Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

Mansuri, Raheleh Mirdar; Shobbar, Zahra‐Sadat; Jelodar, Nadali Babaeian; Ghaffari, Mohammad Reza; Mohammadi, Seyed Mahdi; Daryani, Parisa

doi:10.1186/s12870-020-02679-8

Cited by 42 publications

(30 citation statements)

References 73 publications

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“…Among them, 20 genes localized in the QTL hotspot regions for yield and ion homeostasis are promising potential candidates for enhancing salt tolerance in rice and are validated for differential gene expression using qRT-PCR. Our results are in broad agreement with those of Mirdar-Mansuri et al (2020) for the families of candidate genes detected in meta-QTL. These potential candidate genes are listed in Online Resource 3 and include pectinesterase, peroxidase, oxidoreductase of the aldo/keto reductase family, inorganic phosphate transporter, transcription regulators and OsHKT1.…”

Section: Candidate Genes Associated With Salinity Tolerancesupporting

confidence: 89%

“…In addition, these meta-QTL regions also possess candidate genes related to a wide range of functions including stress signaling and sensing pathways, genes coding integral membrane components, cell wall organization (wall-associated kinases), serine/threonine (Ser/Thr) kinases, pectinesterases, osmotic adjustment (chitinases, hydrolases), transcription factors regulating stress specific genes, ion homeostasis (Na + and K + transporters and vacuolar Na + /H + exchangers) and other related genes. Some of the candidate genes present in these hotspot regions have been validated (Islam et al 2019;Mirdar-Mansuri et al 2020), while other needs to be validated for their tolerance in different genetic backgrounds. In addition to these QTL hotspots, there are several genomic regions with 5-10 traits associated with salinity tolerance.…”

Section: Qtl Hotspots For Introgression Of Salinity Tolerance In Ricementioning

confidence: 99%

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Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age

2021

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Key message Reproductive stage salinity tolerance is most critical for rice as it determines the yield under stress. Few studies have been undertaken for this trait as phenotyping was cumbersome, but new methodology outlined in this review seeks to redress this deficiency. Sixty-three meta-QTLs, the most important genomic regions to target for enhancing salinity tolerance, are reported. Abstract Although rice has been categorized as a salt-sensitive crop, it is not equally affected throughout its growth, being most sensitive at the seedling and reproductive stages. However, a very poor correlation exists between sensitivity at these two stages, which suggests that the effects of salt are determined by different mechanisms and sets of genes (QTLs) in seedlings and during flowering. Although tolerance at the reproductive stage is arguably the more important, as it translates directly into grain yield, more than 90% of publications on the effects of salinity on rice are limited to the seedling stage. Only a few studies have been conducted on tolerance at the reproductive stage, as phenotyping is cumbersome. In this review, we list the varieties of rice released for salinity tolerance traits, those being commercially cultivated in salt-affected soils and summarize phenotyping methodologies. Since further increases in tolerance are needed to maintain future productivity, we highlight work on phenotyping for salinity tolerance at the reproductive stage. We have constructed an exhaustive list of the 935 reported QTLs for salinity tolerance in rice at the seedling and reproductive stages. We illustrate the chromosome locations of 63 meta-QTLs (with 95% confidence interval) that indicate the most important genomic regions for salt tolerance in rice. Further study of these QTLs should enhance our understanding of salt tolerance in rice and, if targeted, will have the highest probability of success for marker-assisted selections.

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Section: Candidate Genes Associated With Salinity Tolerancesupporting

confidence: 89%

Section: Qtl Hotspots For Introgression Of Salinity Tolerance In Ricementioning

confidence: 99%

Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age

2021

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“…The salt stress tolerance of rice is related to the genotype, and different genotypes show discrepant salt stress tolerance (Ganie et al, 2016;Mansuri et al, 2019). Hundreds of salt stress-related QTLs have been identified among different rice populations to date (Kong et al, 2019b;Mansuri et al, 2020). However, only four salt stress-related genes have been cloned and experimentally verified in rice, namely, SKC1 (Lin et al, 2004;Hauser and Horie, 2010), HST1 (Takagi et al, 2015), OsHAK21 (He et al, 2019), and OsSTLK (Lin et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…11 salt stress-related Meta-QTLs were reported via integrating QTL information from 12 studies (Islam et al, 2019). Recently, Mansuri et al (2020) identified 46 Meta-QTLs of salt stress-related traits, including salinity tolerance score, shoot potassium concentration, shoot sodium concentration, chlorophyll content, shoot dry weight trait, etc., (Mansuri et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Analysis Reveals the Mechanisms Underlying Differences in Salt Tolerance Between indica and japonica Rice at Seedling Stage

