Association mapping and genetic dissection of nitrogen use efficiency-related traits in rice (Oryza sativa L.)

Funct Integr Genomics. 2016 May;16(3):323-33. doi: 10.1007/s10142-016-0486-z. Epub 2016 Feb 27.


The increases in the usage of nitrogen fertilizer result in deleterious impacts on the environment; thus, there is an urgent need to improve nitrogen use efficiency (NUE) in crops including rice (Oryza sativa L.). Attentions have focused on quantitative trait loci (QTL) mapping of NUE-related traits using single experimental population, but to date, very few studies have taken advantage of association mapping to examine hundreds of lines for identifying potentially novel QTLs in rice. Here, we conducted association analysis on NUE-related traits using a population containing 184 varieties, which were genotyped with 157 genome-wide simple sequence repeat (SSR) markers. We detected eight statistically significant marker loci associating with NUE-related traits, of which two QTLs at RM5639 and RM3628 harbored known NUE-related genes GS1;2 and AspAt3, respectively. At a novel NUE-related locus RM5748, we developed Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers and searched for putative NUE-related genes which are close to the associated SNP marker. Based on a transcriptional map of N stress responses constructed by our lab, we evaluated expressions of the NUE-related genes in this region and validated their effect on NUE. Meanwhile, we analyzed NUE-related alleles of the eight loci that could be utilized in marker-assisted selection. Moreover, we estimated breeding values of all the varieties through genomic prediction approach that could be beneficial for rice NUE enhancement.

Keywords: Association mapping; Breeding value; NUE; Rice.

MeSH terms

  • Alleles
  • Chromosome Mapping
  • Genetic Association Studies*
  • Genetic Linkage
  • Genomics
  • Genotype
  • Microsatellite Repeats / genetics
  • Nitrogen / metabolism*
  • Oryza / genetics*
  • Oryza / metabolism
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci / genetics*


  • Nitrogen