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Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree cropTheobroma cacaoL., as well as four non-cacaoTheobromaspecies, with the goal of identifying genetic elements essential for protection against the oomycete pathogenPhytophthora palmivora.

We began by creating a new, highly contiguous genome assembly for theP. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k–900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao’s defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor ofPhytophthora spp.

Our results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance toP. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.

The chemo-mechanical loading of rocks causes the dissolution and precipitation of multiple phases in the rock. This dissolution and precipitation of load-bearing mineral phases lead to the stress redistribution in neighboring phases, which in turn results in deformational changes of the sample composite. The aim of this study is to investigate the link between microstructural evolution and creep behavior of shale rocks subjected to chemo-mechanical loading through modeling time-dependent deformation induced by the dissolution-precipitation process. The model couples the microstructural evolution of the shale rocks with the stress/strain fields inside the material as a function of time. The modeling effort is supplemented with an experimental study where shale rocks were exposed to CO2-rich brine under high temperature and pressure conditions. 3D snapshots of the sample microstructure were generated using segmented micro-CT images of the shale sample. The time-evolving microstructures were then integrated with the Finite element-based mechanical model to simulate the creep induced by dissolution and precipitation processes independent of the intrinsic viscoelasticity/viscoplasticity of the mineral phases. After computation of the time-dependent viscoelastic properties of the shale composite, the combined microstructure model and finite element model were utilized to predict the time-dependent stress and strain fields in different zones of reacted shale.

Determination of viscous behavior of shale rocks is key in wide range of applications such as stability of reservoirs, stability of geo-structures subjected to environmental forcing, underground storage of hazardous materials and hydraulic fracturing. Short-term creep strains in hydraulic fracturing can change stress fields and in turn can impact the hydraulic fracturing procedures(H. Sone & Zoback, 2010; Hiroki Sone & Zoback, 2013). While long-term creep strains can hamper the reservoir performance due to the reduction in permeability of the reservoir by closing of fractures and fissures(Du, Hu, Meegoda, & Zhang, 2018; Rybacki, Meier, & Dresen, 2016; Sharma, Prakash, & Abedi, 2019; Hiroki Sone & Zoback, 2014). Owing to these significance of creep strain, it is important to understand the viscoelastic/viscoplastic behavior of shales.