Association analysis of single nucleotide polymorphisms in candidate genes with root traits in maize (Zea mays L.) seedlings

Plant Sci. 2014 Jul;224:9-19. doi: 10.1016/j.plantsci.2014.03.019. Epub 2014 Apr 3.


Several genes involved in maize root development have been isolated. Identification of SNPs associated with root traits would enable the selection of maize lines with better root architecture that might help to improve N uptake, and consequently plant growth particularly under N deficient conditions. In the present study, an association study (AS) panel consisting of 74 maize inbred lines was screened for seedling root traits in 6, 10, and 14-day-old seedlings. Allele re-sequencing of candidate root genes Rtcl, Rth3, Rum1, and Rul1 was also carried out in the same AS panel lines. All four candidate genes displayed different levels of nucleotide diversity, haplotype diversity and linkage disequilibrium. Gene based association analyses were carried out between individual polymorphisms in candidate genes, and root traits measured in 6, 10, and 14-day-old maize seedlings. Association analyses revealed several polymorphisms within the Rtcl, Rth3, Rum1, and Rul1 genes associated with seedling root traits. Several nucleotide polymorphisms in Rtcl, Rth3, Rum1, and Rul1 were significantly (P<0.05) associated with seedling root traits in maize suggesting that all four tested genes are involved in the maize root development. Thus considerable allelic variation present in these root genes can be exploited for improving maize root characteristics.

Keywords: Gene based association mapping; Linkage disequilibrium; Maize; Nucleotide diversity; Root traits; Single nucleotide polymorphism.

Publication types

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

MeSH terms

  • Alleles
  • Genes, Plant*
  • Genotype
  • Haplotypes
  • Linkage Disequilibrium
  • Phenotype*
  • Plant Roots / growth & development*
  • Polymorphism, Single Nucleotide*
  • Seedlings / growth & development
  • Zea mays / genetics*
  • Zea mays / growth & development