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Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population

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Abstract

Key message

A whole genome bin map was developed for a MAGIC population. Association studies for heading date at bin level exhibited powerful QTL mapping and identified favorable alleles.

Abstract

The presumed advantages of multiparent advanced generation intercross (MAGIC) population in quantitative trait locus (QTL) mapping were not fully utilized in the previous studies in which genome-wide association studies (GWAS) were conducted at only single nucleotide polymorphism level. In this study, we genotyped a rice four-way MAGIC population of 247 F7 lines and their parents by sequencing. A total of 5934 bins with an average length of 65 kb were constructed and covered 97% of the genome. The MAGIC population showed low population structure and balanced parental contributions. A bin-based GWAS for heading date identified 4 QTLs in three environments. Three major QTLs were mapped exactly to the bins where the major heading date genes DTH3, Ghd7.1 and Ghd8 were located. Multiple comparisons showed that different parental alleles had varied genetic effects. Like DTH3, the alleles of the Guichao 2/YJSM, IR34 and Cypress had larger, intermediate and no effects, respectively. Based on comparative sequencing of 8 known heading date genes undetected in this MAGIC population, only Ghd7 exhibited diverse function among parents. The failure in Ghd7 mapping was well explained by its interaction with Hd1 because Ghd7 had no effects on heading date when combined with the nonfunctional hd1 carried by all four parents. Overall, bin-based GWAS have more mapping power and higher resolution with a MAGIC population and provide favorable alleles to breeders. The use of more diversified parents is encouraged to develop a MAGIC population for detecting more QTLs for important agronomical traits.

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Acknowledgements

We thank the field technician Mr. JB Wang for his excellent work in the field. This work is partly supported by grants National Natural Science Foundation of China (31701391 and 31821005), and National Key Research and Development Program of China (2016YFD0100301).

Author information

ZH analyzed the data and wrote the article; GH performed most of the experiments; HL and FL investigated the phenotypes; LY developed the MAGIC population; HZ provided technical assistance to ZH; QZ gathered the sequencing data; ZL supervised the phenotypic investigation; QZ helped in experimental design; YX conceived the research plans, supervised and completed the writing and agrees to serve as the author responsible for contact and ensures communication.

Correspondence to Yongzhong Xing.

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Communicated by Christine A. Hackett.

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Han, Z., Hu, G., Liu, H. et al. Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population. Theor Appl Genet 133, 59–71 (2020) doi:10.1007/s00122-019-03440-y

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