epistatic variation

Manicacci D, Camus-Kulandaivelu L, Fourmann M, Arar C, Barrault S, Rousselet A, Feminias N, Consoli L, Francès L, Méchin V, Murigneux A, Prioul J-L, Charcosset A & Damerval C 2009 Epistatic interactions between Opaque2 transcriptional activator and its target gene CyPPDK1 control kernel trait variation in maize. Plant Physiol 150:506-520.

  • a polymorphism in the Opaque2 coding sequence and several polymorphisms in the CyPPDK1 promoter nonadditively interact to modify both lysine content and the protein-versus-starch balance
  • revealing the role in quantitative variation in plants of epistatic interactions between a transcriptional activator and one of its target genes
  • in the maize kernel, the great majority of PPDK enzyme is cytosolic and encoded by a specific gene
  • whose transcription has been shown to be up-regulated by Opaque2
  • through binding to specific sequences in the CyPPDK1 promoter
  • while physiological studies are aimed at understanding the role of Opaque2 and CyPPDK1 maize mutations, nothing is known about the role of nonmutant allele diversity in maize phenotypic variation
  • maize is a particularly suitable species for association genetic studies
  • it contains a substantial amount of genetic diversity, local LD rapidly decreases with physical distance, remaining low at about 2 kb on average for a diverse population
  • population structure may easily be characterized through neutral markers
  • we first characterized the molecular diversity of both candidate genes among a large collection representative of cultivated maize
  • we finally tested for associations between these phenotypic traits and either individual gene polymorphisms or combined polymorphisms from CyPPDK1 and Opaque2 in order to assess possible epistatic interaction between the transcriptional activator and its target gene
  • fourteen polymorphisms from CyPPDK1 and 10 from Opaque2 were chosen from these sequence data, based on their position, frequency, LD, and potential function, and were then genotyped on the 375 inbred lines
  • LD between genes is very low (r2 < 0.10, P > 0.01) and, given the large number of pairs of polymorphisms that were tested, could be considered as nonsignificant
  • we investigated whether pairs of SNPs from CyPPDK1 and Opaque2 have complementary or synergistic effects on kernel phenotypes
  • the natural polymorphism of the CyPPDK1 gene itself only slightly affects endosperm protein content and is not associated with starch content
  • whereas we found that protein and starch contents as well as protein-starch balance are affected by epistatic interaction between the Opaque2 coding sequence and the CyPPDK1 promoter
  • an increase in the protein-starch ratio is unlikely to be achieved through selection of more efficient CyPPDK1 alleles
  • but rather through specific combinations of compatible alleles that allow an increased activation of CyPPDK1 by its transcriptional activator Opaque2
  • the CyPPDK1 promoter SNPs that we studied are in complete or very strong LD both between each other and with many other polymorphisms observed in the initial sequencing all along the promoter