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:10.21203/rs.3.rs-15979/v3

Cited by 7 publications

(8 citation statements)

References 53 publications

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“…41 Meta-QTLs related to salt tolerance were collected from Mansuri et al study (Mansuri et al 2020 ) and the genomic positions of these Meta-QTLs were obtained based on the method we previously described (Kong et al 2020 ). Based on location information, Meta-QTLs and identified QTLs were visualized using TBtools (Additional file 2 : Table S1) (Chen et al 2020 ).…”

Section: Methodsmentioning

confidence: 99%

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

Kong

Zhang

et al. 2021

Rice

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Salinity 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.

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Section: Methodsmentioning

confidence: 99%

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

Kong

Zhang

et al. 2021

Rice

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“…Studies on QTL mapping from bi‐parental mapping populations often have very large QTL intervals and are difficult to validate in a large set of germplasms (Mansuri et al, 2020). Most of the QTLs are robust enough to get detected but very difficult to use in breeding programs because of larger confidence intervals (more recombination and difficult to follow) encompassing, more number of molecular markers and more distant from QTL peaks.…”

Section: Discussionmentioning

confidence: 99%

“…For a trait such as salinity which is highly affected by all the underlying traits, the meta‐analysis approach is very much useful, and a thorough meta‐analysis of QTL mapping studies along with gene expression and proteomic studies is a good way to predict, validate, summarize, and refine the genomic locations responsible (Mansuri et al, 2020). In our study, we identified, validated and predicted the candidate genes underlying the MSQTL4.2 , which can be a very useful tool for marker‐assisted introgression in rice breeding.…”

Section: Discussionmentioning

confidence: 99%

“…A genetic map data containing 19,180 SSR markers from the Gramene database (https://archive.gramene.org/markers/) was used as reference map. Meta‐QTLs were predicted individually for each chromosome as per instructions given in the manual and keeping salt tolerance (SalT) as meta‐trait (governed by several component traits) at the seedling and reproductive stage, separately (Mansuri et al, 2020). If the number of QTLs on particular chromosomes are >9, then the “Veyrieras” method was used or else the “Gerber and Goffinet” method was used (Sosnowski et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

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Meta‐analysis and validation of genomic loci governing seedling and reproductive stage salinity tolerance in rice

Prakash

Lokeshkumar

Rathor

et al. 2022

Physiologia Plantarum

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Identification of concurrent genomic regions contributing tolerance to salinity at the seedling and reproductive stages were done using 45 quantitative trait loci (QTL) mapping studies reporting 915 individual QTLs. The QTL-data were used to perform a meta-analysis to predict, validate and analyze the Meta-QTLs governing component traits contributing to salinity tolerance. We predicted a total of 65 and 49 Meta-QTLs distributed across the genome governing seedling and reproductive stage salinity tolerance, respectively. Salinity stress (EC ~10.0 dSm À1 ) was evaluated in a set of 32 genotypes grown hydroponically, from these eight extreme (highly tolerant and highly susceptible) genotypes were selected for validation of significant Meta-QTLs.Another set of eight previously known and reported (highly tolerant and highly susceptible) genotypes were evaluated under saline micro plot conditions (EC ~8.0 dSm À1 ) and used for validation of significant Meta-QTLs for reproductive stage salinity tolerance. The microsatellite marker "RM5635" linked to MSQTL4.2 (~295.43 kb) was able to clearly differentiate contrasting genotypes for seedling stage salinity tolerance, whereas at the reproductive stage, none of the markers were able to validate the predicted Meta-QTL for salinity tolerance. Earlier reported, gene expression studies were used for candidate gene analysis of validated MSQTL4.2, which indicated the down regulation of Os04g0423100, a gene encoding Monooxygenase-FAD binding domain containing protein. The traits associated with this Meta-QTL were root and shoot sodium and potassium concentration and leaf chlorophyll content. The identified and validated genomic region assumes a great significant role in seedling stage salinity tolerance in rice, and it can be used for marker-assisted backcross breeding programs.

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“…Therefore, understanding the mechanisms underlying the trait became a focal point of crop improvement schemes to develop salt-responsive cultivars. Development of molecular/DNA markers and software-enabled genome-wide mapping of markers combined with high throughput statistical tools paved the way for the identification of quantitative trait loci (QTLs) governing quantitate (polygenic) traits [ 61 , 74 ].…”

Section: The Genetic Basis Of Tolerance To Salinity In Plantsmentioning

confidence: 99%

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

Saradadevi

Das

Mangrauthia

et al. 2021

Biology

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Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.

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

Cited by 7 publications

References 53 publications

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

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

Meta‐analysis and validation of genomic loci governing seedling and reproductive stage salinity tolerance in rice

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

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