Genome-Wide Association Study identifies SNP markers and putative candidate genes for terpene traits important for Leptocybe invasa resistance in Eucalyptus grandis

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College of Forest Resources and Environmental Science


Terpenes are an important group of plant specialized metabolites (PSM) influencing, amongst other functions, defence mechanisms against pests. We used a Genome-Wide Association Study (GWAS) to identify single nucleotide polymorphism (SNP) markers and putative candidate genes for terpene traits. We tested 15,387 informative SNP markers derived from genotyping 416 Eucalyptus grandis individuals for association with three terpene traits, 1,8-cineole, γ-terpinene and p-cymene. A Multi-Locus Mixed Model (MLMM) analysis identified 21 SNP markers for 1,8-cineole on chromosomes 2, 4, 6, 7, 8, 9, 10 and 11, that individually explained 3.0% to 8.4% and jointly 42.7% of the phenotypic variation. Association analysis of γ-terpinene found 32 significant SNP markers on chromosomes 1, 2, 4, 5, 6, 9 and 11, explaining 3.4 to 15.5% and jointly 54.5% of phenotypic variation. For p-cymene 28 significant SNP markers were identified on chromosomes 1, 2, 3, 5, 6, 7, 10 and 11, explaining 3.4% to 16.1% of the phenotypic variation and jointly 46.9%. Our results show that variation underlying the three terpene traits is influenced by a few minor loci in combination with a few major effect loci, suggesting an oligogenic nature of the traits.

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G3 (Bethesda, Md.)