Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis
Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline–alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root leng...
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MDPI AG
2023-05-01
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| author | Rui Wang Zhenzhen Zhou Mengyuan Xiong Mingyu Du Xingxing Lin Cuiping Liu Mingwei Lu Zhengbo Liu Yinping Chang Erbao Liu |
| author_facet | Rui Wang Zhenzhen Zhou Mengyuan Xiong Mingyu Du Xingxing Lin Cuiping Liu Mingwei Lu Zhengbo Liu Yinping Chang Erbao Liu |
| author_sort | Rui Wang |
| collection | DOAJ |
| description | Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline–alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR (<i>qGPR2</i>) and SLR (<i>qSLR9</i>), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: <i>LOC_Os02g40664, LOC_Os02g40810</i>, and <i>LOC_Os09g28310</i>. At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties. |
| first_indexed | 2024-03-11T02:59:58Z |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T02:59:58Z |
| publishDate | 2023-05-01 |
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| series | Plants |
| spelling | doaj.art-b1eaad4c4b23440bb25b2c759ccc4cac2023-11-18T08:24:12ZengMDPI AGPlants2223-77472023-05-011211216310.3390/plants12112163Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association AnalysisRui Wang0Zhenzhen Zhou1Mengyuan Xiong2Mingyu Du3Xingxing Lin4Cuiping Liu5Mingwei Lu6Zhengbo Liu7Yinping Chang8Erbao Liu9College of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei 230036, ChinaMining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline–alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR (<i>qGPR2</i>) and SLR (<i>qSLR9</i>), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: <i>LOC_Os02g40664, LOC_Os02g40810</i>, and <i>LOC_Os09g28310</i>. At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties.https://www.mdpi.com/2223-7747/12/11/2163ricegermination stagesalt toleranceSNP locigenome-wide association analysis |
| spellingShingle | Rui Wang Zhenzhen Zhou Mengyuan Xiong Mingyu Du Xingxing Lin Cuiping Liu Mingwei Lu Zhengbo Liu Yinping Chang Erbao Liu Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis Plants rice germination stage salt tolerance SNP loci genome-wide association analysis |
| title | Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis |
| title_full | Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis |
| title_fullStr | Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis |
| title_full_unstemmed | Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis |
| title_short | Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis |
| title_sort | mining salt tolerance snp loci and prediction of candidate genes in the rice bud stage by genome wide association analysis |
| topic | rice germination stage salt tolerance SNP loci genome-wide association analysis |
| url | https://www.mdpi.com/2223-7747/12/11/2163 |
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