Abstract:
Terpenes are an important group of plant specialized metabolites influencing, amongst other functions, defence mechanisms against
pests. We used a genome-wide association study 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 3 terpene traits, 1,8-cineole, c-terpinene, and p-cymene. A multilocus mixed model 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%–8.4% and jointly 42.7% of the phenotypic variation.
Association analysis of c-terpinene found 32 significant SNP markers on chromosomes 1, 2, 4, 5, 6, 9, and 11, explaining 3.4–15.5% 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 3.4–16.1% of the phenotypic variation and jointly 46.9%. Our results show that variation underlying the 3 terpene traits is
influenced by a few minor loci in combination with a few major effect loci, suggesting an oligogenic nature of the traits.
Description:
DATA AVAILABILITY : All datasets used in GWAS analysis are available at https://figshare.com/s/92751d332fd45a1b58f1. Data of the results obtained from the GWAS analysis was used to generate the figures Manhattan plots, LD decay, and PCA plot. Gene expression data were obtained from a previous study by Oates et al. (2015). The raw data are available through the NCBI (BioProject PRJNA305347), https://www.ncbi.nlm.nih.gov/bioproject/PRJNA305347. Resistant infested (Egr TAG 5 infested: SRA, SRX1470128), resistant uninfested (Egr TAG 5 uninfested: SRA, SRX1470127), susceptible infested (Egr GC540 infested: SRA, SRX1471865), and susceptible uninfested (Egr GC540 uninfested: SRA, SRX1470184). The FPKM is available at https://figshare.com/s/92751d332fd45a1b58f1
