scholarly journals Uncovering the Novel QTLs and Candidate Genes of Salt Tolerance in Rice with Linkage Mapping, RTM-GWAS, and RNA-seq

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Weilong Kong ◽  
Chenhao Zhang ◽  
Shengcheng Zhang ◽  
Yalin Qiang ◽  
Yue Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Salt Tolerance ◽  
Stress Tolerance ◽  
Candidate Genes ◽  
Linkage Mapping ◽  
Recombinant Inbred Lines ◽  
Abiotic Stress Tolerance ◽  
Parental Genotype ◽  
Rice Varieties

AbstractSalinity is a major abiotic stress that limits plant growth and crop productivity. Indica rice and japonica rice show significant differences in tolerance to abiotic stress, and it is considered a feasible method to breed progeny with stronger tolerance to abiotic stress by crossing indica and japonica rice. We herein developed a high-generation recombinant inbred lines (RILs) from Luohui 9 (indica) X RPY geng (japonica). Based on the high-density bin map of this RILs population, salt tolerance QTLs controlling final survival rates were analyzed by linkage mapping and RTM-GWAS methods. A total of seven QTLs were identified on chromosome 3, 4, 5, 6, and 8. qST-3.1, qST-5.1, qST-6.1, and qST-6.2 were novel salt tolerance QTLs in this study and their function were functionally verified by comparative analysis of parental genotype RILs. The gene aggregation result of these four new QTLs emphasized that the combination of the four QTL synergistic genotypes can significantly improve the salt stress tolerance of rice. By comparing the transcriptomes of the root tissues of the parents’ seedlings, at 3 days and 7 days after salt treatment, we then achieved fine mapping of QTLs based on differentially expressed genes (DEGs) identification and DEGs annotations, namely, LOC_Os06g01250 in qST-6.1, LOC_Os06g37300 in qST-6.2, LOC_Os05g14880 in qST-5.1. The homologous genes of these candidate genes were involved in abiotic stress tolerance in different plants. These results indicated that LOC_Os05g14880, LOC_Os06g01250, and LOC_Os06g37300 were the candidate genes of qST-5.1, qST-6.1, and qST-6.2. Our finding provided novel salt tolerance-related QTLs, candidate genes, and several RILs with better tolerance, which will facilitate breeding for improved salt tolerance of rice varieties and promote the exploration tolerance mechanisms of rice salt stress.

scholarly journals Overexpression of a Novel ROP Gene from the Banana (MaROP5g) Confers Increased Salt Stress Tolerance

2018 ◽  
Vol 19 (10) ◽  
pp. 3108 ◽  
Author(s):  
Hongxia Miao ◽  
Peiguang Sun ◽  
Juhua Liu ◽  
Jingyi Wang ◽  
Biyu Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Salt Tolerance ◽  
Stress Tolerance ◽  
Abiotic Stress Tolerance ◽  
Survival Rates ◽  
Wild Type ◽  
Ion Distribution ◽  
Membrane Injury ◽  
Primary Roots

Rho-like GTPases from plants (ROPs) are plant-specific molecular switches that are crucial for plant survival when subjected to abiotic stress. We identified and characterized 17 novel ROP proteins from Musa acuminata (MaROPs) using genomic techniques. The identified MaROPs fell into three of the four previously described ROP groups (Groups II–IV), with MaROPs in each group having similar genetic structures and conserved motifs. Our transcriptomic analysis showed that the two banana genotypes tested, Fen Jiao and BaXi Jiao, had similar responses to abiotic stress: Six genes (MaROP-3b, -5a, -5c, -5f, -5g, and -6) were highly expressed in response to cold, salt, and drought stress conditions in both genotypes. Of these, MaROP5g was most highly expressed in response to salt stress. Co-localization experiments showed that the MaROP5g protein was localized at the plasma membrane. When subjected to salt stress, transgenic Arabidopsis thaliana overexpressing MaROP5g had longer primary roots and increased survival rates compared to wild-type A. thaliana. The increased salt tolerance conferred by MaROP5g might be related to reduced membrane injury and the increased cytosolic K+/Na+ ratio and Ca2+ concentration in the transgenic plants as compared to wild-type. The increased expression of salt overly sensitive (SOS)-pathway genes and calcium-signaling pathway genes in MaROP5g-overexpressing A. thaliana reflected the enhanced tolerance to salt stress by the transgenic lines in comparison to wild-type. Collectively, our results suggested that abiotic stress tolerance in banana plants might be regulated by multiple MaROPs, and that MaROP5g might enhance salt tolerance by increasing root length, improving membrane injury and ion distribution.

