Abstract
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 rhizosphere microbiome, have been neglected. Better understanding of rootstock and scion effects on cacao-specific traits, particularly those involved in root-microbe interactions and nutrient acquisition, could contribute to more efficient rootstock selection and breeding. A rootstock-scion interaction study was conducted using three scion genotypes and eight rootstock populations under greenhouse conditions to better understand the relationships among rootstock and scion identities, soil fertility, and rhizobiome composition and the impacts of these factors on plant uptake of macro- and micronutrients. We show that rootstock genotype has a stronger influence than scion on nutrient uptake, bacterial and fungal diversity, and rhizobiome composition, and that the relative contributions of rootstock and scion genotype to foliar nutrient status are dynamic over time. Correlation analysis and stepwise regression revealed complex relationships of soil physicochemical parameters and the rhizobiome to plant nutrition and emphasized strong impacts of microbial diversity and composition on specific nutrients. Linear discriminant analysis effect size estimation identified rootstock-responsive taxa potentially related to plant nutrition. This study highlights the importance of considering root-associated microbial communities as a factor in cacao rootstock breeding and the need for further investigation into mechanisms underlying nutrient acquisition and microbial interactions in grafted plants.
Highlights
Grafting is a common practice in perennial crops to combine desirable combinations of rootstock and scion traits
Our findings of dominant rootstock effects on plant nutrition and microbial interactions in cacao suggest that rootstock breeding could be employed to increase nutrient use efficiency
If differences had been observed among rootstocks in nutrient accumulation at both time points, it would have warranted investigation of the genetic basis of differences in nutrient uptake and partitioning as well as rootstock-specific microbial taxa that may have contributed
Summary
Grafting is a common practice in perennial crops to combine desirable combinations of rootstock and scion traits. Modern cacao breeding programs have only existed since the 1930s, despite the popularity of this crop, which translates to a limited number of generations given the timeframe required for breeding perennials (DuVal et al, 2017) To date, these programs have focused primarily on generating elite scions, leaving the development of nutrient-efficient, stresstolerant, disease-resistant rootstocks as a significant research gap. One reason may be that at least two of the three primary breeding objectives (bean quality, yield, and disease resistance) are controlled by scions, and soil-borne pathogens that can be controlled with resistant rootstocks are not as significant as foliar and pod pathogens in cacao (Bailey and Meinhardt, 2016). Meeting rising consumer demand without conversion of additional land to cacao production will require increasing resource use efficiency, especially at the rootsoil interface
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