Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice

San Mar Lar, Jeonghwan Seo, Seong-Gyu Jang, Hongjia Zhang, Ah-Rim Lee, Fang-Yuan Cao, Ja-Hong Lee, Na-Eun Kim, Yoonjung Lee, Yong-Jin Park, Joohyun Lee and Soon-Wook Kwon
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San Mar Lar: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
Jeonghwan Seo: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
Seong-Gyu Jang: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
Hongjia Zhang: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
Ah-Rim Lee: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
Fang-Yuan Cao: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
Ja-Hong Lee: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
Na-Eun Kim: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea
Yoonjung Lee: Department of Crop Science, Konkuk University, Seoul 05029, Korea
Yong-Jin Park: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea
Joohyun Lee: Department of Crop Science, Konkuk University, Seoul 05029, Korea
Soon-Wook Kwon: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Korea

Agriculture, 2021, vol. 11, issue 11, 1-17

Abstract: 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( P ) threshold of ≥3.66. The QTL of qSIS2 , showed −log10( P ) = 3.80 and the lead SNP explained 7.87% of total phenotypic variation. The QTL of qSIS4 , showed −log10( P ) = 4.05 and the lead SNP explained 10.53% of total phenotypic variation. The QTL of qSIS8 showed −log10( P ) = 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 ( Os04g0481600 , Os04g0485300 , Os04g0493000 , Os04g0493300 , and Os 08g0390200 ) for salt tolerance in rice seedlings based on the gene expression database and their previously known functions.

Keywords: GWAS; salt-tolerance; Korean landrace rice; candidate gene (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2021
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