scholarly journals Enhanced Abiotic Stress Tolerance of Vicia faba L. Plants Heterologously Expressing the PR10a Gene from Potato

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 173
Author(s):  
Abeer F. Desouky ◽  
Ahmed H. Ahmed ◽  
Hartmut Stützel ◽  
Hans-Jörg Jacobsen ◽  
Yi-Chen Pao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Vicia Faba ◽  
Faba Bean ◽  
Abiotic Stress Tolerance ◽  
Wild Type ◽  
Stress Injury ◽  
Bean Plants ◽  
Vicia Faba L

Pathogenesis-related (PR) proteins are known to play relevant roles in plant defense against biotic and abiotic stresses. In the present study, we characterize the response of transgenic faba bean (Vicia faba L.) plants encoding a PR10a gene from potato (Solanum tuberosum L.) to salinity and drought. The transgene was under the mannopine synthetase (pMAS) promoter. PR10a-overexpressing faba bean plants showed better growth than the wild-type plants after 14 days of drought stress and 30 days of salt stress under hydroponic growth conditions. After removing the stress, the PR10a-plants returned to a normal state, while the wild-type plants could not be restored. Most importantly, there was no phenotypic difference between transgenic and non-transgenic faba bean plants under well-watered conditions. Evaluation of physiological parameters during salt stress showed lower Na+-content in the leaves of the transgenic plants, which would reduce the toxic effect. In addition, PR10a-plants were able to maintain vegetative growth and experienced fewer photosystem changes under both stresses and a lower level of osmotic stress injury under salt stress compared to wild-type plants. Taken together, our findings suggest that the PR10a gene from potato plays an important role in abiotic stress tolerance, probably by activation of stress-related physiological processes.

scholarly journals Transcriptome Changes Reveal the Molecular Mechanisms of Humic Acid-Induced Salt Stress Tolerance in Arabidopsis

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 782
Author(s):  
Joon-Yung Cha ◽  
Sang-Ho Kang ◽  
Myung Geun Ji ◽  
Gyeong-Im Shin ◽  
Song Yi Jeong ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Humic Acid ◽  
Stress Tolerance ◽  
Plant Development ◽  
Molecular Mechanisms ◽  
Abiotic Stress Tolerance ◽  
Principal Component ◽  
Salt Stress Tolerance ◽  
Genes Encoding

Humic acid (HA) is a principal component of humic substances, which make up the complex organic matter that broadly exists in soil environments. HA promotes plant development as well as stress tolerance, however the precise molecular mechanism for these is little known. Here we conducted transcriptome analysis to elucidate the molecular mechanisms by which HA enhances salt stress tolerance. Gene Ontology Enrichment Analysis pointed to the involvement of diverse abiotic stress-related genes encoding HEAT-SHOCK PROTEINs and redox proteins, which were up-regulated by HA regardless of salt stress. Genes related to biotic stress and secondary metabolic process were mainly down-regulated by HA. In addition, HA up-regulated genes encoding transcription factors (TFs) involved in plant development as well as abiotic stress tolerance, and down-regulated TF genes involved in secondary metabolic processes. Our transcriptome information provided here provides molecular evidences and improves our understanding of how HA confers tolerance to salinity stress in plants.

scholarly journals Down-Regulation of SlGRAS10 in Tomato Confers Abiotic Stress Tolerance

