Genome-wide association study

Biotechnology

Population

Agronomy

Biology

Gene

Trait

Genotype

Allele

Single-nucleotide polymorphism

Artificial intelligence

Principal component analysis

Programming language

Computer science

Computational biology

Panicle

Genetics

Medicine

Quantitative trait locus

Genetic architecture

Environmental health

Proceedings of the National Academy of Sciences

Elucidation of the genetic control of rice architecture is crucial due to the global demand for high crop yields. Rice architecture is a complex trait affected by plant height, tillering, and panicle morphology. In this study, principal component analysis (PCA) on 8 typical traits related to plant architecture revealed that the first principal component (PC), PC1, provided the most information on traits that determine rice architecture. A genome-wide association study (GWAS) using PC1 as a dependent variable was used to isolate a gene encoding rice, SPINDLY (OsSPY), that activates the gibberellin (GA) signal suppression protein SLR1. The effect of GA signaling on the regulation of rice architecture was confirmed in 9 types of isogenic plant having different levels of GA responsiveness. Further population genetics analysis demonstrated that the functional allele of OsSPY associated with semidwarfism and small panicles was selected in the process of rice breeding. In summary, the use of PCA in GWAS will aid in uncovering genes involved in traits with complex characteristics.

GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture