Abstract
Egyptian rice landraces represent a unique genetic reservoir shaped by arid environments, yet their genomic and transcriptional response to salt stress remains largely unexplored. Here, we integrated genomic, transcriptomic, and population genetic analyses to systematically unravel the mechanisms of salt tolerance in this vital germplasm. Resequencing 56 Egyptian accessions uncovered a treasure trove of genetic variation, including 18,204 novel SNPs. An expanded GWAS on 258 accessions discovered 17 novel loci for salt tolerance. Parallel RNA-Seq analysis of a salt-tolerant-susceptible pair (Giza 176 vs. 9311) under stress delineated a defense network centered on phenylpropanoid and lipid metabolic pathways in the tolerant genotype. The power of our integrated approach was exemplified by the convergent identification of ONAC063, where GWAS loci, transcriptional responsiveness, and haplotype-phenotype association collectively validated its role. Furthermore, selection sweep analysis highlighted 62 candidate genes under divergent selection. Our study not only positions Egyptian rice as a key resource for allele mining but also establishes a robust multi-omics pipeline for bridging genetic diversity with complex traits, accelerating the discovery of functional genes for breeding climate-resilient crops.
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Claims 5
Claim · model-written summary
Resequencing found 18,204 novel SNPs in Egyptian rice accessions.
- Taxon
- rice
Oryza sativat0 - Outcome
- novel SNPse0
- Value
- 18,204 novel SNPse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Resequencing 56 Egyptian accessions uncovered a treasure trove of genetic variation, including 18,204 novel SNPs.”
t0“Egyptian Rice Germplasm”
Claim · model-written summary
GWAS discovered 17 novel salt-tolerance loci.
- Taxon
- riceOryza sativat0
- Outcome
- novel loci for salt tolerancee0
- Value
- 17 novel locie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“An expanded GWAS on 258 accessions discovered 17 novel loci for salt tolerance.”
t0“Egyptian Rice Germplasm”
Claim · model-written summary
RNA-Seq identified a salt-stress defense network centered on phenylpropanoid and lipid metabolic pathways in the tolerant genotype.
- Taxon
- riceOryza sativat0
- Material
- Giza 176e0
- Outcome
- defense network centered on phenylpropanoid and lipid metabolic pathwayse0
- Comparator
- 9311e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Parallel RNA-Seq analysis of a salt-tolerant-susceptible pair (Giza 176 vs. 9311) under stress delineated a defense network centered on phenylpropanoid and lipid metabolic pathways in the tolerant genotype.”
t0“Egyptian Rice Germplasm”
Claim · model-written summary
Converging GWAS, transcriptional, and haplotype evidence supported a role for ONAC063.
- Taxon
- riceOryza sativat0
- Gene
- ONAC063e0
- Outcome
- validated its rolee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the convergent identification of ONAC063, where GWAS loci, transcriptional responsiveness, and haplotype-phenotype association collectively validated its role”
t0“Egyptian Rice Germplasm”
Claim · model-written summary
Selection sweep analysis highlighted 62 genes under divergent selection.
- Taxon
- riceOryza sativat0
- Outcome
- candidate genes under divergent selectione0
- Value
- 62 candidate genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“selection sweep analysis highlighted 62 candidate genes under divergent selection”
t0“Egyptian Rice Germplasm”