detect salt-tolerant qualitative-trait loci (QTLs) and candidate genes in 196 upland cotton genotypes at the germination stage. Using comprehensive evaluation values of salt tolerance in four environments, we identified 33 significant single-nucleotide polymorphisms (SNPs), including 17 and 7 SNPs under at least two and four environments, respectively. The 17 stable SNPs were located within or near 98 candidate genes in 13 QTLs, including 35 genes that were functionally annotated to be involved in salt stress responses. RNA-seq analysis indicated that among the 98 candidate genes, 13 were stably differentially expressed. Furthermore, 12 of the 13 candidate genes were verified by qRT-PCR. RNA-seq analysis detected 6640, 3878, and 6462 differentially expressed genes at three sampling time points, of which 869 were shared. Conclusions These results, including the elite cotton accessions with accurate salt tolerance evaluation, the significant SNP markers, the candidate genes, and the salt-tolerant pathways, could improve our understanding of the molecular regulatory mechanisms under salt stress tolerance and genetic manipulation for cotton improvement.

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