Association mapping for important agronomic traits in core collection of rice (Oryza sativa L.) with SSR markers

PLoS One. 2014 Oct 31;9(10):e111508. doi: 10.1371/journal.pone.0111508. eCollection 2014.

Abstract

Mining elite genes within rice landraces is of importance for the improvement of cultivated rice. An association mapping for 12 agronomic traits was carried out using a core collection of rice consisting of 150 landraces (Panel 1) with 274 simple sequence repeat (SSR) markers, and the mapping results were further verified using a Chinese national rice micro-core collection (Panel 2) and a collection from a global molecular breeding program (Panel 3). Our results showed that (1) 76 significant (P<0.05) trait-marker associations were detected using mixed linear model (MLM) within Panel 1 in two years, among which 32% were identical with previously mapped QTLs, and 11 significant associations had >10% explained ratio of genetic variation; (2) A total of seven aforementioned trait-marker associations were verified within Panel 2 and 3 when using a general linear model (GLM) and 55 SSR markers of the 76 significant trait-marker associations. However, no significant trait-marker association was found to be identical within three panels when using the MLM model; (3) several desirable alleles of the loci which showed significant trait-marker associations were identified. The research provided important information for further mining these elite genes within rice landraces and using them for rice breeding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agriculture*
  • Alleles
  • Chromosome Mapping*
  • Gene Frequency / genetics
  • Genetic Markers
  • Inheritance Patterns / genetics
  • Linear Models
  • Microsatellite Repeats / genetics*
  • Models, Genetic
  • Oryza / genetics*
  • Phenotype
  • Quantitative Trait Loci / genetics
  • Quantitative Trait, Heritable*
  • Reproducibility of Results

Substances

  • Genetic Markers

Grants and funding

This work was supported by Fund of the National Natural Science Foundation of China grant 30700494. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.