Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice
Salt stress is a major constraint in rice production worldwide. Salt stress is estimated to cause annual losses of 30–50% in rice production. Discovering and deploying salt-resistance genes are the most effective ways to control salt stress. We performed a genome-wide association study (GWAS) to det...
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MDPI AG
2023-03-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/6/1401 |
| _version_ | 1797609361452826624 |
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| author | Tae-Heon Kim Suk-Man Kim |
| author_facet | Tae-Heon Kim Suk-Man Kim |
| author_sort | Tae-Heon Kim |
| collection | DOAJ |
| description | Salt stress is a major constraint in rice production worldwide. Salt stress is estimated to cause annual losses of 30–50% in rice production. Discovering and deploying salt-resistance genes are the most effective ways to control salt stress. We performed a genome-wide association study (GWAS) to detect QTLs related to salt tolerance at the seedling stage using the <i>japonica</i>-multiparent advanced generation intercross (MAGIC) population. Four QTLs (<i>qDTS1-1</i>, <i>qDTS1-2</i>, <i>qDTS2</i>, and <i>qDTS9</i>) associated with salt tolerance were identified on chromosomes 1, 2, and 9. Among these QTLs, a novel QTL, <i>qDTS1-2</i>, was located between flanking SNPs (1354576 and id1028360) on chromosome 1, with the largest −log10(P) value of 5.81 and a total phenotypic variance of 15.2%. RNA-seq analysis revealed that among the seven differentially expressed genes (DEGs) commonly identified in both P6 and JM298 showing salt tolerance, two upregulated genes, <i>Os01g0963600</i> (ASR transcription factor) and <i>Os01g0975300</i> (<i>OsMYB48</i>), related to salt and drought tolerance, were also involved in the target region of <i>qDTS1-2</i>. The results of this study can provide insights into further understanding of salt tolerance mechanisms and developing DNA markers for marker-assisted selection (MAS) breeding to improve the salt tolerance of cultivars in rice breeding programs. |
| first_indexed | 2024-03-11T06:00:24Z |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T06:00:24Z |
| publishDate | 2023-03-01 |
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| series | Plants |
| spelling | doaj.art-8f9a574904fe457d9cea86611397557f2023-11-17T13:23:24ZengMDPI AGPlants2223-77472023-03-01126140110.3390/plants12061401Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in RiceTae-Heon Kim0Suk-Man Kim1Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 41566, Republic of KoreaDepartment of Ecological & Environmental System, Kyungpook National University, Sangju 37224, Republic of KoreaSalt stress is a major constraint in rice production worldwide. Salt stress is estimated to cause annual losses of 30–50% in rice production. Discovering and deploying salt-resistance genes are the most effective ways to control salt stress. We performed a genome-wide association study (GWAS) to detect QTLs related to salt tolerance at the seedling stage using the <i>japonica</i>-multiparent advanced generation intercross (MAGIC) population. Four QTLs (<i>qDTS1-1</i>, <i>qDTS1-2</i>, <i>qDTS2</i>, and <i>qDTS9</i>) associated with salt tolerance were identified on chromosomes 1, 2, and 9. Among these QTLs, a novel QTL, <i>qDTS1-2</i>, was located between flanking SNPs (1354576 and id1028360) on chromosome 1, with the largest −log10(P) value of 5.81 and a total phenotypic variance of 15.2%. RNA-seq analysis revealed that among the seven differentially expressed genes (DEGs) commonly identified in both P6 and JM298 showing salt tolerance, two upregulated genes, <i>Os01g0963600</i> (ASR transcription factor) and <i>Os01g0975300</i> (<i>OsMYB48</i>), related to salt and drought tolerance, were also involved in the target region of <i>qDTS1-2</i>. The results of this study can provide insights into further understanding of salt tolerance mechanisms and developing DNA markers for marker-assisted selection (MAS) breeding to improve the salt tolerance of cultivars in rice breeding programs.https://www.mdpi.com/2223-7747/12/6/1401genome-wide association studyRNA-Seqricesalt stressseedling stage |
| spellingShingle | Tae-Heon Kim Suk-Man Kim Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice Plants genome-wide association study RNA-Seq rice salt stress seedling stage |
| title | Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice |
| title_full | Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice |
| title_fullStr | Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice |
| title_full_unstemmed | Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice |
| title_short | Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice |
| title_sort | identification of candidate genes for salt tolerance at the seedling stage using integrated genome wide association study and transcriptome analysis in rice |
| topic | genome-wide association study RNA-Seq rice salt stress seedling stage |
| url | https://www.mdpi.com/2223-7747/12/6/1401 |
| work_keys_str_mv | AT taeheonkim identificationofcandidategenesforsalttoleranceattheseedlingstageusingintegratedgenomewideassociationstudyandtranscriptomeanalysisinrice AT sukmankim identificationofcandidategenesforsalttoleranceattheseedlingstageusingintegratedgenomewideassociationstudyandtranscriptomeanalysisinrice |