Comparative RNA-seq analysis of resistant and susceptible Theobroma cacao fruits in response to infection with frosty pod pathogen (Moniliophthora roreri)

Authors: Puig, Alina; Cohen, Stephen; Koch Bach, Rachel; ARCINIEGAS LEAL, ADRIANA - CATIE TROPICAL AGRICULTURAL RESEARCH; Gutierrez, Osman; Bailey, Bryan

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2023
Publication Date: 4/25/2023
Citation: Puig, A.S., Cohen, S.P., Koch Bach, R.A., Arciniegas Leal, A., Gutierrez, O.A., Bailey, B.A. 2023. Comparative RNA-seq analysis of resistant and susceptible Theobroma cacao fruits in response to infection with frosty pod pathogen (Moniliophthora roreri). PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-09-22-0101-R.
DOI: https://doi.org/10.1094/PHYTOFR-09-22-0101-R

Interpretive Summary: Frosty pod rot, caused by the fungus Moniliophthora roreri, is one of the most economically significant diseases of cacao. It causes losses of up to 90% in areas, yet only a limited number of resistant clones have been identified. To understand resistance to this disease at the molecular level, we looked at gene expression in resistant and susceptible plant hosts. The gene expression data shows that the resistant plants express more genes responsible for defense and cellular communication compared with susceptible plants, even when they are not infected. Ten of these genes were located in areas of the genome that had been previously associated with resistance to frosty pod rot disease. These findings improve our understanding of resistance to frosty pod rot disease and will be used by scientists and breeders to identify additional sources of resistance in this crop. This disease is actively spreading throughout the western hemisphere and farmers will benefit from having resistant plant varieties available.

Technical Abstract: Frosty pod rot (FPR), caused by Moniliophthora roreri (MR), is one of the most important diseases of cacao, causing losses of up to 90% in areas where the disease is present. A limited number of resistant clones have been identified and are in use in Central America, but additional sources of disease resistance are being sought by breeding programs. RNA-sequencing was used to identify differences in constitutive (mock-inoculated) and pathogen-induced gene expression in cacao pods from trees resistant and susceptible to M. roreri. The greatest number of differentially expressed genes (DEGs) (n=2,039) were identified in susceptible material following inoculation with MR (7 days post inoculation), with the most common pathway categories being cell growth/death (n=102), signaling (n=308), and carbohydrate metabolism (n=141). Resistant material showed little overall change in gene expression (5 DEGs) following pathogen inoculation, suggesting that infection had not become established. For this reason, differences in constitutive gene expression are likely to provide the most relevant information on FPR resistance in this study. In the absence of the pathogen, 144 genes were expressed at a higher level in the resistant material, and 265 were expressed at a higher level in the susceptible material. The genes most highly upregulated in resistant material encode for disease resistance proteins in the leucine rich repeat family and cysteine-rich receptor-like protein kinases. Ten DEGs were located within QTL on chromosomes 2, 7, and 9 previously associated with FPR resistance in this population. This study provides the first analysis of constitutively expressed genes contributing to FPR resistance and identifies significant genes within previously identified disease resistance QTL.