ArticleNational science review2024
Powerful QTL mapping and favorable allele mining in an all-in-one population: a case study of heading date.
Article in National science review, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Identification and Functional Characterization of the Mungbean Yellow Mosaic India Virus Resistant GeneJournal of agricultural and food chemistry · 2026Article
- Multi-parent mapping reveals epistatic architecture and elite haplotypes for multi-trait improvement in cotton.Genome biology · 2026Article
- GWAS and Candidate Gene Prediction of Elemental Accumulation Traits in Rice Using a Multiparental Population.Rice (New York, N.Y.) · 2026Article
- Article
- MAGIC populations: a next-generation framework for dissecting complex quantitative traits and accelerating molecular breeding in crops.Frontiers in plant science · 2026Review
- Comparison of the Genetic Basis of Yield Traits Between Main and Ratoon Rice in an Eight-Way MAGIC Population.Plants (Basel, Switzerland) · 2025Article
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Authors and funding
10 authors.
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Abstract
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 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 <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.
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