Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis

Nat Commun. 2015 Feb 5;6:6258. doi: 10.1038/ncomms7258.


Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. Here we develop an integrated genomic approach to construct a genome map for 1,495 elite hybrid rice varieties and their inbred parental lines. We investigate 38 agronomic traits and identify 130 associated loci. In-depth analyses of the effects of heterozygous genotypes reveal that there are only a few loci with strong overdominance effects in hybrids, but a strong correlation is observed between the yield and the number of superior alleles. While most parental inbred lines have only a small number of superior alleles, high-yielding hybrid varieties have several. We conclude that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agriculture
  • Alleles*
  • Gene-Environment Interaction
  • Genome, Plant*
  • Genome-Wide Association Study
  • Heterozygote
  • Hybrid Vigor / genetics*
  • Hybridization, Genetic*
  • Oryza / genetics*
  • Phenotype
  • Quantitative Trait, Heritable