Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice
Salinity is one of the major constraints causing soil problems and is considered a limitation to increased rice production in rice-growing countries. This genome-wide association study (GWAS) experiment was conducted to understand the genetic basis of salt tolerance at the seedling stage in Korean r...
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| Auteurs principaux: | , , , , , , , , , , , |
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| Format: | article |
| Langue: | EN |
| Publié: |
MDPI AG
2021
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| Sujets: | |
| Accès en ligne: | https://doaj.org/article/a1ed6836e4594e68b3330cb25c569f4f |
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| Résumé: | Salinity is one of the major constraints causing soil problems and is considered a limitation to increased rice production in rice-growing countries. This genome-wide association study (GWAS) experiment was conducted to understand the genetic basis of salt tolerance at the seedling stage in Korean rice. After 10 days of salt stress treatment, salt tolerance was evaluated with a standard evaluation system using a visual salt injury score. With 191 Korean landrace accessions and their genotypes, including 266,040 single-nucleotide polymorphisms (SNPs), using a KNU Axiom Oryza 580K Genotyping Array, GWAS was conducted to detect three QTLs with significant SNPs with a −log10(<i>P</i>) threshold of ≥3.66. The QTL of <i>qSIS2</i>, showed −log10(<i>P</i>) = 3.80 and the lead SNP explained 7.87% of total phenotypic variation. The QTL of <i>qSIS4</i>, showed −log10(<i>P</i>) = 4.05 and the lead SNP explained 10.53% of total phenotypic variation. The QTL of <i>qSIS8</i> showed −log10(<i>P</i>) = 3.78 and the lead SNP explained 7.83% of total phenotypic variation. Among the annotated genes located in these three QTL regions, five genes were selected as candidates (<i>Os04g0481600</i>, <i>Os04g0485300</i>, <i>Os04g0493000</i>, <i>Os04g0493300</i>, and <i>Os</i><i>08g0390200</i>) for salt tolerance in rice seedlings based on the gene expression database and their previously known functions. |
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