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, Pengfei Wang National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070 , China Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences , Haikou 571101 , China Search for other works by this author on: Oxford Academic Ying Yang National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070 , China Search for other works by this author on: Oxford Academic Daoyang Li National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070 , China Search for other works by this author on: Oxford Academic Zhichao Yu National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070 , China Search for other works by this author on: Oxford Academic Bo zhang National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070 , China Search for other works by this author on: Oxford Academic Xiangchun Zhou National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070 , China Search for other works by this author on: Oxford Academic Lizhong Xiong National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070 , China Search for other works by this author on: Oxford Academic Jianwei Zhang National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070 , China Search for other works by this author on: Oxford Academic Yongzhong Xing National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , Wuhan 430070 , China Yazhou Bay National Laboratory , Sanya 572024 , China Corresponding author. E-mail: yzxing@mail.hzau.edu.cn Search for other works by this author on: Oxford Academic
These authors equally contributed to this work
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National Science Review, nwae222, https://doi.org/10.1093/nsr/nwae222
Published:
26 June 2024
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Pengfei Wang, Ying Yang, Daoyang Li, Zhichao Yu, Bo zhang, Xiangchun Zhou, Lizhong Xiong, Jianwei Zhang, Yongzhong Xing, Powerful QTL mapping and favorable allele mining in an all-in-one population: a case study of heading date, National Science Review, 2024;, nwae222, https://doi.org/10.1093/nsr/nwae222
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Abstract
The multiparent advanced generation intercross (MAGIC) population is characterized with great potentials in power and resolution of QTL mapping, but SNP-based GWAS does not fully play its potential. In this study, a MAGIC population of 1021 lines was developed from four Xian and four Geng varieties from 5 subgroups of rice. A total of 44,000 genes showed functional polymorphisms among eight parents, including frameshift variations or premature stop codon variations, which provides the potential to map almost all genes of the MAGIC population. Principal component analysis results showed that the MAGIC population had a weak population structure. A high-density bin map of 24,414 bins was constructed. Segregation distortion occurred in the regions possessing the genes underlying genetic incompatibility and gamete development. SNP-based association analysis and bin-based linkage analysis identified 25 significant loci and 47 QTLs for heading date, including 14 known heading date genes. The mapping resolution of genes is dependent on genetic effects with offset distances of less than 55 kb for major effect genes and less than 123 kb for moderate effect genes. Four causal variants and noncoding structure variants were identified to be associated with heading date. Three to four types of alleles with strong, intermediate, weak, and no genetic effects were identified from eight parents, providing flexibility for the improvement of rice heading date. In most cases, japonica rice carries weak alleles, and indica rice carries strong alleles and nonfunctional alleles. These results confirmed that the MAGIC population provides the exceptional opportunity to detect QTLs, and its use is encouraged for mapping genes and mining favorable alleles for breeding.
MAGIC population, Population structure, bin map, novel casual variant, superior allele
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Author notes
These authors equally contributed to this work
© The Author(s) 2024. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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