Comparative RNA-seq Analysis of Resistant and Susceptible Theobromacacao Fruits in Response to Infection with Frosty Pod Pathogen(Moniliophthora roreri)

Abstract

Frosty pod rot (FPR), caused by Moniliophthora roreri (MR), is one of the mostimportant diseases of cacao, causing losses of up to 90% in areas where it ispresent. A limited number of resistant clones have been identified, but additionalsources of disease resistance are being sought by breeding programs. RNA se-quencing was used to identify differences in constitutive (mock-inoculated) andpathogen-induced gene expression in cacao pods from trees resistant and sus-ceptible to MR. The greatest number of differentially expressed genes (DEGs)(n = 2,039) was identified in susceptible material following inoculation withMR (7 days postinoculation), with the most common pathway categories beingcell growth/death (n = 102), signaling (n = 308), and carbohydrate metabolism(n = 141). Resistant material showed little overall change in gene expression (fiveDEGs) following pathogen inoculation, suggesting that infection had not becomeestablished. For this reason, differences in constitutive gene expression are likelyto provide the most relevant information on FPR resistance in this study. In theabsence of the pathogen,144 genes were expressed at a higher level in the resis-tant material and 265 at a higher level in the susceptible material. The genes mosthighly upregulated in resistant material encode for disease resistance proteins inthe leucine-rich repeat family and cysteine-rich receptor-like protein kinases. TenDEGs were located within quantitative trait loci on chromosomes 2, 7, and 9 previ-ously associated with FPR resistance in this population. This study provides thefirst analysis of constitutively expressed genes contributing to FPR resistanceand identifies significant genes within known disease resistance quantitative traitloci.