Identification of cacao genes responsive to P. palmivora infection in resistant and susceptible cacao clones

Authors: BARAUH, INDRANI - Orise Fellow; ALI, SHAHIN - University Of California, Davis; Shao, Jonathan; LARY, DAVID - University Of Texas; Bailey, Bryan

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2022
Publication Date: 2/8/2022
Citation: Barauh, I., Ali, S., Shao, J.Y., Lary, D., Bailey, B.A. 2022. Identification of cacao genes responsive to P. palmivora infection in resistant and susceptible cacao clones. Frontiers in Plant Science. 12:780805. https://doi.org/10.3389/fpls.2021.780805.
DOI: https://doi.org/10.3389/fpls.2021.780805

Interpretive Summary: Black pod rot of cacao, caused by Phytophthora palmivora, can greatly reduce cacao yields everywhere cacao is grown. The pathogen consumes and destroys the fruit of cacao, the seeds of which are the source of chocolate. Some cacao varieties show resistance to the black pod rot pathogen. Research indicates resistance to black pod rot in cacao pods correlates with resistance observed in cacao leaves, although exactly how this works is unclear. We studied the gene responses in cacao leaves of two black pod rot susceptible cacao varieties and one resistant cacao variety. The resistant variety consistently showed less cell death than the two susceptible varieties after infection. Although many cacao defense genes were induced after infection in all three varieties, the response in the resistance variety was more focused allowing the identification of a unique set of defense genes that were expressed at higher levels in the resistant variety when compared to the two susceptible clones. These genes will serve as candidates for selection by plant breeders in their efforts to provide farmers with cacao varieties resistant to black pod rot.

Technical Abstract: Black pod rot, caused by Phytophthora palmivora, is one of the most devastating diseases of Theobroma cacao L. (cacao) leading to huge losses for farmers and limiting supplies to the chocolate industry. In order to understand resistance response of cacao leaves to Phytophthora palmivora, young red leaves of three different cacao clones (ICS1 , CCN51, and Pound7) were inoculated with zoospores of Phytophthora palmivora and monitored for disease symptom development out to 48 hours before harvesting for RNA-Seq analysis. Pound7 consistently showed less necrosis than ICS1 and CCN51 48 h after inoculation. RNA-Seq was carried out on samples 24 h post Phytophthora palmivora inoculation. A total of 24,672 expressed cacao genes were identified, out of which 2521 transcripts showed induction in at least one Phytophthora palmivora treated clone compared to its respective control and 1917 transcripts showed repression in the same comparisons. There were 115 transcripts showing induction in the Phytophthora palmivora treated samples compared to respective controls in all 3 clones. KEGG analysis revealed that many of the differentially genes were components of pathways important in plant defense against pathogens: Plant MAPK signaling pathway, Plant Hormone signal transduction, Phenylpropanoid biosynthesis, Plant Pathogen Interactions, Alpha-Linolenic acid metabolism, Ethylene biosynthesis, and Terpenoid backbone biosynthesis. We further analyzed the cacao leaf transcriptome in detail focusing on gene families important in plant defense: Germins, WRKYs, Ubiquitin, Lectins, PR-proteins, Glutathione-S-Transferases, Cytochrome P450 enzymes, proteases. A domain search of putative cacao resistance genes within the cacao transcriptome identified 89 genes with prominent LRR domains, 170 protein kinases encoding genes, 210 genes with prominent NB-ARC domains, many of which were constitutively differentially expressed. There is a massive re-programming of the defense gene process in cacao leaf tissue after infection even in susceptible clone. Many defense associated genes are uniquely expressed depending on the clone. The identified candidate genes may be useful as markers for breeding disease resistant cacao varieties against Phytophthora palmivora.