Genome-wide association study reveals the genes associated with the leaf inclusion contents in Chinese medical tree Eucommia ulmoides

Eucommia ulmoides is an economic tree that can biosynthesize secondary metabolites with pharmacological functions. Genetic basis of biosynthesis of these compounds is almost unknown. Therefore, genomic-wide association study was performed to exploit the genetic loci maybe involved in biosynthetic pathways of 5 leaf inclusions (aucubin, chlorogenic acid, gutta-percha, polyphenols, total flavonoids). It was shown that contents of the 5 leaf metabolites have a wide variation following normal distribution. A total of 2 013 102 single nucleotide polymorphism (SNP) markers were identified in a population containing 62 individual clones. Through genome-wide association study analysis, many SNP loci were identified perhaps associated with phenotypes of the leaf inclusions. Higher transcriptional levels of the candidate genes denoted by significant SNPs in leaves suggested they may be involved in biosynthesis of the leaf inclusions. These genetic loci provide with invaluable information for further studies on the gene functions in biosynthesis of the leaf inclusions and selective breeding of the plus trees.