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 623
Author(s):  
Sidra Habib ◽  
Yee Yee Lwin ◽  
Ning Li
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Plant Growth ◽  
Stress Tolerance ◽  
Abiotic Stresses ◽  
Abiotic Stress Tolerance ◽  
Functional Characterization ◽  
Flavonoid Biosynthesis ◽  
Ros Scavenging ◽  
Down Regulation

Adverse environmental factors like salt stress, drought, and extreme temperatures, cause damage to plant growth, development, and crop yield. GRAS transcription factors (TFs) have numerous functions in biological processes. Some studies have reported that the GRAS protein family plays significant functions in plant growth and development under abiotic stresses. In this study, we demonstrated the functional characterization of a tomato SlGRAS10 gene under abiotic stresses such as salt stress and drought. Down-regulation of SlGRAS10 by RNA interference (RNAi) produced dwarf plants with smaller leaves, internode lengths, and enhanced flavonoid accumulation. We studied the effects of abiotic stresses on RNAi and wild-type (WT) plants. Moreover, SlGRAS10-RNAi plants were more tolerant to abiotic stresses (salt, drought, and Abscisic acid) than the WT plants. Down-regulation of SlGRAS10 significantly enhanced the expressions of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) to reduce the effects of reactive oxygen species (ROS) such as O2− and H2O2. Malondialdehyde (MDA) and proline contents were remarkably high in SlGRAS10-RNAi plants. Furthermore, the expression levels of chlorophyll biosynthesis, flavonoid biosynthesis, and stress-related genes were also enhanced under abiotic stress conditions. Collectively, our conclusions emphasized the significant function of SlGRAS10 as a stress tolerate transcription factor in a certain variety of abiotic stress tolerance by enhancing osmotic potential, flavonoid biosynthesis, and ROS scavenging system in the tomato plant.

scholarly journals Arabidopsis Plastid-RNA Polymerase RPOTp Is Involved in Abiotic Stress Tolerance

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 834
Author(s):  
Abel Lidón-Soto ◽  
Eva Núñez-Delegido ◽  
Iván Pastor-Martínez ◽  
Pedro Robles ◽  
Víctor Quesada
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Rna Polymerase ◽  
Stress Tolerance ◽  
Abiotic Stress Tolerance ◽  
Retrograde Signaling ◽  
Compensatory Mechanism ◽  
Transcript Levels ◽  
Plastid Rna Polymerase

Plastid gene expression (PGE) must adequately respond to changes in both development and environmental cues. The transcriptional machinery of plastids in land plants is far more complex than that of prokaryotes. Two types of DNA-dependent RNA polymerases transcribe the plastid genome: a multimeric plastid-encoded polymerase (PEP), and a monomeric nuclear-encoded polymerase (NEP). A single NEP in monocots (RPOTp, RNA polymerase of the T3/T7 phage-type) and two NEPs in dicots (plastid-targeted RPOTp, and plastid- and mitochondrial-targeted RPOTmp) have been hitherto identified. To unravel the role of PGE in plant responses to abiotic stress, we investigated if Arabidopsis RPOTp could function in plant salt tolerance. To this end, we studied the sensitivity of T-DNA mutants scabra3-2 (sca3-2) and sca3-3, defective in the RPOTp gene, to salinity, osmotic stress and the phytohormone abscisic acid (ABA) required for plants to adapt to abiotic stress. sca3 mutants were hypersensitive to NaCl, mannitol and ABA during germination and seedling establishment. Later in development, sca3 plants displayed reduced sensitivity to salt stress. A gene ontology (GO) analysis of the nuclear genes differentially expressed in the sca3-2 mutant (301) revealed that many significantly enriched GO terms were related to chloroplast function, and also to the response to several abiotic stresses. By quantitative RT-PCR (qRT-PCR), we found that genes LHCB1 (LIGHT-HARVESTING CHLOROPHYLL a/b-BINDING1) and AOX1A (ALTERNATIVE OXIDASE 1A) were respectively down- and up-regulated in the Columbia-0 (Col-0) salt-stressed plants, which suggests the activation of plastid and mitochondria-to-nucleus retrograde signaling. The transcript levels of genes RPOTp, RPOTmp and RPOTm significantly increased in these salt-stressed seedlings, but this enhanced expression did not lead to the up-regulation of the plastid genes solely transcribed by NEP. Similar to salinity, carotenoid inhibitor norflurazon (NF) also enhanced the RPOTp transcript levels in Col-0 seedlings. This shows that besides salinity, inhibition of chloroplast biogenesis also induces RPOTp expression. Unlike salt and NF, the NEP genes were significantly down-regulated in the Col-0 seedlings grown in ABA-supplemented media. Together, our findings demonstrate that RPOTp functions in abiotic stress tolerance, and RPOTp is likely regulated positively by plastid-to-nucleus retrograde signaling, which is triggered when chloroplast functionality is perturbed by environmental stresses, e.g., salinity or NF. This suggests the existence of a compensatory mechanism, elicited by impaired chloroplast function. To our knowledge, this is the first study to suggest the role of a nuclear-encoded plastid-RNA polymerase in salt stress tolerance in plants.

