Powerful QTL mapping and favorable allele mining in an all-in-one population: a case study of heading date  

作　　者：Pengfei Wang Ying Yang Daoyang Li Zhichao Yu Bo zhang Xiangchun Zhou Lizhong Xiong Jianwei Zhang Lei Wang Yongzhong Xing 

机构地区：[1]National Key Laboratory of Crop Genetic Improvement,Hubei Hongshan Laboratory,Huazhong Agricultural University,Wuhan 430070,China [2]Institute of Tropical Crop Genetic Resources,Chinese Academy of Tropical Agricultural Sciences,Haikou 571101,China [3]Yazhouwan National Laboratory,Sanya 572024,China

出　　处：《National Science Review》2024年第8期54-68,共15页国家科学评论（英文版）

基　　金：supported by the National Key Research and Development Program of China(2023ZD04073);STI2030-Major Projects(2022ZD04001);the National Natural Science Foundation of China(31821005,U20A2031,32061143042);the Earmarked Fund for China Agriculture Research System(CARS-01);the National Key Laboratory of Crop Genetic Improvement Self-Research Program(ZW22B0204).

摘　　要：The multiparent advanced generation intercross(MAGIC)population is characterized with great potentials in power and resolution of quantitative trait locus(QTL)mapping,but single nucleotide polymorphism(SNP)-based GWAS does not fully reach its potential.In this study,a MAGIC population of 1021 lines was developed from four Xian and four Geng varieties from five subgroups of rice.A total of 44000 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 24414 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<55 kb for major effect genes and<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 confirm 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.

关 键 词：MAGIC population population structure bin map novel casual variant superior allele 

分 类 号：S511[农业科学—作物学]