Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri population
Grain appearance is one of the most important attributes of rice. It is determined by grain size, shape, and weight, which in turn influences the rice yield and market value. In this study, QTLs for grain length, grain width, grain length/width ratio, and grain weight were mapped using the high-thro...
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| Format: | Article |
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Frontiers Media S.A.
2022-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.955347/full |
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| author | Kashif Aslam Kashif Aslam Shahzad Amir Naveed Shahzad Amir Naveed Muhammad Sabar Ghulam Shabir Shahid Masood Shah Abdul Rehman Khan Muhammad Musaddiq Shah Sajid Fiaz Jianlong Xu Jianlong Xu Muhammad Arif |
| author_facet | Kashif Aslam Kashif Aslam Shahzad Amir Naveed Shahzad Amir Naveed Muhammad Sabar Ghulam Shabir Shahid Masood Shah Abdul Rehman Khan Muhammad Musaddiq Shah Sajid Fiaz Jianlong Xu Jianlong Xu Muhammad Arif |
| author_sort | Kashif Aslam |
| collection | DOAJ |
| description | Grain appearance is one of the most important attributes of rice. It is determined by grain size, shape, and weight, which in turn influences the rice yield and market value. In this study, QTLs for grain length, grain width, grain length/width ratio, and grain weight were mapped using the high-throughput indica/indica SNP platforms. The population of the mega indica variety IR64 and the high-quality aromatic variety Sadri from Iran was phenotyped. Based on this phenotypic data, plants of 94 F2:3 families including both parents were selected. A linkage map analysis of 210 SNP markers identified 14 QTLs controlling the grain length, grain width, length/width ratio, and 1,000 grain weight. Among these 14, one important region containing the QTLs for all the four studies’ traits was mapped on chromosome 8. It was derived from Sadri for the decreased length/width ratio and increased grain weight. This study demonstrated the speed and efficiency in using multiplex SNP genotyping for QTL analysis. Moreover, this study identified four novel QTLs (qGL8, qTGW8, qLWR8, and qGW8) sharing the same position on chromosome 8 which were linked with grain quality characteristics between one indica and one aromatic variety. It will enable more precise marker-assisted selection for grain weight, shape, and size. Further in-depth studies are required to dissect this region of interest and identify the related gene(s). |
| first_indexed | 2024-04-11T22:32:47Z |
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| id | doaj.art-44b42be2b42c459c9cc98fab9358654c |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-11T22:32:47Z |
| publishDate | 2022-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-44b42be2b42c459c9cc98fab9358654c2022-12-22T03:59:18ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-08-011310.3389/fgene.2022.955347955347Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri populationKashif Aslam0Kashif Aslam1Shahzad Amir Naveed2Shahzad Amir Naveed3Muhammad Sabar4Ghulam Shabir5Shahid Masood Shah6Abdul Rehman Khan7Muhammad Musaddiq Shah8Sajid Fiaz9Jianlong Xu10Jianlong Xu11Muhammad Arif12National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, PakistanInstitute of Molecular Biology and Biotechnology, BZ University, Multan, PakistanNational Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, PakistanNational Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, PakistanRice Research Institute, Kala Shah Kaku, PakistanNational Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, PakistanDepartment of Biotechnology, COMSATS University Islamabad, Abbottabad, PakistanDepartment of Biotechnology, COMSATS University Islamabad, Abbottabad, PakistanDepartment of Biological Sciences, International Islamic University Islamabad, Islamabad, PakistanDepartment of Plant Breeding and Genetics, The University of Haripur, Haripur, PakistanShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaInstitute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaNational Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, PakistanGrain appearance is one of the most important attributes of rice. It is determined by grain size, shape, and weight, which in turn influences the rice yield and market value. In this study, QTLs for grain length, grain width, grain length/width ratio, and grain weight were mapped using the high-throughput indica/indica SNP platforms. The population of the mega indica variety IR64 and the high-quality aromatic variety Sadri from Iran was phenotyped. Based on this phenotypic data, plants of 94 F2:3 families including both parents were selected. A linkage map analysis of 210 SNP markers identified 14 QTLs controlling the grain length, grain width, length/width ratio, and 1,000 grain weight. Among these 14, one important region containing the QTLs for all the four studies’ traits was mapped on chromosome 8. It was derived from Sadri for the decreased length/width ratio and increased grain weight. This study demonstrated the speed and efficiency in using multiplex SNP genotyping for QTL analysis. Moreover, this study identified four novel QTLs (qGL8, qTGW8, qLWR8, and qGW8) sharing the same position on chromosome 8 which were linked with grain quality characteristics between one indica and one aromatic variety. It will enable more precise marker-assisted selection for grain weight, shape, and size. Further in-depth studies are required to dissect this region of interest and identify the related gene(s).https://www.frontiersin.org/articles/10.3389/fgene.2022.955347/fullgrain weightQTL mappingSNP markersgrain sizegenotyping |
| spellingShingle | Kashif Aslam Kashif Aslam Shahzad Amir Naveed Shahzad Amir Naveed Muhammad Sabar Ghulam Shabir Shahid Masood Shah Abdul Rehman Khan Muhammad Musaddiq Shah Sajid Fiaz Jianlong Xu Jianlong Xu Muhammad Arif Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri population Frontiers in Genetics grain weight QTL mapping SNP markers grain size genotyping |
| title | Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri population |
| title_full | Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri population |
| title_fullStr | Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri population |
| title_full_unstemmed | Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri population |
| title_short | Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri population |
| title_sort | identification of qtls for rice grain size and weight by high throughput snp markers in the ir64 x sadri population |
| topic | grain weight QTL mapping SNP markers grain size genotyping |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.955347/full |
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