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Background  Understanding the effects of resistance QTL on pathogen development cycle is an important issue for the creation of QTL combination strategies to durably increase disease resistance in plants. The oomycete pathogen  Aphanomyces euteiches , causing root rot disease, is one of the major factors limiting the pea crop in the main producing countries. No commercial resistant varieties are currently available in Europe. Resistance alleles at seven main QTL were recently identified and introgressed into pea agronomic lines, resulting in the creation of Near Isogenic Lines (NILs) at the QTL. This study aimed to determine the effect of main  A. euteiches  resistance QTL in NILs on different steps of the pathogen life cycle.    Results  NILs carrying resistance alleles at main QTL in susceptible genetic backgrounds were evaluated in a destructive test under controlled conditions. The development of root rot disease severity and pathogen DNA levels in the roots was measured during ten days after inoculation. Significant effects of several resistance alleles at the two major QTL  Ae-Ps7.6  and  Ae-Ps4.5  were observed on symptom appearance and root colonization by  A. euteiches . Some resistance alleles at three other minor-effect QTL ( Ae-Ps2.2 ,  Ae-Ps3.1  and  Ae-Ps5.1 ) significantly decreased root colonization. The combination of resistance alleles at two or three QTL including the major QTL  Ae-Ps7.6  ( Ae-Ps5.1 / Ae-Ps7.6  or  Ae-Ps2.2 / Ae-Ps3.1 / Ae-Ps7.6 ) had an increased effect on delaying symptom appearance and/or slowing down root colonization by  A. euteiches  and on plant resistance levels, compared to the effects of individual or no resistance alleles.    Conclusions  This study demonstrated the effects of single or multiple resistance QTL on delaying symptom appearance and/or slowing down colonization by  A. euteiches  in pea roots, using original plant material and a precise pathogen quantification method. Our findings suggest that single resistance QTL can act on multiple or specific steps of the disease development cycle and that their actions could be pyramided to increase partial resistance in future pea varieties. Further studies are needed to investigate QTL effects on different steps of the pathogen life cycle, as well as the efficiency and durability of pyramiding strategies using QTL which appear to act on the same stage of the pathogen cycle.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-016-0822-4) contains supplementary material, which is available to authorized users.

Single and multiple resistance QTL delay symptom appearance and slow down root colonization by Aphanomyces euteiches in pea near isogenic lines