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

Author: 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

Nature Communications. 28 Sep 2021. 5673(2021)

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.

Full Article:The identification of grain size genes by RapMap reveals directional selection during rice domestication | Nature Communications