4.3 Article

Genome-wide association study identifies SNP markers and putative candidate genes for terpene traits important for Leptocybe invasa resistance in Eucalyptus grandis

Journal

G3-GENES GENOMES GENETICS
Volume 12, Issue 4, Pages -

Publisher

OXFORD UNIV PRESS INC
DOI: 10.1093/g3journal/jkac004

Keywords

Eucalyptus grandis; Leptocybe invasa; genome-wide association study; terpenes; single nucleotide polymorphism; multilocus mixed model; Genomic Prediction; GenPred; Shared Data Resource

Funding

  1. Department of Science and Innovation (DSI)
  2. Technology Innovation Agency (TIA) of South Africa
  3. South African National Research Foundation (NRF) [UID105767, UID95807]
  4. Forest Molecular Genetics (FMG) Programme at the University of Pretoria
  5. Forest Sector Innovation Fund
  6. Mondi

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This study identified SNP markers associated with terpene traits in Eucalyptus grandis, indicating that these traits are influenced by a combination of minor and major effect loci.
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, gamma-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 gamma-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.

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