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Background   Phytophthora nicotianae  Breda de Haan ( Phytophthora parasitica  Dastur) causes severe damage to citrus crops worldwide. A population of citrandarins was created from the cross between the susceptible parent  Citrus sunki  Hort. Ex Tan. and the resistant parent  Poncirus trifoliata  (L.) Raf. cv. Rubidoux, both parents and two reference rootstocks (Rangpur lime and Swingle citrumelo) were grafted in a greenhouse on Rangpur lime. Inoculations were performed at 10 cm and 15 cm above the grafting region and the resulting lesions were evaluated by measuring the lesion length 60 days after inoculation. As control, non-inoculated plants of each genotype were used. In addition, we evaluated the expression of 19 candidate genes involved in citrus defense response 48 h after pathogen infection by quantitative Real-Time PCR (qPCR). We mapped genomic regions of Quantitative Trait Loci (QTLs) and Expression Quantitative Trait Loci (eQTLs) associated with resistance to  P. parasitica  in the linkage groups (LGs) of the previously constructed maps of  C. sunki  and  P. trifoliata .    Results  We found disease severity differences among the generated hybrids, with lesion lengths varying from 1.15 to 11.13 mm. The heritability of the character was 65%. These results indicate that there is a great possibility of success in the selection of resistant hybrids within this experiment. The analysis of gene expression profile demonstrated a great variation of responses regarding the activation of plant defense pathways, indicating that citrandarins have several defense strategies to control oomycete infection. The information of the phenotypic and gene expression data made possible to detect genomic regions associated with resistance. Three QTLs and 84 eQTLs were detected in the linkage map of  P. trifoliata , while one QTL and 110 eQTLs were detected in  C. sunki .    Conclusions  This is the first study to use eQTLs mapping in the  Phytophthora -citrus interaction .  Our results from the QTLs and eQTLs mapping allow us to conclude that the resistance of some citrandarins to the infection by  P. parasitica  is due to a favorable combination of QTLs and eQTLs transmitted by both parents.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4888-2) contains supplementary material, which is available to authorized users.

QTLs and eQTLs mapping related to citrandarins’ resistance to citrus gummosis disease