Epistatic interactions between Opaque2 transcriptional activator and its target gene CyPPDK1 control kernel trait variation in maize

Abstract

Association genetics is a powerful method to track gene polymorphisms responsible for phenotypic variation, since it takes advantage of existing collections and historical recombination to study the correlation between large genetic diversity and phenotypic variation. We used a collection of 375 maize (Zea mays ssp. mays) inbred lines representative of tropical, American, and European diversity, previously characterized for genome-wide neutral markers and population structure, to investigate the roles of two functionally related candidate genes, Opaque2 and CyPPDK1, on kernel quality traits. Opaque2 encodes a basic leucine zipper transcriptional activator specifically expressed during endosperm development that controls the transcription of many target genes, including CyPPDK1, which encodes a cytosolic pyruvate orthophosphate dikinase. Using statistical models that correct for population structure and individual kinship, Opaque2 polymorphism was found to be strongly associated with variation of the essential amino acid lysine. This effect could be due to the direct role of Opaque2 on either zein transcription, zeins being major storage proteins devoid of lysine, or lysine degradation through the activation of lysine ketoglutarate reductase. Moreover, we found that 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, thus revealing the role in quantitative variation in plants of epistatic interactions between a transcriptional activator and one of its target genes.

Figure 1.

Allelic frequency at CyPPDK1 and Opaque2 polymorphisms among 375 inbred lines. Black, gray, and white bars indicate different alleles. Polymorphism positions are indicated along genes (solid arrows, polymorphisms in exons; dashed arrows, polymorphisms in introns; SNP names starting with OP or CP are located upstream the ATG start codon). For each gene, one SNP leads to a change in an amino acid.

Figure 2.

Half-matrix of LD among Opaque2 and CyPPDK1 polymorphisms. Multiallelic polymorphisms shown in Figure 1 were converted into biallelic data (see “Materials and Methods”). [See online article for color version of this figure.]

Figure 3.

Average protein-starch ratio (p/s) and Lys (lysin) content depending on combined genotypes at CyPPDK1 and Opaque2 SNPs. The letters a and b indicate group classification of the four phenotypic means through Duncan's test at a 0.05 threshold.