scholarly journals De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rasmita Rani Das ◽  
Seema Pradhan ◽  
Ajay Parida
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Differentially Expressed Genes ◽  
Salinity Stress ◽  
Abiotic Stress Tolerance ◽  
Differentially Expressed ◽  
Little Millet ◽  
Drought And Salt Stress

AbstractScreening the transcriptome of drought tolerant variety of little millet (Panicum sumatrense), a marginally cultivated, nutritionally rich, susbsistent crop, can identify genes responsible for its hardiness and enable identification of new sources of genetic variation which can be used for crop improvement. RNA-Seq generated ~ 230 million reads from control and treated tissues, which were assembled into 86,614 unigenes. In silico differential gene expression analysis created an overview of patterns of gene expression during exposure to drought and salt stress. Separate gene expression profiles for leaf and root tissue revealed the differences in regulatory mechanisms operating in these tissues during exposure to abiotic stress. Several transcription factors were identified and studied for differential expression. 61 differentially expressed genes were found to be common to both tissues under drought and salinity stress and were further validated using qRT-PCR. Transcriptome of P. sumatrense was also used to mine for genic SSR markers relevant to abiotic stress tolerance. This study is first report on a detailed analysis of molecular mechanisms of drought and salinity stress tolerance in a little millet variety. Resources generated in this study can be used as potential candidates for further characterization and to improve abiotic stress tolerance in food crops.

scholarly journals QTL mapping and candidate gene identification in rice using a Kalarata-Azucena population under salt stress

2020 ◽  
Author(s):  
Marjorie P. de Ocampo ◽  
Ho Viet The ◽  
Michael J. Thomson ◽  
Shiro Mitsuya ◽  
Akira Yamauchi ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Gene ◽  
Candidate Genes ◽  
Evaluation System ◽  
Average Distance ◽  
Chlorophyll Concentration ◽  
Interval Mapping ◽  
Chromosome 1 ◽  
Rice Varieties

Abstract Background Salt stress is a major constraint across large rice production areas in Asia, because of the high sensitivity of modern rice varieties. To identify quantitative trait loci (QTL) associated with salt tolerance in rice, we developed an F2 population from a cross between the salt-tolerant landrace, Kalarata, and the salt-sensitive parent, Azucena. An F2 population was used for DNA extraction, and F2:3 families from this population were screened in a phytotron in a saline nutrient solution at the seedling stage. Results After 2 weeks at an EC of 12 dS m− 1, the F2:3 families were scored for salt tolerance using IRRI’s Standard evaluation system (SES). Growth, biomass, Na+ and K+ concentrations in leaf tissues, and chlorophyll concentration were determined. A genetic linkage map was constructed with 151 SSRs and InDel markers, which cover 1463 cM with an average distance of 9.69 cM between loci. A total of 13 QTL were identified using Composite Interval Mapping for 16 traits. The short arm of chromosome 1 had the highest density of QTL associated with salt tolerance, which coincides with the Saltol locus; emphasizing the importance of this locus for candidate gene discovery and for use in rice breeding. Several novel QTL were identified on other chromosomes. Conclusions The novel QTL identified in this study constitute future targets for molecular breeding, to combine them with other QTLs identified before, for higher and stable performance of rice varieties in salt affected soils. Candidate genes for the large effect QTL on chromosome 3 were found to be involved in diverse biological processes, cellular components, and molecular functions. Several candidate genes in this locus were functionally associated with salt stress tolerance and should further be considered for genetic improvement of rice varieties.

