Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies
A tiller number is the key determinant of rice plant architecture and panicle number and consequently controls grain yield. Thus, it is necessary to optimize the tiller number to achieve the maximum yield in rice. However, comprehensive analyses of the genetic basis of the tiller number, considering...
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MDPI AG
2020-12-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/9/12/1695 |
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| author | Shuyu Zhao Su Jang Yoon Kyung Lee Dong-Gwan Kim Zhengxun Jin Hee-Jong Koh |
| author_facet | Shuyu Zhao Su Jang Yoon Kyung Lee Dong-Gwan Kim Zhengxun Jin Hee-Jong Koh |
| author_sort | Shuyu Zhao |
| collection | DOAJ |
| description | A tiller number is the key determinant of rice plant architecture and panicle number and consequently controls grain yield. Thus, it is necessary to optimize the tiller number to achieve the maximum yield in rice. However, comprehensive analyses of the genetic basis of the tiller number, considering the development stage, tiller type, and related traits, are lacking. In this study, we sequence 219 Korean rice accessions and construct a high-quality single nucleotide polymorphism (SNP) dataset. We also evaluate the tiller number at different development stages and heading traits involved in phase transitions. By genome-wide association studies (GWASs), we detected 20 significant association signals for all traits. Five signals were detected in genomic regions near known candidate genes. Most of the candidate genes were involved in the phase transition from vegetative to reproductive growth. In particular, <i>HD1</i> was simultaneously associated with the productive tiller ratio and heading date, indicating that the photoperiodic heading gene directly controls the productive tiller ratio. Multiple linear regression models of lead SNPs showed coefficients of determination (<i>R</i><sup>2</sup>) of 0.49, 0.22, and 0.41 for the tiller number at the maximum tillering stage, productive tiller number, and productive tiller ratio, respectively. Furthermore, the model was validated using independent japonica rice collections, implying that the lead SNPs included in the linear regression model were generally applicable to the tiller number prediction. We revealed the genetic basis of the tiller number in rice plants during growth, By GWASs, and formulated a prediction model by linear regression. Our results improve our understanding of tillering in rice plants and provide a basis for breeding high-yield rice varieties with the optimum the tiller number. |
| first_indexed | 2024-03-10T14:22:04Z |
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| last_indexed | 2024-03-10T14:22:04Z |
| publishDate | 2020-12-01 |
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| record_format | Article |
| series | Plants |
| spelling | doaj.art-198e4369861045f6b62ae256ebc38ff72023-11-20T23:17:34ZengMDPI AGPlants2223-77472020-12-01912169510.3390/plants9121695Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association StudiesShuyu Zhao0Su Jang1Yoon Kyung Lee2Dong-Gwan Kim3Zhengxun Jin4Hee-Jong Koh5Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, KoreaDepartment of Bioindustry and Bioresource Engineering, Department of Molecular Biology and Plant Engineering Research Institute, Sejong University, Seoul 05006, KoreaDepartment of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin 150030, ChinaDepartment of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, KoreaA tiller number is the key determinant of rice plant architecture and panicle number and consequently controls grain yield. Thus, it is necessary to optimize the tiller number to achieve the maximum yield in rice. However, comprehensive analyses of the genetic basis of the tiller number, considering the development stage, tiller type, and related traits, are lacking. In this study, we sequence 219 Korean rice accessions and construct a high-quality single nucleotide polymorphism (SNP) dataset. We also evaluate the tiller number at different development stages and heading traits involved in phase transitions. By genome-wide association studies (GWASs), we detected 20 significant association signals for all traits. Five signals were detected in genomic regions near known candidate genes. Most of the candidate genes were involved in the phase transition from vegetative to reproductive growth. In particular, <i>HD1</i> was simultaneously associated with the productive tiller ratio and heading date, indicating that the photoperiodic heading gene directly controls the productive tiller ratio. Multiple linear regression models of lead SNPs showed coefficients of determination (<i>R</i><sup>2</sup>) of 0.49, 0.22, and 0.41 for the tiller number at the maximum tillering stage, productive tiller number, and productive tiller ratio, respectively. Furthermore, the model was validated using independent japonica rice collections, implying that the lead SNPs included in the linear regression model were generally applicable to the tiller number prediction. We revealed the genetic basis of the tiller number in rice plants during growth, By GWASs, and formulated a prediction model by linear regression. Our results improve our understanding of tillering in rice plants and provide a basis for breeding high-yield rice varieties with the optimum the tiller number.https://www.mdpi.com/2223-7747/9/12/1695rice tilleringtiller numberproductive tiller numberheading datephase transitiongenome-wide association study |
| spellingShingle | Shuyu Zhao Su Jang Yoon Kyung Lee Dong-Gwan Kim Zhengxun Jin Hee-Jong Koh Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies Plants rice tillering tiller number productive tiller number heading date phase transition genome-wide association study |
| title | Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies |
| title_full | Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies |
| title_fullStr | Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies |
| title_full_unstemmed | Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies |
| title_short | Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies |
| title_sort | genetic basis of tiller dynamics of rice revealed by genome wide association studies |
| topic | rice tillering tiller number productive tiller number heading date phase transition genome-wide association study |
| url | https://www.mdpi.com/2223-7747/9/12/1695 |
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