Whole-genome quantitative trait locus mapping reveals major role of epistasis on yield of rice

PLoS One. 2014 Jan 29;9(1):e87330. doi: 10.1371/journal.pone.0087330. eCollection 2014.


Although rice yield has been doubled in most parts of the world since 1960s, thanks to the advancements in breeding technologies, the biological mechanisms controlling yield are largely unknown. To understand the genetic basis of rice yield, a number of quantitative trait locus (QTL) mapping studies have been carried out, but whole-genome QTL mapping incorporating all interaction effects is still lacking. In this paper, we exploited whole-genome markers of an immortalized F2 population derived from an elite rice hybrid to perform QTL mapping for rice yield characterized by yield per plant and three yield component traits. Our QTL model includes additive and dominance main effects of 1,619 markers and all pair-wise interactions, with a total of more than 5 million possible effects. The QTL mapping identified 54, 5, 28 and 4 significant effects involving 103, 9, 52 and 7 QTLs for the four traits, namely the number of panicles per plant, the number of grains per panicle, grain weight, and yield per plant. Most identified QTLs are involved in digenic interactions. An extensive literature survey of experimentally characterized genes related to crop yield shows that 19 of 54 effects, 4 of 5 effects, 12 of 28 effects and 2 of 4 effects for the four traits, respectively, involve at least one QTL that locates within 2 cM distance to at least one yield-related gene. This study not only reveals the major role of epistasis influencing rice yield, but also provides a set of candidate genetic loci for further experimental investigation.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bayes Theorem
  • Chromosome Mapping
  • Chromosomes, Plant / genetics*
  • Epistasis, Genetic*
  • Genetic Association Studies
  • Genetic Markers
  • Genome, Plant
  • Models, Genetic
  • Oryza / anatomy & histology
  • Oryza / genetics*
  • Phenotype
  • Quantitative Trait Loci
  • Seeds / anatomy & histology
  • Seeds / genetics*


  • Genetic Markers

Grant support

This work was supported by the National Science Foundation (NSF) under NSF CAREER Award no. 0746882 to XC and by the Agriculture and Food Research Initiative (AFRI) of the USDA National Institute of Food and Agriculture under the Plant Genome, Genetics and Breeding Program 2007-35300-18285 to SX. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.