Gene

Demography

Population genomics

Biology

Heterosis

Local adaptation

Single-nucleotide polymorphism

Genetics

Genome

Genotype

Agronomy

Population

Sociology

Genomics

Hybrid

Quantitative trait locus

Allele

Genetic variation

Domestication

Nature Genetics

Extensive allelic variation in agronomically important genes serves as the basis of rice breeding. Here, we present a comprehensive map of rice quantitative trait nucleotides (QTNs) and inferred QTN effects based on eight genome-wide association study cohorts. Population genetic analyses revealed that domestication, local adaptation and heterosis are all associated with QTN allele frequency changes. A genome navigation system, RiceNavi, was developed for QTN pyramiding and breeding route optimization, and implemented in the improvement of a widely cultivated indica variety. This work presents an efficient platform that bridges ever-increasing genomic knowledge and diverse improvement needs in rice. A comprehensive rice quantitative trait nucleotide map provides new genetic insights and serves as the basis for RiceNavi, a tool to optimize breeding schemes.

A quantitative genomics map of rice provides genetic insights and guides breeding