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.

This study sought to quantify and characterize diverse rootstock scion interactions in cacao around graft compatibility, disease resistance, nutrient use efficiency, vigor traits, and translocation of nonstructural carbohydrates. In total, 106 grafts were performed with three scion cultivars (Matina 1/6, Criollo 22, Pound 7) and nine diverse open-pollinated seedling populations (BYNC, EQX 3348, GNV 360, IMC 14, PA 107, SCA 6, T 294, T 384, T 484). We found evidence for both local and translocated graft incompatibility. Cross sections and Micro-XCT imaging revealed anatomical anomalies, including necrosis and cavitation at the junction and accumulation of starch in the rootstock directly below the graft junction. Scion genetics were a significant factor in explaining differences in graft take, and graft take varied from 47% (Criollo 22) to 72% (Pound 7). Rootstock and scion identity both accounted for differences in survival over the course of the 30-month greenhouse study, with a low of 28.5% survival of Criollo 22 scions and a high of 72% for Pound 7 scions. Survival by rootstocks varied from 14.3% on GNV 360 to 100% survival on T 294 rootstock. A positive correlation of 0.34 (p = 0.098) was found between the graft success of different rootstock–scion combinations and their kinship coefficient, suggesting that relatedness of stock and scion could be a driver of incompatibility. Significant rootstock–scion effects were also observed for nutrient use efficiency, plant vigor, and resistance to Phytophthora palmivora. These findings, while preliminary in nature, highlight the potential of rootstock breeding to improve plant nutrition, resilience, and disease resistance in cacao.