Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (<i>Oryza sativa</i> L.)
Zinc (Zn) is an essential micronutrient for rice, but it is toxic at a high concentration, especially in acid soils. It is yet unknown which genes regulate Zn tolerance in rice. In the present study, a genome-wide association study (GWAS) was performed for Zn tolerance in rice at the seedling stage...
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| Format: | Article |
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MDPI AG
2022-11-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/22/3138 |
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| author | Kaizhen Zhong Lihong Xie Shikai Hu Gaoneng Shao Zhonghua Sheng Guiai Jiao Ling Wang Ying Chen Shaoqing Tang Xiangjin Wei Peng Zhang Peisong Hu |
| author_facet | Kaizhen Zhong Lihong Xie Shikai Hu Gaoneng Shao Zhonghua Sheng Guiai Jiao Ling Wang Ying Chen Shaoqing Tang Xiangjin Wei Peng Zhang Peisong Hu |
| author_sort | Kaizhen Zhong |
| collection | DOAJ |
| description | Zinc (Zn) is an essential micronutrient for rice, but it is toxic at a high concentration, especially in acid soils. It is yet unknown which genes regulate Zn tolerance in rice. In the present study, a genome-wide association study (GWAS) was performed for Zn tolerance in rice at the seedling stage within a rice core collection, named Ting’s core collection, which showed extensive phenotypic variations in Zn toxicity with high-density single-nucleotide polymorphisms (SNPs). A total of 7 and 19 quantitative trait loci (QTL) were detected using root elongation (RE) and relative root elongation (RRE) under high Zn toxicity, respectively. Among them, 24 QTL were novel, and <i>qRRE15</i> was located in the same region where 3 QTL were reported previously. In addition, <i>qRE4</i> and <i>qRRE9</i> were identical. Furthermore, we found eight candidate genes that are involved in abiotic and biotic stress, immunity, cell expansion, and phosphate transport in the loci of <i>qRRE8</i>, <i>qRRE9</i>, and <i>qRRE15</i>. Moreover, four candidate genes, i.e., <i>Os01g0200700</i>, <i>Os06g0621900</i>, <i>Os06g0493600</i>, and <i>Os06g0622700</i>, were verified correlating to Zn tolerance in rice by quantitative real time-PCR (qRT-PCR). Taken together, these results provide significant insight into the genetic basis for Zn toxicity tolerance and tolerant germplasm for developing rice tolerance to Zn toxicity and improving rice production in Zn-contaminated soils. |
| first_indexed | 2024-03-09T18:03:46Z |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T18:03:46Z |
| publishDate | 2022-11-01 |
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| series | Plants |
| spelling | doaj.art-2cb374779a014772abf5f66066fcb1d22023-11-24T09:40:14ZengMDPI AGPlants2223-77472022-11-011122313810.3390/plants11223138Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (<i>Oryza sativa</i> L.)Kaizhen Zhong0Lihong Xie1Shikai Hu2Gaoneng Shao3Zhonghua Sheng4Guiai Jiao5Ling Wang6Ying Chen7Shaoqing Tang8Xiangjin Wei9Peng Zhang10Peisong Hu11College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, ChinaZinc (Zn) is an essential micronutrient for rice, but it is toxic at a high concentration, especially in acid soils. It is yet unknown which genes regulate Zn tolerance in rice. In the present study, a genome-wide association study (GWAS) was performed for Zn tolerance in rice at the seedling stage within a rice core collection, named Ting’s core collection, which showed extensive phenotypic variations in Zn toxicity with high-density single-nucleotide polymorphisms (SNPs). A total of 7 and 19 quantitative trait loci (QTL) were detected using root elongation (RE) and relative root elongation (RRE) under high Zn toxicity, respectively. Among them, 24 QTL were novel, and <i>qRRE15</i> was located in the same region where 3 QTL were reported previously. In addition, <i>qRE4</i> and <i>qRRE9</i> were identical. Furthermore, we found eight candidate genes that are involved in abiotic and biotic stress, immunity, cell expansion, and phosphate transport in the loci of <i>qRRE8</i>, <i>qRRE9</i>, and <i>qRRE15</i>. Moreover, four candidate genes, i.e., <i>Os01g0200700</i>, <i>Os06g0621900</i>, <i>Os06g0493600</i>, and <i>Os06g0622700</i>, were verified correlating to Zn tolerance in rice by quantitative real time-PCR (qRT-PCR). Taken together, these results provide significant insight into the genetic basis for Zn toxicity tolerance and tolerant germplasm for developing rice tolerance to Zn toxicity and improving rice production in Zn-contaminated soils.https://www.mdpi.com/2223-7747/11/22/3138riceTing’s core collectionZn toxicityGWASQTL |
| spellingShingle | Kaizhen Zhong Lihong Xie Shikai Hu Gaoneng Shao Zhonghua Sheng Guiai Jiao Ling Wang Ying Chen Shaoqing Tang Xiangjin Wei Peng Zhang Peisong Hu Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (<i>Oryza sativa</i> L.) Plants rice Ting’s core collection Zn toxicity GWAS QTL |
| title | Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (<i>Oryza sativa</i> L.) |
| title_full | Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (<i>Oryza sativa</i> L.) |
| title_fullStr | Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (<i>Oryza sativa</i> L.) |
| title_full_unstemmed | Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (<i>Oryza sativa</i> L.) |
| title_short | Genome-Wide Association Study of Zinc Toxicity Tolerance within a Rice Core Collection (<i>Oryza sativa</i> L.) |
| title_sort | genome wide association study of zinc toxicity tolerance within a rice core collection i oryza sativa i l |
| topic | rice Ting’s core collection Zn toxicity GWAS QTL |
| url | https://www.mdpi.com/2223-7747/11/22/3138 |
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