The identification of grain size genes by RapMap reveals directional selection during rice domestication

Juncheng Zhang, Dejian Zhang, Yawei Fan, Cuicui Li, Pengkun Xu, Wei Li, Qi Sun, Xiaodong Huang, Chunyu Zhang, Linyue Wu, Huaizhou Yang, Shiyu Wang, Xiaomin Su, Xingxing Li, Yingying Song, Meng-en Wu, Xingming Lian and Yibo Li ()
Additional contact information
Juncheng Zhang: Huazhong Agricultural University
Dejian Zhang: Huazhong Agricultural University
Yawei Fan: Huazhong Agricultural University
Cuicui Li: Huazhong Agricultural University
Pengkun Xu: Huazhong Agricultural University
Wei Li: Huazhong Agricultural University
Qi Sun: Huazhong Agricultural University
Xiaodong Huang: Huazhong Agricultural University
Chunyu Zhang: Huazhong Agricultural University
Linyue Wu: Huazhong Agricultural University
Huaizhou Yang: Huazhong Agricultural University
Shiyu Wang: Huazhong Agricultural University
Xiaomin Su: Huazhong Agricultural University
Xingxing Li: Huazhong Agricultural University
Yingying Song: Huazhong Agricultural University
Meng-en Wu: Huazhong Agricultural University
Xingming Lian: Huazhong Agricultural University
Yibo Li: Huazhong Agricultural University

Nature Communications, 2021, vol. 12, issue 1, 1-18

Abstract: Abstract Cloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity. Here, we introduce RapMap, a method for rapid multi-QTL mapping by employing F2 gradient populations (F2GPs) constructed by minor-phenotypic-difference accessions. The co-segregation standard of the single-locus genetic models ensures simultaneous integration of a three-in-one framework in RapMap i.e. detecting a real QTL, confirming its effect, and obtaining its near-isogenic line-like line (NIL-LL). We demonstrate the feasibility of RapMap by cloning eight rice grain-size genes using 15 F2GPs in three years. These genes explain a total of 75% of grain shape variation. Allele frequency analysis of these genes using a large germplasm collection reveals directional selection of the slender and long grains in indica rice domestication. In addition, major grain-size genes have been strongly selected during rice domestication. We think application of RapMap in crops will accelerate gene discovery and genomic breeding.

Date: 2021
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DOI: 10.1038/s41467-021-25961-1

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