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- Title
The identification of grain size genes by RapMap reveals directional selection during rice domestication.
- Authors
Zhang, Juncheng; Zhang, Dejian; Fan, Yawei; Li, Cuicui; Xu, Pengkun; Li, Wei; Sun, Qi; Huang, Xiaodong; Zhang, Chunyu; Wu, Linyue; Yang, Huaizhou; Wang, Shiyu; Su, Xiaomin; Li, Xingxing; Song, Yingying; Wu, Meng-en; Lian, Xingming; Li, Yibo
- 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. Cloning quantitative trait loci (QTL) in crops is often slow and laborious. Here, the authors describe RapMap, a method to rapidly clone multiple QTL based on F2 gradient populations coupled with a co-segregation standard, and show how it can be used to identify genes controlling grain size in rice.
- Subjects
LOCUS (Genetics); GENETIC variation; GRAIN size; GENETIC models; RICE; HYBRID rice
- Publication
Nature Communications, 2021, Vol 12, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-021-25961-1