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.
Highlights
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
Plant breeders are interested in screening large collections of genetic resources in order to identify haplotypes of interest involved in agronomic trait variation
We found no correlation between allelic frequency and average phenotypic values among groups, suggesting that no CyPPDK1 or Opaque2 single nucleotide polymorphisms (SNPs) are involved in local adaptation for kernel quality
Summary
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. Using statistical models that correct for population structure and individual kinship, Opaque 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 Opaque on either zein transcription, zeins being major storage proteins devoid of lysine, or lysine degradation through the activation of lysine ketoglutarate reductase. Maize (Zea mays), one of the main crops in the world, accumulates a large amount of starch (75%280% of endosperm dry matter at maturity) and storage proteins (12%215%, mainly zeins) in its kernel endosperm Such resources are accumulated to support seed germination and initial seedling growth, which are major traits in both agronomical and natural conditions. An increase in PPDK activity in the endosperm cytosol could induce a reduction in starch accumulation as well as an increase in protein content
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