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Perennial agroecosystems often seek to optimize productivity by breeding nutrient-efficient, disease-resistant rootstocks. In cacao (Theobroma cacao L.), however, rootstock selection has traditionally relied on locally available open pollinated populations with limited data on performance. Furthermore, rootstock associations with the rhizobiome, or...
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... T. cacao has been studied for decades but comparatively little molecular research has been done on the cacao root-associated microbiome (Schmidt et al. 2022). With the sequencing of the cacao genome in the past decade (Argout et al. 2011), new understanding of its population genetics (Motamayor et al. 2008), and recent evidence of genetic effects on its rhizosphere microbiome (Schmidt et al. 2021), there is a clear need for further investigation of the cacao microbiome and how to optimize beneficial microbial interactions in this perennial crop. The prevalence of grafting in field-grown cacao means that the genotype (G), environment (E), and G-E influences on the microbiome that must be considered for annual crops must be expanded to include rootstock (R), scion (S), E, R-S, and R-S-E interactions, a much more complex model (Albacete et al. 2015). ...
... Consistent with other recent work in cacao (Schmidt et al. 2021), we found that rootstock but not scion identity affects composition of the cacao root endophyte and rhizosphere microbiomes, though that study did not address root endophytes or study the microbiome before and after grafting. A similar study in ungrafted apple seedlings found greater differences among bacterial and fungal shoot endophytes between a semidwarfing rootstock and dwarfing rootstock than among three scion cultivars, and grafting did not alter endophyte diversity or composition in that study either (Liu et al. 2018). ...
... ASVs are identified to genus level where possible. genotype on the microbiome under different circumstances; however, that is unlikely in cacao given documented rootstock effects and rootstock-responsive taxa (Schmidt et al. 2021). It is plausible that (i) the set of SNPs used here did not cover loci relevant to plant-microbe interactions, (ii) the microbial communities in the greenhouse substrate do not include numerous genotype-responsive taxa, or (iii) this experiment did not capture the environmental or developmental conditions under which genetic variation in the root and rhizosphere microbiome would be most pronounced. ...
Recent advances in understanding microbial contributions to plant growth and soil health have sparked interest in breeding plants that cultivate a beneficial microbiome. Yet optimizing phytobiomes requires knowledge of the genetic architecture of host influence on the associated microbiome, and this knowledge is particularly lacking in perennial crops such as Theobroma cacao. Grafting adds an additional layer of complexity: What are the relative impacts of rootstock and scion on the root and rhizosphere microbiomes? Plant-microbe interactions have rarely been investigated in Theobroma cacao despite the global significance of this crop. We sought to 1) characterize the effect of host genotype on the cacao root endophyte and rhizosphere microbiomes, 2) identify a core microbiome across six open-pollinated rootstock groups, and 3) investigate whether members of the core microbiome were linked to plant growth traits in greenhouse-grown trees. Rootstock and scion identity did not affect within-sample diversity of the root or rhizosphere microbiomes, but rootstock explained 7-13% of variation in prokaryotic communities and 9-12% of variation in fungal communities. However, rootstock genetic distance was not related to taxonomic or phylogenetic dissimilarity of the root or rhizosphere microbiomes. We identified a conserved core microbiome that contained numerous taxa found in both root and rhizosphere microbiomes. Structural topic model and multivariate regression approaches identified both co-varying groups and individual taxa within the core microbiome that were associated with metrics of plant growth and development. These preliminary results could be used to inform breeding programs and potentially soil bio-amendment strategies for cacao seedlings.
