Heritability of the Pinus radiata root microbiome

Both evolutionary history and recent breeding selections can influence plant microbiomes, with closely-related individuals often having more similar microbiomes. Pinus radiata D.Don is an emerging conifer model species for investigating tree-microbiome interactions. However, little is known about how the P. radiata microbiome covaries with host genotype, especially beyond the seedling stage.

We sampled the root microbiome of 528 individual P. radiata trees (age = 9 yrs), comprising four clonal copies each of 132 host genotypes from 28 full-sib families, from a clonal breeding trial in New Zealand. We determined whether variations in the bacterial and fungal root microbiomes were associated with host ancestry (i.e., provenance), family, and genotype.

Host family was associated with fungal but not bacterial root microbiome composition, whereas broader ancestry and individual genotype within families had no detectable effect on either bacterial or fungal microbiome composition. While core (in ≥80% samples) amplicon sequence variants (ASVs) typically had negligible heritability, the relative abundances of 83 bacterial and 13 fungal non-core ASVs had low to moderate broad-sense heritabilities (0.2 to 0.46). Host genetic effects associated with abundances of heritable ASVs were primarily non-additive and likely involve complex gene interactions.

Our study revealed subtle host family effects for the root fungal microbiome of P. radiata, with several heritable bacterial and fungal ASVs. This study broadens our understanding of host genetic influences on the composition of the root microbiome of P. radiata and indicates there are both opportunities and challenges for including microbiome-related traits in tree breeding programmes.