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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Autores principales: 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, Soon-Wook Kwon
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Publicado: MDPI AG 2021
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Acceso en línea:https://doaj.org/article/a1ed6836e4594e68b3330cb25c569f4f
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spelling oai:doaj.org-article:a1ed6836e4594e68b3330cb25c569f4f2021-11-25T16:02:05ZGenome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice10.3390/agriculture111111742077-0472https://doaj.org/article/a1ed6836e4594e68b3330cb25c569f4f2021-11-01T00:00:00Zhttps://www.mdpi.com/2077-0472/11/11/1174https://doaj.org/toc/2077-0472Salinity 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.San Mar LarJeonghwan SeoSeong-Gyu JangHongjia ZhangAh-Rim LeeFang-Yuan CaoJa-Hong LeeNa-Eun KimYoonjung LeeYong-Jin ParkJoohyun LeeSoon-Wook KwonMDPI AGarticleGWASsalt-toleranceKorean landrace ricecandidate geneAgriculture (General)S1-972ENAgriculture, Vol 11, Iss 1174, p 1174 (2021)
institution DOAJ
collection DOAJ
language EN
topic GWAS
salt-tolerance
Korean landrace rice
candidate gene
Agriculture (General)
S1-972
spellingShingle GWAS
salt-tolerance
Korean landrace rice
candidate gene
Agriculture (General)
S1-972
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
Soon-Wook Kwon
Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice
description 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.
format article
author 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
Soon-Wook Kwon
author_facet 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
Soon-Wook Kwon
author_sort San Mar Lar
title Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice
title_short Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice
title_full Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice
title_fullStr Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice
title_full_unstemmed Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice
title_sort genome-wide association study for detecting salt-tolerance loci and candidate genes in rice
publisher MDPI AG
publishDate 2021
url https://doaj.org/article/a1ed6836e4594e68b3330cb25c569f4f
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