Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Yadav, Ashutosh Kumar; Kumar, Aruna; Grover, Nitasha; Ellur, Ranjith Kumar; Bollinedi, Haritha; Krishnan, Subbaiyan Gopala; Bhowmick, Prolay Kumar; Vinod, K. K.; Nagarajan, M.; Singh, Ashok Kumar

doi:10.3390/plants10030559

Cited by 20 publications

(13 citation statements)

References 83 publications

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“…There are various GWAS applications in rice with unique growth stages and features in saline environments. Recently, GWAS application found 23 Marker–Trait Associations in rice salinity tolerance at early vegetative stage [ 106 ]. Using GWAS, 20 QTN were found, among 6 and 14 associated with salt tolerance at germination and seedling stage, respectively [ 107 ].…”

Section: Omics Platforms Used For Rice Improvementmentioning

confidence: 99%

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Ullah

Abdullah‐Zawawi

Zainal-Abidin

et al. 2022

Plants

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Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

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Section: Omics Platforms Used For Rice Improvementmentioning

confidence: 99%

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Ullah

Abdullah‐Zawawi

Zainal-Abidin

et al. 2022

Plants

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“…GWAS enables high-resolution mapping, utilizing single nucleotide polymorphisms (SNPs) as genetic markers instead of the QTL linkage mapping approach [93]. In the indica subspecies of rice, GWAS has been conducted for agronomic characteristics such as tiller number, grain width, grain length, and spikelet number using single nucleotide polymorphisms (SNPs) discovered by whole-genome sequencing [94]. GWAS has been applied for mapping traits associated with loci responsible for salinity tolerance.…”

Section: Genome-wide Association Study (Gwas) Techniquementioning

confidence: 99%

Advanced Breeding Strategies and Future Perspectives of Salinity Tolerance in Rice

Rafii

Yusoff

et al. 2021

Agronomy

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Rice, generally classified as a typical glycophyte, often faces abiotic stresses such as excessive drought, high salinity, prolonged submergence, cold, and temperature, which significantly affects growth, development, and ultimately, grain yield. Among these negative impacts of abiotic factors in rice production, salinity stress is a major constraint, followed by drought. There is considerable research on the use of marker-assisted selection (MAS), genome editing techniques, and transgenic studies that have profoundly improved the present-day rice breeders’ toolboxes for developing salt-tolerant varieties. Salinity stresses significantly affect rice plants during seedling and reproductive stages. Hence, greater understanding and manipulation of genetic architecture in developing salt-tolerant rice varieties will significantly impact sustainable rice production. Rice plants’ susceptibility or tolerance to high salinity has been reported to be the result of coordinated actions of multiple stress-responsive quantitative trait loci (QTLs)/genes. This paper reviews recent literature, updating the effects of salinity stress on rice plants and germplasm collections and screening for salinity tolerance by different breeding techniques. Mapping and identification of QTLs salt tolerance genes are illuminated. The present review updates recent breeding for improvement in rice tolerance to salinity stress and how state-of-the-art tools such as MAS or genetic engineering and genome editing techniques, including mutagenesis and conventional breeding techniques, can assist in transferring salt-tolerant QTLs genes into elite rice genotypes, accelerating breeding of salt-resistant rice cultivars.

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“…These studies showed that there were some genes expected to be involved in salt resistance in rice, including a nitrate transporter gene OsNRT2.1 [ 97 ], a MADS-box family transcription factor gene OsMADS31 [ 94 ], a sucrose transport protein gene OsSUT1 , a transcript factor gene OsGAMYB , and some function gene s OsCTR3 , OsMYB6 and OsHKT1;4 [ 88 ], etc. With the development of variety resequencing, salt tolerance GWAS has rapidly developed [ 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 ]. GWAS has exploited the natural variation in root architecture remodeling under salt tolerance to uncover the genetic controls underlying plant responses [ 83 , 106 ].…”

Section: Association Analysis Of Rice Salt Tolerancementioning

confidence: 99%

Gene Mapping, Cloning and Association Analysis for Salt Tolerance in Rice

Fan

Jiang

Meng

et al. 2021

IJMS

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Soil salinization caused by the accumulation of sodium can decrease rice yield and quality. Identification of rice salt tolerance genes and their molecular mechanisms could help breeders genetically improve salt tolerance. We studied QTL mapping of populations for rice salt tolerance, period and method of salt tolerance identification, salt tolerance evaluation parameters, identification of salt tolerance QTLs, and fine-mapping and map cloning of salt tolerance QTLs. We discuss our findings as they relate to other genetic studies of salt tolerance association.

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Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Cited by 20 publications

References 83 publications

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Advanced Breeding Strategies and Future Perspectives of Salinity Tolerance in Rice

Gene Mapping, Cloning and Association Analysis for Salt Tolerance in Rice

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