Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease

Cacao ( Theobroma cacao ) is a highly valuable crop with growing demands in the global market. However, cacao farmers often face challenges posed by black pod disease caused by Phytophthora spp. with P. palmivora as the most dominant. Regulations of various gene expression influence plant resistance to pathogens. One mechanism involves targeting mRNA of virulence genes in the invading pathogens, suppressing their infection. However, resistance also could be suppressed by plant-derived miRNAs that target their own defense genes. The objective of this study is to identify differentially expressed miRNAs in black pod resistant and susceptible cacao varieties and to predict their targets in T. cacao and P. palmivora transcripts. In total, 54 known miRNAs from 40 miRNA families and 67 Novel miRNAs were identified. 17 miRNAs were differentially expressed in susceptible variety compared to resistant one, with 9 miRNAs were upregulated and 8 miRNAs downregulated. In T. cacao transcripts, the upregulated miRNAs were predicted to target several genes, including defense genes. The suppression of these defense genes can lead to a reduction in plant resistance against pathogen infection. While in P. palmivora transcripts, the upregulated miRNAs were predicted to target several genes, including P. palmivora effector genes. In the future, limiting expression of miRNAs that target T. cacao 's defense genes and applying miRNAs that target P. palmivora effector genes hold promise for enhancing cacao plant resistance against P. palmivora infection.