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Reference Detail
| Reference | ||
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| Author | Lv Y., Ma J., Wei H., Xiao F., Wang Y., Jahan N., Hazman M., Qian Q., Shang L., Guo L. | |
| Title | Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of salt tolerance in Rice (<i>Oryza sativa</i> L.). | |
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Abstract: Soil salinity poses a serious threat to the sustainable production of rice (<i>Oryza sativa</i> L.) throughout the world. Thus, the detection of loci and alleles responsible for salt tolerance is fundamental to accelerating the improvement of rice and producing the resilient varieties that will ensure future harvests. In this study, we collected a set of 191 mini-core rice populations from around the world, evaluated their salt tolerance based on plant growth and development phenotypes at the seedling stage, and divided a standard evaluation score (SES) of visual salt injury into five different grades. We used ∼3.82 million single nucleotide polymorphisms (SNPs) to identify 155 significant SNPs and 275 genes associated with salt sensitivity based on a genome-wide association study (GWAS) of SES. In particular, two candidate genes, <i>ZFP179</i> and <i>OsDSR2</i>, were associated with salt tolerance, and <i>OsHKT1;1</i> was co-detected in the entire GWAS of all the panels and <i>indica</i>. Additionally, we investigated the transcriptional changes in cultivars 93-11 and PA64s under normal and salinity stress conditions and found 517 co-upregulated and 223 co-downregulated genes. These differentially expressed genes (DEGs) were highly enriched in "response to chemical" and "stress" based on the gene ontology enrichment analysis. Notably, 30 candidate genes that were associated with the salt tolerance analysis were obtained by integrating GWAS and transcriptomic DEG analyses, including 13 cloned genes that had no reports of tolerance to salt and 17 candidate genes whose functions were unknown. To further explore these genes and their alleles, we performed haplotype analysis, genome-wide domestication detection, and transcriptome analysis to breed improved varieties. This data and the genetic resources provided will be valuable for the development of salt tolerant rice varieties. |
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| Journal | Front Plant Sci | |
| Country | China | |
| Volume | 13 | |
| Pages | 912637 | |
| Year | 2022 | |
| PubMed ID | 35783926 | |
| PubMed Central ID | 9248812 | |
| DOI | 10.3389/fpls.2022.912637 | |
| URL | - | |
| Relation | ||
| Gene | AKT2 CBL8 CBSCLC1 CYP94C2B DHODH1 DSG1 DSR2 EIL1A FBOX396 HKT4 HSP23.7 IDS1 LEA17 LEA8 MPK6 MSRA4 NBL3 PUP4 REP2 RPK1 RS2 SIDP366 SIK2 SLR1 TIFY10C ZFP179 ZFP182 | |
| INSD | - | |
| Strain | Wild Core Collection | - |
| Induced Mutation Lines(NIG Collection) | - | |
| Sterile Seed Strain | - | |
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Lethal Embryo Mutantion Strain |
- | |
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Stages in Each Organ - Muant Lines (Gene) |
- | |
| Cultivated Varieties(NIG Collection) | - | |
| Stages in Each Organ | - | |
