Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 19, 2005
Publication Date: April 2, 2005
Citation: Szalma, S.J., Buckler Iv, E.S., Snook, M.E., Mcmullen, M.D. 2005. Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Journal of Theoretical and Applied Genetics. 110(7):1324-1333. Interpretive Summary: An important area of current research for crop improvement is to identify the genes, and the DNA sequence variation with genes, that control variation in agronomic traits. Association analysis is a genetic approach that links DNA sequence differences to variation in trait expression. A potential limitation to the power of association analysis is that the effect of one gene often is dependent on specific DNA variation at other genes. In this study, we use genes involved in the synthesis of maysin, an insect resistance factor in maize silks, to determine how variation in one gene affects our ability to detect significant associations in a second gene. We demonstrate that the power of association analysis to detect significant DNA variation in one gene can be enhanced by conditioning the analysis on the variation at other genes. Our results are important to geneticists and plant breeders in improving our ability to i) define agronomically important genes and ii) identify functionally important DNA sequence variation.
Technical Abstract: Two compounds, the C-glycosyl flavone maysin and the phenylpropanoid product chlorogenic acid (CGA) have been implicated in corn earworm (Helicoverpa zea Boddie) resistance in maize (Zea mays L.). Previous quantitative trait locus (QTL) analyses identified the pericarp color (p) locus as the major QTL for maysin and CGA. Quantitative trait analysis has also implicated the dihydroflavanol reductase locus anthocyaninless1 (a1), and the duplicate chalcone synthase (CHS) loci, colorless2 (c2) and white pollen1 (whp1), as QTL for maysin and/or CGA synthesis. Epistatic interactions between p and a1, and p and c2, were also defined. To examine if sequence variation among maize lines at these candidate structural loci affected maysin and CGA synthesis, association analysis was performed. The promoter of the a1 gene, and the promoter and coding regions of the duplicate CHS loci, c2 and whp1, were sequenced in diverse maize lines. Because the p locus was the major QTL and was involved in epistatic relationships with the structural loci under investigation, association analysis at the structural loci was conditioned on p genotype. We demonstrated a highly significant association of two sequence polymorphisms in the promoter of a1 with maysin synthesis. Additional conditioning on the genotype of the significant a1 polymorphism, in addition to p, allowed the detection of a significant polymorphism within the whp1 promoter. Our analyses demonstrate that conditioning for epistatic factors greatly increases the power of association testing.