scholarly journals Ectopic overexpression of abiotic stress-induced rice annexin, OsAnn5 potentiates tolerance to abiotic stresses

2019 ◽  
Author(s):  
Prasanna Boyidi ◽  
Trishla Vikas Shalibhadra ◽  
Halidev Krishna Botta ◽  
Deepanker Yadav ◽  
Pulugurtha Bharadwaja Kirti
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Abiotic Stress Tolerance ◽  
Peripheral Region ◽  
Upstream Region ◽  
Synthesis Inhibitor ◽  
Post Translational Modifications ◽  
Over Expression ◽  
Onion Epidermal Cells

AbstractThe current study on putative rice annexin OsAnn5 was tried to know its functional role in the abiotic stress tolerance. For this an in silico analysis of its protein sequence and upstream region was carried out. This results in identification of several probable potential sites for post-translational modifications and cis-elements respectively. We have studied the effect of OsAnn5 in the amelioration of abiotic stress tolerance through heterologous expression in transgenic tobacco and E.coli. It is observed that OsAnn5 over expression leads to enhanced tolerance to abiotic stress through efficient scavenging of the ROS and balanced expression of SOD and CAT antioxidant enzymes in both the systems, under stress treatments. Fluorescent signal for transiently expressed EGFP:OsANN5 fusion protein was localized in the peripheral region of the onion epidermal cells under salt stress treatment. Expression analysis of OsAnn5 under ABA synthesis inhibitor, fluridone and salinity stress revealed that OsAnn5 appears to act through an ABA-independent pathway under salt stress and in support to this 35S:OsAnn5 transgenics seedlings exhibited less sensitivity to externally applied ABA.

scholarly journals Meta-analysis of the effect of expression of MYB transcription factor genes on abiotic stress

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11268
Author(s):  
Zhaolan Han ◽  
Xiaowen Shang ◽  
Lingxia Shao ◽  
Ya Wang ◽  
Xujun Zhu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Abiotic Stress Tolerance ◽  
Meta Analysis ◽  
Plant Performance ◽  
Myb Transcription Factor ◽  
Published Data ◽  
Experimental Conditions ◽  
Donor Type

Background MYB proteins are a large group of transcription factors. The overexpression of MYB genes has been reported to improve abiotic stress tolerance in plant. However, due to the variety of plant species studied and the types of gene donors/recipients, along with different experimental conditions, it is difficult to interpret the roles of MYB in abiotic stress tolerance from published data. Methods Using meta-analysis approach, we investigated the plant characteristics involved in cold, drought, and salt stress in MYB-overexpressing plants and analyzed the degrees of influence on plant performance by experimental variables. Results The results show that two of the four measured plant parameters in cold-stressed plants, two of the six in drought-stressed, and four of the 13 in salt-stressed were significantly impacted by MYB overexpression by 22% or more, and the treatment medium, donor/recipient species, and donor type significantly influence the effects of MYB-overexpression on drought stress tolerance. Also, the donor/recipient species, donor type, and stress duration all significantly affected the extent of MYB-mediated salt stress tolerance. In summary, this study compiles and analyzes the data across studies to help us understand the complex interactions that dictate the efficacy of heterologous MYB expression designed for improved abiotic stress tolerance in plants.

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