Plants encounter numerous abiotic and biotic stressors throughout their lifecycle. The extracellular plant cuticle is the first protective layer between the plant and the external environment. This hydrophobic barrier is produced by epidermal cells and consists of a cutin matrix that is infused with and coated by a diverse array of very long chain fatty acids and their derivatives. This metabolome can vary between plant species, between organs of a single plant species, and across development of a single tissue. While the framework of surface lipid biosynthesis, which includes de novo fatty acid biosynthesis in the plastid and fatty acid elongation in the endoplasmic reticulum, has been well-studied in plants, the genetic and biochemical networks underlying surface lipid biosynthesis in epidermal cells and subsequent accumulation on the extracellular surface are not fully understood. The stigmatic surfaces of maize, known as silks, are particularly rich in hydrocarbons, providing a unique opportunity to further characterize the biosynthesis of surface hydrocarbons in more detail. To test the hypotheses that genetics and environment influence the accumulation of surface hydrocarbons on silks and to examine the breadth of metabolome compositions across genetically diverse germplasm, cuticular hydrocarbons were analyzed on husk-encased silks and silks that emerged from the husk leaves from a diverse set maize inbred lines. Total hydrocarbon accumulation varied ~10-fold, and up to 5-fold between emerged and husk-encased silks. The surface hydrocarbon metabolomes of the inbred lines B73 and Mo17 are quite distinct, with B73 accumulating ~2-fold more hydrocarbons than Mo17, making quantitative genetic approaches with populations derived from these agronomically important inbreds attractive.

To better understand the genetic network that underlies the diversity in cuticular lipid compositions, metabolite-quantitative trait locus mapping was employed to identify genomic loci associated with the silk surface lipid metabolome. This analysis identified approximately 100 loci associated with accumulation of individual surface lipid metabolites, classes of metabolites and relative composition of the metabolome, with dozens of loci identified in two independent mQTL experiments. Loci identified to be associated with more than one surface lipid trait suggested pleiotropic actions by the causal polymorphisms at eight genomic locations with four locations identified in both experiments.

To further define two genomic loci of interest, fine mapping was conducted using dual testcross QTL analysis and heterozygous inbred family analysis. A locus near the Chromosome 1 centromere that influences the accumulation of unsaturated lipids, was found to fractionate into linked QTL, with a stearoyl-acyl carrier protein desaturase gene residing in each segment of the fractionation (sacd3 and sacd4). A second locus on the long arm of Chromosome 4 that influences carbon chain length of surface lipids was narrowed from ~7.5 Mbp (239 genes) to ~6 Mbp (198 genes), allowing for the exclusion of a known surface lipid biosynthesis gene, glossy4, and retention of a putative fatty aldehyde decarbonylase. These fine mapping results provide functional insights into the candidate genes that may underlie these loci and suggest the use of dual testcross QTL analysis as a standard fine mapping approach.

In conclusion, this work advances our understanding of silk metabolome compositions, the relative influence of genetics and the environment on surface lipid accumulation, and the genomic loci associated with surface lipid accumulation. Collectively, this work builds a foundation for future identification of maize surface lipid biosynthesis genes that may aid plant breeding efforts for enhanced crop protection from environmental stressors.