QTL and association analyses of the phenylpropanoid pathway in maize silks

The C-glycosyl flavone maysin is an important component of corn earworm (Helicoverpa zea Boddie); (CEW) resistance in maize (Zea mays L.) silks. Chlorogenic acid (CGA), a product of the phenylpropanoid pathway, has also been implicated in CEW antibiosis. The transition from the 9-carbon phenylpropanoid to the 15-carbon flavonoid pathway represents a potentially important regulation point in C-glycosyl flavone biosynthesis. Chalcone synthase (CHS) catalyzes this reaction and is encoded by a pair of duplicate loci in maize, colorless2 (c2) and white pollen1 (whp1). Chromosomal regions of the maize genome corresponding to these two loci have been identified as quantitative trait loci (QTL) for maysin synthesis. Our objective was to investigate the role of CHS in flavone and CGA biosynthesis.; c2 and whp1 were tested as candidate loci using three related F₂ populations segregating for variation at both structural and regulatory loci. Results from statistical and QTL analyses: (i) support earlier findings of the requirement of a functional pericarp color (p) allele for C-glycosyl flavone biosynthesis; (ii) demonstrate that variation at the c2 region on chromosome 4 influences both maysin and CGA levels in silks; (iii) reveal a dosage-dependent relationship between c2 and whp1 in which the whp1 region acts cooperatively with functional c2 to increase flavones and partially compensates for nonfunctional c2; and (iv) demonstrate that mutations in c2 and whp1 shunt intermediates from maysin synthesis to CGA. These results indicate that CHS function is a regulatory focal point of substrate flow between the flavone and phenylpropanoid pathways.; To examine whether sequence variation at structural loci in the flavone pathway affected maysin synthesis, association analysis was performed. The promoter of the anthocyaninless1 (a1) gene, and both promoter and coding regions of the duplicate CHS loci, c2 and whp1, were sequenced in maize lines representing a broad spectrum of available maize genetic diversity. The data were used to generate haplotype information to test for association with accumulation of maysin and CGA in silks. After accounting for p genotype, we found a highly significant association of sequence polymorphisms in the promoter of a1 and whp1 with maysin synthesis. Our analysis showed that the conditioning for epistatic factors increased the power of association testing.