Uncovering genetic determinants of antioxidant properties in Thai landrace rice through genome-wide association analysis
Abstract Pigmented rice (Oryza sativa L.) is recognized as a source of natural antioxidant compounds, such as flavonoids, oryzanol, tocopherol, and anthocyanin. Because of their nutritional benefits, anthocyanin-enriched or pigmented rice varieties are feasible alternatives for promoting human healt...
| Autori principali: | , , , , , , , , , , , |
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| Natura: | Articolo |
| Lingua: | English |
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Nature Portfolio
2025-01-01
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| Serie: | Scientific Reports |
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| Accesso online: | https://doi.org/10.1038/s41598-024-83926-y |
| _version_ | 1826879563065458688 |
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| author | Putut Rakhmad Purnama Pipob Suwanchaikasem Supaporn Junbuathong Somsong Chotechuen Peerapon Moung-Ngam Waraluk Kasettranan Chanita Paliyavuth Monnat Pongpanich Sittiruk Roytrakul Luca Comai Teerapong Buaboocha Supachitra Chadchawan |
| author_facet | Putut Rakhmad Purnama Pipob Suwanchaikasem Supaporn Junbuathong Somsong Chotechuen Peerapon Moung-Ngam Waraluk Kasettranan Chanita Paliyavuth Monnat Pongpanich Sittiruk Roytrakul Luca Comai Teerapong Buaboocha Supachitra Chadchawan |
| author_sort | Putut Rakhmad Purnama |
| collection | DOAJ |
| description | Abstract Pigmented rice (Oryza sativa L.) is recognized as a source of natural antioxidant compounds, such as flavonoids, oryzanol, tocopherol, and anthocyanin. Because of their nutritional benefits, anthocyanin-enriched or pigmented rice varieties are feasible alternatives for promoting human health. Pigment biosynthesis in rice is a complex process that involves multiple biosynthetic and regulatory genes. This study aimed to identify the genes associated with antioxidant traits in local Thai rice and develop molecular markers for breeding programs. Single nucleotide polymorphisms (SNPs) in 233 rice cultivars, 119,541 SNPs from the promoters, and the first 5 exons of all genes were associated with antioxidant phenotypes determined using 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid), 2,2-diphenyl-1-picrylhydrazyl, ferric reducing antioxidant power, total flavonoid content, and total phenolic content assays through a mixed linear model (MLM) genome-wide association study (GWAS). GWAS analysis detected 336 quantitative trait nucleotides located at 93 loci, 83% of which were consistently mapped to the reported quantitative trait loci of antioxidant traits. Ten loci, including the OsRc gene, were consistently co-associated with all phenotypic traits. Two genetic markers for polymerase chain reaction detection were developed for the OsTT8 gene and the OsRc promoter, both of which were positively correlated with antioxidant properties. These markers can be applied for antioxidant trait selection in rice breeding programs. |
| first_indexed | 2025-02-17T02:00:35Z |
| format | Article |
| id | doaj.art-bccb9fe35e204d31bb2fce7e4ee111e5 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2025-02-17T02:00:35Z |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-bccb9fe35e204d31bb2fce7e4ee111e52025-01-12T12:14:30ZengNature PortfolioScientific Reports2045-23222025-01-0115111710.1038/s41598-024-83926-yUncovering genetic determinants of antioxidant properties in Thai landrace rice through genome-wide association analysisPutut Rakhmad Purnama0Pipob Suwanchaikasem1Supaporn Junbuathong2Somsong Chotechuen3Peerapon Moung-Ngam4Waraluk Kasettranan5Chanita Paliyavuth6Monnat Pongpanich7Sittiruk Roytrakul8Luca Comai9Teerapong Buaboocha10Supachitra Chadchawan11Bioinformatics and Computational Biology Program, Graduate School, Chulalongkorn UniversityCenter of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn UniversityPathum Thani Rice Research CenterDivision of Rice Research and Development, Rice DepartmentPathum Thani Rice Research CenterDepartment of Botany, Faculty of Science, Chulalongkorn UniversityDepartment of Botany, Faculty of Science, Chulalongkorn UniversityDepartment of Mathematics and Computer Science, Faculty of Science, Chulalongkorn UniversityGenome Technology Research Unit, Proteomics Research Laboratory National Science and Technology Development Agency Department of Plant Biology and Genome Center, University of California DavisCenter of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn UniversityCenter of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn UniversityAbstract Pigmented rice (Oryza sativa L.) is recognized as a source of natural antioxidant compounds, such as flavonoids, oryzanol, tocopherol, and anthocyanin. Because of their nutritional benefits, anthocyanin-enriched or pigmented rice varieties are feasible alternatives for promoting human health. Pigment biosynthesis in rice is a complex process that involves multiple biosynthetic and regulatory genes. This study aimed to identify the genes associated with antioxidant traits in local Thai rice and develop molecular markers for breeding programs. Single nucleotide polymorphisms (SNPs) in 233 rice cultivars, 119,541 SNPs from the promoters, and the first 5 exons of all genes were associated with antioxidant phenotypes determined using 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid), 2,2-diphenyl-1-picrylhydrazyl, ferric reducing antioxidant power, total flavonoid content, and total phenolic content assays through a mixed linear model (MLM) genome-wide association study (GWAS). GWAS analysis detected 336 quantitative trait nucleotides located at 93 loci, 83% of which were consistently mapped to the reported quantitative trait loci of antioxidant traits. Ten loci, including the OsRc gene, were consistently co-associated with all phenotypic traits. Two genetic markers for polymerase chain reaction detection were developed for the OsTT8 gene and the OsRc promoter, both of which were positively correlated with antioxidant properties. These markers can be applied for antioxidant trait selection in rice breeding programs.https://doi.org/10.1038/s41598-024-83926-yAnthocyaninsGenetic markerLociProanthocyanidinsQTNs |
| spellingShingle | Putut Rakhmad Purnama Pipob Suwanchaikasem Supaporn Junbuathong Somsong Chotechuen Peerapon Moung-Ngam Waraluk Kasettranan Chanita Paliyavuth Monnat Pongpanich Sittiruk Roytrakul Luca Comai Teerapong Buaboocha Supachitra Chadchawan Uncovering genetic determinants of antioxidant properties in Thai landrace rice through genome-wide association analysis Scientific Reports Anthocyanins Genetic marker Loci Proanthocyanidins QTNs |
| title | Uncovering genetic determinants of antioxidant properties in Thai landrace rice through genome-wide association analysis |
| title_full | Uncovering genetic determinants of antioxidant properties in Thai landrace rice through genome-wide association analysis |
| title_fullStr | Uncovering genetic determinants of antioxidant properties in Thai landrace rice through genome-wide association analysis |
| title_full_unstemmed | Uncovering genetic determinants of antioxidant properties in Thai landrace rice through genome-wide association analysis |
| title_short | Uncovering genetic determinants of antioxidant properties in Thai landrace rice through genome-wide association analysis |
| title_sort | uncovering genetic determinants of antioxidant properties in thai landrace rice through genome wide association analysis |
| topic | Anthocyanins Genetic marker Loci Proanthocyanidins QTNs |
| url | https://doi.org/10.1038/s41598-024-83926-y |
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