Abstract
BACKGROUND: Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages. RESULTS: Large phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms "biological processes" and "molecular function" with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions. CONCLUSIONS: Using high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.
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Claims 7
Claim · model-written summary
The 708 rice accessions showed large phenotypic variation.
- Taxon
- rice
Oryza sativae0 - Material
- 708 rice accessionse0
- Outcome
- phenotypic variationse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Large phenotypic variations were observed in 708 rice accessions”
Claim · model-written summary
Salt stress considerably limited rice yield and related traits.
- Taxon
- rice plantsOryza sativat0
- Treatment
- salt stresse0
- Outcome
- yield and its related traitse0
- Direction
- considerably limitede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“yield and its related traits were considerably limited when exposed to salt stress”
t0“rice plants”
Claim · model-written summary
GWAS detected 2255 marker-trait association signals and significant SNPs in 903 genes.
- Taxon
- rice plantsOryza sativat0
- Outcome
- marker-trait association signalse0
- Value
- 2255e0
- Qualifier
- 903 genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes”
t0“rice plants”
Claim · model-written summary
Forty-three genes shared functional annotations with known salt-responsive rice genes.
- Taxon
- riceOryza sativae0
- Outcome
- same functional annotatione0
- Value
- 43 genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“43 genes processed same functional annotation, and the gene ontology terms "biological processes" and "molecular function" with the known genes responsive to salt stress in rice”
Claim · model-written summary
Haplotype analysis identified 15 candidate genes associated with target traits, including five known and 10 novel genes.
- Taxon
- rice plantsOryza sativat0
- Gene
- 15 promising candidatese0
- Outcome
- target traitse0
- Value
- five known genes and 10 novel genese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes”
t0“rice plants”
Claim · model-written summary
Seven accessions with favorable haplotypes of four grain-yield-associated genes performed well under salinity.
- Taxon
- rice plantsOryza sativat0
- Material
- seven accessionse0
- Outcome
- performed well under saline stress conditionse0
- Value
- four genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions”
t0“rice plants”
Claim · model-written summary
Five known and two new genes were significantly associated with grain yield and related traits under saline stress.
- Taxon
- rice plantsOryza sativat0
- Gene
- OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1e0
- Outcome
- grain yield and its related traitse0
- Qualifier
- under saline stress conditionse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions”
t0“rice plants”
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salinity · yield · Oryza sativa (rice)Positive and negative results
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