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

Juncheng Zhang,Chunyu Zhang,Cuicui Li,Yawei Fan,Shiyu Wang,Xingming Lian,Xiaomin Su,Meng-En Wu,Xingxing Li,Qi Sun,Wei Li,Yibo Li,Yingying Song,Xiaodong Huang,Pengkun Xu,Huaizhou Yang,Dejian Zhang,Linyue Wu

doi:10.1038/s41467-021-25961-1

Juncheng Zhang, Chunyu Zhang + Show 16 more

Open Access

https://doi.org/10.1038/s41467-021-25961-1

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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.

Highlights

Cloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity
From all the cases of QTL cloning in rice[12], it can be seen that not more than four QTL genes (QTGs) for a specific trait could be isolated in a traditional genetic population constructed by largephenotypic-difference bi-parents
Rapid Mapping (RapMap) has several notable advantages over traditional schemes of linkage and association analyses (F2, recombinant inbred line (RIL), doubled haploid (DH), Genome-wide association studies (GWAS), nested association mapping (NAM), and multiparent advanced generation intercross (MAGIC))[7,8,9,10,11,12,13,14,15,16,17,18,19] and those recently reported methods (QTL-seq, QTG-seq, MutMap, and others)[32,47,48,49,50]. These advantages include the flexibility of parent selection, the simplicity of constructing multi-parental F2 gradient populations (F2GPs), high mapping power and resolution, high genetic diversity to achieve multi-loci mapping with higher reliability and higher phenotypic variation explained (PVE), mapping QTL of minor effect or low allele frequency, fast gene discovery using near-isogenic linelike line (NIL-LL), and the three-in-one framework integrated by the cosegregation standard

Summary

Introduction

Cloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity. We demonstrate the feasibility of RapMap by cloning eight rice grain-size genes using 15 F2GPs in three years. The identification and dissection of a QTL into a single Mendelian factor using the traditional approaches often require the complex construction of advanced generation populations and near-isogenic lines (NILs) by repeated backcrossing, which are rate-limiting steps of cloning a QTL and remain time-consuming and laborious[3,5,9]. MAGIC and NAM populations mainly offer preliminary mapping with high resolution for some loci, and the causal genes of a trait have rarely been identified effectively[14]. More grain-size QTGs need to be identified to reveal the regulatory mechanism of QTG interactions in rice[4,7,8,20,21]

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