et al. 2021

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Screening and breeding more salt-tolerant varieties is an effective way to deal with the global reduction in rice (Oryza sativa L.) yield caused by salt stress. However, the molecular mechanism underlying differences in salt tolerance between varieties, especially between the subspecies, is still unclear. We herein performed a comparative transcriptomic analysis under salt stress in contrasting two rice genotypes, namely RPY geng (japonica, tolerant variety) and Luohui 9 (named as Chao 2R in this study, indica, susceptible variety). 7208 and 3874 differentially expressed genes (DEGs) were identified under salt stress in Chao 2R and RPY geng, separately. Of them, 2714 DEGs were co-expressed in both genotypes, while 4494 and 1190 DEGs were specifically up/down-regulated in Chao 2R and RPY geng, respectively. Gene ontology (GO) analysis results provided a more reasonable explanation for the salt tolerance difference between the two genotypes. The expression of normal life process genes in Chao 2R were severely affected under salt stress, but RPY geng regulated the expression of multiple stress-related genes to adapt to the same intensity of salt stress, such as secondary metabolic process (GO:0019748), oxidation-reduction process (GO:0009067), etc. Furthermore, we highlighted important pathways and transcription factors (TFs) related to salt tolerance in RPY geng specific DEGs sets based on MapMan annotation and TF identification. Through Meta-QTLs mapping and homologous analysis, we screened out 18 salt stress-related candidate genes (RPY geng specific DEGs) in 15 Meta-QTLs. Our findings not only offer new insights into the difference in salt stress tolerance between the rice subspecies but also provide critical target genes to facilitate gene editing to enhance salt stress tolerance in rice.

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“…In addition, these meta-QTL regions also possess candidate genes related to a wide range of functions including stress signaling and sensing pathways, genes coding integral membrane components, cell wall organization (Wall Associated Kinases), Serine/Threonine (Ser/Thr) kinases, pectinesterases, osmotic adjustment (chitinases, hydrolases), transcription factors regulating stress speci c genes, ion homeostasis (Na + and K + transporters and vacuolar Na + /H + exchangers) and other related genes. Some of the candidate genes present in these hotspot regions have been validated (Islam et al 2019;Mirdar Mansuri, 2020), while other needs to be validated for their tolerance in different genetic backgrounds. In addition to these QTL hotspots, there are several genomic regions with 5-10 traits associated with salinity tolerance.…”

Section: Qtl Hotspots For Introgression Of Salinity Tolerance In Ricementioning

confidence: 99%

Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age

Singh

Kota

Flowers

2021

Preprint

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Although rice has been categorized as a salt-sensitive crop, it is not equally affected throughout its growth, being most sensitive at the seedling and reproductive stages. However, a very poor correlation exists between sensitivity at these two stages, which suggests that the effects of salt are determined by different mechanisms and sets of genes (QTLs) in seedlings and during flowering. Although tolerance at the reproductive stage is arguably the more important, as it translates directly into grain yield, more than 90% of publications on the effects of salinity on rice are limited to the seedling stage. Only a few studies have been conducted on tolerance at the reproductive stage, as phenotyping is cumbersome. In this review, we list the varieties of rice released for salinity tolerance traits, those being commercially cultivated in salt-affected soils and summarise phenotyping methodologies. Since further increases in tolerance are needed to maintain future productivity, we highlight work on phenotyping for salinity tolerance at the reproductive stage. We have constructed an exhaustive list of the 935 reported QTLs for salinity tolerance in rice at the seedling and reproductive stages. We illustrate the chromosome locations of 63 meta-QTLs (with 95% confidence interval) that indicate the most important genomic regions for salt tolerance in rice. Further study of these QTLs should enhance our understanding of salt tolerance in rice and, if targeted, will have the highest probability of success for marker assisted selections.

show abstract

Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

Cited by 42 publications

References 73 publications

Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age

Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age

Comparative Transcriptome Analysis Reveals the Mechanisms Underlying Differences in Salt Tolerance Between indica and japonica Rice at Seedling Stage

Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age

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